DFT application for chlorin derivatives photosensitizer drugs modeling

NASA Astrophysics Data System (ADS)

Machado, Neila; Carvalho, B. G.; Téllez Soto, C. A.; Martin, A. A.; Favero, P. P.

2018-04-01

Photodynamic therapy is an alternative form of cancer treatment that meets the desire for a less aggressive approach to the body. It is based on the interaction between a photosensitizer, activating light, and molecular oxygen. This interaction results in a cascade of reactions that leads to localized cell death. Many studies have been conducted to discover an ideal photosensitizer, which aggregates all the desirable characteristics of a potent cell killer and generates minimal side effects. Using Density Functional Theory (DFT) implemented in the program Vienna Ab-initio Simulation Package, new chlorin derivatives with different functional groups were simulated to evaluate the different absorption wavelengths to permit resonant absorption with the incident laser. Gaussian 09 program was used to determine vibrational wave numbers and Natural Bond Orbitals. The chosen drug with the best characteristics for the photosensitizer was a modified model of the original chlorin, which was called as Thiol chlorin. According to our calculations it is stable and is 19.6% more efficient at optical absorption in 708 nm in comparison to the conventional chlorin e6. Vibrational modes, optical and electronic properties were predicted. In conclusion, this study is an attempt to improve the development of new photosensitizer drugs through computational methods that save time and contribute to decrease the numbers of animals for model application.

Spectral analysis of the Earth's topographic potential via 2D-DFT: a new data-based degree variance model to degree 90,000

NASA Astrophysics Data System (ADS)

Rexer, Moritz; Hirt, Christian

2015-09-01

Classical degree variance models (such as Kaula's rule or the Tscherning-Rapp model) often rely on low-resolution gravity data and so are subject to extrapolation when used to describe the decay of the gravity field at short spatial scales. This paper presents a new degree variance model based on the recently published GGMplus near-global land areas 220 m resolution gravity maps (Geophys Res Lett 40(16):4279-4283, 2013). We investigate and use a 2D-DFT (discrete Fourier transform) approach to transform GGMplus gravity grids into degree variances. The method is described in detail and its approximation errors are studied using closed-loop experiments. Focus is placed on tiling, azimuth averaging, and windowing effects in the 2D-DFT method and on analytical fitting of degree variances. Approximation errors of the 2D-DFT procedure on the (spherical harmonic) degree variance are found to be at the 10-20 % level. The importance of the reference surface (sphere, ellipsoid or topography) of the gravity data for correct interpretation of degree variance spectra is highlighted. The effect of the underlying mass arrangement (spherical or ellipsoidal approximation) on the degree variances is found to be crucial at short spatial scales. A rule-of-thumb for transformation of spectra between spherical and ellipsoidal approximation is derived. Application of the 2D-DFT on GGMplus gravity maps yields a new degree variance model to degree 90,000. The model is supported by GRACE, GOCE, EGM2008 and forward-modelled gravity at 3 billion land points over all land areas within the SRTM data coverage and provides gravity signal variances at the surface of the topography. The model yields omission errors of 9 mGal for gravity (1.5 cm for geoid effects) at scales of 10 km, 4 mGal (1 mm) at 2-km scales, and 2 mGal (0.2 mm) at 1-km scales.

Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost

NASA Astrophysics Data System (ADS)

Bajaj, Akash; Janet, Jon Paul; Kulik, Heather J.

2017-11-01

The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and molecules. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such physically intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT.

The structure of N2 adsorbed on the rumpled NaCl(100) surface—A combined LEED and DFT-D study

NASA Astrophysics Data System (ADS)

Vogt, Jochen

2012-11-01

The structure of N2 physisorbed on the NaCl(100) single crystal surface is investigated by means of quantitative low-energy electron diffraction (LEED) in combination with dispersion corrected density functional theory (DFT-D). In the temperature range between 20 K and 45 K, a p(1 × 1) structure is observed in the LEED experiment. According to the structure analysis based on the measured diffraction spot intensity profiles, the N2 molecules are adsorbed over the topmost Na+ ions. The experimental distance of the lower nitrogen to the Na+ ion underneath is (2.55 ± 0.07) Å; the corresponding DFT-D value is 2.65 Å. The axes of the molecules are tilted (26 ± 3)° with respect to the surface normal, while in the zero Kelvin optimum structure from DFT-D, the molecules have a perpendicular orientation. The experimental monolayer heat of adsorption, deduced from a Fowler-Guggenheim kinetic model of adsorption is -(13.6 ± 1.6) kJ mol-1, including a lateral molecule-molecule interaction energy of -(2.0 ± 0.4) kJ mol-1. The zero Kelvin adsorption energy from DFT-D, including zero point energy correction, is -15.6 kJ mol-1; the molecule-molecule interaction is -2.4 kJ mol-1. While the rumpling of the NaCl(100) surface is unchanged upon adsorption of nitrogen, the best-fit root mean square thermal displacements of the ions in the topmost substrate layer are significantly reduced.

Ab initio DFT+U study of He atom incorporation into UO(2) crystals.

PubMed

Gryaznov, Denis; Heifets, Eugene; Kotomin, Eugene

2009-09-07

We present and discuss results of the density functional theory (DFT) for perfect UO(2) crystals with He atoms in octahedral interstitial positions therein. We have calculated basic bulk crystal properties and He incorporation energies into the low temperature anti-ferromagnetic UO(2) phase using several exchange-correlation functionals within the spin-polarized local density (LDA) and generalized gradient (GGA) approximations. In all DFT calculations we included the on-site correlation corrections using the Hubbard model (DFT+U approach). We analysed a potential crystalline symmetry reduction from tetragonal down to orthorhombic structure and confirmed the presence of the Jahn-Teller effect in a perfect UO(2). We discuss also the problem of a conducting electronic state arising when He is placed into a tetragonal antiferromagnetic phase of UO(2) commonly used in defect modelling. Consequently, we found a specific monoclinic lattice distortion which allowed us to restore the semiconducting state and properly estimate He incorporation energies. Unlike the bulk properties, the He incorporation energy strongly depends on several factors, including the supercell size, the use of spin polarization, the exchange-correlation functionals and on-site correlation corrections. We compare our results for the He incorporation with the previous shell model and ab initio DFT calculations.

Study of vibrational spectra and hydrogen bonding network in dimeric and tetrameric model of ampicillin using DFT and AIM approach

NASA Astrophysics Data System (ADS)

Shukla, Anuradha; Khan, Eram; Tandon, Poonam; Sinha, Kirti

2017-03-01

Ampicillin is a β-lactam antibiotic that is active against both gram-positive and gram-negative bacteria and is widely used for the treatment of infections. In this work, molecular properties of ampicillin are calculated on the basis of calculations on its dimeric and tetrameric models using DFT/B3LYP/6-311G(d,p). HOMO-LUMO energy gap shows that chemical reactivity of tetrameric model of ampicillin is higher than the dimeric and monomeric model of ampicillin. To get a better understanding of intra and intermolecular bonding and interactions among bonds, NBO analysis is carried out with tetrameric model of ampicillin, and is further finalized with an 'quantum theory of atoms-in-molecules' (QTAIM) analysis. The binding energy of dimeric model of ampicillin is calculated as -26.84 kcal/mol and -29.34 kcal/mol using AIM and DFT calculations respectively. The global electrophilicity index (ω = 2.8118 eV) of tetrameric model of ampicillin shows that this behaves as a strong electrophile in comparison to dimeric and monomeric model of ampicillin. The FT-Raman and FT-IR spectra were recorded in the solid phase, and interpreted in terms of potential energy distribution analysis. A collective theoretical and experimental vibrational analysis approves the presence of hydrogen bonds in the ampicillin molecule.

Optimized structure and thermochemical properties of flavonoids determined by the CHIH(medium) DFT model chemistry versus experimental techniques

NASA Astrophysics Data System (ADS)

Mendoza-Wilson, Ana María.; Lardizabal-Gutiérrez, Daniel; Torres-Moye, Enrique; Fuentes-Cobas, Luis; Balandrán-Quintana, René R.; Camacho-Dávila, Alejandro; Quintero-Ramos, Armando; Glossman-Mitnik, Daniel

2007-12-01

The purpose of this work was to evaluate the accuracy of the CHIH(medium)-DFT model chemistry (PBEg/CBSB2 ∗∗//PBEg/CBSB4) in the determination of the optimized structure and thermochemical properties of heterocyclic systems of medium size such as flavonoids, wherefore were selected three of the most abundant flavonoids in vegetable tissues, and which posses the higher antioxidant activity: quercetin, (+)-catechin and cyanidin. As reference systems were employed three cyclic compounds: phenol, catechol and resorcinol. The thermochemical properties evaluated were enthalpy of formation, bond dissociation enthalpy (BDE) and ionization potential (IP), following the scheme of isodesmic reactions. The theoretical results were compared with experimental data generated by X-ray diffraction and calorimetric techniques realized in part by us, whereas other data were taken from the literature. The results obtained in this work reveal that the CHIH(medium)-DFT model chemistry represents an accurate computational tool to calculate structural and thermochemical properties in the studied flavonoid and reference compounds. The average absolute deviation of enthalpy of formation for reference compounds was 3.0 kcal/mol, 2.64 kcal/mol for BDE, and 2.97 kcal/mol for IP.

A real-time fluorescent sensor specific to Mg2+: crystallographic evidence, DFT calculation and its use for quantitative determination of magnesium in drinking water.

PubMed

Men, Guangwen; Chen, Chunrong; Zhang, Shitong; Liang, Chunshuang; Wang, Ying; Deng, Mengyu; Shang, Hongxing; Yang, Bing; Jiang, Shimei

2015-02-14

An "off-the-shelf" fluorescence "turn-on" Mg(2+) chemosensor 3,5-dichlorosalicylaldehyde (BCSA) was rationally designed and developed. This proposed sensor works based on Mg(2+)-induced formation of the 2 : 1 BCSA-Mg(2+) complex. The coordination of BSCA to Mg(2+) increases its structural rigidity generating a chelation-enhanced fluorescence (CHEF) effect which was confirmed by single crystal XRD studies of the BSCA-Mg(2+) complex and TD/DFT calculations. This sensor exhibits high sensitivity and selectivity for the quantitative monitoring of Mg(2+) with a wide detection range (0-40 μM), a low detection limit (2.89 × 10(-7) mol L(-1)) and a short response time (<0.5 s). It can also resist the interference from the other co-existing metal ions, especially Ca(2+). Consequently, this fluorescent sensor can be utilized to monitor Mg(2+) in real time within actual samples from drinking water.

Combined DFT and BS study on the exchange coupling of dinuclear sandwich-type POM: comparison of different functionals and reliability of structure modeling.

PubMed

Yin, Bing; Xue, GangLin; Li, JianLi; Bai, Lu; Huang, YuanHe; Wen, ZhenYi; Jiang, ZhenYi

2012-05-01

The exchange coupling of a group of three dinuclear sandwich-type polyoxomolybdates [MM'(AsMo7O27)2](12-) with MM' = CrCr, FeFe, FeCr are theoretically predicted from combined DFT and broken-symmetry (BS) approach. Eight different XC functionals are utilized to calculate the exchange-coupling constant J from both the full crystalline structures and model structures of smaller size. The comparison between theoretical values and accurate experimental results supports the applicability of DFT-BS method in this new type of sandwich-type dinuclear polyoxomolybdates. However, a careful choice of functionals is necessary to achieve the desired accuracy. The encouraging results obtained from calculations on model structures highlight the great potential of application of structure modeling in theoretical study of POM. Structural modeling may not only reduce the computational cost of large POM species but also be able to take into account the external field effect arising from solvent molecules in solution or counterions in crystal.

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

DFT and TD-DFT calculations of metallotetraphenylporphyrin and metallotetraphenylporphyrin fullerene complexes as potential dye sensitizers for solar cells

NASA Astrophysics Data System (ADS)

El Mahdy, A. M.; Halim, Shimaa Abdel; Taha, H. O.

2018-05-01

Density functional theory (DFT) and time-dependent DFT calculations have been employed to model metallotetraphenylporphyrin dyes and metallotetraphenylporphyrin -fullerene complexes in order to investigate the geometries, electronic structures, the density of states, non-linear optical properties (NLO), IR-vis spectra, molecular electrostatic potential contours, and electrophilicity. To calculate the excited states of the tetraphenyl porphyrin analogs, time-dependent density functional theory (TD-DFT) are used. Their UV-vis spectra were also obtained and a comparison with available experimental and theoretical results is included. The results reveal that the metal and the tertiary butyl groups of the dyes are electron donors, and the tetraphenylporphyrin rings are electron acceptors. The HOMOs of the dyes fall within the (TiO2)60 and Ti38O76 band gaps and support the issue of typical interfacial electron transfer reaction. The resulting potential drop of Mn-TPP-C60 increased by ca. 3.50% under the effect of the tertiary butyl groups. The increase in the potential drop indicates that the tertiary butyl complexes could be a better choice for the strong operation of the molecular rectifiers. The introduction of metal atom and tertiary butyl groups to the tetraphenyl porphyrin moiety leads to a stronger response to the external electric field and induces higher photo-to-current conversion efficiency. This also shifts the absorption in the dyes and makes them potential candidates for harvesting light in the entire visible and near IR region for photovoltaic applications.

Robust 3D DFT video watermarking

NASA Astrophysics Data System (ADS)

Deguillaume, Frederic; Csurka, Gabriela; O'Ruanaidh, Joseph J.; Pun, Thierry

1999-04-01

This paper proposes a new approach for digital watermarking and secure copyright protection of videos, the principal aim being to discourage illicit copying and distribution of copyrighted material. The method presented here is based on the discrete Fourier transform (DFT) of three dimensional chunks of video scene, in contrast with previous works on video watermarking where each video frame was marked separately, or where only intra-frame or motion compensation parameters were marked in MPEG compressed videos. Two kinds of information are hidden in the video: a watermark and a template. Both are encoded using an owner key to ensure the system security and are embedded in the 3D DFT magnitude of video chunks. The watermark is a copyright information encoded in the form of a spread spectrum signal. The template is a key based grid and is used to detect and invert the effect of frame-rate changes, aspect-ratio modification and rescaling of frames. The template search and matching is performed in the log-log-log map of the 3D DFT magnitude. The performance of the presented technique is evaluated experimentally and compared with a frame-by-frame 2D DFT watermarking approach.

Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation.

PubMed

Casida, Mark E; Huix-Rotllant, Miquel

2016-01-01

In their famous paper, Kohn and Sham formulated a formally exact density-functional theory (DFT) for the ground-state energy and density of a system of N interacting electrons, albeit limited at the time by certain troubling representability questions. As no practical exact form of the exchange-correlation (xc) energy functional was known, the xc-functional had to be approximated, ideally by a local or semilocal functional. Nowadays, however, the realization that Nature is not always so nearsighted has driven us up Perdew's Jacob's ladder to find increasingly nonlocal density/wavefunction hybrid functionals. Time-dependent (TD-) DFT is a younger development which allows DFT concepts to be used to describe the temporal evolution of the density in the presence of a perturbing field. Linear response (LR) theory then allows spectra and other information about excited states to be extracted from TD-DFT. Once again the exact TD-DFT xc-functional must be approximated in practical calculations and this has historically been done using the TD-DFT adiabatic approximation (AA) which is to TD-DFT very similar to what the local density approximation (LDA) is to conventional ground-state DFT. Although some of the recent advances in TD-DFT focus on what can be done within the AA, others explore ways around the AA. After giving an overview of DFT, TD-DFT, and LR-TD-DFT, this chapter focuses on many-body corrections to LR-TD-DFT as one way to build hybrid density-functional/wavefunction methodology for incorporating aspects of nonlocality in time not present in the AA.

Quantitative reactive modeling and verification.

PubMed

Henzinger, Thomas A

Formal verification aims to improve the quality of software by detecting errors before they do harm. At the basis of formal verification is the logical notion of correctness , which purports to capture whether or not a program behaves as desired. We suggest that the boolean partition of software into correct and incorrect programs falls short of the practical need to assess the behavior of software in a more nuanced fashion against multiple criteria. We therefore propose to introduce quantitative fitness measures for programs, specifically for measuring the function, performance, and robustness of reactive programs such as concurrent processes. This article describes the goals of the ERC Advanced Investigator Project QUAREM. The project aims to build and evaluate a theory of quantitative fitness measures for reactive models. Such a theory must strive to obtain quantitative generalizations of the paradigms that have been success stories in qualitative reactive modeling, such as compositionality, property-preserving abstraction and abstraction refinement, model checking, and synthesis. The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology. In particular, we will use the quantitative reactive models and fitness measures developed in this project for testing hypotheses about the mechanisms behind data from biological experiments.

Assessment of TD-DFT and LF-DFT for study of d − d transitions in first row transition metal hexaaqua complexes

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

Vlahović, Filip; Perić, Marko; Zlatar, Matija, E-mail: matijaz@chem.bg.ac.rs

2015-06-07

Herein, we present the systematic, comparative computational study of the d − d transitions in a series of first row transition metal hexaaqua complexes, [M(H{sub 2}O){sub 6}]{sup n+} (M{sup 2+/3+} = V {sup 2+/3+}, Cr{sup 2+/3+}, Mn{sup 2+/3+}, Fe{sup 2+/3+}, Co{sup 2+/3+}, Ni{sup 2+}) by the means of Time-dependent Density Functional Theory (TD-DFT) and Ligand Field Density Functional Theory (LF-DFT). Influence of various exchange-correlation (XC) approximations have been studied, and results have been compared to the experimental transition energies, as well as, to the previous high-level ab initio calculations. TD-DFT gives satisfactory results in the cases of d{sup 2}, d{supmore » 4}, and low-spin d{sup 6} complexes, but fails in the cases when transitions depend only on the ligand field splitting, and for states with strong character of double excitation. LF-DFT, as a non-empirical approach to the ligand field theory, takes into account in a balanced way both dynamic and non-dynamic correlation effects and hence accurately describes the multiplets of transition metal complexes, even in difficult cases such as sextet-quartet splitting in d{sup 5} complexes. Use of the XC functionals designed for the accurate description of the spin-state splitting, e.g., OPBE, OPBE0, or SSB-D, is found to be crucial for proper prediction of the spin-forbidden excitations by LF-DFT. It is shown that LF-DFT is a valuable alternative to both TD-DFT and ab initio methods.« less

DFT/TD-DFT study of solvent effect as well the substituents influence on the different features of TPP derivatives for PDT application

NASA Astrophysics Data System (ADS)

Dulski, Mateusz; Kempa, Marta; Kozub, Patrycja; Wójcik, Justyna; Rojkiewicz, Marcin; Kuś, Piotr; Szurko, Agnieszka; Ratuszna, Alicja; Wrzalik, Roman

2013-03-01

Spectral characteristics study of meso-tetraphenylporphyrin derivatives (TPP1 and TPP2) used as photosensitizers for utilization in photodynamic therapy (PDT) has been performed by density functional theory (DFT) and time dependent DFT (TD-DFT) calculations at B3LYP/6-31G(d) level of theory using PCM solvation model. The geometrical parameters of porphyrins have been studied for ground and excited-state geometry to deduce the influence of various substituents as well as solvent effect on the deformation of porphyrin ring. Two theoretical approaches - linear response (LR) and external iteration (EI) - have been performed to replicate absorption and fluorescence emission spectra. Experimental and theoretical investigations have shown that EI method reproduces the absorption energies very well for both singlet-singlet and triplet-triplet transitions, whereas the LR approach is more coherent with experimental fluorescence emission spectra. Spectral features and HOMO-LUMO band gap analysis have shown that TPP1 can be more useful in PDT. Calculations have revealed that two the highest occupied and two the lowest unoccupied molecular orbitals are responsible for the Q-band absorption and are located mainly on the porphyrin ring. In order to verify the substituent effect on the activity of tested compounds in their ground and excited states, the molecular electrostatic potential surfaces have been analyzed.

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

PubMed

Levy, Ronald M; Cui, Di; Zhang, Bin W; Matubayasi, Nobuyuki

2017-04-20

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis

PubMed Central

de la Lande, A.; Maddaluno, J.; Parisel, O.; Darden, T. A.; Piquemal, J-P

2010-01-01

Following our previous study (Piquemal et al., New J. Chem., 2003, 27, 909), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu2O2 metallic core (Piquemal and Pilmé, J. Mol. Struct.: Theochem, 2006, 77, 764). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems. PMID:20396590

DFT modeling, UV-Vis and IR spectroscopic study of acetylacetone-modified zirconia sol-gel materials.

PubMed

Georgieva, Ivelina; Danchova, Nina; Gutzov, Stoyan; Trendafilova, Natasha

2012-06-01

Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as IR and UV-Vis transmittance and diffuse reflectance spectroscopies. Based on DFT model calculations and simulated and experimental UV-Vis and IR spectra of all the studied structures, the most probable building units of the Zr(IV)-AcAc gel were predicted: the dimeric double hydroxo-bridged complex Zr(2)(AcAc)(2)(OH)(4)(OH)(2br) 9 and the monooxo-bridged complex Zr(2)(AcAc)(2)(OH)(4)O(br)·2H(2)O 12. In both structures, the two AcAc ligands are coordinated to one Zr atom. It was shown that building units 9 and 12 determine the photophysical and vibrational properties of the gel material. The observed UV-Vis and IR spectra of Zr(IV)-AcAc gel were interpreted and a relation between the spectroscopic and structural data was derived. The observed UV-Vis bands at 315 nm and 298/288 nm were assigned to partial ligand-metal transitions and to intra-/inter-AcAc ligand transitions, respectively.

Spectroscopic and DFT Study of RhIII Chloro Complex Transformation in Alkaline Solutions.

PubMed

Vasilchenko, Danila B; Berdyugin, Semen N; Korenev, Sergey V; O'Kennedy, Sean; Gerber, Wilhelmus J

2017-09-05

The hydrolysis of [RhCl 6 ] 3- in NaOH-water solutions was studied by spectrophotometric methods. The reaction proceeds via successive substitution of chloride with hydroxide to quantitatively form [Rh(OH) 6 ] 3- . Ligand substitution kinetics was studied in an aqueous 0.434-1.085 M NaOH matrix in the temperature range 5.5-15.3 °C. Transformation of [RhCl 6 ] 3- into [RhCl 5 (OH)] 3- was found to be the rate-determining step with activation parameters of ΔH † = 105 ± 4 kJ mol -1 and ΔS † = 59 ± 10 J K -1 mol -1 . The coordinated hydroxo ligand(s) induces rapid ligand substitution to form [Rh(OH) 6 ] 3- . By simulating ligand substitution as a dissociative mechanism, using density functional theory (DFT), we can now explain the relatively fast and slow kinetics of chloride substitution in basic and acidic matrices, respectively. Moreover, the DFT calculated activation energies corroborated experimental data that the kinetic stereochemical sequence of [RhCl 6 ] 3- hydrolysis in an acidic solution proceeds as [RhCl 6 ] 3- → [RhCl 5 (H 2 O)] 2- → cis-[RhCl 4 (H 2 O) 2 ] - . However, DFT calculations predict in a basic solution the trans route of substitution [RhCl 6 ] 3- → [RhCl 5 (OH)] 3- → trans-[RhCl 4 (OH) 2 ] 3- is kinetically favored.

The mathematics of cancer: integrating quantitative models.

PubMed

Altrock, Philipp M; Liu, Lin L; Michor, Franziska

2015-12-01

Mathematical modelling approaches have become increasingly abundant in cancer research. The complexity of cancer is well suited to quantitative approaches as it provides challenges and opportunities for new developments. In turn, mathematical modelling contributes to cancer research by helping to elucidate mechanisms and by providing quantitative predictions that can be validated. The recent expansion of quantitative models addresses many questions regarding tumour initiation, progression and metastases as well as intra-tumour heterogeneity, treatment responses and resistance. Mathematical models can complement experimental and clinical studies, but also challenge current paradigms, redefine our understanding of mechanisms driving tumorigenesis and shape future research in cancer biology.

Comparison of discrete Fourier transform (DFT) and principal component analysis/DFT as forecasting tools for absorbance time series received by UV-visible probes installed in urban sewer systems.

PubMed

Plazas-Nossa, Leonardo; Torres, Andrés

2014-01-01

The objective of this work is to introduce a forecasting method for UV-Vis spectrometry time series that combines principal component analysis (PCA) and discrete Fourier transform (DFT), and to compare the results obtained with those obtained by using DFT. Three time series for three different study sites were used: (i) Salitre wastewater treatment plant (WWTP) in Bogotá; (ii) Gibraltar pumping station in Bogotá; and (iii) San Fernando WWTP in Itagüí (in the south part of Medellín). Each of these time series had an equal number of samples (1051). In general terms, the results obtained are hardly generalizable, as they seem to be highly dependent on specific water system dynamics; however, some trends can be outlined: (i) for UV range, DFT and PCA/DFT forecasting accuracy were almost the same; (ii) for visible range, the PCA/DFT forecasting procedure proposed gives systematically lower forecasting errors and variability than those obtained with the DFT procedure; and (iii) for short forecasting times the PCA/DFT procedure proposed is more suitable than the DFT procedure, according to processing times obtained.

Methanol Synthesis from CO2 Hydrogenation over a Pd4/In2O3 Model Catalyst: A Combined DFT and Kinetic Study

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

Ye, Jingyun; Liu, Changjun; Mei, Donghai

2014-08-01

Methanol synthesis from CO2 hydrogenation on Pd4/In2O3 has been investigated using density functional theory (DFT) and microkinetic modeling. In this study, three possible routes in the reaction network of CO2 + H2 → CH3OH + H2O have been examined. Our DFT results show that the HCOO route competes with the RWGS route whereas a high activation barrier kinetically blocks the HCOOH route. DFT results also suggest that H2COO* + H* ↔ H2CO* +OH* and cis-COOH* + H* ↔CO* + H2O* are the rate limiting steps in the HCOO route and the RWGS route, respectively. Microkinetic modeling results demonstrate that themore » HCOO route is the dominant reaction route for methanol synthesis from CO2 hydrogenation. We found that the activation of H adatom on the small Pd cluster and the presence of H2O on the In2O3 substrate play important roles in promoting the methanol synthesis. The hydroxyl adsorbed at the interface of Pd4/In2O3 induces the transformation of the supported Pd4 cluster from a butterfly structure into a tetrahedron structure. This important structure change not only indicates the dynamical nature of the supported nanoparticle catalyst structure during the reaction but also shifts the final hydrogenation step from H2COH to CH3O.« less

Using DFT Methods to Study Activators in Optical Materials

DOE PAGES

Du, Mao-Hua

2015-08-17

Density functional theory (DFT) calculations of various activators (ranging from transition metal ions, rare-earth ions, ns 2 ions, to self-trapped and dopant-bound excitons) in phosphors and scintillators are reviewed. As a single-particle ground-state theory, DFT calculations cannot reproduce the experimentally observed optical spectra, which involve transitions between multi-electronic states. However, DFT calculations can generally provide sufficiently accurate structural relaxation and distinguish different hybridization strengths between an activator and its ligands in different host compounds. This is important because the activator-ligand interaction often governs the trends in luminescence properties in phosphors and scintillators, and can be used to search for newmore » materials. DFT calculations of the electronic structure of the host compound and the positions of the activator levels relative to the host band edges in scintillators are also important for finding optimal host-activator combinations for high light yields and fast scintillation response. Mn 4+ activated red phosphors, scintillators activated by Ce 3+, Eu 2+, Tl +, and excitons are shown as examples of using DFT calculations in phosphor and scintillator research.« less

The Hubbard Dimer: A Complete DFT Solution to a Many-Body Problem

NASA Astrophysics Data System (ADS)

Smith, Justin; Carrascal, Diego; Ferrer, Jaime; Burke, Kieron

2015-03-01

In this work we explain the relationship between density functional theory and strongly correlated models using the simplest possible example, the two-site asymmetric Hubbard model. We discuss the connection between the lattice and real-space and how this is a simple model for stretched H2. We can solve this elementary example analytically, and with that we can illuminate the underlying logic and aims of DFT. While the many-body solution is analytic, the density functional is given only implicitly. We overcome this difficulty by creating a highly accurate parameterization of the exact function. We use this parameterization to perform benchmark calculations of correlation kinetic energy, the adiabatic connection, etc. We also test Hartree-Fock and the Bethe Ansatz Local Density Approximation. We also discuss and illustrate the derivative discontinuity in the exchange-correlation energy and the infamous gap problem in DFT. DGE-1321846, DE-FG02-08ER46496.

Chlorophenol sorption on multi-walled carbon nanotubes: DFT modeling and structure-property relationship analysis.

PubMed

Watkins, Marquita; Sizochenko, Natalia; Moore, Quentarius; Golebiowski, Marek; Leszczynska, Danuta; Leszczynski, Jerzy

2017-02-01

The presence of chlorophenols in drinking water can be hazardous to human health. Understanding the mechanisms of adsorption under specific experimental conditions would be beneficial when developing methods to remove toxic substances from drinking water during water treatment in order to limit human exposure to these contaminants. In this study, we investigated the sorption of chlorophenols on multi-walled carbon nanotubes using a density functional theory (DFT) approach. This was applied to study selected interactions between six solvents, five types of nanotubes, and six chlorophenols. Experimental data were used to construct structure-adsorption relationship (SAR) models that describe the recovery process. Specific interactions between solvents and chlorophenols were taken into account in the calculations by using novel specific mixture descriptors.

DFT and TD-DFT computation of charge transfer complex between o-phenylenediamine and 3,5-dinitrosalicylic acid

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

Afroz, Ziya; Zulkarnain,; Ahmad, Afaq, E-mail: afaqahmad3@gmail.com

2016-05-23

DFT and TD-DFT studies of o-phenylenediamine (PDA), 3,5-dinitrosalicylic acid (DNSA) and their charge transfer complex have been carried out at B3LYP/6-311G(d,p) level of theory. Molecular geometry and various other molecular properties like natural atomic charges, ionization potential, electron affinity, band gap, natural bond orbital (NBO) and frontier molecular analysis have been presented at same level of theory. Frontier molecular orbital and natural bond orbital analysis show the charge delocalization from PDA to DNSA.

Plane-Wave DFT Methods for Chemistry

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

Bylaska, Eric J.

A detailed description of modern plane-wave DFT methods and software (contained in the NWChem package) are described that allow for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful for simulating chemistry, including techniques for calculating charged systems, exact exchange (i.e. hybrid DFT methods), and highly efficient AIMD/MM methods. Sample applications on the structure of the goethite+water interface and the hydrolysis of nitroaromatic molecules are described.

Optical Gaps in Pristine and Heavily Doped Silicon Nanocrystals: DFT versus Quantum Monte Carlo Benchmarks.

PubMed

Derian, R; Tokár, K; Somogyi, B; Gali, Á; Štich, I

2017-12-12

We present a time-dependent density functional theory (TDDFT) study of the optical gaps of light-emitting nanomaterials, namely, pristine and heavily B- and P-codoped silicon crystalline nanoparticles. Twenty DFT exchange-correlation functionals sampled from the best currently available inventory such as hybrids and range-separated hybrids are benchmarked against ultra-accurate quantum Monte Carlo results on small model Si nanocrystals. Overall, the range-separated hybrids are found to perform best. The quality of the DFT gaps is correlated with the deviation from Koopmans' theorem as a possible quality guide. In addition to providing a generic test of the ability of TDDFT to describe optical properties of silicon crystalline nanoparticles, the results also open up a route to benchmark-quality DFT studies of nanoparticle sizes approaching those studied experimentally.

Electronic spectroscopy of HRe(CO) 5: a CASSCF/CASPT2 and TD-DFT study

NASA Astrophysics Data System (ADS)

Bossert, J.; Ben Amor, N.; Strich, A.; Daniel, C.

2001-07-01

The low-lying excited states of HRe(CO) 5 have been calculated at the CASSCF/CASPT2 and TD-DFT level of theory using relativistic effective core potentials (ECP) or ab initio model potentials (AIMP). The theoretical absorption spectrum is compared to the experimental one. Despite the similarity between the experimental absorption spectra of HMn(CO) 5 and HRe(CO) 5 in the UV/visible energy domain it is shown that the assignment differs significantly between the two molecules. The low-lying excited states of HRe(CO) 5 correspond to 5d→π *CO excitations whereas the spectrum of HMn(CO) 5 consists mainly of 3d→3d and 3d→ σ*Mn-H excitations. If the CASPT2 and TD-DFT results are quite comparable for the lowest excited states, the upper part assignment is more problematic with the TD-DFT method.

Understanding density functional theory (DFT) and completing it in practice

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

Bagayoko, Diola

2014-12-15

We review some salient points in the derivation of density functional theory (DFT) and of the local density approximation (LDA) of it. We then articulate an understanding of DFT and LDA that seems to be ignored in the literature. We note the well-established failures of many DFT and LDA calculations to reproduce the measured energy gaps of finite systems and band gaps of semiconductors and insulators. We then illustrate significant differences between the results from self consistent calculations using single trial basis sets and those from computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma andmore » Franklin (BZW-EF). Unlike the former, the latter calculations verifiably attain the absolute minima of the occupied energies, as required by DFT. These minima are one of the reasons for the agreement between their results and corresponding, experimental ones for the band gap and a host of other properties. Further, we note predictions of DFT BZW-EF calculations that have been confirmed by experiment. Our subsequent description of the BZW-EF method ends with the application of the Rayleigh theorem in the selection, among the several calculations the method requires, of the one whose results have a full, physics content ascribed to DFT. This application of the Rayleigh theorem adds to or completes DFT, in practice, to preserve the physical content of unoccupied, low energy levels. Discussions, including implications of the method, and a short conclusion follow the description of the method. The successive augmentation of the basis set in the BZW-EF method, needed for the application of the Rayleigh theorem, is also necessary in the search for the absolute minima of the occupied energies, in practice.« less

Charge transfer complex between 2,3-diaminopyridine with chloranilic acid. Synthesis, characterization and DFT, TD-DFT computational studies

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2018-05-01

New charge transfer complex (CTC) between the electron donor 2,3-diaminopyridine (DAP) with the electron acceptor chloranilic (CLA) acid has been synthesized and characterized experimentally and theoretically using a variety of physicochemical techniques. The experimental work included the use of elemental analysis, UV-vis, IR and 1H NMR studies to characterize the complex. Electronic spectra have been carried out in different hydrogen bonded solvents, methanol (MeOH), acetonitrile (AN) and 1:1 mixture from AN-MeOH. The molecular composition of the complex was identified to be 1:1 from Jobs and molar ratio methods. The stability constant was determined using minimum-maximum absorbances method where it recorded high values confirming the high stability of the formed complex. The solid complex was prepared and characterized by elemental analysis that confirmed its formation in 1:1 stoichiometric ratio. Both IR and NMR studies asserted the existence of proton and charge transfers in the formed complex. For supporting the experimental results, DFT computations were carried out using B3LYP/6-31G(d,p) method to compute the optimized structures of the reactants and complex, their geometrical parameters, reactivity parameters, molecular electrostatic potential map and frontier molecular orbitals. The analysis of DFT results strongly confirmed the high stability of the formed complex based on existing charge transfer beside proton transfer hydrogen bonding concordant with experimental results. The origin of electronic spectra was analyzed using TD-DFT method where the observed λmax are strongly consisted with the computed ones. TD-DFT showed the contributed states for various electronic transitions.

Generalized PSF modeling for optimized quantitation in PET imaging.

PubMed

Ashrafinia, Saeed; Mohy-Ud-Din, Hassan; Karakatsanis, Nicolas A; Jha, Abhinav K; Casey, Michael E; Kadrmas, Dan J; Rahmim, Arman

2017-06-21

Point-spread function (PSF) modeling offers the ability to account for resolution degrading phenomena within the PET image generation framework. PSF modeling improves resolution and enhances contrast, but at the same time significantly alters image noise properties and induces edge overshoot effect. Thus, studying the effect of PSF modeling on quantitation task performance can be very important. Frameworks explored in the past involved a dichotomy of PSF versus no-PSF modeling. By contrast, the present work focuses on quantitative performance evaluation of standard uptake value (SUV) PET images, while incorporating a wide spectrum of PSF models, including those that under- and over-estimate the true PSF, for the potential of enhanced quantitation of SUVs. The developed framework first analytically models the true PSF, considering a range of resolution degradation phenomena (including photon non-collinearity, inter-crystal penetration and scattering) as present in data acquisitions with modern commercial PET systems. In the context of oncologic liver FDG PET imaging, we generated 200 noisy datasets per image-set (with clinically realistic noise levels) using an XCAT anthropomorphic phantom with liver tumours of varying sizes. These were subsequently reconstructed using the OS-EM algorithm with varying PSF modelled kernels. We focused on quantitation of both SUV mean and SUV max , including assessment of contrast recovery coefficients, as well as noise-bias characteristics (including both image roughness and coefficient of-variability), for different tumours/iterations/PSF kernels. It was observed that overestimated PSF yielded more accurate contrast recovery for a range of tumours, and typically improved quantitative performance. For a clinically reasonable number of iterations, edge enhancement due to PSF modeling (especially due to over-estimated PSF) was in fact seen to lower SUV mean bias in small tumours. Overall, the results indicate that exactly matched PSF

Accurate Induction Energies for Small Organic Molecules. 2. Development and Testing of Distributed Polarizability Models against SAPT(DFT) Energies.

PubMed

Misquitta, Alston J; Stone, Anthony J; Price, Sarah L

2008-01-01

In part 1 of this two-part investigation we set out the theoretical basis for constructing accurate models of the induction energy of clusters of moderately sized organic molecules. In this paper we use these techniques to develop a variety of accurate distributed polarizability models for a set of representative molecules that include formamide, N-methyl propanamide, benzene, and 3-azabicyclo[3.3.1]nonane-2,4-dione. We have also explored damping, penetration, and basis set effects. In particular, we have provided a way to treat the damping of the induction expansion. Different approximations to the induction energy are evaluated against accurate SAPT(DFT) energies, and we demonstrate the accuracy of our induction models on the formamide-water dimer.

Muon contact hyperfine field in metals: A DFT calculation

NASA Astrophysics Data System (ADS)

Onuorah, Ifeanyi John; Bonfà, Pietro; De Renzi, Roberto

2018-05-01

In positive muon spin rotation and relaxation spectroscopy it is becoming customary to take advantage of density functional theory (DFT) based computational methods to aid the experimental data analysis. DFT-aided muon site determination is especially useful for measurements performed in magnetic materials, where large contact hyperfine interactions may arise. Here we present a systematic analysis of the accuracy of the ab initio estimation of muon's hyperfine contact field on elemental transition metals, performing state-of-the-art spin-polarized plane-wave DFT and using the projector-augmented pseudopotential approach, which allows one to include the core state effects due to the spin ordering. We further validate this method in not-so-simple, noncentrosymmetric metallic compounds, presently of topical interest for their spiral magnetic structure giving rise to skyrmion phases, such as MnSi and MnGe. The calculated hyperfine fields agree with experimental values in all cases, provided the spontaneous spin magnetization of the metal is well reproduced within the approach. To overcome the known limits of the conventional mean-field approximation of DFT on itinerant magnets, we adopt the so-called reduced Stoner theory [L. Ortenzi et al., Phys. Rev. B 86, 064437 (2012), 10.1103/PhysRevB.86.064437]. We establish the accuracy of the estimated muon contact field in metallic compounds with DFT and our results show improved agreement with experiments compared to those of earlier publications.

Modeling Excited States in TiO2 Nanoparticles: On the Accuracy of a TD-DFT Based Description

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

Berardo, Enrico; Hu, Hanshi; Shevlin, S. A.

2014-03-11

We have investigated the suitability of Time-Dependent Density Functional Theory (TD-DFT) to describe vertical low-energy excitations in naked and hydrated titanium dioxide nanoparticles through a comparison with results from Equation-of-Motion Coupled Cluster (EOM-CC) quantum chemistry methods. We demonstrate that for most TiO2 nanoparticles TD-DFT calculations with commonly used exchange-correlation (XC-)potentials (e.g. B3LYP) and EOM-CC methods give qualitatively similar results. Importantly, however, we also show that for an important subset of structures, TD-DFT gives qualitatively different results depending upon the XC-potential used and that in this case only TD-CAM-B3LYP and TD-BHLYP calculations yield results that are consistent with those obtained usingmore » EOM-CC theory. Moreover, we demonstrate that the discrepancies for such structures arise from a particular combination of defects, excitations involving which are charge-transfer excitations and hence are poorly described by XC-potentials that contain no or low fractions of Hartree-Fock like exchange. Finally, we discuss that such defects are readily healed in the presence of ubiquitously present water and that as a result the description of vertical low-energy excitations for hydrated TiO2 nanoparticles is hence non-problematic.« less

Quantitative Modeling of Earth Surface Processes

NASA Astrophysics Data System (ADS)

Pelletier, Jon D.

This textbook describes some of the most effective and straightforward quantitative techniques for modeling Earth surface processes. By emphasizing a core set of equations and solution techniques, the book presents state-of-the-art models currently employed in Earth surface process research, as well as a set of simple but practical research tools. Detailed case studies demonstrate application of the methods to a wide variety of processes including hillslope, fluvial, aeolian, glacial, tectonic, and climatic systems. Exercises at the end of each chapter begin with simple calculations and then progress to more sophisticated problems that require computer programming. All the necessary computer codes are available online at www.cambridge.org/9780521855976. Assuming some knowledge of calculus and basic programming experience, this quantitative textbook is designed for advanced geomorphology courses and as a reference book for professional researchers in Earth and planetary science looking for a quantitative approach to Earth surface processes.

Dehalogenation of persistent halogenated organic compounds: A review of computational studies and quantitative structure-property relationships.

PubMed

Luo, Jin; Hu, Jiwei; Wei, Xionghui; Fu, Liya; Li, Lingyun

2015-07-01

Dehalogenation is one of the highly important degradation reactions for halogenated organic compounds (HOCs) in the environment, which is also being developed as a potential type of the remediation technologies. In combination with the experimental results, intensive efforts have recently been devoted to the development of efficient theoretical methodologies (e.g. multi-scale simulation) to investigate the mechanisms for dehalogenation of HOCs. This review summarizes the structural characteristics of neutral molecules, anionic species and excited states of HOCs as well as their adsorption behavior on the surface of graphene and the Fe cluster. It discusses the key physiochemical properties (e.g. frontier orbital energies and thermodynamic properties) calculated at various levels of theory (e.g. semiempirical, ab initio, density functional theory (DFT) and the periodic DFT) as well as their connections to the reactivity and reaction pathway for the dehalogenation. This paper also reviews the advances in the linear and nonlinear quantitative structure-property relationship models for the dehalogenation kinetics of HOCs and in the mathematical modeling of the dehalogenation processes. Furthermore, prospects of further expansion and exploration of the current research fields are described in this article. Published by Elsevier Ltd.

A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

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

Chavda, Bhavin R., E-mail: chavdabhavin9@gmail.com; Dubey, Rahul P.; Patel, Urmila H.

The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb –London –Paulimore » (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.« less

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship.

PubMed

Wang, Xueding; Xu, Yilian; Yang, Lu; Lu, Xiang; Zou, Hao; Yang, Weiqing; Zhang, Yuanyuan; Li, Zicheng; Ma, Menglin

2018-03-01

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

An EQT-cDFT approach to determine thermodynamic properties of confined fluids.

PubMed

Mashayak, S Y; Motevaselian, M H; Aluru, N R

2015-06-28

We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.

Influence of xc functional on thermal-elastic properties of Ceria: A DFT-based Debye-Grüneisen model approach

NASA Astrophysics Data System (ADS)

Lee, Ji-Hwan; Tak, Youngjoo; Lee, Taehun; Soon, Aloysius

Ceria (CeO2-x) is widely studied as a choice electrolyte material for intermediate-temperature (~ 800 K) solid oxide fuel cells. At this temperature, maintaining its chemical stability and thermal-mechanical integrity of this oxide are of utmost importance. To understand their thermal-elastic properties, we firstly test the influence of various approximations to the density-functional theory (DFT) xc functionals on specific thermal-elastic properties of both CeO2 and Ce2O3. Namely, we consider the local-density approximation (LDA), the generalized gradient approximation (GGA-PBE) with and without additional Hubbard U as applied to the 4 f electron of Ce, as well as the recently popularized hybrid functional due to Heyd-Scuseria-Ernzehof (HSE06). Next, we then couple this to a volume-dependent Debye-Grüneisen model to determine the thermodynamic quantities of ceria at arbitrary temperatures. We find an explicit description of the strong correlation (e.g. via the DFT + U and hybrid functional approach) is necessary to have a good agreement with experimental values, in contrast to the mean-field treatment in standard xc approximations (such as LDA or GGA-PBE). We acknowledge support from Samsung Research Funding Center of Samsung Electronics (SRFC-MA1501-03).

DFT-Assisted Polymorph Identification from Lattice Raman Fingerprinting

PubMed Central

2017-01-01

A combined experimental and theoretical approach, consisting of lattice phonon Raman spectroscopy and density functional theory (DFT) calculations, is proposed as a tool for lattice dynamics characterization and polymorph phase identification. To illustrate the reliability of the method, the lattice phonon Raman spectra of two polymorphs of the molecule 2,7-dioctyloxy[1]benzothieno[3,2-b]benzothiophene are investigated. We show that DFT calculations of the lattice vibrations based on the known crystal structures, including many-body dispersion van der Waals (MBD-vdW) corrections, predict experimental data within an accuracy of ≪5 cm–1 (≪0.6 meV). Due to the high accuracy of the simulations, they can be used to unambiguously identify different polymorphs and to characterize the nature of the lattice vibrations and their relationship to the structural properties. More generally, this work implies that DFT-MBD-vdW is a promising method to describe also other physical properties that depend on lattice dynamics like charge transport. PMID:28731723

A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene.

PubMed

Jaraíz, Martín; Enríquez, Lourdes; Pinacho, Ruth; Rubio, José E; Lesarri, Alberto; López-Pérez, José L

2017-04-07

A novel DFT-based Reaction Kinetics (DFT-RK) simulation approach, employed in combination with real-time data from reaction monitoring instrumentation (like UV-vis, FTIR, Raman, and 2D NMR benchtop spectrometers), is shown to provide a detailed methodology for the analysis and design of complex synthetic chemistry schemes. As an example, it is applied to the opening of epoxides by titanocene in THF, a catalytic system with abundant experimental data available. Through a DFT-RK analysis of real-time IR data, we have developed a comprehensive mechanistic model that opens new perspectives to understand previous experiments. Although derived specifically from the opening of epoxides, the prediction capabilities of the model, built on elementary reactions, together with its practical side (reaction kinetics simulations of real experimental conditions) make it a useful simulation tool for the design of new experiments, as well as for the conception and development of improved versions of the reagents. From the perspective of the methodology employed, because both the computational (DFT-RK) and the experimental (spectroscopic data) components can follow the time evolution of several species simultaneously, it is expected to provide a helpful tool for the study of complex systems in synthetic chemistry.

Design Techniques for Uniform-DFT, Linear Phase Filter Banks

NASA Technical Reports Server (NTRS)

Sun, Honglin; DeLeon, Phillip

1999-01-01

Uniform-DFT filter banks are an important class of filter banks and their theory is well known. One notable characteristic is their very efficient implementation when using polyphase filters and the FFT. Separately, linear phase filter banks, i.e. filter banks in which the analysis filters have a linear phase are also an important class of filter banks and desired in many applications. Unfortunately, it has been proved that one cannot design critically-sampled, uniform-DFT, linear phase filter banks and achieve perfect reconstruction. In this paper, we present a least-squares solution to this problem and in addition prove that oversampled, uniform-DFT, linear phase filter banks (which are also useful in many applications) can be constructed for perfect reconstruction. Design examples are included illustrate the methods.

QSAR, DFT and molecular modeling studies of peptides from HIV-1 to describe their recognition properties by MHC-I.

PubMed

Andrade-Ochoa, S; García-Machorro, J; Bello, Martiniano; Rodríguez-Valdez, L M; Flores-Sandoval, C A; Correa-Basurto, J

2017-08-03

Human immunodeficiency virus type-1 (HIV-1) has infected more than 40 million people around the world. HIV-1 treatment still has several side effects, and the development of a vaccine, which is another potential option for decreasing human infections, has faced challenges. This work presents a computational study that includes a quantitative structure activity relationship(QSAR) using density functional theory(DFT) for reported peptides to identify the principal quantum mechanics descriptors related to peptide activity. In addition, the molecular recognition properties of these peptides are explored on major histocompatibility complex I (MHC-I) through docking and molecular dynamics (MD) simulations accompanied by the Molecular Mechanics Generalized Born Surface Area (MMGBSA) approach for correlating peptide activity reported elsewhere vs. theoretical peptide affinity. The results show that the carboxylic acid and hydroxyl groups are chemical moieties that have an inverse relationship with biological activity. The number of sulfides, pyrroles and imidazoles from the peptide structure are directly related to biological activity. In addition, the HOMO orbital energy values of the total absolute charge and the Ghose-Crippen molar refractivity of peptides are descriptors directly related to the activity and affinity on MHC-I. Docking and MD simulation studies accompanied by an MMGBSA analysis show that the binding free energy without considering the entropic contribution is energetically favorable for all the complexes. Furthermore, good peptide interaction with the most affinity is evaluated experimentally for three proteins. Overall, this study shows that the combination of quantum mechanics descriptors and molecular modeling studies could help describe the immunogenic properties of peptides from HIV-1.

Rate constants of hydroxyl radical oxidation of polychlorinated biphenyls in the gas phase: A single-descriptor based QSAR and DFT study.

PubMed

Yang, Zhihui; Luo, Shuang; Wei, Zongsu; Ye, Tiantian; Spinney, Richard; Chen, Dong; Xiao, Ruiyang

2016-04-01

The second-order rate constants (k) of hydroxyl radical (·OH) with polychlorinated biphenyls (PCBs) in the gas phase are of scientific and regulatory importance for assessing their global distribution and fate in the atmosphere. Due to the limited number of measured k values, there is a need to model the k values for unknown PCBs congeners. In the present study, we developed a quantitative structure-activity relationship (QSAR) model with quantum chemical descriptors using a sequential approach, including correlation analysis, principal component analysis, multi-linear regression, validation, and estimation of applicability domain. The result indicates that the single descriptor, polarizability (α), plays an important role in determining the reactivity with a global standardized function of lnk = -0.054 × α ‒ 19.49 at 298 K. In order to validate the QSAR predicted k values and expand the current k value database for PCBs congeners, an independent method, density functional theory (DFT), was employed to calculate the kinetics and thermodynamics of the gas-phase ·OH oxidation of 2,4',5-trichlorobiphenyl (PCB31), 2,2',4,4'-tetrachlorobiphenyl (PCB47), 2,3,4,5,6-pentachlorobiphenyl (PCB116), 3,3',4,4',5,5'-hexachlorobiphenyl (PCB169), and 2,3,3',4,5,5',6-heptachlorobiphenyl (PCB192) at 298 K at B3LYP/6-311++G**//B3LYP/6-31 + G** level of theory. The QSAR predicted and DFT calculated k values for ·OH oxidation of these PCB congeners exhibit excellent agreement with the experimental k values, indicating the robustness and predictive power of the single-descriptor based QSAR model we developed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantitative Predictive Models for Systemic Toxicity (SOT)

EPA Science Inventory

Models to identify systemic and specific target organ toxicity were developed to help transition the field of toxicology towards computational models. By leveraging multiple data sources to incorporate read-across and machine learning approaches, a quantitative model of systemic ...

Experimental and DFT study of thiol-stabilized Pt/CNTs catalysts.

PubMed

Li, L; Chen, S G; Wei, Z D; Qi, X Q; Xia, M R; Wang, Y Q

2012-12-28

Using a combination of experiments and density functional theory (DFT) calculations, we explored the mechanisms of the stabilization effect of the thiolized (-SH) group on the Pt/SH-CNTs catalyst. Pt particles supported on the hydroxyl functionalized CNTs (Pt/OH-CNTs) are synthesized as a baseline for comparison. Experimentally, the platinum on OH-CNTs has a stronger tendency for aggregation than that on SH-CNTs. The differences in the oxidation resistance, migration activation energy, and corrosion resistance between the Pt/SH-CNTs and Pt/OH-CNTs are calculated using DFT. The DFT calculations indicate that the -SH group enhances the oxidation resistance of the Pt cluster and CNTs and restricts Pt migration on the CNTs. DFT calculations also suggest that the enhanced stability of Pt/SH-CNTs originates from the increased interaction between Pt and SH-CNTs and the depressed d-band center of the Pt NPs. Thus, the functional groups on the CNTs used for stabilization of supported Pt NPs should provide a deposit and anchor site for Pt NPs and maintain the perfect structure of CNTs rather than destroying it.

The standard mean-field treatment of inter-particle attraction in classical DFT is better than one might expect

NASA Astrophysics Data System (ADS)

Archer, Andrew J.; Chacko, Blesson; Evans, Robert

2017-07-01

In classical density functional theory (DFT), the part of the Helmholtz free energy functional arising from attractive inter-particle interactions is often treated in a mean-field or van der Waals approximation. On the face of it, this is a somewhat crude treatment as the resulting functional generates the simple random phase approximation (RPA) for the bulk fluid pair direct correlation function. We explain why using standard mean-field DFT to describe inhomogeneous fluid structure and thermodynamics is more accurate than one might expect based on this observation. By considering the pair correlation function g(x) and structure factor S(k) of a one-dimensional model fluid, for which exact results are available, we show that the mean-field DFT, employed within the test-particle procedure, yields results much superior to those from the RPA closure of the bulk Ornstein-Zernike equation. We argue that one should not judge the quality of a DFT based solely on the approximation it generates for the bulk pair direct correlation function.

The influence of the dispersion corrections on the performance of DFT method in modeling HNgY noble gas molecules and their complexes

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Sadlej, Joanna

2018-01-01

The letter reports a comparative assessment of the usefulness of the two different Grimme's corrections for evaluating dispersion interaction (DFT-D3 and DFT-D3BJ) for the representative molecules of the family of noble-gas hydrides HXeY and their complexes with the HZ molecules, where Y and Z are F/Cl/OH/SH. with special regard to the dispersion term calculated by means of the symmetry-adapted perturbation theory (at the SAPT0 level). The results indicate that despite differences in the total interactions energy (DFT + corrections) versus SAPT0 results, the sequence of contributions of the individual dispersion terms is still maintained. Both dispersion corrections perform similarly and they improve the results suggesting that it is worthwhile to include them in calculations.

FAST TRACK COMMUNICATION A DFT + DMFT approach for nanosystems

NASA Astrophysics Data System (ADS)

Turkowski, Volodymyr; Kabir, Alamgir; Nayyar, Neha; Rahman, Talat S.

2010-11-01

We propose a combined density-functional-theory-dynamical-mean-field-theory (DFT + DMFT) approach for reliable inclusion of electron-electron correlation effects in nanosystems. Compared with the widely used DFT + U approach, this method has several advantages, the most important of which is that it takes into account dynamical correlation effects. The formalism is illustrated through different calculations of the magnetic properties of a set of small iron clusters (number of atoms 2 <= N <= 5). It is shown that the inclusion of dynamical effects leads to a reduction in the cluster magnetization (as compared to results from DFT + U) and that, even for such small clusters, the magnetization values agree well with experimental estimations. These results justify confidence in the ability of the method to accurately describe the magnetic properties of clusters of interest to nanoscience.

Conformational, vibrational, NMR and DFT studies of N-methylacetanilide.

PubMed

Arjunan, V; Santhanam, R; Rani, T; Rosi, H; Mohan, S

2013-03-01

A detailed conformational, vibrational, NMR and DFT studies of N-methylacetanilide have been carried out. In DFT, B3LYP method have been used with 6-31G(**), 6-311++G(**) and cc-pVTZ basis sets. The vibrational frequencies were calculated resulting in IR and Raman frequencies together with intensities and Raman depolarisation ratios. The dipole moment derivatives were computed analytically. Owing to the complexity of the molecule, the potential energy distributions of the vibrational modes of the compound are also calculated. Isoelectronic molecular electrostatic potential surface (MEP) and electron density surface were examined. (1)H and (13)C NMR isotropic chemical shifts were calculated and the assignments made are compared with the experimental values. The energies of important MO's of the compound were also determined from TD-DFT method. Copyright © 2012 Elsevier B.V. All rights reserved.

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

Equation of state of mixtures: density functional theory (DFT) simulations and experiments on Sandia's Z machine

NASA Astrophysics Data System (ADS)

Magyar, R. J.; Root, S.; Haill, T. A.; Schroen, D. G.; Mattsson, T. R.; Flicker, D. G.; Sandia National Laboratories Collaboration

2011-06-01

Mixtures of materials are expected to behave quite differently from their isolated constituents, particularly when the constituents atomic numbers differ significantly. To investigate the mixture behavior, we performed density functional theory (DFT) calculations on xenon/hydrogen, xenon/ethane, and platinum/hydrocarbon mixtures. In addition, we performed shock compression experiments on platinum-doped hydrocarbon foams up to 480 GPa using the Sandia Z-accelerator. Since the DFT simulations treat electrons and nuclei generically, simulations of pure and mix systems are expected to be of comparable accuracy. The DFT and experimental results are compared to hydrodynamic simulations using different mixing models in the equation of state. The role of de-mixing and the relative contributions of the enthalpy of mixing are explored. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Model-Based Linkage Analysis of a Quantitative Trait.

PubMed

Song, Yeunjoo E; Song, Sunah; Schnell, Audrey H

2017-01-01

Linkage Analysis is a family-based method of analysis to examine whether any typed genetic markers cosegregate with a given trait, in this case a quantitative trait. If linkage exists, this is taken as evidence in support of a genetic basis for the trait. Historically, linkage analysis was performed using a binary disease trait, but has been extended to include quantitative disease measures. Quantitative traits are desirable as they provide more information than binary traits. Linkage analysis can be performed using single-marker methods (one marker at a time) or multipoint (using multiple markers simultaneously). In model-based linkage analysis the genetic model for the trait of interest is specified. There are many software options for performing linkage analysis. Here, we use the program package Statistical Analysis for Genetic Epidemiology (S.A.G.E.). S.A.G.E. was chosen because it also includes programs to perform data cleaning procedures and to generate and test genetic models for a quantitative trait, in addition to performing linkage analysis. We demonstrate in detail the process of running the program LODLINK to perform single-marker analysis, and MLOD to perform multipoint analysis using output from SEGREG, where SEGREG was used to determine the best fitting statistical model for the trait.

DFT Modeling of Cross-Linked Polyethylene: Role of Gold Atoms and Dispersion Interactions.

PubMed

Blaško, Martin; Mach, Pavel; Antušek, Andrej; Urban, Miroslav

2018-02-08

Using DFT modeling, we analyze the concerted action of gold atoms and dispersion interactions in cross-linked polyethylene. Our model consists of two oligomer chains (PEn) with 7, 11, 15, 19, or 23 carbon atoms in each oligomer cross-linked with one to three Au atoms through C-Au-C bonds. In structures with a single gold atom the C-Au-C bond is located in the central position of the oligomer. Binding energies (BEs) with respect to two oligomer radical fragments and Au are as high as 362-489 kJ/mol depending on the length of the oligomer chain. When the dispersion contribution in PEn-Au-PEn oligomers is omitted, BE is almost independent of the number of carbon atoms, lying between 293 and 296 kJ/mol. The dispersion energy contributions to BEs in PEn-Au-PEn rise nearly linearly with the number of carbon atoms in the PEn chain. The carbon-carbon distance in the C-Au-C moiety is around 4.1 Å, similar to the bond distance between saturated closed shell chains in the polyethylene crystal. BEs of pure saturated closed shell PEn-PEn oligomers are 51-187 kJ/mol. Both Au atoms and dispersion interactions contribute considerably to the creation of nearly parallel chains of oligomers with reasonably high binding energies.

Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

NASA Astrophysics Data System (ADS)

Srivastava, Santosh K.; Singh, Vipin B.

2013-11-01

Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

Semi-Local DFT Functionals with Exact-Exchange-Like Features: Beyond the AK13

NASA Astrophysics Data System (ADS)

Armiento, Rickard

The Armiento-Kümmel functional from 2013 (AK13) is a non-empirical semi-local exchange functional on generalized gradient approximation form (GGA) in Kohn-Sham (KS) density functional theory (DFT). Recent works have established that AK13 gives improved electronic-structure exchange features over other semi-local methods, with a qualitatively improved orbital description and band structure. For example, the Kohn-Sham band gap is greatly extended, as it is for exact exchange. This talk outlines recent efforts towards new exchange-correlation functionals based on, and extending, the AK13 design ideas. The aim is to improve the quantitative accuracy, the description of energetics, and to address other issues found with the original formulation. Swedish e-Science Research Centre (SeRC).

Implementation of DFT application on ternary optical computer

NASA Astrophysics Data System (ADS)

Junjie, Peng; Youyi, Fu; Xiaofeng, Zhang; Shuai, Kong; Xinyu, Wei

2018-03-01

As its characteristics of huge number of data bits and low energy consumption, optical computing may be used in the applications such as DFT etc. which needs a lot of computation and can be implemented in parallel. According to this, DFT implementation methods in full parallel as well as in partial parallel are presented. Based on resources ternary optical computer (TOC), extensive experiments were carried out. Experimental results show that the proposed schemes are correct and feasible. They provide a foundation for further exploration of the applications on TOC that needs a large amount calculation and can be processed in parallel.

Water at silica/liquid water interfaces investigated by DFT-MD simulations

NASA Astrophysics Data System (ADS)

Gaigeot, Marie-Pierre

This talk is dedicated to probing the microscopic structural organization of water at silica/liquid water interfaces including electrolytes by first principles DFT-based molecular dynamics simulations (DFT-MD). We will present our very recent DFT-MD simulations of electrolytic (KCl, NaCl, NaI) silica/liquid water interfaces in order to unravel the intertwined structural properties of water and electrolytes at the crystalline quartz/liquid water and amorphous silica/liquid water interfaces. DFT-MD simulations provide direct knowledge of the structural organization of water and the H-Bond network formed between the water molecules within the different water layers above the silica surface. One can furthermore extract vibrational signatures of the water molecules within the interfacial layers from the DFT-MD simulations, especially non-linear SFG (Sum Frequency generation) signatures that are active at solid/liquid interfaces. The strength of the simulated spectra is that a detailed analysis of the signatures in terms of the water/water H-Bond networks formed within the interfacial water layers and in terms of the water/silica or water/electrolytes H-Bond networks can be given. Comparisons of SFG spectra between quartz/water/electrolytes and amorphous silica/water/electrolytes interfaces allow us to definitely conclude on how the structural arrangements of liquid water at these electrolytic interfaces modulate the final spectroscopic signatures. Invited speaker.

Why is MP2-Water "Cooler" and "Denser" than DFT-Water?

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

Willow, Soohaeng Y.; Zeng, Xiao Cheng; Xantheas, Sotiris S.

To maintain water in the liquid phase at the correct (1 g/cm3) density during first-principles simulations, density-functional theory (DFT) with a dispersionless generalized-gradient-approximation (GGA) functional requires a much higher temperature and pressure than the ambient conditions. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water performed by Del Ben et al. [J. Chem. Phys. Lett. 4, 3753 (2013); J. Chem. Phys. 143, 054506 (2015)] and by us [Willow et al., Sci. Rep. 5, 14358 (2015)] required a lower temperature and a negative pressure than DFT to keep water liquid. Here, we present a unifying explanation of these trendsmore » derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the calculated temperature and pressure of the liquid phase are strongly correlated with the polarizability of water and the dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for water to be liquid. In MP2 and DFT/GGA, the dispersion interaction is stronger and weaker (or lacking), respectively. This explains why liquid water contracts uniformly and becomes too dense in MP2, whereas the opposite is the case for dispersionless DFT/GGA.« less

SERS and DFT study of p-hydroxybenzoic acid adsorbed on colloidal silver particles.

PubMed

Chen, Y; Chen, S J; Li, S; Wei, J J

2015-10-16

In this study, normal Raman spectra of p—hydroxybenzoic acid (PHBA) powder and its surface—enhanced Raman scattering (SERS) spectra in silver colloidal solutions were measured under near infrared excitation conditions. In theoretical calculation, two models of PHBA adsorbed on the surfaces of silver nanoparticles were established. The Raman frequencies of these two models using density functional theory (DFT) method were calculated, and compared with the experimental results. It was found that the calculated Raman frequencies were in good agreement with experimental values, which indicates that there are two enhanced mechanism physical (electromagnetic, EM) enhancement and chemical (charge—transfer, CT) enhancement, in silver colloidal solutions regarding SERS effect. Furthermore, from high—quality SERS spectrum of PHBA obtained in silver colloids, we inferred that PHBA molecules in silver colloids adsorb onto the metal surfaces through carboxyl at a perpendicular orientation. The combination of SERS spectra and DFT calculation is thus useful for studies of the adsorption—orientation of a molecule on a metal colloid.

On the number of multiplications necessary to compute a length-2 exp n DFT

NASA Technical Reports Server (NTRS)

Heideman, M. T.; Burrus, C. S.

1986-01-01

The number of multiplications necessary and sufficient to compute a length-2 exp n DFT is determined. The method of derivation is shown to apply to the multiplicative complexity results of Winograd (1980, 1981) for a length-p exp n DFT, for p an odd prime number. The multiplicative complexity of the one-dimensional DFT is summarized for many possible lengths.

Ethane and Xenon mixing: density functional theory (DFT) simulations and experiments on Sandia's Z machine

NASA Astrophysics Data System (ADS)

Magyar, Rudolph; Root, Seth; Mattsson, Thomas; Cochrane, Kyle

2012-02-01

The combination of ethane and xenon is one of the simplest binary mixtures in which bond breaking is expected to play a role under shock conditions. At cryogenic conditions, xenon is often understood to mix with alkanes such as Ethane as if it were also an alkane, but this model is expected to break down at higher temperatures and pressures. To investigate the breakdown, we have performed density functional theory (DFT) calculations on several xenon/ethane mixtures. Additionally, we have performed shock compression experiments on Xenon-Ethane using the Sandia Z - accelerator. The DFT and experimental results are compared to hydrodynamic simulations using different mixing models in the equation of state. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Adaptive DFT-based Interferometer Fringe Tracking

NASA Technical Reports Server (NTRS)

Wilson, Edward; Pedretti, Ettore; Bregman, Jesse; Mah, Robert W.; Traub, Wesley A.

2004-01-01

An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) observatory at Mt. Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on off-line data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately 2.0 milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse.

Embedding multiple watermarks in the DFT domain using low- and high-frequency bands

NASA Astrophysics Data System (ADS)

Ganic, Emir; Dexter, Scott D.; Eskicioglu, Ahmet M.

2005-03-01

Although semi-blind and blind watermarking schemes based on Discrete Cosine Transform (DCT) or Discrete Wavelet Transform (DWT) are robust to a number of attacks, they fail in the presence of geometric attacks such as rotation, scaling, and translation. The Discrete Fourier Transform (DFT) of a real image is conjugate symmetric, resulting in a symmetric DFT spectrum. Because of this property, the popularity of DFT-based watermarking has increased in the last few years. In a recent paper, we generalized a circular watermarking idea to embed multiple watermarks in lower and higher frequencies. Nevertheless, a circular watermark is visible in the DFT domain, providing a potential hacker with valuable information about the location of the watermark. In this paper, our focus is on embedding multiple watermarks that are not visible in the DFT domain. Using several frequency bands increases the overall robustness of the proposed watermarking scheme. Specifically, our experiments show that the watermark embedded in lower frequencies is robust to one set of attacks, and the watermark embedded in higher frequencies is robust to a different set of attacks.

Electronic structure and equation of state of Sm2Co17 from first-principles DFT+ U

NASA Astrophysics Data System (ADS)

Huang, Patrick; Butch, Nicholas P.; Jeffries, Jason R.; McCall, Scott K.

2013-03-01

Rare-earth intermetallics have important applications as permanent magnet materials, and the rational optimization of their properties would benefit greatly from guidance from ab initio modeling. However, these systems are particularly challenging for current electronic structure methods. Here, we present an ab initio study of the prototype material Sm2Co17 and related compounds, using density functional theory with a Hubbard correction for the Sm 4 f-electrons (DFT+ U method) and ultrasoft pseudopotentials. The Hubbard U parameter is derived from first principles [Cococcioni and de Gironcoli, PRB 71, 035105 (2005)], not fit to experiment. Our calculations are in good agreement with recent photoemission measurements at ambient pressure and the equation of state up to 40 GPa, thus supporting the validity of our DFT+ U model. Prepared by LLNL under Contract DE-AC52-07NA27344.

Modeling with Young Students--Quantitative and Qualitative.

ERIC Educational Resources Information Center

Bliss, Joan; Ogborn, Jon; Boohan, Richard; Brosnan, Tim; Mellar, Harvey; Sakonidis, Babis

1999-01-01

A project created tasks and tools to investigate quality and nature of 11- to 14-year-old pupils' reasoning with quantitative and qualitative computer-based modeling tools. Tasks and tools were used in two innovative modes of learning: expressive, where pupils created their own models, and exploratory, where pupils investigated an expert's model.…

A fast D.F.T. algorithm using complex integer transforms

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1978-01-01

Winograd (1976) has developed a new class of algorithms which depend heavily on the computation of a cyclic convolution for computing the conventional DFT (discrete Fourier transform); this new algorithm, for a few hundred transform points, requires substantially fewer multiplications than the conventional FFT algorithm. Reed and Truong have defined a special class of finite Fourier-like transforms over GF(q squared), where q = 2 to the p power minus 1 is a Mersenne prime for p = 2, 3, 5, 7, 13, 17, 19, 31, 61. In the present paper it is shown that Winograd's algorithm can be combined with the aforementioned Fourier-like transform to yield a new algorithm for computing the DFT. A fast method for accurately computing the DFT of a sequence of complex numbers of very long transform-lengths is thus obtained.

Molecular structure, vibrational spectra and DFT molecular orbital calculations (TD-DFT and NMR) of the antiproliferative drug Methotrexate

NASA Astrophysics Data System (ADS)

Ayyappan, S.; Sundaraganesan, N.; Aroulmoji, V.; Murano, E.; Sebastian, S.

2010-09-01

The FT-IR and FT-Raman spectral studies of the Methotrexate (MTX) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of MTX have been investigated with the help of B3LYP density functional theory (DFT) using 6-31G(d) as basis set. Detailed analysis of the vibrational spectra has been made with the aid of theoretically predicted vibrational frequencies. The vibrational analysis confirms the differently acting ring modes, steric repulsion, conjugation and back-donation. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complement with the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Good correlations between the experimental 1H and 13C NMR chemical shifts in DMSO solution and calculated GIAO shielding tensors were found.

Zinc binding in HDAC inhibitors: a DFT study.

PubMed

Wang, Difei; Helquist, Paul; Wiest, Olaf

2007-07-06

Histone deacetylases (HDACs) are attractive targets for the treatment of cancers and a variety of other diseases. Most currently studied HDAC inhibitors contain hydroxamic acids, which are potentially problematic in the development of practical drugs. DFT calculations of the binding modes and free energies of binding for a variety of other functionalities in a model active site of HDAC are described. The protonation state of hydroxamic acids in the active site and the origin of the high affinity are discussed. These results emphasize the importance of a carefully chosen pKa for zinc binding and provide guidance for the design of novel, non-hydroxamic acid HDAC inhibitors.

Secure Image Transmission over DFT-precoded OFDM-VLC systems based on Chebyshev Chaos scrambling

NASA Astrophysics Data System (ADS)

Wang, Zhongpeng; Qiu, Weiwei

2017-08-01

This paper proposes a physical layer image secure transmission scheme for discrete Fourier transform (DFT) precoded OFDM-based visible light communication systems by using Chebyshev chaos maps. In the proposed scheme, 256 subcarriers and QPSK modulation are employed. The transmitted digital signal of the image is encrypted with a Chebyshev chaos sequence. The encrypted signal is then transformed by a DFT precoding matrix to reduce the PAPR of the OFDM signal. After that, the encrypted and DFT-precoded OFDM are transmitted over a VLC channel. The simulation results show that the proposed image security transmission scheme can not only protect the DFT-precoded OFDM-based VLC from eavesdroppers but also improve BER performance.

Direct Production of Propene from the Thermolysis of Poly(β-hydroxybutyrate) (PHB). An Experimental and DFT Investigation.

PubMed

Clark, Jared M; Pilath, Heidi M; Mittal, Ashutosh; Michener, William E; Robichaud, David J; Johnson, David K

2016-01-28

We demonstrate a synthetic route toward the production of propene directly from poly(β-hydroxybutyrate) (PHB), the most common of a wide range of high-molecular-mass microbial polyhydroxyalkanoates. Propene, a major commercial hydrocarbon, was obtained from the depolymerization of PHB and subsequent decarboxylation of the crotonic acid monomer in good yields (up to 75 mol %). The energetics of PHB depolymerization and the gas-phase decarboxylation of crotonic acid were also studied using density functional theory (DFT). The average activation energy for the cleavage of the R'C(O)O-R linkage is calculated to be 163.9 ± 7.0 kJ mol(-1). Intramolecular, autoacceleration effects regarding the depolymerization of PHB, as suggested in some literature accounts, arising from the formation of crotonyl and carboxyl functional groups in the products could not be confirmed by the results of DFT and microkinetic modeling. DFT results, however, suggest that intermolecular catalysis involving terminal carboxyl groups may accelerate PHB depolymerization. Activation energies for this process were estimated to be about 20 kJ mol(-1) lower than that for the noncatalyzed ester cleavage, 144.3 ± 6.4 kJ mol(-1). DFT calculations predict the decarboxylation of crotonic acid to follow second-order kinetics with an activation energy of 147.5 ± 6.3 kJ mol(-1), consistent with that measured experimentally, 146.9 kJ mol(-1). Microkinetic modeling of the PHB to propene overall reaction predicts decarboxylation of crotonic acid to be the rate-limiting step, consistent with experimental observations. The results also indicate that improvements made to enhance the isomerization of crotonic acid to vinylacetic acid will improve the direct conversion of PHB to propene.

TD-DFT Insight into Photodissociation of Co-C Bond in Coenzyme B12

NASA Astrophysics Data System (ADS)

Kozlowski, Pawel; Liu, Hui; Kornobis, Karina; Lodowski, Piotr; Jaworska, Maria

2013-12-01

Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo-C → σ*Co-C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a MLCT (metal-to-ligand charge transfer) and a σ bonding-ligand charge transfer (SBLCT) states.

DFT-GGA errors in NO chemisorption energies on (111) transition metal surfaces

NASA Astrophysics Data System (ADS)

Huang, Xu; Mason, Sara E.

2014-03-01

We investigate whether well-known DFT-GGA errors in predicting the chemisorption energy (Echem) of CO on transition metal surfaces manifest in analogous NO chemisorption systems. While widely investigated in the case of CO/metal, analogous DFT-GGA errors have long been claimed to be absent in NO/metal chemisorption. Here, we provide theoretical evidence of systematic enhanced back-donation in NO/metal chemisorption at the DFT-GGA level. We use electronic structure analysis to show that the partially filled molecular NO 2π* orbital rehybridizes with the transition metal d-band to form new bonding and anti-bonding states. We relate the back-donation charge transfer associated with chemisorption to the promotion of an electron from the 5σ orbital to the 2π* orbital in the gas-phase NO G2Σ- ← X2Π excitation. We establish linear relationships between Echem and ΔEG ← X and formulate an Echem correction scheme in the style of Mason et al. [Physical Review B 69, 161401(R)]. We apply the NO Echem correction method to the (111) surfaces of Pt, Pd, Rh, and Ir, with NO chemisorption modeled at a coverage of 0.25 ML. We note that the slope of Echemvs. ΔEG ← X and the dipole moment depend strongly on adsorption site for each metal, and we construct an approximate correction scheme which we test using NO/Pt(100) chemisorption.

Quantitative model validation of manipulative robot systems

NASA Astrophysics Data System (ADS)

Kartowisastro, Iman Herwidiana

This thesis is concerned with applying the distortion quantitative validation technique to a robot manipulative system with revolute joints. Using the distortion technique to validate a model quantitatively, the model parameter uncertainties are taken into account in assessing the faithfulness of the model and this approach is relatively more objective than the commonly visual comparison method. The industrial robot is represented by the TQ MA2000 robot arm. Details of the mathematical derivation of the distortion technique are given which explains the required distortion of the constant parameters within the model and the assessment of model adequacy. Due to the complexity of a robot model, only the first three degrees of freedom are considered where all links are assumed rigid. The modelling involves the Newton-Euler approach to obtain the dynamics model, and the Denavit-Hartenberg convention is used throughout the work. The conventional feedback control system is used in developing the model. The system behavior to parameter changes is investigated as some parameters are redundant. This work is important so that the most important parameters to be distorted can be selected and this leads to a new term called the fundamental parameters. The transfer function approach has been chosen to validate an industrial robot quantitatively against the measured data due to its practicality. Initially, the assessment of the model fidelity criterion indicated that the model was not capable of explaining the transient record in term of the model parameter uncertainties. Further investigations led to significant improvements of the model and better understanding of the model properties. After several improvements in the model, the fidelity criterion obtained was almost satisfied. Although the fidelity criterion is slightly less than unity, it has been shown that the distortion technique can be applied in a robot manipulative system. Using the validated model, the importance of

A series of 2, 4, 5-trisubstituted oxazole: Synthesis, characterization and DFT modelling

NASA Astrophysics Data System (ADS)

Kadam, Vinay S.; Shaikh, Saminaparwin G.; Patel, Arun L.

2016-06-01

A new series of 2,4,5-trisubstituted oxazole were synthesized with good yields using simple methodology. All the compounds were thoroughly characterized by IR, NMR (1H and 13C) and mass spectrometry and structures of 2-(4-butyloxyphenyl)-4,5-dimethyloxazole (5b) and 4,5-dimethyl-2-(4-(octyloxy)phenyl)oxazole(5e) were unambiguously determined by X-ray crystallography. Evidently, the crystal structures of these compounds showed C-H⋯N and C-H⋯O intermolecular interactions. The electronic structures of these compounds were also studied by DFT at B3LYP/6-311G ++ level of theory.

What Are We Doing When We Translate from Quantitative Models?

PubMed Central

Critchfield, Thomas S; Reed, Derek D

2009-01-01

Although quantitative analysis (in which behavior principles are defined in terms of equations) has become common in basic behavior analysis, translational efforts often examine everyday events through the lens of narrative versions of laboratory-derived principles. This approach to translation, although useful, is incomplete because equations may convey concepts that are difficult to capture in words. To support this point, we provide a nontechnical introduction to selected aspects of quantitative analysis; consider some issues that translational investigators (and, potentially, practitioners) confront when attempting to translate from quantitative models; and discuss examples of relevant translational studies. We conclude that, where behavior-science translation is concerned, the quantitative features of quantitative models cannot be ignored without sacrificing conceptual precision, scientific and practical insights, and the capacity of the basic and applied wings of behavior analysis to communicate effectively. PMID:22478533

6 Principles for Quantitative Reasoning and Modeling

ERIC Educational Resources Information Center

Weber, Eric; Ellis, Amy; Kulow, Torrey; Ozgur, Zekiye

2014-01-01

Encouraging students to reason with quantitative relationships can help them develop, understand, and explore mathematical models of real-world phenomena. Through two examples--modeling the motion of a speeding car and the growth of a Jactus plant--this article describes how teachers can use six practical tips to help students develop quantitative…

FT-IR and DFT study of lemon peel

NASA Astrophysics Data System (ADS)

Berezin, K. V.; Likhter, A. M.; Shagautdinova, I. T.; Chernavina, M. L.; Novoselova, A. V.

2017-03-01

Experimental FT-IR spectra of lemon peel are registered in the 650 - 3800 cm-1 range. The influence of peel artificial and natural dehydration on its vibrational spectrum is studied. The colored outer surface of lemon peel is proved not to have a significant impact on FT-IR spectrum. It is determined that only dehydration processes affect the FT-IR vibrational spectrum of the peel when a lemon is stored for 28 days under natural laboratory conditions. Polymer molecule models for dietary fibers, such as cellulose, hemicellulose, pectin, lignin, as well as hesperidin - flavonoid glycoside, and free moisture cluster are developed within the framework of DFT/B3LYP/6-31G(d) theoretical method. By implementing supramolecular approach, modeling of the vibrational FT-IR spectrum of lemon peel is carried out and its detailed theoretical interpretation is presented.

Structure, IR and Raman spectra of phosphotrihydrazide studied by DFT

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2016-09-01

The FTIR and FT Raman measurements of the phosphotrihydrazide (S)P[N(Me)-NH2]3 have been performed. This compound is a zero generation dendrimer G0 with terminal amine groups. Structural optimization and normal mode analysis were obtained for G0 by the density functional theory (DFT). Optimized geometric bond length and angles obtained by DFT show good agreement with experiment. The amine terminal groups are characterized by the well-defined bands at 3321, 3238, 1614 cm- 1 in the experimental IR spectrum and by bands at 3327, 3241 cm- 1 in the Raman spectrum of G0. The experimental frequencies of asymmetric and symmetric NH2 stretching vibrations of amine group are lower than theoretical values due to intramolecular Nsbnd H ⋯ S hydrogen bond. This hydrogen bond is also responsible for higher experimental infrared intensity of these bands as compared with theoretical values. Relying on DFT calculations a complete vibrational assignment is proposed for the studied dendrimer.

Quantitative modeling of soil genesis processes

NASA Technical Reports Server (NTRS)

Levine, E. R.; Knox, R. G.; Kerber, A. G.

1992-01-01

For fine spatial scale simulation, a model is being developed to predict changes in properties over short-, meso-, and long-term time scales within horizons of a given soil profile. Processes that control these changes can be grouped into five major process clusters: (1) abiotic chemical reactions; (2) activities of organisms; (3) energy balance and water phase transitions; (4) hydrologic flows; and (5) particle redistribution. Landscape modeling of soil development is possible using digitized soil maps associated with quantitative soil attribute data in a geographic information system (GIS) framework to which simulation models are applied.

Assessing the density functional theory-based multireference configuration interaction (DFT/MRCI) method for transition metal complexes

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

Escudero, Daniel, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de; Thiel, Walter, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de

2014-05-21

We report an assessment of the performance of density functional theory-based multireference configuration interaction (DFT/MRCI) calculations for a set of 3d- and 4d-transition metal (TM) complexes. The DFT/MRCI results are compared to published reference data from reliable high-level multi-configurational ab initio studies. The assessment covers the relative energies of different ground-state minima of the highly correlated CrF{sub 6} complex, the singlet and triplet electronically excited states of seven typical TM complexes (MnO{sub 4}{sup −}, Cr(CO){sub 6}, [Fe(CN){sub 6}]{sup 4−}, four larger Fe and Ru complexes), and the corresponding electronic spectra (vertical excitation energies and oscillator strengths). It includes comparisons withmore » results from different flavors of time-dependent DFT (TD-DFT) calculations using pure, hybrid, and long-range corrected functionals. The DFT/MRCI method is found to be superior to the tested TD-DFT approaches and is thus recommended for exploring the excited-state properties of TM complexes.« less

Accurate Energies and Orbital Description in Semi-Local Kohn-Sham DFT

NASA Astrophysics Data System (ADS)

Lindmaa, Alexander; Kuemmel, Stephan; Armiento, Rickard

2015-03-01

We present our progress on a scheme in semi-local Kohn-Sham density-functional theory (KS-DFT) for improving the orbital description while still retaining the level of accuracy of the usual semi-local exchange-correlation (xc) functionals. DFT is a widely used tool for first-principles calculations of properties of materials. A given task normally requires a balance of accuracy and computational cost, which is well achieved with semi-local DFT. However, commonly used semi-local xc functionals have important shortcomings which often can be attributed to features of the corresponding xc potential. One shortcoming is an overly delocalized representation of localized orbitals. Recently a semi-local GGA-type xc functional was constructed to address these issues, however, it has the trade-off of lower accuracy of the total energy. We discuss the source of this error in terms of a surplus energy contribution in the functional that needs to be accounted for, and offer a remedy for this issue which formally stays within KS-DFT, and, which does not harshly increase the computational effort. The end result is a scheme that combines accurate total energies (e.g., relaxed geometries) with an improved orbital description (e.g., improved band structure).

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

Adaptive DFT-Based Interferometer Fringe Tracking

NASA Astrophysics Data System (ADS)

Wilson, Edward; Pedretti, Ettore; Bregman, Jesse; Mah, Robert W.; Traub, Wesley A.

An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) Observatory at Mount Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier-transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on offline data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately 2.0 milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse. One example of such an application might be to the field of thin-film measurement by ellipsometry, using a broadband light source and a Fourier-transform spectrometer to detect the resulting fringe patterns.

Behaviour of DFT-based approaches to the spin-orbit term of zero-field splitting tensors: a case study of metallocomplexes, MIII(acac)3 (M = V, Cr, Mn, Fe and Mo).

PubMed

Sugisaki, Kenji; Toyota, Kazuo; Sato, Kazunobu; Shiomi, Daisuke; Takui, Takeji

2017-11-15

Spin-orbit contributions to the zero-field splitting (ZFS) tensor (D SO tensor) of M III (acac) 3 complexes (M = V, Cr, Mn, Fe and Mo; acac = acetylacetonate anion) are evaluated by means of ab initio (a hybrid CASSCF/MRMP2) and DFT (Pederson-Khanna (PK) and natural orbital-based Pederson-Khanna (NOB-PK)) methods, focusing on the behaviour of DFT-based approaches to the D SO tensors against the valence d-electron configurations of the transition metal ions in octahedral coordination. Both the DFT-based approaches reproduce trends in the D tensors. Significantly, the differences between the theoretical and experimental D (D = D ZZ - (D XX + D YY )/2) values are smaller in NOB-PK than in PK, emphasising the usefulness of the natural orbital-based approach to the D tensor calculations of transition metal ion complexes. In the case of d 2 and d 4 electronic configurations, the D SO (NOB-PK) values are considerably underestimated in the absolute magnitude, compared with the experimental ones. The D SO tensor analysis based on the orbital region partitioning technique (ORPT) revealed that the D SO contributions attributed to excitations from the singly occupied region (SOR) to the unoccupied region (UOR) are significantly underestimated in the DFT-based approaches to all the complexes under study. In the case of d 3 and d 5 configurations, the (SOR → UOR) excitations contribute in a nearly isotropic manner, which causes fortuitous error cancellations in the DFT-based D SO values. These results indicate that more efforts to develop DFT frameworks should be directed towards the reproduction of quantitative D SO tensors of transition metal complexes with various electronic configurations and local symmetries around metal ions.

Testing process predictions of models of risky choice: a quantitative model comparison approach

PubMed Central

Pachur, Thorsten; Hertwig, Ralph; Gigerenzer, Gerd; Brandstätter, Eduard

2013-01-01

This article presents a quantitative model comparison contrasting the process predictions of two prominent views on risky choice. One view assumes a trade-off between probabilities and outcomes (or non-linear functions thereof) and the separate evaluation of risky options (expectation models). Another view assumes that risky choice is based on comparative evaluation, limited search, aspiration levels, and the forgoing of trade-offs (heuristic models). We derived quantitative process predictions for a generic expectation model and for a specific heuristic model, namely the priority heuristic (Brandstätter et al., 2006), and tested them in two experiments. The focus was on two key features of the cognitive process: acquisition frequencies (i.e., how frequently individual reasons are looked up) and direction of search (i.e., gamble-wise vs. reason-wise). In Experiment 1, the priority heuristic predicted direction of search better than the expectation model (although neither model predicted the acquisition process perfectly); acquisition frequencies, however, were inconsistent with both models. Additional analyses revealed that these frequencies were primarily a function of what Rubinstein (1988) called “similarity.” In Experiment 2, the quantitative model comparison approach showed that people seemed to rely more on the priority heuristic in difficult problems, but to make more trade-offs in easy problems. This finding suggests that risky choice may be based on a mental toolbox of strategies. PMID:24151472

Building a Database for a Quantitative Model

NASA Technical Reports Server (NTRS)

Kahn, C. Joseph; Kleinhammer, Roger

2014-01-01

A database can greatly benefit a quantitative analysis. The defining characteristic of a quantitative risk, or reliability, model is the use of failure estimate data. Models can easily contain a thousand Basic Events, relying on hundreds of individual data sources. Obviously, entering so much data by hand will eventually lead to errors. Not so obviously entering data this way does not aid linking the Basic Events to the data sources. The best way to organize large amounts of data on a computer is with a database. But a model does not require a large, enterprise-level database with dedicated developers and administrators. A database built in Excel can be quite sufficient. A simple spreadsheet database can link every Basic Event to the individual data source selected for them. This database can also contain the manipulations appropriate for how the data is used in the model. These manipulations include stressing factors based on use and maintenance cycles, dormancy, unique failure modes, the modeling of multiple items as a single "Super component" Basic Event, and Bayesian Updating based on flight and testing experience. A simple, unique metadata field in both the model and database provides a link from any Basic Event in the model to its data source and all relevant calculations. The credibility for the entire model often rests on the credibility and traceability of the data.

Uranyl extraction by N,N-dialkylamide ligands studied using static and dynamic DFT simulations.

PubMed

Sieffert, Nicolas; Wipff, Georges

2015-02-14

We report DFT static and dynamic studies on uranyl complexes [UO(2)(NO(3))x(H(2)O)(y)L(z)](2-x) involved in the uranyl extraction from water to an "oil" phase (hexane) by an amide ligand L (N,N-dimethylacetamide). Static DFT results "in solution" (continuum SMD models for water and hexane) predict that the stepwise formation of [UO(2)(NO(3))(2)L(2)] from the UO(2)(H(2)O)(5)(2+) species is energetically favourable, and allow us to compare cis/trans isomers of penta- and hexa-coordinated complexes and key intermediates in the two solvents. DFT-MD simulations of [UO(2)(NO(3))(2)L(2)], [UO(2)(NO(3))(2)(H(2)O)L(2)], and [UO(2)(NO(3))(H(2)O)L(2)](+) species in explicit solvent environments (water, hexane, or the water/hexane interface) represented at the MM or full-DFT level reveal a versatile solvent dependent binding mode of nitrates, also evidenced by metadynamics simulations. In water and at the interface, the latter exchange from bi- to monodentate, via in plane rotational motions in some cases. Remarkably, structures of complexes at the interface are more "water-like" than gas phase- or hexane-like. Thus, the order of U-O(NO(3))/U-O(L) bond distances observed in the gas phase (U-O(nit) < U-OL) is inverted at the interface and in water. Overall, the results are consistent with the experimental observation of uranyl extraction from nitric acid solutions by amide analogues (bearing "fatty" substituents), and allow us to propose possible extraction mechanisms, involving complexation of L "right at the interface". They also point to the importance of the solvent environment and the dynamics on the structure and stability of the complexes.

Optical properties of alkali halide crystals from all-electron hybrid TD-DFT calculations

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

Webster, R., E-mail: ross.webster07@imperial.ac.uk; Harrison, N. M.; Bernasconi, L.

2015-06-07

We present a study of the electronic and optical properties of a series of alkali halide crystals AX, with A = Li, Na, K, Rb and X = F, Cl, Br based on a recent implementation of hybrid-exchange time-dependent density functional theory (TD-DFT) (TD-B3LYP) in the all-electron Gaussian basis set code CRYSTAL. We examine, in particular, the impact of basis set size and quality on the prediction of the optical gap and exciton binding energy. The formation of bound excitons by photoexcitation is observed in all the studied systems and this is shown to be correlated to specific features ofmore » the Hartree-Fock exchange component of the TD-DFT response kernel. All computed optical gaps and exciton binding energies are however markedly below estimated experimental and, where available, 2-particle Green’s function (GW-Bethe-Salpeter equation, GW-BSE) values. We attribute this reduced exciton binding to the incorrect asymptotics of the B3LYP exchange correlation ground state functional and of the TD-B3LYP response kernel, which lead to a large underestimation of the Coulomb interaction between the excited electron and hole wavefunctions. Considering LiF as an example, we correlate the asymptotic behaviour of the TD-B3LYP kernel to the fraction of Fock exchange admixed in the ground state functional c{sub HF} and show that there exists one value of c{sub HF} (∼0.32) that reproduces at least semi-quantitatively the optical gap of this material.« less

Integrated Environmental Modeling: Quantitative Microbial Risk Assessment

EPA Science Inventory

The presentation discusses the need for microbial assessments and presents a road map associated with quantitative microbial risk assessments, through an integrated environmental modeling approach. A brief introduction and the strengths of the current knowledge are illustrated. W...

DFT-MD simulations of shocked Xenon

NASA Astrophysics Data System (ADS)

Magyar, Rudolph J.; Mattsson, Thomas R.

2009-03-01

Xenon is not only a technologically important element used in laser technologies, jet propulsion and dental anesthesia, but it is also arguably the simplest material in which to study the metal-insulator transition at high pressure. Because of its closed shell electronic configuration, Xenon is often assumed to be chemically inert, interacting almost entirely through the van der Waals interaction, and at liquid density, is typically modeled well using Leonard-Jones potentials. However, such modeling has a limited range of validity as Xenon is known to form compounds at normal conditions and likely exhibits considerably more chemistry at higher densities when hybridization of occupied orbitals becomes significant. In this talk, we present DFT-MD simulations of shocked liquid Xenon with the goal of developing an improved equation of state. The relative importance of the van der Waals interaction compared to other Coulomb interactions is considered, and estimates of the relative accuracy of various density functionals are quantified. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

An evidential reasoning extension to quantitative model-based failure diagnosis

NASA Technical Reports Server (NTRS)

Gertler, Janos J.; Anderson, Kenneth C.

1992-01-01

The detection and diagnosis of failures in physical systems characterized by continuous-time operation are studied. A quantitative diagnostic methodology has been developed that utilizes the mathematical model of the physical system. On the basis of the latter, diagnostic models are derived each of which comprises a set of orthogonal parity equations. To improve the robustness of the algorithm, several models may be used in parallel, providing potentially incomplete and/or conflicting inferences. Dempster's rule of combination is used to integrate evidence from the different models. The basic probability measures are assigned utilizing quantitative information extracted from the mathematical model and from online computation performed therewith.

ERBB3: A potential serum biomarker for early detection and therapeutic target for devil facial tumour 1 (DFT1)

PubMed Central

Kunde, Dale A.; Taylor, Robyn L.; Pyecroft, Stephen B.; Sohal, Sukhwinder Singh; Snow, Elizabeth T.

2017-01-01

Devil Facial Tumour 1 (DFT1) is one of two transmissible neoplasms of Tasmanian devils (Sarcophilus harrisii) predominantly affecting their facial regions. DFT1’s cellular origin is that of Schwann cell lineage where lesions are evident macroscopically late in the disease. Conversely, the pre-clinical timeframe from cellular transmission to appearance of DFT1 remains uncertain demonstrating the importance of an effective pre-clinical biomarker. We show that ERBB3, a marker expressed normally by the developing neural crest and Schwann cells, is immunohistohemically expressed by DFT1, therefore the potential of ERBB3 as a biomarker was explored. Under the hypothesis that serum ERBB3 levels may increase as DFT1 invades local and distant tissues our pilot study determined serum ERBB3 levels in normal Tasmanian devils and Tasmanian devils with DFT1. Compared to the baseline serum ERBB3 levels in unaffected Tasmanian devils, Tasmanian devils with DFT1 showed significant elevation of serum ERBB3 levels. Interestingly Tasmanian devils with cutaneous lymphoma (CL) also showed elevation of serum ERBB3 levels when compared to the baseline serum levels of Tasmanian devils without DFT1. Thus, elevated serum ERBB3 levels in otherwise healthy looking devils could predict possible DFT1 or CL in captive or wild devil populations and would have implications on the management, welfare and survival of Tasmanian devils. ERBB3 is also a therapeutic target and therefore the potential exists to consider modes of administration that may eradicate DFT1 from the wild. PMID:28591206

A VLSI pipeline design of a fast prime factor DFT on a finite field

NASA Technical Reports Server (NTRS)

Truong, T. K.; Hsu, I. S.; Shao, H. M.; Reed, I. S.; Shyu, H. C.

1986-01-01

A conventional prime factor discrete Fourier transform (DFT) algorithm is used to realize a discrete Fourier-like transform on the finite field, GF(q sub n). A pipeline structure is used to implement this prime factor DFT over GF(q sub n). This algorithm is developed to compute cyclic convolutions of complex numbers and to decode Reed-Solomon codes. Such a pipeline fast prime factor DFT algorithm over GF(q sub n) is regular, simple, expandable, and naturally suitable for VLSI implementation. An example illustrating the pipeline aspect of a 30-point transform over GF(q sub n) is presented.

A new DFT approach to model small polarons in oxides with proper account for long-range polarization

NASA Astrophysics Data System (ADS)

Kokott, Sebastian; Levchenko, Sergey V.; Scheffler, Matthias; Theory Department Team

In this work, we address two important challenges in the DFT description of small polarons (excess charges localized within one unit cell): sensitivity to the errors in exchange-correlation (XC) treatment and finite-size effects in supercell calculations. The polaron properties are obtained using a modified neutral potential-energy surface (PES). Using the hybrid HSE functional and considering the whole range 0 <= α <= 1 , we show that the modified PES model significantly reduces the dependence of the polaron level and binding energy in MgO and TiO2 on the XC functional. It does not eliminate the dependence on supercell size. Based on Pekar's model, we derive the proper long-range behavior of the polaron and a finite-size correction that allows to obtain the polaron properties in the dilute limit (tested for supercells containing up to 1,000 atoms). The developed approach reduces drastically the computational time for exploring the polaron PES, and gives a consistent description of polarons for the whole range of α. It allowed us to find a self-trapped hole in MgO that is noticeably more stable than reported previously. partially supported by UniCat (Deutsche Forschungsgemeinschaft).

DFT Study of Optical Properties of Pt-based Complexes

NASA Astrophysics Data System (ADS)

Oprea, Corneliu I.; Dumbravǎ, Anca; Moscalu, Florin; Nicolaides, Atnanassios; Gîrţu, Mihai A.

2010-01-01

We report Density Functional Theory (DFT) calculations providing the geometrical and electronic structures, as well as the vibrational and optical properties of the homologous series of Pt-pyramidalized olefin complexes (CH2)n-(C8H10)Pt(PH3)2, where n = 0, 1, and 2, in their neutral and oxidized states. All complexes were geometry optimized for the singlet ground state in vacuum using DFT methods with B3LYP exchange-correlation functional and the Effective Core Potential LANL2DZ basis set, within the frame of Gaussian03 quantum chemistry package. We find the coordination geometry of Pt to be distorted square planar, with dihedral angles ranging from 0°, for n = 0 and 1, which have C2V symmetry to 3.4°, for n = 2 with C2 symmetry. The Mulliken charge analysis allows a discussion of the oxidation state of the Pt ion. Electronic transitions were calculated at the same level of theory by means of Time Dependant-DFT. For n = 2 the electronic absorption bands are located in the UV region of the spectrum, the transitions being assigned to metal to ligand charge transfers. The relevance of these Pt-based compounds as possible pigments for dye-sensitized solar cells is discussed.

Adaptive DFT-Based Interferometer Fringe Tracking

NASA Astrophysics Data System (ADS)

Wilson, Edward; Pedretti, Ettore; Bregman, Jesse; Mah, Robert W.; Traub, Wesley A.

2005-12-01

An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) Observatory at Mount Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier-transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on offline data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately [InlineEquation not available: see fulltext.] milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse. One example of such an application might be to the field of thin-film measurement by ellipsometry, using a broadband light source and a Fourier-transform spectrometer to detect the resulting fringe patterns.

Quantitative collision induced mass spectrometry of substituted piperazines - A correlative analysis between theory and experiment

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2017-12-01

The present paper deals with quantitative kinetics and thermodynamics of collision induced dissociation (CID) reactions of piperazines under different experimental conditions together with a systematic description of effect of counter-ions on common MS fragment reactions of piperazines; and intra-molecular effect of quaternary cyclization of substituted piperazines yielding to quaternary salts. There are discussed quantitative model equations of rate constants as well as free Gibbs energies of series of m-independent CID fragment processes in GP, which have been evidenced experimentally. Both kinetic and thermodynamic parameters are also predicted by computational density functional theory (DFT) and ab initio both static and dynamic methods. The paper examines validity of Maxwell-Boltzmann distribution to non-Boltzmann CID processes in quantitatively as well. The experiments conducted within the latter framework yield to an excellent correspondence with theoretical quantum chemical modeling. The important property of presented model equations of reaction kinetics is the applicability in predicting unknown and assigning of known mass spectrometric (MS) patterns. The nature of "GP" continuum of CID-MS coupled scheme of measurements with electrospray ionization (ESI) source is discussed, performing parallel computations in gas-phase (GP) and polar continuum at different temperatures and ionic strengths. The effect of pressure is presented. The study contributes significantly to methodological and phenomenological developments of CID-MS and its analytical implementations for quantitative and structural analyses. It also demonstrates great prospective of a complementary application of experimental CID-MS and computational quantum chemistry studying chemical reactivity, among others. To a considerable extend this work underlies the place of computational quantum chemistry to the field of experimental analytical chemistry in particular highlighting the structural analysis.

Advantages of GPU technology in DFT calculations of intercalated graphene

NASA Astrophysics Data System (ADS)

Pešić, J.; Gajić, R.

2014-09-01

Over the past few years, the expansion of general-purpose graphic-processing unit (GPGPU) technology has had a great impact on computational science. GPGPU is the utilization of a graphics-processing unit (GPU) to perform calculations in applications usually handled by the central processing unit (CPU). Use of GPGPUs as a way to increase computational power in the material sciences has significantly decreased computational costs in already highly demanding calculations. A level of the acceleration and parallelization depends on the problem itself. Some problems can benefit from GPU acceleration and parallelization, such as the finite-difference time-domain algorithm (FTDT) and density-functional theory (DFT), while others cannot take advantage of these modern technologies. A number of GPU-supported applications had emerged in the past several years (www.nvidia.com/object/gpu-applications.html). Quantum Espresso (QE) is reported as an integrated suite of open source computer codes for electronic-structure calculations and materials modeling at the nano-scale. It is based on DFT, the use of a plane-waves basis and a pseudopotential approach. Since the QE 5.0 version, it has been implemented as a plug-in component for standard QE packages that allows exploiting the capabilities of Nvidia GPU graphic cards (www.qe-forge.org/gf/proj). In this study, we have examined the impact of the usage of GPU acceleration and parallelization on the numerical performance of DFT calculations. Graphene has been attracting attention worldwide and has already shown some remarkable properties. We have studied an intercalated graphene, using the QE package PHonon, which employs GPU. The term ‘intercalation’ refers to a process whereby foreign adatoms are inserted onto a graphene lattice. In addition, by intercalating different atoms between graphene layers, it is possible to tune their physical properties. Our experiments have shown there are benefits from using GPUs, and we reached an

Refining the quantitative pathway of the Pathways to Mathematics model.

PubMed

Sowinski, Carla; LeFevre, Jo-Anne; Skwarchuk, Sheri-Lynn; Kamawar, Deepthi; Bisanz, Jeffrey; Smith-Chant, Brenda

2015-03-01

In the current study, we adopted the Pathways to Mathematics model of LeFevre et al. (2010). In this model, there are three cognitive domains--labeled as the quantitative, linguistic, and working memory pathways--that make unique contributions to children's mathematical development. We attempted to refine the quantitative pathway by combining children's (N=141 in Grades 2 and 3) subitizing, counting, and symbolic magnitude comparison skills using principal components analysis. The quantitative pathway was examined in relation to dependent numerical measures (backward counting, arithmetic fluency, calculation, and number system knowledge) and a dependent reading measure, while simultaneously accounting for linguistic and working memory skills. Analyses controlled for processing speed, parental education, and gender. We hypothesized that the quantitative, linguistic, and working memory pathways would account for unique variance in the numerical outcomes; this was the case for backward counting and arithmetic fluency. However, only the quantitative and linguistic pathways (not working memory) accounted for unique variance in calculation and number system knowledge. Not surprisingly, only the linguistic pathway accounted for unique variance in the reading measure. These findings suggest that the relative contributions of quantitative, linguistic, and working memory skills vary depending on the specific cognitive task. Copyright © 2014 Elsevier Inc. All rights reserved.

Modeling conflict : research methods, quantitative modeling, and lessons learned.

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

Rexroth, Paul E.; Malczynski, Leonard A.; Hendrickson, Gerald A.

2004-09-01

This study investigates the factors that lead countries into conflict. Specifically, political, social and economic factors may offer insight as to how prone a country (or set of countries) may be for inter-country or intra-country conflict. Largely methodological in scope, this study examines the literature for quantitative models that address or attempt to model conflict both in the past, and for future insight. The analysis concentrates specifically on the system dynamics paradigm, not the political science mainstream approaches of econometrics and game theory. The application of this paradigm builds upon the most sophisticated attempt at modeling conflict as a resultmore » of system level interactions. This study presents the modeling efforts built on limited data and working literature paradigms, and recommendations for future attempts at modeling conflict.« less

Water adsorption in SAPO-34: elucidating the role of local heterogeneities and defects using dispersion-corrected DFT calculations.

PubMed

Fischer, Michael

2015-10-14

The chabazite-type silicoaluminophosphate SAPO-34 is a promising adsorbent for applications in thermal energy storage using water adsorption-desorption cycles. In order to develop a microscopic understanding of the impact of local heterogeneities and defects on the water adsorption properties, the interaction of different models of SAPO-34 with water was studied using dispersion-corrected density-functional theory (DFT-D) calculations. In addition to SAPO-34 with isolated silicon atoms, the calculations considered models incorporating two types of heterogeneities (silicon islands, aluminosilicate domains), and two defect-containing (partially and fully desilicated) systems. DFT-D optimisations were performed for systems with small amounts of adsorbed water, in which all H2O molecules can interact with framework protons, and systems with large amounts of adsorbed water (30 H2O molecules per unit cell). At low loadings, the host-guest interaction energy calculated for SAPO-34 with isolated Si atoms amounts to approximately -90 kJ mol(-1). While the presence of local heterogeneities leads to the creation of some adsorption sites that are energetically slightly more favourable, the interaction strength is drastically reduced in systems with defects. At high water loadings, energies in the range of -70 kJ mol(-1) are obtained for all models. The DFT-D interaction energies are in good agreement with experimentally measured heats of water adsorption. A detailed analysis of the equilibrium structures was used to gain insights into the binding modes at low coverages, and to assess the extent of framework deprotonation and changes in the coordination environment of aluminium atoms at high water loadings.

Mathematical modelling and quantitative methods.

PubMed

Edler, L; Poirier, K; Dourson, M; Kleiner, J; Mileson, B; Nordmann, H; Renwick, A; Slob, W; Walton, K; Würtzen, G

2002-01-01

The present review reports on the mathematical methods and statistical techniques presently available for hazard characterisation. The state of the art of mathematical modelling and quantitative methods used currently for regulatory decision-making in Europe and additional potential methods for risk assessment of chemicals in food and diet are described. Existing practices of JECFA, FDA, EPA, etc., are examined for their similarities and differences. A framework is established for the development of new and improved quantitative methodologies. Areas for refinement, improvement and increase of efficiency of each method are identified in a gap analysis. Based on this critical evaluation, needs for future research are defined. It is concluded from our work that mathematical modelling of the dose-response relationship would improve the risk assessment process. An adequate characterisation of the dose-response relationship by mathematical modelling clearly requires the use of a sufficient number of dose groups to achieve a range of different response levels. This need not necessarily lead to an increase in the total number of animals in the study if an appropriate design is used. Chemical-specific data relating to the mode or mechanism of action and/or the toxicokinetics of the chemical should be used for dose-response characterisation whenever possible. It is concluded that a single method of hazard characterisation would not be suitable for all kinds of risk assessments, and that a range of different approaches is necessary so that the method used is the most appropriate for the data available and for the risk characterisation issue. Future refinements to dose-response characterisation should incorporate more clearly the extent of uncertainty and variability in the resulting output.

A general framework for numerical simulation of improvised explosive device (IED)-detection scenarios using density functional theory (DFT) and terahertz (THz) spectra.

PubMed

Shabaev, Andrew; Lambrakos, Samuel G; Bernstein, Noam; Jacobs, Verne L; Finkenstadt, Daniel

2011-04-01

We have developed a general framework for numerical simulation of various types of scenarios that can occur for the detection of improvised explosive devices (IEDs) through the use of excitation using incident electromagnetic waves. A central component model of this framework is an S-matrix representation of a multilayered composite material system. Each layer of the system is characterized by an average thickness and an effective electric permittivity function. The outputs of this component are the reflectivity and the transmissivity as functions of frequency and angle of the incident electromagnetic wave. The input of the component is a parameterized analytic-function representation of the electric permittivity as a function of frequency, which is provided by another component model of the framework. The permittivity function is constructed by fitting response spectra calculated using density functional theory (DFT) and parameter adjustment according to any additional information that may be available, e.g., experimentally measured spectra or theory-based assumptions concerning spectral features. A prototype simulation is described that considers response characteristics for THz excitation of the high explosive β-HMX. This prototype simulation includes a description of a procedure for calculating response spectra using DFT as input to the Smatrix model. For this purpose, the DFT software NRLMOL was adopted. © 2011 Society for Applied Spectroscopy

Modelling realistic TiO2 nanospheres: A benchmark study of SCC-DFTB against hybrid DFT

NASA Astrophysics Data System (ADS)

Selli, Daniele; Fazio, Gianluca; Di Valentin, Cristiana

2017-10-01

TiO2 nanoparticles (NPs) are nowadays considered fundamental building blocks for many technological applications. Morphology is found to play a key role with spherical NPs presenting higher binding properties and chemical activity. From the experimental point of view, the characterization of these nano-objects is extremely complex, opening a large room for computational investigations. In this work, TiO2 spherical NPs of different sizes (from 300 to 4000 atoms) have been studied with a two-scale computational approach. Global optimization to obtain stable and equilibrated nanospheres was performed with a self-consistent charge density functional tight-binding (SCC-DFTB) simulated annealing process, causing a considerable atomic rearrangement within the nanospheres. Those SCC-DFTB relaxed structures have been then optimized at the DFT(B3LYP) level of theory. We present a systematic and comparative SCC-DFTB vs DFT(B3LYP) study of the structural properties, with particular emphasis on the surface-to-bulk sites ratio, coordination distribution of surface sites, and surface energy. From the electronic point of view, we compare HOMO-LUMO and Kohn-Sham gaps, total and projected density of states. Overall, the comparisons between DFTB and hybrid density functional theory show that DFTB provides a rather accurate geometrical and electronic description of these nanospheres of realistic size (up to a diameter of 4.4 nm) at an extremely reduced computational cost. This opens for new challenges in simulations of very large systems and more extended molecular dynamics.

Quantitative model analysis with diverse biological data: applications in developmental pattern formation.

PubMed

Pargett, Michael; Umulis, David M

2013-07-15

Mathematical modeling of transcription factor and signaling networks is widely used to understand if and how a mechanism works, and to infer regulatory interactions that produce a model consistent with the observed data. Both of these approaches to modeling are informed by experimental data, however, much of the data available or even acquirable are not quantitative. Data that is not strictly quantitative cannot be used by classical, quantitative, model-based analyses that measure a difference between the measured observation and the model prediction for that observation. To bridge the model-to-data gap, a variety of techniques have been developed to measure model "fitness" and provide numerical values that can subsequently be used in model optimization or model inference studies. Here, we discuss a selection of traditional and novel techniques to transform data of varied quality and enable quantitative comparison with mathematical models. This review is intended to both inform the use of these model analysis methods, focused on parameter estimation, and to help guide the choice of method to use for a given study based on the type of data available. Applying techniques such as normalization or optimal scaling may significantly improve the utility of current biological data in model-based study and allow greater integration between disparate types of data. Copyright © 2013 Elsevier Inc. All rights reserved.

DFT study of CO2 and H2O co-adsorption on carbon models of coal surface.

PubMed

Gao, Zhengyang; Ding, Yi

2017-06-01

The moisture content of coal affects the adsorption capacity of CO 2 on the coal surface. Since the hydrogen bonds are formed between H 2 O and oxygen functional group, the H 2 O cluster more easily adsorbs on the coal micropore than CO 2 molecule. The coal micropores are occupied by H 2 O molecules that cannot provide extra space for CO 2 adsorption, which may leads to the reduction of CO 2 adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO 2 and adsorbed H 2 O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H 2 O to CO 2 adsorption. This study reports some typical coal-H 2 O···CO 2 complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H 2 O molecule can more stably adsorb on the aromatic ring surface than CO 2 molecule, and the absolute values of local ESP maximum and minimum of H 2 O cluster are greater than CO 2 . AIM analysis shows a detailed interaction path and strength between atoms in CO 2 and H 2 O, and RDG analysis shows that the interactions among CO 2 , H 2 O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO 2 and H 2 O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H 2 O can promote CO 2 adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO 2 adsorption capacity, the attractive interaction of adsorbed H 2 O to CO 2 makes little contribution.

Discrete Fourier Transform-Based Multivariate Image Analysis: Application to Modeling of Aromatase Inhibitory Activity.

PubMed

Barigye, Stephen J; Freitas, Matheus P; Ausina, Priscila; Zancan, Patricia; Sola-Penna, Mauro; Castillo-Garit, Juan A

2018-02-12

We recently generalized the formerly alignment-dependent multivariate image analysis applied to quantitative structure-activity relationships (MIA-QSAR) method through the application of the discrete Fourier transform (DFT), allowing for its application to noncongruent and structurally diverse chemical compound data sets. Here we report the first practical application of this method in the screening of molecular entities of therapeutic interest, with human aromatase inhibitory activity as the case study. We developed an ensemble classification model based on the two-dimensional (2D) DFT MIA-QSAR descriptors, with which we screened the NCI Diversity Set V (1593 compounds) and obtained 34 chemical compounds with possible aromatase inhibitory activity. These compounds were docked into the aromatase active site, and the 10 most promising compounds were selected for in vitro experimental validation. Of these compounds, 7419 (nonsteroidal) and 89 201 (steroidal) demonstrated satisfactory antiproliferative and aromatase inhibitory activities. The obtained results suggest that the 2D-DFT MIA-QSAR method may be useful in ligand-based virtual screening of new molecular entities of therapeutic utility.

Structural characterization, surface characteristics and non covalent interactions of a heterocyclic Schiff base: Evaluation of antioxidant potential by UV-visible spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Chithiraikumar, S.; Gandhimathi, S.; Neelakantan, M. A.

2017-06-01

A heterocyclic Schiff base, (E)-4-(1-((pyridin-2-ylmethyl)imino)ethyl)benzene-1,3-diol (L) was synthesized and isolated as single crystals. Its structure was characterized by FT-IR, UV, 1H and 13C NMR, and further confirmed by X-ray crystallography. Qualitatively and quantitatively the various interactions in the crystal structure of L has been analyzed by Hirshfeld surfaces and 2D fingerprint plots. Non covalent interactions have been studied by electron localization function (ELF) and mapped with reduced density gradient (RDG) analysis. The molecular structure was studied computationally by DFT-B3LYP/6-311G(d,p) calculations. HOMO-LUMO energy levels, chemical reactivity descriptors and thermodynamic parameters have been investigated at the same level of theory. The antioxidant potential of L was evaluated experimentally by measuring DPPH free radical scavenging effect using UV-visible spectroscopy and theoretically by DFT. Theoretical parameters, such as bond dissociation enthalpy (BDE) and spin density calculated suggests that antioxidant potential of L is due to H atom abstraction from the sbnd OH group.

Interpretation of protein quantitation using the Bradford assay: comparison with two calculation models.

PubMed

Ku, Hyung-Keun; Lim, Hyuk-Min; Oh, Kyong-Hwa; Yang, Hyo-Jin; Jeong, Ji-Seon; Kim, Sook-Kyung

2013-03-01

The Bradford assay is a simple method for protein quantitation, but variation in the results between proteins is a matter of concern. In this study, we compared and normalized quantitative values from two models for protein quantitation, where the residues in the protein that bind to anionic Coomassie Brilliant Blue G-250 comprise either Arg and Lys (Method 1, M1) or Arg, Lys, and His (Method 2, M2). Use of the M2 model yielded much more consistent quantitation values compared with use of the M1 model, which exhibited marked overestimations against protein standards. Copyright © 2012 Elsevier Inc. All rights reserved.

CO2 adsorption-assisted CH4 desorption on carbon models of coal surface: A DFT study

NASA Astrophysics Data System (ADS)

Xu, He; Chu, Wei; Huang, Xia; Sun, Wenjing; Jiang, Chengfa; Liu, Zhongqing

2016-07-01

Injection of CO2 into coal is known to improve the yields of coal-bed methane gas. However, the technology of CO2 injection-enhanced coal-bed methane (CO2-ECBM) recovery is still in its infancy with an unclear mechanism. Density functional theory (DFT) calculations were performed to elucidate the mechanism of CO2 adsorption-assisted CH4 desorption (AAD). To simulate coal surfaces, different six-ring aromatic clusters (2 × 2, 3 × 3, 4 × 4, 5 × 5, 6 × 6, and 7 × 7) were used as simplified graphene (Gr) carbon models. The adsorption and desorption of CH4 and/or CO2 on these carbon models were assessed. The results showed that a six-ring aromatic cluster model (4 × 4) can simulate the coal surface with limited approximation. The adsorption of CO2 onto these carbon models was more stable than that in the case of CH4. Further, the adsorption energies of single CH4 and CO2 in the more stable site were -15.58 and -18.16 kJ/mol, respectively. When two molecules (CO2 and CH4) interact with the surface, CO2 compels CH4 to adsorb onto the less stable site, with a resulting significant decrease in the adsorption energy of CH4 onto the surface of the carbon model with pre-adsorbed CO2. The Mulliken charges and electrostatic potentials of CH4 and CO2 adsorbed onto the surface of the carbon model were compared to determine their respective adsorption activities and changes. At the molecular level, our results showed that the adsorption of the injected CO2 promoted the desorption of CH4, the underlying mechanism of CO2-ECBM.

Error compensation of IQ modulator using two-dimensional DFT

NASA Astrophysics Data System (ADS)

Ohshima, Takashi; Maesaka, Hirokazu; Matsubara, Shinichi; Otake, Yuji

2016-06-01

It is important to precisely set and keep the phase and amplitude of an rf signal in the accelerating cavity of modern accelerators, such as an X-ray Free Electron Laser (XFEL) linac. In these accelerators an acceleration rf signal is generated or detected by an In-phase and Quadrature (IQ) modulator, or a demodulator. If there are any deviations of the phase and the amplitude from the ideal values, crosstalk between the phase and the amplitude of the output signal of the IQ modulator or the demodulator arises. This causes instability of the feedback controls that simultaneously stabilize both the rf phase and the amplitude. To compensate for such deviations, we developed a novel compensation method using a two-dimensional Discrete Fourier Transform (DFT). Because the observed deviations of the phase and amplitude of an IQ modulator involve sinusoidal and polynomial behaviors on the phase angle and the amplitude of the rf vector, respectively, the DFT calculation with these basis functions makes a good approximation with a small number of compensation coefficients. Also, we can suppress high-frequency noise components arising when we measure the deviation data. These characteristics have advantages compared to a Look Up Table (LUT) compensation method. The LUT method usually demands many compensation elements, such as about 300, that are not easy to treat. We applied the DFT compensation method to the output rf signal of a C-band IQ modulator at SACLA, which is an XFEL facility in Japan. The amplitude deviation of the IQ modulator after the DFT compensation was reduced from 15.0% at the peak to less than 0.2% at the peak for an amplitude control range of from 0.1 V to 0.9 V (1.0 V full scale) and for a phase control range from 0 degree to 360 degrees. The number of compensation coefficients is 60, which is smaller than that of the LUT method, and is easy to treat and maintain.

Application of DFT Filter Banks and Cosine Modulated Filter Banks in Filtering

NASA Technical Reports Server (NTRS)

Lin, Yuan-Pei; Vaidyanathan, P. P.

1994-01-01

None given. This is a proposal for a paper to be presented at APCCAS '94 in Taipei, Taiwan. (From outline): This work is organized as follows: Sec. II is devoted to the construction of the new 2m channel under-decimated DFT filter bank. Implementation and complexity of this DFT filter bank are discussed therein. IN a similar manner, the new 2m channel cosine modulated filter bank is discussed in Sec. III. Design examples are given in Sec. IV.

Benchmarks and Reliable DFT Results for Spin Gaps of Small Ligand Fe(II) Complexes

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

Song, Suhwan; Kim, Min-Cheol; Sim, Eunji

2017-05-01

All-electron fixed-node diffusion Monte Carlo provides benchmark spin gaps for four Fe(II) octahedral complexes. Standard quantum chemical methods (semilocal DFT and CCSD(T)) fail badly for the energy difference between their high- and low-spin states. Density-corrected DFT is both significantly more accurate and reliable and yields a consistent prediction for the Fe-Porphyrin complex

Symmetry properties of the electron density and following from it limits on the KS-DFT applications

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.

2018-03-01

At present, the Density Functional Theory (DFT) approach elaborated by Kohn with co-authors more than 50 years ago became the most widely used method for study molecules and solids. Using modern computation facilities, it can be applied to systems with million atoms. In the atmosphere of such great popularity, it is particularly important to know the limits of the applicability of DFT methods. In this report, I will discuss two cases when the conventional DFT approaches, using only electron density ρ and its gradients, cannot be applied (I will not consider the Ψ-versions of DFT). The first case is quite evident. In the degenerated states, the electron density may not be defined, since electronic and nuclear motions cannot be separated, the vibronic interaction mixed them. The second case is related to the spin of the state. As it was rigorously proved by group theoretical methods at the theorem level, the electron density does not depend on the total spin S of the arbitrary N-electron state. It means that the Kohn-Sham equations have the same form for states with different S. The critical survey of elaborated DFT procedures, taking into account spin, shows that they modified only exchange functionals, the correlation functionals do not correspond to the spin of the state. The point is that the conception of spin cannot be defined in the framework of the electron density formalism, which corresponds to the one-particle reduced density matrix. This is the main reason of the problems arising in the study by DFT of magnetic properties of the transition metals. The possible way of resolving these problems can be found in the two-particle reduced density matrix formulation of DFT.

Optical characterization of shock-induced chemistry in the explosive nitromethane using DFT and time-dependent DFT

NASA Astrophysics Data System (ADS)

Pellouchoud, Lenson; Reed, Evan

2014-03-01

With continual improvements in ultrafast optical spectroscopy and new multi-scale methods for simulating chemistry for hundreds of picoseconds, the opportunity is beginning to exist to connect experiments with simulations on the same timescale. We compute the optical properties of the liquid phase energetic material nitromethane (CH3NO2) for the first 100 picoseconds behind the front of a simulated shock at 6.5km/s, close to the experimentally observed detonation shock speed. We utilize molecular dynamics trajectories computed using the multi-scale shock technique (MSST) for time-resolved optical spectrum calculations based on both linear response time-dependent DFT (TDDFT) and the Kubo-Greenwood (KG) formula within Kohn-Sham DFT. We find that TDDFT predicts optical conductivities 25-35% lower than KG-based values and provides better agreement with the experimentally measured index of refraction of unreacted nitromethane. We investigate the influence of electronic temperature on the KG spectra and find no significant effect at optical wavelengths. With all methods, the spectra evolve non-monotonically in time as shock-induced chemistry takes place. We attribute the time-resolved absorption at optical wavelengths to time-dependent populations of molecular decomposition products, including NO, CNO, CNOH, H2O, and larger molecules. Supported by NASA Space Technology Research Fellowship (NSTRF) #NNX12AM48H.

Understanding Density Functional Theory (DFT) and Completing it in Practice

NASA Astrophysics Data System (ADS)

Bagayoko, Diola

2015-03-01

A brief review of the seminal article by Hohenberg and Kohn leads to two conditions that have to be met by electronic structure calculations in order for their results to represent the physics content of DFT. One of these conditions is often the verifiable attainment of the absolute minima of the occupied energies. Using the second Hohenberg Kohn theorem, we show that results of calculations that do not meet this condition, when it applies, do not necessarily represent DFT findings. We illustrate this fact with over 100 calculated band gaps that are much smaller than corresponding, measured ones; in contrast, we list calculations that strictly adhered to the aforementioned conditions and whose results are in excellent agreement with experiment. We describe two crucial steps in the latter calculations that add to or complete DFT in practice. Some implications of our findings for academia, industry, and program package developers will be discussed. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

Insufficient Hartree–Fock Exchange in Hybrid DFT Functionals Produces Bent Alkynyl Radical Structures

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

Oyeyemi, Victor B.; Keith, John A.; Pavone, Michele

2012-01-11

Density functional theory (DFT) is often used to determine the electronic and geometric structures of molecules. While studying alkynyl radicals, we discovered that DFT exchange-correlation (XC) functionals containing less than ~22% Hartree–Fock (HF) exchange led to qualitatively different structures than those predicted from ab initio HF and post-HF calculations or DFT XCs containing 25% or more HF exchange. We attribute this discrepancy to rehybridization at the radical center due to electron delocalization across the triple bonds of the alkynyl groups, which itself is an artifact of self-interaction and delocalization errors. Inclusion of sufficient exact exchange reduces these errors and suppressesmore » this erroneous delocalization; we find that a threshold amount is needed for accurate structure determinations. Finally, below this threshold, significant errors in predicted alkyne thermochemistry emerge as a consequence.« less

Asynchronous adaptive time step in quantitative cellular automata modeling

PubMed Central

Zhu, Hao; Pang, Peter YH; Sun, Yan; Dhar, Pawan

2004-01-01

Background The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in cellular automata based multi-cellular modeling: how to introduce differential equation based quantitative computing to precisely describe cellular activity, and upon it, how to solve the heavy time consumption issue in simulation. Results Based on a modified, language based cellular automata system we extended that allows ordinary differential equations in models, we introduce a method implementing asynchronous adaptive time step in simulation that can considerably improve efficiency yet without a significant sacrifice of accuracy. An average speedup rate of 4–5 is achieved in the given example. Conclusions Strategies for reducing time consumption in simulation are indispensable for large-scale, quantitative multi-cellular models, because even a small 100 × 100 × 100 tissue slab contains one million cells. Distributed and adaptive time step is a practical solution in cellular automata environment. PMID:15222901

Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2017-06-01

With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.

The Mapping Model: A Cognitive Theory of Quantitative Estimation

ERIC Educational Resources Information Center

von Helversen, Bettina; Rieskamp, Jorg

2008-01-01

How do people make quantitative estimations, such as estimating a car's selling price? Traditionally, linear-regression-type models have been used to answer this question. These models assume that people weight and integrate all information available to estimate a criterion. The authors propose an alternative cognitive theory for quantitative…

Density Functional Theory (DFT) Simulations of Shocked Liquid Xenon

NASA Astrophysics Data System (ADS)

Mattsson, Thomas R.; Magyar, Rudolph J.

2009-06-01

Xenon is not only a technologically important element used in laser technologies and jet propulsion, but it is also one of the most accessible materials in which to study the metal-insulator transition with increasing pressure. Because of its closed shell electronic configuration, Xenon is often assumed to be chemically inert, interacting almost entirely through the van der Waals interaction, and at liquid density, is typically modeled well using Leonard-Jones potentials. However, such modeling has a limited range of validity as Xenon is known to form compounds at normal conditions and likely exhibits considerably more chemistry at higher densities when hybridization of occupied orbitals becomes significant. In this talk, we present DFT-MD simulations of shocked liquid Xenon with the goal of developing an improved equation of state. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

DFT and ENDOR Study of Bixin Radical Cations and Neutral Radicals on Silica-Alumina.

PubMed

Tay-Agbozo, Sefadzi S; Krzyaniak, Matthew D; Bowman, Michael K; Street, Shane; Kispert, Lowell D

2015-06-18

Bixin, a carotenoid found in annatto (Bixa orellana), is unique among natural carotenoids by being water-soluble. We stabilized free radicals from bixin on the surface of silica-alumina (Si-Al) and characterized them by pulsed electron-nuclear double resonance (ENDOR). DFT calculations of unpaired electron spin distribution for various bixin radicals predict the EPR hyperfine couplings. Least-square fitting of experimental ENDOR spectra by spectra calculated from DFT hyperfine couplings characterized the radicals trapped on Si-Al. DFT predicts that the trans bixin radical cation is more stable than the cis bixin radical cation by 1.26 kcal/mol. This small energy difference is consistent with the 26% trans and 23% cis radical cations in the ENDOR spectrum. The remainder of the ENDOR spectrum is due to several neutral radicals formed by loss of a H(+) ion from the 9, 9', 13, or 13' methyl group, a common occurrence in all water-insoluble carotenoids previously studied. Although carboxyl groups of bixin strongly affect its solubility relative to other natural carotenoids, they do not alter properties of its free radicals based on DFT calculations and EPR measurements which remain similar to typical water-insoluble carotenoids.

DFT treatment of transport through Anderson junction: exact results and approximations

NASA Astrophysics Data System (ADS)

Burke, Kieron

2012-02-01

Since the pioneering break-junction experiments of Reed and Tour measuring the conductance of dithiolated benzene between gold leads, many researchers in physics and chemistry have been calculating conductance for such systems using density functional theory (DFT). Off resonance, the predicted current is often 10-100 times larger than that measured. This error is often ascribed to the application of ground-state DFT to a non-equilibrium problem. I will argue that, in fact, this is largely due to errors in the density functional approximations in popular use, rather than necessarily errors in the methodology. A stark illustration of this principle is the ability of DFT to reproduce the exact transmission through an Anderson junction at zero-temperature and weak bias, including the Kondo plateau, but only if the exact ground-state density functional is used. In fact, this case can be used to reverse-engineer the exact functional for this problem. Popular approximations can also be tested, including both smooth and discontinuous functionals of the density, as well as symmetry-broken approaches. [4pt] [1] Kondo effect given exactly by density functional theory, J. P. Bergfield, Z. Liu, K. Burke, and C. A. Stafford, arXiv:1106.3104; [0pt] [2] Broadening of the Derivative Discontinuity in Density Functional Theory, F. Evers, and P. Schmitteckert, arXiv:1106.3658; [0pt] [3] DFT-based transport calculations, Friedel's sum rule and the Kondo effect, P. Tr"oster, P. Schmitteckert, and F. Evers, arXiv:1106.3669; [0pt] [4] Towards a description of the Kondo effect using time-dependent density functional theory, G. Stefanucci, and S. Kurth, arXiv:1106.3728.

An EQT-based cDFT approach for thermodynamic properties of confined fluid mixtures

NASA Astrophysics Data System (ADS)

Motevaselian, M. H.; Aluru, N. R.

2017-04-01

We present an empirical potential-based quasi-continuum theory (EQT) to predict the structure and thermodynamic properties of confined fluid mixtures. The central idea in the EQT is to construct potential energies that integrate important atomistic details into a continuum-based model such as the Nernst-Planck equation. The EQT potentials can be also used to construct the excess free energy functional, which is required for the grand potential in the classical density functional theory (cDFT). In this work, we use the EQT-based grand potential to predict various thermodynamic properties of a confined binary mixture of hydrogen and methane molecules inside graphene slit channels of different widths. We show that the EQT-cDFT predictions for the structure, surface tension, solvation force, and local pressure tensor profiles are in good agreement with the molecular dynamics simulations. Moreover, we study the effect of different bulk compositions and channel widths on the thermodynamic properties. Our results reveal that the composition of methane in the mixture can significantly affect the ordering of molecules and thermodynamic properties under confinement. In addition, we find that graphene is selective to methane molecules.

Investigation of the Fe{sup 3+} centers in perovskite KMgF{sub 3} through a combination of ab initio (density functional theory) and semi-empirical (superposition model) calculations

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

Emül, Y.; Department of Software Engineering, Cumhuriyet University, 58140 Sivas; Erbahar, D.

2015-08-14

Analyses of the local crystal and electronic structure in the vicinity of Fe{sup 3+} centers in perovskite KMgF{sub 3} crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe{sup 3+} centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe{sup 3+} centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe{sup 3+} center case), FeF{sub 5}Omore » cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe{sup 3+} centers in KMgF{sub 3}.« less

Quantitative Evidence for Lanthanide-Oxygen Orbital Mixing in CeO2, PrO2, and TbO2.

PubMed

Minasian, Stefan G; Batista, Enrique R; Booth, Corwin H; Clark, David L; Keith, Jason M; Kozimor, Stosh A; Lukens, Wayne W; Martin, Richard L; Shuh, David K; Stieber, S Chantal E; Tylisczcak, Tolek; Wen, Xiao-Dong

2017-12-13

Understanding the nature of covalent (band-like) vs ionic (atomic-like) electrons in metal oxides continues to be at the forefront of research in the physical sciences. In particular, the development of a coherent and quantitative model of bonding and electronic structure for the lanthanide dioxides, LnO 2 (Ln = Ce, Pr, and Tb), has remained a considerable challenge for both experiment and theory. Herein, relative changes in mixing between the O 2p orbitals and the Ln 4f and 5d orbitals in LnO 2 are evaluated quantitatively using O K-edge X-ray absorption spectroscopy (XAS) obtained with a scanning transmission X-ray microscope and density functional theory (DFT) calculations. For each LnO 2 , the results reveal significant amounts of Ln 5d and O 2p mixing in the orbitals of t 2g (σ-bonding) and e g (π-bonding) symmetry. The remarkable agreement between experiment and theory also shows that significant mixing with the O 2p orbitals occurs in a band derived from the 4f orbitals of a 2u symmetry (σ-bonding) for each compound. However, a large increase in orbital mixing is observed for PrO 2 that is ascribed to a unique interaction derived from the 4f orbitals of t 1u symmetry (σ- and π-bonding). O K-edge XAS and DFT results are compared with complementary L 3 -edge and M 5,4 -edge XAS measurements and configuration interaction calculations, which shows that each spectroscopic approach provides evidence for ground state O 2p and Ln 4f orbital mixing despite inducing very different core-hole potentials in the final state.

Quantitative trait nucleotide analysis using Bayesian model selection.

PubMed

Blangero, John; Goring, Harald H H; Kent, Jack W; Williams, Jeff T; Peterson, Charles P; Almasy, Laura; Dyer, Thomas D

2005-10-01

Although much attention has been given to statistical genetic methods for the initial localization and fine mapping of quantitative trait loci (QTLs), little methodological work has been done to date on the problem of statistically identifying the most likely functional polymorphisms using sequence data. In this paper we provide a general statistical genetic framework, called Bayesian quantitative trait nucleotide (BQTN) analysis, for assessing the likely functional status of genetic variants. The approach requires the initial enumeration of all genetic variants in a set of resequenced individuals. These polymorphisms are then typed in a large number of individuals (potentially in families), and marker variation is related to quantitative phenotypic variation using Bayesian model selection and averaging. For each sequence variant a posterior probability of effect is obtained and can be used to prioritize additional molecular functional experiments. An example of this quantitative nucleotide analysis is provided using the GAW12 simulated data. The results show that the BQTN method may be useful for choosing the most likely functional variants within a gene (or set of genes). We also include instructions on how to use our computer program, SOLAR, for association analysis and BQTN analysis.

Mesoscale models for stacking faults, deformation twins and martensitic transformations: Linking atomistics to continuum

NASA Astrophysics Data System (ADS)

Kibey, Sandeep A.

We present a hierarchical approach that spans multiple length scales to describe defect formation---in particular, formation of stacking faults (SFs) and deformation twins---in fcc crystals. We link the energy pathways (calculated here via ab initio density functional theory, DFT) associated with formation of stacking faults and twins to corresponding heterogeneous defect nucleation models (described through mesoscale dislocation mechanics). Through the generalized Peieirls-Nabarro model, we first correlate the width of intrinsic SFs in fcc alloy systems to their nucleation pathways called generalized stacking fault energies (GSFE). We then establish a qualitative dependence of twinning tendency in fee metals and alloys---specifically, in pure Cu and dilute Cu-xAl (x= 5.0 and 8.3 at.%)---on their twin-energy pathways called the generalized planar fault energies (GPFE). We also link the twinning behavior of Cu-Al alloys to their electronic structure by determining the effect of solute Al on the valence charge density redistribution at the SF through ab initio DFT. Further, while several efforts have been undertaken to incorporate twinning for predicting stress-strain response of fcc materials, a fundamental law for critical twinning stress has not yet emerged. We resolve this long-standing issue by linking quantitatively the twin-energy pathways (GPFE) obtained via ab initio DFT to heterogeneous, dislocation-based twin nucleation models. We establish an analytical expression that quantitatively predicts the critical twinning stress in fcc metals in agreement with experiments without requiring any empiricism at any length scale. Our theory connects twinning stress to twin-energy pathways and predicts a monotonic relation between stress and unstable twin stacking fault energy revealing the physics of twinning. We further demonstrate that the theory holds for fcc alloys as well. Our theory inherently accounts for directional nature of twinning which available

Quantitative modelling in cognitive ergonomics: predicting signals passed at danger.

PubMed

Moray, Neville; Groeger, John; Stanton, Neville

2017-02-01

This paper shows how to combine field observations, experimental data and mathematical modelling to produce quantitative explanations and predictions of complex events in human-machine interaction. As an example, we consider a major railway accident. In 1999, a commuter train passed a red signal near Ladbroke Grove, UK, into the path of an express. We use the Public Inquiry Report, 'black box' data, and accident and engineering reports to construct a case history of the accident. We show how to combine field data with mathematical modelling to estimate the probability that the driver observed and identified the state of the signals, and checked their status. Our methodology can explain the SPAD ('Signal Passed At Danger'), generate recommendations about signal design and placement and provide quantitative guidance for the design of safer railway systems' speed limits and the location of signals. Practitioner Summary: Detailed ergonomic analysis of railway signals and rail infrastructure reveals problems of signal identification at this location. A record of driver eye movements measures attention, from which a quantitative model for out signal placement and permitted speeds can be derived. The paper is an example of how to combine field data, basic research and mathematical modelling to solve ergonomic design problems.

Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT.

PubMed

Ringe, Stefan; Oberhofer, Harald; Hille, Christoph; Matera, Sebastian; Reuter, Karsten

2016-08-09

The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.

Investigating fold structures of 2D materials by quantitative transmission electron microscopy.

PubMed

Wang, Zhiwei; Zhang, Zengming; Liu, Wei; Wang, Zhong Lin

2017-04-01

We report an approach developed for deriving 3D structural information of 2D membrane folds based on the recently-established quantitative transmission electron microscopy (TEM) in combination with density functional theory (DFT) calculations. Systematic multislice simulations reveal that the membrane folding leads to sufficiently strong electron scattering which enables a precise determination of bending radius. The image contrast depends also on the folding angles of 2D materials due to the variation of projection potentials, which however exerts much smaller effect compared with the bending radii. DFT calculations show that folded edges are typically characteristic of (fractional) nanotubes with the same curvature retained after energy optimization. Owing to the exclusion of Stobbs factor issue, numerical simulations were directly used in comparison with the experimental measurements on an absolute contrast scale, which results in a successful determination of bending radius of folded monolayer MoS 2 films. The method should be applicable to characterizing all 2D membranes with 3D folding features. Copyright © 2017 Elsevier Ltd. All rights reserved.

FT-Raman, FT-IR spectroscopic and DFT studies of hexaphenoxycyclotriphosphazene

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Padie, C.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2016-07-01

The FTIR and FT Raman measurements of zero Gc0‧ -H and first Gc1‧ -H generations of phosphorus dendrimer built from cyclotriphosphazene core with phenoxy and deuterophenoxy terminal groups have been performed. In order to evaluate how much the frequencies, shift when changing the electronics of the system the FTIR and FT Raman spectra of phosphorus‒containing dendron with five terminal oxybenzaldehyde and one ester function Gci‧ have been also studied. Structural optimization and normal mode analysis were obtained for Gc0‧ -H and Gc0‧ -D by the density functional theory (DFT). It is discovered that dendrimer molecule exists in a stable conformation with six phenoxy terminal groups spaced above and below the flat cyclotriphosphazene core. Optimized geometric bond length and angles obtained by DFT show good agreement with a previously-published X-ray study. The phenoxy terminal groups are characterized by the well-defined line at 993 cm-1 in the experimental Raman spectrum of Gc0‧ -H and by line at 960 cm-1 in the Raman spectrum of Gc0‧ -D. Relying on DFT calculations a complete vibrational assignment is proposed for the studied dendrimers. The frequencies and relative intensity of the bands at 1589, 1487 cm-1 in the IR spectra show marked difference in dependence of the substituents on the aromatic ring.

DFT Calculation of IR Absorption Spectra for PCE-nH2O, TCE-nH2O, DCE-nH2O, VC-nH2O for Small and Water-Dominated Molecular Clusters

DTIC Science & Technology

2017-10-31

of isolated molecules and that of bulk systems. DFT calculated absorption spectra represent quantitative estimates that can be correlated with...spectra, can be correlated with the presence of these hydrocarbons (see reference [1]). Accordingly, the molecular structure and IR absorption spectra of...associated with different types of ambient molecules, e.g., H2O, in order to apply background subtraction or spectral-signature- correlation algorithms

Performance Theories for Sentence Coding: Some Quantitative Models

ERIC Educational Resources Information Center

Aaronson, Doris; And Others

1977-01-01

This study deals with the patterns of word-by-word reading times over a sentence when the subject must code the linguistic information sufficiently for immediate verbatim recall. A class of quantitative models is considered that would account for reading times at phrase breaks. (Author/RM)

Detection of Prostate Cancer: Quantitative Multiparametric MR Imaging Models Developed Using Registered Correlative Histopathology.

PubMed

Metzger, Gregory J; Kalavagunta, Chaitanya; Spilseth, Benjamin; Bolan, Patrick J; Li, Xiufeng; Hutter, Diane; Nam, Jung W; Johnson, Andrew D; Henriksen, Jonathan C; Moench, Laura; Konety, Badrinath; Warlick, Christopher A; Schmechel, Stephen C; Koopmeiners, Joseph S

2016-06-01

Purpose To develop multiparametric magnetic resonance (MR) imaging models to generate a quantitative, user-independent, voxel-wise composite biomarker score (CBS) for detection of prostate cancer by using coregistered correlative histopathologic results, and to compare performance of CBS-based detection with that of single quantitative MR imaging parameters. Materials and Methods Institutional review board approval and informed consent were obtained. Patients with a diagnosis of prostate cancer underwent multiparametric MR imaging before surgery for treatment. All MR imaging voxels in the prostate were classified as cancer or noncancer on the basis of coregistered histopathologic data. Predictive models were developed by using more than one quantitative MR imaging parameter to generate CBS maps. Model development and evaluation of quantitative MR imaging parameters and CBS were performed separately for the peripheral zone and the whole gland. Model accuracy was evaluated by using the area under the receiver operating characteristic curve (AUC), and confidence intervals were calculated with the bootstrap procedure. The improvement in classification accuracy was evaluated by comparing the AUC for the multiparametric model and the single best-performing quantitative MR imaging parameter at the individual level and in aggregate. Results Quantitative T2, apparent diffusion coefficient (ADC), volume transfer constant (K(trans)), reflux rate constant (kep), and area under the gadolinium concentration curve at 90 seconds (AUGC90) were significantly different between cancer and noncancer voxels (P < .001), with ADC showing the best accuracy (peripheral zone AUC, 0.82; whole gland AUC, 0.74). Four-parameter models demonstrated the best performance in both the peripheral zone (AUC, 0.85; P = .010 vs ADC alone) and whole gland (AUC, 0.77; P = .043 vs ADC alone). Individual-level analysis showed statistically significant improvement in AUC in 82% (23 of 28) and 71% (24 of 34

Why use DFT methods in the study of carbohydrates?

USDA-ARS?s Scientific Manuscript database

The recent advances in density functional theory (DFT) and computer technology allow us to study systems with more than 100 atoms routinely. This makes it feasible to study large carbohydrate molecules via quantum mechanical methods, whereas in the past, studies of carbohydrates were restricted to ...

Modeling the weak hydrogen bonding of pyrrole and dichloromethane through Raman and DFT study.

PubMed

Singh, Dheeraj Kumar; Asthana, Birendra Pratap; Srivastava, Sunil Kumar

2012-08-01

Raman spectra of neat pyrrole (C(4)H(5)N) and its binary mixtures with dichloromethane (CH(2)Cl(2), DCM) with varying mole fractions of C(4)H(5)N from 0.1 to 0.9 were recorded in order to monitor the influence of molecular interaction on spectral features of selected vibrational bands of pyrrole in the region 600-1600 cm(-1). Only 1369 cm(-1) vibrational band of pyrrole shows a significant change in its peak position in going from neat pyrrole to the complexes. The 1369 cm(-1) band shows (∼6 cm(-1)) blue shift upon dilution and the corresponding linewidth shows the maximum shift at C = 0.5 mole fraction of pyrrole upon dilution which clearly indicates that the concentration fluctuation model plays major role. Quantum chemical calculation using density functional theory (DFT) and ab-initio (MP2 and HF) methods were performed employing high level basis set, 6-311++G(d,p) to obtain the ground state geometry of neat pyrrole and its complexes with DCM in gas phase. Basis set superimpose error (BSSE) correction was also introduced by using the counterpoise method. In order to account for the solvent effect on vibrational features and changes in optimized structural parameters of pyrrole, polarizable continuum model (PCM) (bulk solvations) and PCM (specific plus bulk solvations) calculations were performed. Two possible configurations of pyrrole + DCM complex have been predicted by B3LYP and HF methods, whereas the MP2 method gave only single configuration in which H atom of DCM is bonded to π ring of the pyrrole molecule. This affects significantly the ring vibrations of pyrrole molecule, which was also observed in our experimental results.

Understanding the Relativistic Generalization of Density Functional Theory (DFT) and Completing it in Practice

NASA Astrophysics Data System (ADS)

Bagayoko, Diola

In 2014, 50 years following the introduction of density functional theory (DFT), a rigorous understanding of it was published [AIP Advances, 4, 127104 (2014)]. This understanding included necessary steps ab initio electronic structure calculations have to take if their results are to possess the full physical content of DFT. These steps guarantee the fulfillment of conditions of validity of DFT; not surprisingly, they have led to accurate descriptions of several dozens of semiconductors, from first principle, without invoking derivative discontinuity or self-interaction correction. This presentation shows the mathematically and physically rigorous understanding of the relativistic extension of DFT by Rajagopal and Callaway {Phys. Rev. B 7, 1912 (1973)]. As in the non-relativistic case, the attainment of the absolute minima of the occupied energies is a necessary condition for the corresponding current density to be that of the ground state of the system and for computational results to agree with corresponding, experimental ones. Acknowledgments:This work was funded in part by the US National Science Foundation [NSF, Award Nos. EPS-1003897, NSF (2010-2015)-RII-SUBR, and HRD-1002541], the US Department of Energy, National Nuclear Security Administration (NNSA, Award No. DE-NA0002630), LaSPACE, and LONI-SUBR.

Quantitative assessment model for gastric cancer screening

PubMed Central

Chen, Kun; Yu, Wei-Ping; Song, Liang; Zhu, Yi-Min

2005-01-01

AIM: To set up a mathematic model for gastric cancer screening and to evaluate its function in mass screening for gastric cancer. METHODS: A case control study was carried on in 66 patients and 198 normal people, then the risk and protective factors of gastric cancer were determined, including heavy manual work, foods such as small yellow-fin tuna, dried small shrimps, squills, crabs, mothers suffering from gastric diseases, spouse alive, use of refrigerators and hot food, etc. According to some principles and methods of probability and fuzzy mathematics, a quantitative assessment model was established as follows: first, we selected some factors significant in statistics, and calculated weight coefficient for each one by two different methods; second, population space was divided into gastric cancer fuzzy subset and non gastric cancer fuzzy subset, then a mathematic model for each subset was established, we got a mathematic expression of attribute degree (AD). RESULTS: Based on the data of 63 patients and 693 normal people, AD of each subject was calculated. Considering the sensitivity and specificity, the thresholds of AD values calculated were configured with 0.20 and 0.17, respectively. According to these thresholds, the sensitivity and specificity of the quantitative model were about 69% and 63%. Moreover, statistical test showed that the identification outcomes of these two different calculation methods were identical (P>0.05). CONCLUSION: The validity of this method is satisfactory. It is convenient, feasible, economic and can be used to determine individual and population risks of gastric cancer. PMID:15655813

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

PubMed Central

2010-01-01

Background Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation

13C CPMAS NMR studies and DFT calculations of triterpene xylosides isolated from Actaea racemosa

NASA Astrophysics Data System (ADS)

Jamróz, Marta K.; Paradowska, Katarzyna; Gliński, Jan A.; Wawer, Iwona

2011-05-01

13C CPMAS NMR spectra of four triterpene glycosides: cimigenol xyloside ( 1), 26-deoxyactein ( 2), cimicifugoside H-1 ( 3) and 24-acethylhydroshengmanol xyloside ( 4) were recorded and analyzed to characterize their solid-state structure. Experimental data were supported by theoretical calculations of NMR shielding constants with the GIAO/6-31G**-su1 approach. A number of methods for the conformational search and a number of functionals for the DFT calculations were applied to ( 1). The best method was proven to be MMFF or MMFFAQ for the conformational search and the PBE1PBE functional for the DFT calculations. Extra calculations simulating C16 dbnd O⋯HOH hydrogen bond yield the isotropic shielding closer to the experimental solid-state value. For all the compounds CP kinetics parameters were calculated using either the I-S or the I-I*-S model. The analysis of CP kinetics data for methyl groups revealed differences in the T2 time constant for two methyl groups (C29 and C30) linked at C4.

A pipeline design of a fast prime factor DFT on a finite field

NASA Technical Reports Server (NTRS)

Truong, T. K.; Hsu, In-Shek; Shao, H. M.; Reed, Irving S.; Shyu, Hsuen-Chyun

1988-01-01

A conventional prime factor discrete Fourier transform (DFT) algorithm is used to realize a discrete Fourier-like transform on the finite field, GF(q sub n). This algorithm is developed to compute cyclic convolutions of complex numbers and to decode Reed-Solomon codes. Such a pipeline fast prime factor DFT algorithm over GF(q sub n) is regular, simple, expandable, and naturally suitable for VLSI implementation. An example illustrating the pipeline aspect of a 30-point transform over GF(q sub n) is presented.

A DFT based ligand field model for magnetic exchange coupling in transition metal dimer complexes:. (ii) application to magnetic systems with more than one unpaired electron per site

NASA Astrophysics Data System (ADS)

Atanasov, M.; Daul, C. A.

2003-11-01

The DFT based ligand field model for magnetic exchange coupling proposed recently, has been extended to systems containing more than one unpaired electron per site. The guidelines for this extension are described using a model example - the complex (NH 3) 3Cr III(OH) 3Cr III (NH 3) 33+. The exchange Hamiltonian, H ex=-J 12S1S2 has been simplified using symmetry principles, i.e. utilizing the D 3h(C 3v) Cr III - dimer(site) symmetry. Both antiferro- and ferromagnetic exchange coupling constants are found to yield important contributions to the value of the (negative, antiferromagnetic) exchange coupling constant in good agreement with experiment.

Stereochemical and conformational study on fenoterol by ECD spectroscopy and TD-DFT calculations.

PubMed

Tedesco, Daniele; Zanasi, Riccardo; Wainer, Irving W; Bertucci, Carlo

2014-03-01

Fenoterol and its derivatives are selective β2-adrenergic receptor (β2-AR) agonists whose stereoselective biological activities have been extensively investigated in the past decade; a complete stereochemical characterization of fenoterol derivatives is therefore crucial for a better understanding of the effects of stereochemistry on β2-AR binding. In the present project, the relationship between chiroptical properties and absolute stereochemistry of the stereoisomers of fenoterol (1) was investigated by experimental ECD spectroscopy and time-dependent density functional theory (TD-DFT). DFT geometry optimizations were carried out at the RI-B97D/TZVP/IEFPCM(MeOH) level and subsequent TD-DFT calculations were performed using the PBE0 hybrid functional. Despite the large pool of equilibrium conformers found for the investigated compounds and the known limitations of the level of theory employed, the computational protocol was able to reproduce the experimental ECD spectra of the stereoisomers of 1. The main contribution to the overall chiroptical properties was found to arise from the absolute configuration of the chiral center in α-position to the resorcinol moiety. Based on this evidence, a thorough conformational analysis was performed on the optimized DFT conformers, which revealed the occurrence of a different equilibrium between conformational patterns for the diastereomers of fenoterol: the (R,R')/(S,S') enantiomeric pair showed a higher population of folded conformations than the (R,S')/(S,R') pair. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantitative metal magnetic memory reliability modeling for welded joints

NASA Astrophysics Data System (ADS)

Xing, Haiyan; Dang, Yongbin; Wang, Ben; Leng, Jiancheng

2016-03-01

Metal magnetic memory(MMM) testing has been widely used to detect welded joints. However, load levels, environmental magnetic field, and measurement noises make the MMM data dispersive and bring difficulty to quantitative evaluation. In order to promote the development of quantitative MMM reliability assessment, a new MMM model is presented for welded joints. Steel Q235 welded specimens are tested along the longitudinal and horizontal lines by TSC-2M-8 instrument in the tensile fatigue experiments. The X-ray testing is carried out synchronously to verify the MMM results. It is found that MMM testing can detect the hidden crack earlier than X-ray testing. Moreover, the MMM gradient vector sum K vs is sensitive to the damage degree, especially at early and hidden damage stages. Considering the dispersion of MMM data, the K vs statistical law is investigated, which shows that K vs obeys Gaussian distribution. So K vs is the suitable MMM parameter to establish reliability model of welded joints. At last, the original quantitative MMM reliability model is first presented based on the improved stress strength interference theory. It is shown that the reliability degree R gradually decreases with the decreasing of the residual life ratio T, and the maximal error between prediction reliability degree R 1 and verification reliability degree R 2 is 9.15%. This presented method provides a novel tool of reliability testing and evaluating in practical engineering for welded joints.

Techniques for Computing the DFT Using the Residue Fermat Number Systems and VLSI

NASA Technical Reports Server (NTRS)

Truong, T. K.; Chang, J. J.; Hsu, I. S.; Pei, D. Y.; Reed, I. S.

1985-01-01

The integer complex multiplier and adder over the direct sum of two copies of a finite field is specialized to the direct sum of the rings of integers modulo Fermat numbers. Such multiplications and additions can be used in the implementation of a discrete Fourier transform (DFT) of a sequence of complex numbers. The advantage of the present approach is that the number of multiplications needed for the DFT can be reduced substantially over the previous approach. The architectural designs using this approach are regular, simple, expandable and, therefore, naturally suitable for VLSI implementation.

Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT.

PubMed

Götz, Andreas W; Kollmar, Christian; Hess, Bernd A

2005-09-01

We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by Löwdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods. (c) 2005 Wiley Periodicals, Inc.

A Quantitative Cost Effectiveness Model for Web-Supported Academic Instruction

ERIC Educational Resources Information Center

Cohen, Anat; Nachmias, Rafi

2006-01-01

This paper describes a quantitative cost effectiveness model for Web-supported academic instruction. The model was designed for Web-supported instruction (rather than distance learning only) characterizing most of the traditional higher education institutions. It is based on empirical data (Web logs) of students' and instructors' usage…

A quantitative systems physiology model of renal function and blood pressure regulation: Model description.

PubMed

Hallow, K M; Gebremichael, Y

2017-06-01

Renal function plays a central role in cardiovascular, kidney, and multiple other diseases, and many existing and novel therapies act through renal mechanisms. Even with decades of accumulated knowledge of renal physiology, pathophysiology, and pharmacology, the dynamics of renal function remain difficult to understand and predict, often resulting in unexpected or counterintuitive therapy responses. Quantitative systems pharmacology modeling of renal function integrates this accumulated knowledge into a quantitative framework, allowing evaluation of competing hypotheses, identification of knowledge gaps, and generation of new experimentally testable hypotheses. Here we present a model of renal physiology and control mechanisms involved in maintaining sodium and water homeostasis. This model represents the core renal physiological processes involved in many research questions in drug development. The model runs in R and the code is made available. In a companion article, we present a case study using the model to explore mechanisms and pharmacology of salt-sensitive hypertension. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

Synthesis and spectroscopical study of rhodanine derivative using DFT approaches

NASA Astrophysics Data System (ADS)

Anbarasan, R.; Dhandapani, A.; Manivarman, S.; Subashchandrabose, S.; Saleem, H.

2015-07-01

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of (E)-5-benzylidene-2-thioxothiazolidine-4-one (E5BTTO) have been investigated experimentally and theoretically based on Density Functional Theory (DFT) approach. The FT-Raman and FT-IR spectra of E5BTTO were recorded in solid phase. Theoretical calculations were performed at the DFT level using the Gaussian 03 program. The experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumber by their Total Energy Distribution (TED). The results of the calculation were applied to simulate infrared and raman spectra of the title compound which showed good agreement with the observed spectra. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Stability arising from hyperconjugative interactions leading to its NLO activity and charge delocalization were analyzed using Natural Bond Orbital (NBO) analysis.

Thiol reduction of arsenite and selenite: DFT modeling of the pathways to an as-se bond.

PubMed

Harper, Lenora K; Antony, Sonia; Bayse, Craig A

2014-12-15

The reactivity of arsenite and selenite with biological thiols plays an important role in the toxicity of these elements. However, toxic effects are eliminated when the species are coadministered, due to the antagonistic relationship between selenium and arsenic. The reduction of arsenous acid and selenious acid by thiol and the formation of an As-Se species have been modeled using density functional theory (DFT) and solvent-assisted proton exchange (SAPE), a microsolvation technique that uses a network of water molecules to mimic the participation of bulk solvent in proton transfer processes. Activation barriers and relative energies were calculated for the stepwise thiol reduction of arsenite to form As(SR)3 and selenious acid to first form a selenotrisulfide (Se(SR)2) and then H2Se. Several pathways were explored for the formation of an As-Se bond: the nucleophilic attack of selenide or selenopersulfide on As(OH)3, (RS)As(OH)2, and (RS)2AsOH to form (RS)2AsSeH. On the basis of the lower activation barrier and bioavailability of (RS)2AsOH, the reaction of H2Se with (RS)2AsOH is deemed the most favorable, consistent with previous experimental studies.

Geometric interpretations of the Discrete Fourier Transform (DFT)

NASA Technical Reports Server (NTRS)

Campbell, C. W.

1984-01-01

One, two, and three dimensional Discrete Fourier Transforms (DFT) and geometric interpretations of their periodicities are presented. These operators are examined for their relationship with the two sided, continuous Fourier transform. Discrete or continuous transforms of real functions have certain symmetry properties. The symmetries are examined for the one, two, and three dimensional cases. Extension to higher dimension is straight forward.

Density Functional Theory (dft) Simulations of Shocked Liquid Xenon

NASA Astrophysics Data System (ADS)

Mattsson, Thomas R.; Magyar, Rudolph J.

2009-12-01

Xenon is not only a technologically important element used in laser technologies and jet propulsion, but it is also one of the most accessible materials in which to study the metal-insulator transition with increasing pressure. Because of its closed shell electronic configuration, xenon is often assumed to be chemically inert, interacting almost entirely through the van der Waals interaction, and at liquid density, is typically modeled well using Leonard-Jones potentials. However, such modeling has a limited range of validity as xenon is known to form compounds under normal conditions and likely exhibits considerably more chemistry at higher densities when hybridization of occupied orbitals becomes significant. We present DFT-MD simulations of shocked liquid xenon with the goal of developing an improved equation of state. The calculated Hugoniot to 2 MPa compares well with available experimental shock data. Sandia is a mul-tiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Designing automation for human use: empirical studies and quantitative models.

PubMed

Parasuraman, R

2000-07-01

An emerging knowledge base of human performance research can provide guidelines for designing automation that can be used effectively by human operators of complex systems. Which functions should be automated and to what extent in a given system? A model for types and levels of automation that provides a framework and an objective basis for making such choices is described. The human performance consequences of particular types and levels of automation constitute primary evaluative criteria for automation design when using the model. Four human performance areas are considered--mental workload, situation awareness, complacency and skill degradation. Secondary evaluative criteria include such factors as automation reliability, the risks of decision/action consequences and the ease of systems integration. In addition to this qualitative approach, quantitative models can inform design. Several computational and formal models of human interaction with automation that have been proposed by various researchers are reviewed. An important future research need is the integration of qualitative and quantitative approaches. Application of these models provides an objective basis for designing automation for effective human use.

A two-factor error model for quantitative steganalysis

NASA Astrophysics Data System (ADS)

Böhme, Rainer; Ker, Andrew D.

2006-02-01

Quantitative steganalysis refers to the exercise not only of detecting the presence of hidden stego messages in carrier objects, but also of estimating the secret message length. This problem is well studied, with many detectors proposed but only a sparse analysis of errors in the estimators. A deep understanding of the error model, however, is a fundamental requirement for the assessment and comparison of different detection methods. This paper presents a rationale for a two-factor model for sources of error in quantitative steganalysis, and shows evidence from a dedicated large-scale nested experimental set-up with a total of more than 200 million attacks. Apart from general findings about the distribution functions found in both classes of errors, their respective weight is determined, and implications for statistical hypothesis tests in benchmarking scenarios or regression analyses are demonstrated. The results are based on a rigorous comparison of five different detection methods under many different external conditions, such as size of the carrier, previous JPEG compression, and colour channel selection. We include analyses demonstrating the effects of local variance and cover saturation on the different sources of error, as well as presenting the case for a relative bias model for between-image error.

A transformative model for undergraduate quantitative biology education.

PubMed

Usher, David C; Driscoll, Tobin A; Dhurjati, Prasad; Pelesko, John A; Rossi, Louis F; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B

2010-01-01

The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions.

A Transformative Model for Undergraduate Quantitative Biology Education

PubMed Central

Driscoll, Tobin A.; Dhurjati, Prasad; Pelesko, John A.; Rossi, Louis F.; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B.

2010-01-01

The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions. PMID:20810949

A Quantitative Model of Expert Transcription Typing

DTIC Science & Technology

1993-03-08

side of pure psychology, several researchers have argued that transcription typing is a particularly good activity for the study of human skilled...phenomenon with a quantitative METT prediction. The first, quick and dirty analysis gives a good prediction of the copy span, in fact, it is even...typing, it should be demonstrated that the mechanism of the model does not get in the way of good predictions. If situations occur where the entire

Impact of implementation choices on quantitative predictions of cell-based computational models

NASA Astrophysics Data System (ADS)

Kursawe, Jochen; Baker, Ruth E.; Fletcher, Alexander G.

2017-09-01

'Cell-based' models provide a powerful computational tool for studying the mechanisms underlying the growth and dynamics of biological tissues in health and disease. An increasing amount of quantitative data with cellular resolution has paved the way for the quantitative parameterisation and validation of such models. However, the numerical implementation of cell-based models remains challenging, and little work has been done to understand to what extent implementation choices may influence model predictions. Here, we consider the numerical implementation of a popular class of cell-based models called vertex models, which are often used to study epithelial tissues. In two-dimensional vertex models, a tissue is approximated as a tessellation of polygons and the vertices of these polygons move due to mechanical forces originating from the cells. Such models have been used extensively to study the mechanical regulation of tissue topology in the literature. Here, we analyse how the model predictions may be affected by numerical parameters, such as the size of the time step, and non-physical model parameters, such as length thresholds for cell rearrangement. We find that vertex positions and summary statistics are sensitive to several of these implementation parameters. For example, the predicted tissue size decreases with decreasing cell cycle durations, and cell rearrangement may be suppressed by large time steps. These findings are counter-intuitive and illustrate that model predictions need to be thoroughly analysed and implementation details carefully considered when applying cell-based computational models in a quantitative setting.

Quantitative Systems Pharmacology: A Case for Disease Models.

PubMed

Musante, C J; Ramanujan, S; Schmidt, B J; Ghobrial, O G; Lu, J; Heatherington, A C

2017-01-01

Quantitative systems pharmacology (QSP) has emerged as an innovative approach in model-informed drug discovery and development, supporting program decisions from exploratory research through late-stage clinical trials. In this commentary, we discuss the unique value of disease-scale "platform" QSP models that are amenable to reuse and repurposing to support diverse clinical decisions in ways distinct from other pharmacometrics strategies. © 2016 The Authors Clinical Pharmacology & Therapeutics published by Wiley Periodicals, Inc. on behalf of The American Society for Clinical Pharmacology and Therapeutics.

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

USGS Publications Warehouse

Anderson, Ryan; Clegg, Samuel M.; Frydenvang, Jens; Wiens, Roger C.; McLennan, Scott M.; Morris, Richard V.; Ehlmann, Bethany L.; Dyar, M. Darby

2017-01-01

Accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “sub-model” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. The sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

Ferrocenyl-substituted dinuclear Cu(II) complex: Synthesis, spectroscopy, electrochemistry, DFT calculations and catecholase activity

NASA Astrophysics Data System (ADS)

Emirik, Mustafa; Karaoğlu, Kaan; Serbest, Kerim; Menteşe, Emre; Yilmaz, Ismail

2016-02-01

A new ferrocenyl-substituted heterocyclic hydrazide ligand and its Cu(II) complex were prepared. The DFT calculations were performed to determine the electronic and molecular structures of the title compounds. The electronic spectra were calculated by using time-dependent DFT method, and the transitions were correlated with the molecular orbitals of the compounds. The bands assignments of IR spectra were achieved in the light of the theoretical vibrational spectral data and total energy distribution values calculated at DFT/B3LYP/6-311++G(d,p) level. The redox behaviors of the ferrocene derivatives were investigated by cyclic voltammetry. The compounds show reversible redox couple assignable to Fc+/Fc couple. The copper(II) complex behaves as an effective catalyst towards oxidation of 3,5-di-tert-butylcatechol to its corresponding quinone derivative in DMF saturated with O2. The reaction follows Michaelis-Menten enzymatic reaction kinetics with turnover numbers 2.32 × 103.

An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing.

PubMed

Wu, Zujian; Pang, Wei; Coghill, George M

2015-01-01

Both qualitative and quantitative model learning frameworks for biochemical systems have been studied in computational systems biology. In this research, after introducing two forms of pre-defined component patterns to represent biochemical models, we propose an integrative qualitative and quantitative modelling framework for inferring biochemical systems. In the proposed framework, interactions between reactants in the candidate models for a target biochemical system are evolved and eventually identified by the application of a qualitative model learning approach with an evolution strategy. Kinetic rates of the models generated from qualitative model learning are then further optimised by employing a quantitative approach with simulated annealing. Experimental results indicate that our proposed integrative framework is feasible to learn the relationships between biochemical reactants qualitatively and to make the model replicate the behaviours of the target system by optimising the kinetic rates quantitatively. Moreover, potential reactants of a target biochemical system can be discovered by hypothesising complex reactants in the synthetic models. Based on the biochemical models learned from the proposed framework, biologists can further perform experimental study in wet laboratory. In this way, natural biochemical systems can be better understood.

Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast

PubMed Central

Pang, Wei; Coghill, George M.

2015-01-01

In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed. PMID:25864377

Predicting the properties of the lead alloys from DFT calculations

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

Buimaga-Iarinca, L., E-mail: luiza.iarinca@itim-cj.ro; Calborean, A.

2015-12-23

We provide qualitative results for the physical properties of the lead alloys at atomic scale by using DFT calculations. Our approach is based on the two assumptions: (i) the geometric structure of lead atoms provides a matrix where the alloying elements can take their positions in the structure as substitutions and (ii) there is a small probability of a direct interaction between the alloying elements, thus the interactions of each alloying element may be approximated by the interactions to the lead matrix. DFT calculations are used to investigate the interaction between several types of impurities and the lead matrix formore » low concentrations of the alloying element. We report results such as the enthalpy of formation, charge transfer and mechanical stress induced by the impurities in the lead matrix; these results can be used as qualitative guide in tuning the physico-chemical properties of the lead alloys.« less

Understanding the HIV-1 protease reactivity with DFT: what do we gain from recent functionals?

PubMed

Garrec, J; Sautet, P; Fleurat-Lessard, P

2011-07-07

The modeling of HIV-1 plays a crucial role in the understanding of its reactivity and its interactions with specific drugs. In this work, we propose a medium sized model to test the ability of a variety of quantum chemistry approaches to provide reasonable geometric parameters and energetics for this system. Although our model is large enough to include the main polarizing groups of the active site, it is small enough to be used within full quantum studies up to the second order Møller-Plesset (MP2) level with extrapolations to coupled cluster CCSD(T) level. These high level calculations are used as reference to assess the ability of electronic structure methods (semiempirical and DFT) to provide accurate geometries and energies for the HIV-1 protease reaction. All semiempirical methods fail to describe the geometry of the protease active site. Within DFT, pure generalized gradient approximation (GGA) functionals have difficulty in reproducing the reaction energy and underestimate the barrier. Hybrid and/or meta GGA approaches do not yield a consistent improvement. The best results are obtained with hybrid GGA B3LYP or X3LYP and with hybrid meta GGA functionals with a fraction of exact exchange around 30-40%, such as M06, B1B95, or BMK functionals. On the basis of these results, we propose an accurate and computationally efficient strategy, employing quantum chemistry methods. This is applied here to study the protonation state of the reaction intermediate and could be easily used in further QM/MM studies.

DFT and ab initio study of the unimolecular decomposition of the lowest singlet and triplet states of nitromethane

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

Manaa, M.R.; Fried, L.E.

1998-11-26

The fully optimized potential energy curves for the unimolecular decomposition of the lowest singlet and triplet states of nitromethane through the C-NO{sub 2} bond dissociation pathway are calculated using various DFT and high-level ab initio electronic structure methods. The authors perform gradient corrected density functional theory (DFT) and multiconfiguration self-consistent field (MCSCF) to conclusively demonstrate that the triplet state of nitromethane is bound. The adiabatic curve of this state exhibits a 33 kcal/mol energy barrier as determined at the MCSCF level. DFT methods locate this barrier at a shorter C-N bond distance with 12--16 kcal/mol lower energy than does MCSCF.more » In addition to MCSCF and DFT, quadratic configuration interactions with single and double substitutions (QCISD) calculations are also performed for the singlet curve. The potential energy profiles of this state predicted by FT methods based on Becke`s 1988 exchange functional differ by as much as 17 kcal/mol from the predictions of MCSCF and QCISD in the vicinity of the equilibrium structure. The computational methods predict bond dissociation energies 5--9 kcal/mol lower than the experimental value. DFT techniques based on Becke`s 3-parameter exchange functional show the best overall agreement with the higher level methods.« less

Diffusion of anthracene derivatives on Cu(111) studied by STM and DFT

NASA Astrophysics Data System (ADS)

Wyrick, Jonathan; Bartels, Ludwig; Einstein, Theodore

2014-03-01

Substituted anthracenes have drawn attention due to their ability to diffuse uniaxially on a Cu(111) surface. We compare anthracene to three of its derivatives whose 9,10 hydrogens are replaced by elements of the chalcogen group that act as linkers binding the molecules to a Cu(111) substrate. DFT calculations shed light on STM imaging and diffusion studies on the three substituted species. We present an analysis of the DFT results in which energetic contributions to the diffusion barriers are partitioned among the Kohn-Sham orbitals, allowing us to make assignments as to how each orbital affects diffusion for each species and draw comparisons between them. Present address: Center for Nanoscale Science and Technology, NIST, Gaithersburg, MD.

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast.

PubMed

Pang, Wei; Coghill, George M

2015-05-01

In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

The linearized multistage model and the future of quantitative risk assessment.

PubMed

Crump, K S

1996-10-01

The linearized multistage (LMS) model has for over 15 years been the default dose-response model used by the U.S. Environmental Protection Agency (USEPA) and other federal and state regulatory agencies in the United States for calculating quantitative estimates of low-dose carcinogenic risks from animal data. The LMS model is in essence a flexible statistical model that can describe both linear and non-linear dose-response patterns, and that produces an upper confidence bound on the linear low-dose slope of the dose-response curve. Unlike its namesake, the Armitage-Doll multistage model, the parameters of the LMS do not correspond to actual physiological phenomena. Thus the LMS is 'biological' only to the extent that the true biological dose response is linear at low dose and that low-dose slope is reflected in the experimental data. If the true dose response is non-linear the LMS upper bound may overestimate the true risk by many orders of magnitude. However, competing low-dose extrapolation models, including those derived from 'biologically-based models' that are capable of incorporating additional biological information, have not shown evidence to date of being able to produce quantitative estimates of low-dose risks that are any more accurate than those obtained from the LMS model. Further, even if these attempts were successful, the extent to which more accurate estimates of low-dose risks in a test animal species would translate into improved estimates of human risk is questionable. Thus, it does not appear possible at present to develop a quantitative approach that would be generally applicable and that would offer significant improvements upon the crude bounding estimates of the type provided by the LMS model. Draft USEPA guidelines for cancer risk assessment incorporate an approach similar to the LMS for carcinogens having a linear mode of action. However, under these guidelines quantitative estimates of low-dose risks would not be developed for

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

PubMed

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

A computational DFT study of structural transitions in textured solid-fluid interfaces

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Parry, Andrew O.; Kalliadasis, Serafim

2015-11-01

Fluids adsorbed at walls, in capillary pores and slits, and in more exotic, sculpted geometries such as grooves and wedges can exhibit many new phase transitions, including wetting, pre-wetting, capillary-condensation and filling, compared to their bulk counterparts. As well as being of fundamental interest to the modern statistical mechanical theory of inhomogeneous fluids, these are also relevant to nanofluidics, chemical- and bioengineering. In this talk we will show using a microscopic Density Functional Theory (DFT) for fluids how novel, continuous, interfacial transitions associated with the first-order prewetting line, can occur on steps, in grooves and in wedges, that are sensitive to both the range of the intermolecular forces and interfacial fluctuation effects. These transitions compete with wetting, filling and condensation producing very rich phase diagrams even for relatively simple geometries. We will also discuss practical aspects of DFT calculations, and demonstrate how this statistical-mechanical framework is capable of yielding complex fluid structure, interfacial tensions, and regions of thermodynamic stability of various fluid configurations. As a side note, this demonstrates that DFT is an excellent tool for the investigations of complex multiphase systems. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031.

Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

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

Schober, Christoph; Reuter, Karsten; Oberhofer, Harald, E-mail: harald.oberhofer@ch.tum.de

2016-02-07

We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or “flavors” of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer),more » we find that our new scheme gives improved electronic couplings for HAB7 (−6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (−15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.« less

Two-dimensional auto-correlation analysis and Fourier-transform analysis of second-harmonic-generation image for quantitative analysis of collagen fiber in human facial skin

NASA Astrophysics Data System (ADS)

Ogura, Yuki; Tanaka, Yuji; Hase, Eiji; Yamashita, Toyonobu; Yasui, Takeshi

2018-02-01

We compare two-dimensional auto-correlation (2D-AC) analysis and two-dimensional Fourier transform (2D-FT) for evaluation of age-dependent structural change of facial dermal collagen fibers caused by intrinsic aging and extrinsic photo-aging. The age-dependent structural change of collagen fibers for female subjects' cheek skin in their 20s, 40s, and 60s were more noticeably reflected in 2D-AC analysis than in 2D-FT analysis. Furthermore, 2D-AC analysis indicated significantly higher correlation with the skin elasticity measured by Cutometer® than 2D-AC analysis. 2D-AC analysis of SHG image has a high potential for quantitative evaluation of not only age-dependent structural change of collagen fibers but also skin elasticity.

A quantitative model of optimal data selection in Wason's selection task.

PubMed

Hattori, Masasi

2002-10-01

The optimal data selection model proposed by Oaksford and Chater (1994) successfully formalized Wason's selection task (Wason, 1966). The model, however, involved some questionable assumptions and was also not sufficient as a model of the task because it could not provide quantitative predictions of the card selection frequencies. In this paper, the model was revised to provide quantitative fits to the data. The model can predict the selection frequencies of cards based on a selection tendency function (STF), or conversely, it enables the estimation of subjective probabilities from data. Past experimental data were first re-analysed based on the model. In Experiment 1, the superiority of the revised model was shown. However, when the relationship between antecedent and consequent was forced to deviate from the biconditional form, the model was not supported. In Experiment 2, it was shown that sufficient emphasis on probabilistic information can affect participants' performance. A detailed experimental method to sort participants by probabilistic strategies was introduced. Here, the model was supported by a subgroup of participants who used the probabilistic strategy. Finally, the results were discussed from the viewpoint of adaptive rationality.

Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids

NASA Astrophysics Data System (ADS)

Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

2013-06-01

Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

Quantitative modeling of reservoir-triggered seismicity

NASA Astrophysics Data System (ADS)

Hainzl, S.; Catalli, F.; Dahm, T.; Heinicke, J.; Woith, H.

2017-12-01

Reservoir-triggered seismicity might occur as the response to the crustal stress caused by the poroelastic response to the weight of the water volume and fluid diffusion. Several cases of high correlations have been found in the past decades. However, crustal stresses might be altered by many other processes such as continuous tectonic stressing and coseismic stress changes. Because reservoir-triggered stresses decay quickly with distance, even tidal or rainfall-triggered stresses might be of similar size at depth. To account for simultaneous stress sources in a physically meaningful way, we apply a seismicity model based on calculated stress changes in the crust and laboratory-derived friction laws. Based on the observed seismicity, the model parameters can be determined by maximum likelihood method. The model leads to quantitative predictions of the variations of seismicity rate in space and time which can be used for hypothesis testing and forecasting. For case studies in Talala (India), Val d'Agri (Italy) and Novy Kostel (Czech Republic), we show the comparison of predicted and observed seismicity, demonstrating the potential and limitations of the approach.

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

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

Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

DOE PAGES

Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens; ...

2016-12-15

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

In Vitro Antioxidant Activity of Selected 4-Hydroxy-chromene-2-one Derivatives—SAR, QSAR and DFT Studies

PubMed Central

Mladenović, Milan; Mihailović, Mirjana; Bogojević, Desanka; Matić, Sanja; Nićiforović, Neda; Mihailović, Vladimir; Vuković, Nenad; Sukdolak, Slobodan; Solujić, Slavica

2011-01-01

The series of fifteen synthesized 4-hydroxycoumarin derivatives was subjected to antioxidant activity evaluation in vitro, through total antioxidant capacity, 1,1-diphenyl-2-picryl-hydrazyl (DPPH), hydroxyl radical, lipid peroxide scavenging and chelating activity. The highest activity was detected during the radicals scavenging, with 2b, 6b, 2c, and 4c noticed as the most active. The antioxidant activity was further quantified by the quantitative structure-activity relationships (QSAR) studies. For this purpose, the structures were optimized using Paramethric Method 6 (PM6) semi-empirical and Density Functional Theory (DFT) B3LYP methods. Bond dissociation enthalpies of coumarin 4-OH, Natural Bond Orbital (NBO) gained hybridization of the oxygen, acidity of the hydrogen atom and various molecular descriptors obtained, were correlated with biological activity, after which we designed 20 new antioxidant structures, using the most favorable structural motifs, with much improved predicted activity in vitro. PMID:21686153

Solvatochromic benzo[h] coumarins: Synthesis, solvatochromism, NLO and DFT study

NASA Astrophysics Data System (ADS)

Warde, Umesh; Sekar, Nagaiyan

2017-10-01

Three benzo[h] coumarins were synthesized and analyzed for their potential NLOphoric properties. Coumarins were synthesized using Knoevenagel condensation method by reacting hydroxyl-naphthalene aldehyde with cyano-methylelene-benzazoles containing NH, O and S elements respectively as the active methylene compounds. The absorption maxima for the coumarins are not affected by the solvent polarity but emission maxima does. Emission solvatochromism was analyzed using various solvent polarity functions which highlights the polarity dependency of the emission profile. Coumarins showed satisfactory values for first and second hyperpolarizability which are comparable using solvatochromism and DFT. NLO properties are also compared with the limits of hyperpolarizability calculated using sum rule of quantum mechanics. Results show that the NLO properties predicted by DFT are close to the upper limits of hyperpolarizability. The functional CAM-B3LYP is proven to be suitable for predicting NLO properties for these coumarins compared to functional B3LYP. The present study highlights the importance of such molecules for incorporating in advanced NLOphores.

Accuracy of Td-DFT in the Ultraviolet and Circular Dichroism Spectra of Deoxyguanosine and Uridine.

PubMed

Miyahara, Tomoo; Nakatsuji, Hiroshi

2018-01-11

Accuracy of the time-dependent density functional theory (Td-DFT) was examined for the ultraviolet (UV) and circular dichroism (CD) spectra of deoxyguanosine (dG) and uridine, using 11 different DFT functionals and two different basis sets. The Td-DFT results of the UV and CD spectra were strongly dependent on the functionals used. The basis-set dependence was observed only for the CD spectral calculations. For the UV spectra, the B3LYP and PBE0 functionals gave relatively good results. For the CD spectra, the B3LYP and PBE0 with 6-311G(d,p) basis gave relatively permissible result only for dG. The results of other functionals were difficult to be used for the studies of the UV and CD spectra, though the symmetry adapted cluster-configuration interaction (SAC-CI) method reproduced well the experimental spectra of these molecules. To obtain valuable information from the theoretical calculations of the UV and CD spectra, the theoretical tool must be able to reproduce correctly both of the intensities and peak positions of the UV and CD spectra. Then, we can analyze the reasons of the changes of the intensity and/or the peak position to clarify the chemistry involved. It is difficult to recommend Td-DFT as such tools of science, at least from the examinations using dG and uridine.

Quantitative Systems Pharmacology: A Case for Disease Models

PubMed Central

Ramanujan, S; Schmidt, BJ; Ghobrial, OG; Lu, J; Heatherington, AC

2016-01-01

Quantitative systems pharmacology (QSP) has emerged as an innovative approach in model‐informed drug discovery and development, supporting program decisions from exploratory research through late‐stage clinical trials. In this commentary, we discuss the unique value of disease‐scale “platform” QSP models that are amenable to reuse and repurposing to support diverse clinical decisions in ways distinct from other pharmacometrics strategies. PMID:27709613

DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

NASA Astrophysics Data System (ADS)

Stawoska, I.; Dudzik, A.; Wasylewski, M.; Jemioła-Rzemińska, M.; Skoczowski, A.; Strzałka, K.; Szaleniec, M.

2017-06-01

The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, ( S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2' ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R2 = 0.93) and a good prediction of the reaction kinetics (R2 = 0.89). The observed relations were validated in prediction of log K eq obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.

Investigation of ground state charge transfer complex between paracetamol and p-chloranil through DFT and UV-visible studies

NASA Astrophysics Data System (ADS)

Shukla, Madhulata; Srivastava, Nitin; Saha, Satyen

2012-08-01

The present report deals with the theoretical investigation on ground state structure and charge transfer (CT) transitions in paracetamol (PA)/p-chloranil (CA) complex using Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TD-DFT) method. It is found that Cdbnd O bond length of p-chloranil increases on complexation with paracetamol along with considerable amount of charge transfer from PA to CA. TD-DFT calculations have been performed to analyse the observed UV-visible spectrum of PA-CA charge transferred complex. Interestingly, in addition to expected CT transition, a weak symmetry relieved π-π* transition in the chloranil is also observed.

A Systematic Quantitative-Qualitative Model: How To Evaluate Professional Services

ERIC Educational Resources Information Center

Yoda, Koji

1973-01-01

The proposed evaluation model provides for the assignment of relative weights to each criterion, and establishes a weighting system for calculating a quantitative-qualitative raw score for each service activity of a faculty member being reviewed. (Author)

DFT study of ethyl xanthate interaction with sphalerite (1 1 0) surface in the absence and presence of copper

NASA Astrophysics Data System (ADS)

Liu, Jian; Wen, Shuming; Deng, Jiushuai; Chen, Xiumin; Feng, Qicheng

2014-08-01

The interaction among sphalerite (1 1 0) surface, copper and ethyl xanthate (EX) was simulated using the density functional theory (DFT). The results of DFT indicate that four types of stable interaction models exist among sphalerite surface, copper and EX, i.e., EX interacts with the Cu substituted for Zn, Cu adsorbed on the top site of S, Cu adsorbed on the bridge site of S and Cu(OH)2 adsorbed on the sphalerite surface. The four interaction models can result in the activation flotation of sphalerite. Density of states (DOS) analysis shows that the energy level discrepancy of the Zn 3d orbital in ZnS and the bonding S 3p orbital in EX results in the weak adsorption of EX on un-activated sphalerite surface. However, after copper activation, the Cu 3d orbital peak and bonding S 3p orbital peak are just maximally overlapped nearby the Fermi level. This study provides an insight into the nature that sphalerite responds not well to EX and also a comprehensive understanding on the possible interaction cases existing among sphalerite surface, copper and EX.

OH-initiated transformation and hydrolysis of aspirin in AOPs system: DFT and experimental studies.

PubMed

He, Lin; Sun, Xiaomin; Zhu, Fanping; Ren, Shaojie; Wang, Shuguang

2017-08-15

Advanced oxidation processes (AOPs) are widely used in wastewater treatment of pharmaceutical and personal care products (PPCPs). In this work, the OH-initiated transformation as well as the hydrolysis of a typical PPCPs, aspirin, was investigated using density functional theory (DFT) calculations and laboratory experiments. For DFT calculations, the frontier electron densities and bond dissociation energies were analyzed. Profiles of the potential energy surface were constructed, and all the possible pathways were discussed. Additionally, rate constants for each pathway were calculated with transition state theory (TST) method. UV/H 2 O 2 experiments of aspirin were performed and degradation intermediates were identified by UPLC-MS-MS analysis. Different findings from previous experimental works were reported that the H-abstraction pathways at methyl position were dominated and OH-addition pathways on benzene ring were also favored. Meantime, hydroxyl ASA was confirmed as the main stable intermediate. Moreover, it was the first time to use DFT method to investigate the hydrolysis mechanisms of organic ester compound. Copyright © 2017 Elsevier B.V. All rights reserved.

The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies

NASA Astrophysics Data System (ADS)

Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L.; Sinha, Chittaranjan

2015-02-01

Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)sbnd H(7A)---O(2), N(7)sbnd H(7B)---O(3), N(1)sbnd H(1)---N(2), C(5)sbnd H(5)---O(3)sbnd S(1) and N(7)sbnd (H7A)---O(2)sbnd S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37 × 104 M-1. The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach.

PubMed

Cecchet, F; Lis, D; Caudano, Y; Mani, A A; Peremans, A; Champagne, B; Guthmuller, J

2012-03-28

The knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular, DFT calculations have been carried out on three classes of models for the aliphatic chains. The first class of models consists of aliphatic chains, containing from 3 to 12 carbon atoms, in which only one methyl group can freely vibrate, while the rest of the chain is frozen by a strong overweight of its C and H atoms. This enables us to localize the probed vibrational modes on the methyl group. In the second class, only one methyl group is frozen, while the entire remaining chain is allowed to vibrate. This enables us to analyse the influence of the aliphatic chain on the methyl stretching vibrations. Finally, the dodecanethiol (DDT) molecule is considered, for which the effects of two dielectrics, i.e. n-hexane and n-dodecane, are investigated. Moreover, DDT calculations are also carried out by using different exchange-correlation (XC) functionals in order to assess the DFT approximations. Using the DFT IR vectors and Raman tensors, the SFG spectrum of DDT has been simulated and the orientation of the methyl group has then been deduced and compared with that obtained using an analytical approach based on a bond additivity model. This analysis shows that when using DFT molecular properties, the predicted orientation of the terminal methyl group tends to converge as a function of the alkyl chain length and that the effects of the chain as well as of the dielectric environment are small. Instead, a more significant difference is observed when comparing the DFT-based results with those obtained from the analytical approach, thus indicating

Human judgment vs. quantitative models for the management of ecological resources.

PubMed

Holden, Matthew H; Ellner, Stephen P

2016-07-01

Despite major advances in quantitative approaches to natural resource management, there has been resistance to using these tools in the actual practice of managing ecological populations. Given a managed system and a set of assumptions, translated into a model, optimization methods can be used to solve for the most cost-effective management actions. However, when the underlying assumptions are not met, such methods can potentially lead to decisions that harm the environment and economy. Managers who develop decisions based on past experience and judgment, without the aid of mathematical models, can potentially learn about the system and develop flexible management strategies. However, these strategies are often based on subjective criteria and equally invalid and often unstated assumptions. Given the drawbacks of both methods, it is unclear whether simple quantitative models improve environmental decision making over expert opinion. In this study, we explore how well students, using their experience and judgment, manage simulated fishery populations in an online computer game and compare their management outcomes to the performance of model-based decisions. We consider harvest decisions generated using four different quantitative models: (1) the model used to produce the simulated population dynamics observed in the game, with the values of all parameters known (as a control), (2) the same model, but with unknown parameter values that must be estimated during the game from observed data, (3) models that are structurally different from those used to simulate the population dynamics, and (4) a model that ignores age structure. Humans on average performed much worse than the models in cases 1-3, but in a small minority of scenarios, models produced worse outcomes than those resulting from students making decisions based on experience and judgment. When the models ignored age structure, they generated poorly performing management decisions, but still outperformed

Evaluation of DFT methods for computing the interaction energies of homomolecular and heteromolecular dimers of monosubstituted benzene

NASA Astrophysics Data System (ADS)

Godfrey-Kittle, Andrew; Cafiero, Mauricio

We present density functional theory (DFT) interaction energies for the sandwich and T-shaped conformers of substituted benzene dimers. The DFT functionals studied include TPSS, HCTH407, B3LYP, and X3LYP. We also include Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory calculations (MP2), as well as calculations using a new functional, P3LYP, which includes PBE and HF exchange and LYP correlation. Although DFT methods do not explicitly account for the dispersion interactions important in the benzene-dimer interactions, we find that our new method, P3LYP, as well as HCTH407 and TPSS, match MP2 and CCSD(T) calculations much better than the hybrid methods B3LYP and X3LYP methods do.

Experimental demonstration of OFDM/OQAM transmission with DFT-based channel estimation for visible laser light communications

NASA Astrophysics Data System (ADS)

He, Jing; Shi, Jin; Deng, Rui; Chen, Lin

2017-08-01

Recently, visible light communication (VLC) based on light-emitting diodes (LEDs) is considered as a candidate technology for fifth-generation (5G) communications, VLC is free of electromagnetic interference and it can simplify the integration of VLC into heterogeneous wireless networks. Due to the data rates of VLC system limited by the low pumping efficiency, small output power and narrow modulation bandwidth, visible laser light communication (VLLC) system with laser diode (LD) has paid more attention. In addition, orthogonal frequency division multiplexing/offset quadrature amplitude modulation (OFDM/OQAM) is currently attracting attention in optical communications. Due to the non-requirement of cyclic prefix (CP) and time-frequency domain well-localized pulse shapes, it can achieve high spectral efficiency. Moreover, OFDM/OQAM has lower out-of-band power leakage so that it increases the system robustness against inter-carrier interference (ICI) and frequency offset. In this paper, a Discrete Fourier Transform (DFT)-based channel estimation scheme combined with the interference approximation method (IAM) is proposed and experimentally demonstrated for VLLC OFDM/OQAM system. The performance of VLLC OFDM/OQAM system with and without DFT-based channel estimation is investigated. Moreover, the proposed DFT-based channel estimation scheme and the intra-symbol frequency-domain averaging (ISFA)-based method are also compared for the VLLC OFDM/OQAM system. The experimental results show that, the performance of EVM using the DFT-based channel estimation scheme is improved about 3dB compared with the conventional IAM method. In addition, the DFT-based channel estimation scheme can resist the channel noise effectively than that of the ISFA-based method.

Comparison of blood flow models and acquisitions for quantitative myocardial perfusion estimation from dynamic CT

NASA Astrophysics Data System (ADS)

Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R.; La Riviere, Patrick J.; Alessio, Adam M.

2014-04-01

Myocardial blood flow (MBF) can be estimated from dynamic contrast enhanced (DCE) cardiac CT acquisitions, leading to quantitative assessment of regional perfusion. The need for low radiation dose and the lack of consensus on MBF estimation methods motivates this study to refine the selection of acquisition protocols and models for CT-derived MBF. DCE cardiac CT acquisitions were simulated for a range of flow states (MBF = 0.5, 1, 2, 3 ml (min g)-1, cardiac output = 3, 5, 8 L min-1). Patient kinetics were generated by a mathematical model of iodine exchange incorporating numerous physiological features including heterogenenous microvascular flow, permeability and capillary contrast gradients. CT acquisitions were simulated for multiple realizations of realistic x-ray flux levels. CT acquisitions that reduce radiation exposure were implemented by varying both temporal sampling (1, 2, and 3 s sampling intervals) and tube currents (140, 70, and 25 mAs). For all acquisitions, we compared three quantitative MBF estimation methods (two-compartment model, an axially-distributed model, and the adiabatic approximation to the tissue homogeneous model) and a qualitative slope-based method. In total, over 11 000 time attenuation curves were used to evaluate MBF estimation in multiple patient and imaging scenarios. After iodine-based beam hardening correction, the slope method consistently underestimated flow by on average 47.5% and the quantitative models provided estimates with less than 6.5% average bias and increasing variance with increasing dose reductions. The three quantitative models performed equally well, offering estimates with essentially identical root mean squared error (RMSE) for matched acquisitions. MBF estimates using the qualitative slope method were inferior in terms of bias and RMSE compared to the quantitative methods. MBF estimate error was equal at matched dose reductions for all quantitative methods and range of techniques evaluated. This suggests that

Spectroscopic investigation, HOMO-LUMO and NLO studies on L-histidinium maleate based on DFT approach

NASA Astrophysics Data System (ADS)

Dhanavel, S.; Stephen, A.; Asirvatham, P. Samuel

2017-05-01

The molecular structure of the title compound L-Histidinium Maleate (LHM) was constructed and optimized based on Density Functional Theory method (DFT-B3LYP) with the 6-31G (d,p) basis set. The fundamental vibrational spectral assignment was analyzed with the aid of optimized structure of LHM. The study on electronic properties such as, HOMO-LUMO energies and absorption wavelength were performed using Time dependent DFT (TD-DFT) approach which reveals that energy transfer occur within the molecule. 13C NMR chemical shift values were measured using Gauge independent atomic orbital method (GIAO) and the obtained values are in good agreement with the reported experimental values. Hardness, ionization potential and electrophilicity index also calculated. The electric dipole moment (μtot) and hyperpolarizability (βtot) values of the investigated molecules were computed. The calculated value (β) was 3.7 times higher than that of urea, which confirms the LHM molecule is a potential candidate for NLO applications.

Models of Quantitative Estimations: Rule-Based and Exemplar-Based Processes Compared

ERIC Educational Resources Information Center

von Helversen, Bettina; Rieskamp, Jorg

2009-01-01

The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model--the mapping model--that outperformed the…

Semiempirical and DFT Investigations of the Dissociation of Alkyl Halides

ERIC Educational Resources Information Center

Waas, Jack R.

2006-01-01

Enthalpy changes corresponding to the gas phase heats of dissociation of 12 organic halides were calculated using two semiempirical methods, the Hartree-Fock method, and two DFT methods. These calculated values were compared to experimental values where possible. All five methods agreed generally with the expected empirically known trends in the…

Activation mechanism of ammonium ions on sulfidation of malachite (-201) surface by DFT study

NASA Astrophysics Data System (ADS)

Wu, Dandan; Mao, Yingbo; Deng, Jiushuai; Wen, Shuming

2017-07-01

The activation mechanism of ammonium ions on the sulfidation of malachite (-201) was determined by density functional theory (DFT) calculations. Results of DFT calculations indicated that interlayer sulfidation occurs during the sulfidation process of malachite (-201). The absorption of both the ammonium ion and sulfide ion on the malachite (-201) surface is stronger than that of sulfur ion. After sulfidation was activated with ammonium ion, the Cu 3d orbital peak is closer to the Fermi level and characterized by a stronger peak value. Therefore, the addition of ammonium ions activated the sulfidation of malachite (-201), thereby improving the flotation performance.

Structures, mechanical properties, equations of state, and electronic properties of β-HMX under hydrostatic pressures: a DFT-D2 study.

PubMed

Peng, Qing; Rahul; Wang, Guangyu; Liu, Gui-Rong; De, Suvranu

2014-10-07

We report the hydrostatic compression studies of the β-polymorph of a cyclotetramethylene tetranitramine (HMX) energetic molecular crystal using DFT-D2, a first-principles calculation based on density functional theory (DFT) with van der Waals (vdW) corrections. The molecular structure, mechanical properties, electronic properties, and equations of state of β-HMX are investigated. For the first time, we predict the elastic constants of β-HMX using DFT-D2 studies. The equations of state under hydrostatic compression are studied for pressures up to 100 GPa. We found that the N-N bonds along the minor axis are responsible for the sensitivity of β-HMX. The analysis of the charge distribution shows that the electronic charge is transferred from hydrogen atoms to nitro groups with the amount of 0.131 and 0.064e for the nitro groups along the minor axis and major axis, respectively, when pressure changes from 0 GPa to 100 GPa. The electronic energy band gap changes from direct at a pressure of 0 GPa to indirect at a pressure of 50 GPa and higher. The band gap decreases with respect to an increase in pressure, implying that the impact sensitivity increases with compression. Our study suggests that the van der Waals interactions are critically important in modeling the mechanical properties of this molecular crystal.

DFT, Its Impact on Condensed Matter and on ``Materials-Genome'' Research

NASA Astrophysics Data System (ADS)

Scheffler, Matthias

About 40 years ago, two seminal works demonstrated the power of density-functional theory (DFT) for real materials. These studies by Moruzzi, Janak, and Williams on metals and Yin and Cohen on semiconductors visualized the spatial distribution of electrons, predicted the equation of state of solids, crystal stability, pressure-induced phase transitions, and more. They also stressed the importance of identifying trends by looking at many systems (e.g. the whole transition-metal series). Since then, the field has seen numerous applications of DFT to solids, liquids, defects, surfaces, and interfaces providing important descriptions and explanations as well as predictions of experimentally not yet identified systems. - ∖ ∖ About 10 years ago, G. Ceder and his group [Ref. 3 and references therein] started with high-throughput screening calculations in the spirit of what in 2011 became the ``Materials Genome Initiative''. The idea of high-throughput screening is old (a key example is the ammonia catalyst found by A. Mittasch at BASF more than 100 years ago), but it is now increasingly becoming clear that big data of materials does not only provide direct information but that the data is structured. This enables interpolation, (modest) extrapolation, and new routes towards understanding [Ref. 5 and references therein]. - ∖ ∖ The amount of data created by ``computational materials science'' is significant. For instance, the NoMaD Repository (which includes also data from other repositories, e.g. AFLOWLIB and OQMD) now holds more than 18 million total-energy calculations. In fact, the amount of data of computational materials science is steadily increasing, and about hundred million CPU core hours are nowadays used every day, worldwide, for DFT calculations for materials. - ∖ ∖ The talk will summarize this enormous impact of DFT on materials science, and it will address the next steps, e.g. the issue how to exploit big data of materials for doing forefront

Quantitative Structure--Activity Relationship Modeling of Rat Acute Toxicity by Oral Exposure

EPA Science Inventory

Background: Few Quantitative Structure-Activity Relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity endpoints. Objective: In this study, a combinatorial QSAR approach has been employed for the creation of robust and predictive models of acute toxi...

DFT +U Modeling of Hole Polarons in Organic Lead Halide Perovskites

NASA Astrophysics Data System (ADS)

Welch, Eric; Erhart, Paul; Scolfaro, Luisa; Zakhidov, Alex

Due to the ever present drive towards improved efficiencies in solar cell technology, new and improved materials are emerging rapidly. Organic halide perovskites are a promising prospect, yet a fundamental understanding of the organic perovskite structure and electronic properties is missing. Particularly, explanations of certain physical phenomena, specifically a low recombination rate and high mobility of charge carriers still remain controversial. We theoretically investigate possible formation of hole polarons adopting methodology used for oxide perovskites. The perovskite studied here is the ABX3structure, with A being an organic cation, B lead and C a halogen; the combinations studied allow for A1,xA2 , 1 - xBX1,xX2 , 3 - xwhere the alloy convention is used to show mixtures of the organic cations and/or the halogens. Two organic cations, methylammonium and formamidinium, and three halogens, iodine, chlorine and bromine are studied. Electronic structures and polaron behavior is studied through first principle density functional theory (DFT) calculations using the Vienna Ab Initio Simulation Package (VASP). Local density approximation (LDA) pseudopotentials are used and a +U Hubbard correction of 8 eV is added; this method was shown to work with oxide perovskites. It is shown that a localized state is realized with the Hubbard correction in systems with an electron removed, residing in the band gap of each different structure. Thus, hole polarons are expected to be seen in these perovskites.

A systematic theoretical study of the electronic structures of porphyrin dimers: DFT and TD-DFT calculations on diporphyrins linked by ethane, ethene, ethyne, imine, and azo bridges.

PubMed

Rintoul, Llew; Harper, Shannon R; Arnold, Dennis P

2013-11-21

Theoretical calculations of the geometries, electronic structures and electronic absorption spectra of a series of covalently-linked porphyrin dimers are reported. The diporphyrins comprise 5,10,15-triphenylporphyrinatozinc(II) (ZnTriPP) units linked through the meso carbons by two-atom bridges, namely 1,2-ethanediyl (1), trans-1,2-ethenediyl (2), ethynediyl (3), 1,2-iminomethenediyl (4), and transdiazenediyl (5). The structures were optimised in toluene solvent by Density Functional Theory (DFT), using the integral equation formalism variant of the polarizable continuum model. The calculations were performed using the B3LYP functional and the 6-31G(d,p) basis set. The complete molecules were modelled, with no substitution of smaller groups on the periphery. In parallel, the compounds 2–5 were prepared by known or novel synthetic routes, to enable comparisons of experimental electronic absorption spectra with those calculated using time dependent-DFT at the same level of theory. As the ethane dimer 1 is not yet synthetically accessible, the model monomer meso-2-phenylethylZnTriPP was used for comparisons with the theoretical predictions. The results form a self-consistent set, enabling for the first time legitimate comparisons of the electronic structures of the series, especially regarding the degree to which the porphyrin p-systems interact by conjugation across the bridges. The theoretical calculations of the electronic transitions match the observed spectra in toluene to a remarkable degree, especially with respect to the peak maximum of the Q band, which represents to a large degree the energy of the HOMO–LUMO transition. The imine 4 is intrinsically polar due to the asymmetric bridge, and the HOMO is located almost exclusively on the ZnTriPP unit attached to the nitrogen of the imine, and the LUMO on the C-attached ring. Thus the Q-band transition is mapped as a comprehensive charge-transfer from the former ring to the latter. This may have consequences

The electronic spectra and the structures of the individual copper(II) chloride and bromide complexes in acetonitrile according to steady-state absorption spectroscopy and DFT/TD-DFT calculations

NASA Astrophysics Data System (ADS)

Olshin, Pavel K.; Myasnikova, Olesya S.; Kashina, Maria V.; Gorbunov, Artem O.; Bogachev, Nikita A.; Kompanets, Viktor O.; Chekalin, Sergey V.; Pulkin, Sergey A.; Kochemirovsky, Vladimir A.; Skripkin, Mikhail Yu.; Mereshchenko, Andrey S.

2018-03-01

The results of spectrophotometric study and quantum chemical calculations for copper(II) chloro- and bromocomplexes in acetonitrile are reported. Electronic spectra of the individual copper(II) halide complexes were obtained in a wide spectral range 200-2200 nm. Stability constants of the individual copper(II) halide complexes in acetonitrile were calculated: log β1 = 8.5, log β2 = 15.6, log β3 = 22.5, log β4 = 25.7 for [CuCln]2-n and log β1 = 17.0, log β2 = 24.6, log β3 = 28.1, log β4 = 30.4 for [CuBrn]2-n. Structures of the studied complexes were optimized and electronic spectra were simulated using DFT and TD-DFT methodologies, respectively. According to the calculations, the more is the number of halide ligands the less is coordination number of copper ion.

Global Quantitative Modeling of Chromatin Factor Interactions

PubMed Central

Zhou, Jian; Troyanskaya, Olga G.

2014-01-01

Chromatin is the driver of gene regulation, yet understanding the molecular interactions underlying chromatin factor combinatorial patterns (or the “chromatin codes”) remains a fundamental challenge in chromatin biology. Here we developed a global modeling framework that leverages chromatin profiling data to produce a systems-level view of the macromolecular complex of chromatin. Our model ultilizes maximum entropy modeling with regularization-based structure learning to statistically dissect dependencies between chromatin factors and produce an accurate probability distribution of chromatin code. Our unsupervised quantitative model, trained on genome-wide chromatin profiles of 73 histone marks and chromatin proteins from modENCODE, enabled making various data-driven inferences about chromatin profiles and interactions. We provided a highly accurate predictor of chromatin factor pairwise interactions validated by known experimental evidence, and for the first time enabled higher-order interaction prediction. Our predictions can thus help guide future experimental studies. The model can also serve as an inference engine for predicting unknown chromatin profiles — we demonstrated that with this approach we can leverage data from well-characterized cell types to help understand less-studied cell type or conditions. PMID:24675896

Modeling ferroelectric film properties and size effects from tetragonal interlayer in Hf1-xZrxO2 grains

NASA Astrophysics Data System (ADS)

Künneth, Christopher; Materlik, Robin; Kersch, Alfred

2017-05-01

Size effects from surface or interface energy play a pivotal role in stabilizing the ferroelectric phase in recently discovered thin film Zirconia-Hafnia. However, sufficient quantitative understanding has been lacking due to the interference with the stabilizing effect from dopants. For the important class of undoped Hf1-xZrxO2, a phase stability model based on free energy from Density functional theory (DFT) and surface energy values adapted to the sparse experimental and theoretical data has been successful to describe key properties of the available thin film data. Since surfaces and interfaces are prone to interference, the predictive capability of the model is surprising and directs to a hitherto undetected, underlying reason. New experimental data hint on the existence of an interlayer on the grain surface fixed in the tetragonal phase possibly shielding from external influence. To explore the consequences of such a mechanism, we develop an interface free energy model to include the fixed interlayer, generalize the grain model to include a grain radius distribution, calculate average polarization and permittivity, and compare the model with available experimental data. Since values for interface energies are sparse or uncertain, we obtain its values from minimizing the least square difference between predicted key parameters to experimental data in a global optimization. Since the detailed values for DFT energies depend on the chosen method, we repeat the search for different computed data sets and come out with quantitatively different but qualitatively consistent values for interface energies. The resulting values are physically very reasonable and the model is able to give qualitative prediction. On the other hand, the optimization reveals that the model is not able to fully capture the experimental data. We discuss possible physical effects and directions of research to possibly close this gap.

DFT investigations of hydrogen storage materials

NASA Astrophysics Data System (ADS)

Wang, Gang

Hydrogen serves as a promising new energy source having no pollution and abundant on earth. However the most difficult problem of applying hydrogen is to store it effectively and safely, which is smartly resolved by attempting to keep hydrogen in some metal hydrides to reach a high hydrogen density in a safe way. There are several promising metal hydrides, the thermodynamic and chemical properties of which are to be investigated in this dissertation. Sodium alanate (NaAlH4) is one of the promising metal hydrides with high hydrogen storage capacity around 7.4 wt. % and relatively low decomposition temperature of around 100 °C with proper catalyst. Sodium hydride is a product of the decomposition of NaAlH4 that may affect the dynamics of NaAlH4. The two materials with oxygen contamination such as OH- may influence the kinetics of the dehydriding/rehydriding processes. Thus the solid solubility of OH - groups (NaOH) in NaAlH4 and NaH is studied theoretically by DFT calculations. Magnesium boride [Mg(BH4)2] is has higher hydrogen capacity about 14.9 wt. % and the decomposition temparture of around 250 °C. However one flaw restraining its application is that some polyboron compounds like MgB12H12 preventing from further release of hydrogen. Adding some transition metals that form magnesium transition metal ternary borohydride [MgaTMb(BH4)c] may simply the decomposition process to release hydrogen with ternary borides (MgaTMbBc). The search for the probable ternary borides and the corresponding pseudo phase diagrams as well as the decomposition thermodynamics are performed using DFT calculations and GCLP method to present some possible candidates.

Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car-Parrinello calculations

NASA Astrophysics Data System (ADS)

Varini, Nicola; Ceresoli, Davide; Martin-Samos, Layla; Girotto, Ivan; Cavazzoni, Carlo

2013-08-01

One of the most promising techniques used for studying the electronic properties of materials is based on Density Functional Theory (DFT) approach and its extensions. DFT has been widely applied in traditional solid state physics problems where periodicity and symmetry play a crucial role in reducing the computational workload. With growing compute power capability and the development of improved DFT methods, the range of potential applications is now including other scientific areas such as Chemistry and Biology. However, cross disciplinary combinations of traditional Solid-State Physics, Chemistry and Biology drastically improve the system complexity while reducing the degree of periodicity and symmetry. Large simulation cells containing of hundreds or even thousands of atoms are needed to model these kind of physical systems. The treatment of those systems still remains a computational challenge even with modern supercomputers. In this paper we describe our work to improve the scalability of Quantum ESPRESSO (Giannozzi et al., 2009 [3]) for treating very large cells and huge numbers of electrons. To this end we have introduced an extra level of parallelism, over electronic bands, in three kernels for solving computationally expensive problems: the Sternheimer equation solver (Nuclear Magnetic Resonance, package QE-GIPAW), the Fock operator builder (electronic ground-state, package PWscf) and most of the Car-Parrinello routines (Car-Parrinello dynamics, package CP). Final benchmarks show our success in computing the Nuclear Magnetic Response (NMR) chemical shift of a large biological assembly, the electronic structure of defected amorphous silica with hybrid exchange-correlation functionals and the equilibrium atomic structure of height Porphyrins anchored to a Carbon Nanotube, on many thousands of CPU cores.

Reactive sites influence in PMMA oligomers reactivity: a DFT study

NASA Astrophysics Data System (ADS)

Paz, C. V.; Vásquez, S. R.; Flores, N.; García, L.; Rico, J. L.

2018-01-01

In this work, we present a theoretical study of methyl methacrylate (MMA) living anionic polymerization. The study was addressed to understanding two important experimental observations made for Michael Szwarc in 1956. The unexpected effect of reactive sites concentration in the propagation rate, and the self-killer behavior of MMA (deactivating of living anionic polymerization). The theoretical calculations were performed by density functional theory (DFT) to obtain the frontier molecular orbitals values. These values were used to calculate and analyze the chemical interaction descriptors in DFT-Koopmans’ theorem. As a result, it was observed that the longest chain-length species (related with low concentration of reactive sites) exhibit the highest reactivity (behavior associated with the increase of the propagation rate). The improvement in this reactivity was attributed to the crosslinking produced in the polymethyl methacrylate chains. Meanwhile, the self-killer behavior was associated with the intermolecular forces present in the reactive sites. This behavior was associated to an obstruction in solvation, since the active sites remained active through all propagation species. The theoretical results were in good agreement with the Szwarc experiments.

Self-consistent DFT +U method for real-space time-dependent density functional theory calculations

NASA Astrophysics Data System (ADS)

Tancogne-Dejean, Nicolas; Oliveira, Micael J. T.; Rubio, Angel

2017-12-01

We implemented various DFT+U schemes, including the Agapito, Curtarolo, and Buongiorno Nardelli functional (ACBN0) self-consistent density-functional version of the DFT +U method [Phys. Rev. X 5, 011006 (2015), 10.1103/PhysRevX.5.011006] within the massively parallel real-space time-dependent density functional theory (TDDFT) code octopus. We further extended the method to the case of the calculation of response functions with real-time TDDFT+U and to the description of noncollinear spin systems. The implementation is tested by investigating the ground-state and optical properties of various transition-metal oxides, bulk topological insulators, and molecules. Our results are found to be in good agreement with previously published results for both the electronic band structure and structural properties. The self-consistent calculated values of U and J are also in good agreement with the values commonly used in the literature. We found that the time-dependent extension of the self-consistent DFT+U method yields improved optical properties when compared to the empirical TDDFT+U scheme. This work thus opens a different theoretical framework to address the nonequilibrium properties of correlated systems.

Water dissociation and CO oxidation over Au/anatase catalyst. A DFT-D2 study

NASA Astrophysics Data System (ADS)

Saqlain, Muhammad Adnan; Hussain, Akhtar; Siddiq, Muhammad; Leitão, Alexandre A.

2018-03-01

With the help of DFT-D2 methodology, we have investigated the adsorption of water on clean anatase(001) and Au/anatase(001). In the former case, adsorption energies of H2O differ to small extent computed employing GGA = PW91 and DFT-D2 methods. While the GGA = PW91 predicts that water would desorb close to 650 K on the TiO2 surface, the DFT-D2 predicts that desorption is most likely to occur above 700 K. A comparison of water adsorption on TiO2 and Au/TiO2 surfaces shows that the TiO2 prefers dimer adsorption whereas the Au/TiO2 prefers monomer adsorption. We found that the diffusion of surface hydroxyls on to the Au cluster from the Au/TiO2 periphery is unlikely and it seems that the CO oxidation would occur at the Au/TiO2 boundary. The results show that water dissociation and CO oxidation steps occur easily on Au/TiO2 indicating that this could be good alternative catalyst for water gas shift reaction industry.

Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.

2018-03-01

Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.

Adsorption behavior and mechanism of acidic blue 25 dye onto cucurbit[8]uril: A spectral and DFT study

NASA Astrophysics Data System (ADS)

Luo, Hanhan; Huang, Xiangyu; Luo, Yuhan; Li, Zhuang; Li, Lan; Gao, Chao; Xiong, Jinyan; Li, Wei

2018-03-01

The acidic blue 25 (AB25) dye was efficiently adsorbed by CB [8]; the saturated adsorption capacity (qexp) reached 434.8 mg/g and was far higher than those of previous reported adsorbents. The Langmuir and Freundich isotherms were used to fit the equilibrium data, and the results showed that the Freundlich isotherm seemed to agree better with the AB25 adsorption. The adsorption kinetics followed the pseudo-second-order model. Calculated thermodynamic parameters showed that the adsorption of AB25 onto CB [8] was a spontaneous and enthalpy-driven process. The adsorption mechanism was explored by N2 adsorption-desorption, TG, FT-IR, UV-vis as well as MD simulation and DFT calculations. TG analysis revealed that a new inclusion complex was produced, and FT-IR,UV-vis spectrum and DFT calculations verify its structure. In this inclusion complex, the AB25 dye molecule inserted into cavities of CB [8] from portal, and the sulfonate and phenyl groups stayed in the hydrophobic cavity. TDDFT calculations indicated that all excitation arisen from π → π* transition.

Structure and electronic absorption spectra of nematogenic alkoxycinnamic acids - a comparative study based on semiempirical and DFT methods.

PubMed

Praveen, Pogula Lakshmi; Ojha, Durga Prasad

2012-04-01

Structure of nematogenic p-n-Alkoxy cinnamic acids (nOCAC) with various alkyl chain carbon atoms (n = 2, 4, 6, 8) has been optimized using density functional B3LYP with 6-31+G (d) basis set using crystallographic geometry as input. Using the optimized geometry, electronic structure of the molecules has been evaluated using the semiempirical methods and DFT calculations. Molecular charge distribution and phase stability of these systems have been analyzed based on Mulliken and Löwdin population analysis. The electronic absorption spectra of nOCAC molecules have been simulated by employing DFT method, semiempirical CNDO/S and INDO/S parameterizations. Two types of calculations have been performed for model systems containing single and double molecules of nOCAC. UV-Visible spectra have been calculated for all single molecules. The UV stability of the molecules has been discussed in light of the electronic transition oscillator strength (f). The dimer complexes of higher homologues (n = 6, 8) have also been reported to enable the comparison between single and double molecules.

A projection-free method for representing plane-wave DFT results in an atom-centered basis

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

Dunnington, Benjamin D.; Schmidt, J. R., E-mail: schmidt@chem.wisc.edu

2015-09-14

Plane wave density functional theory (DFT) is a powerful tool for gaining accurate, atomic level insight into bulk and surface structures. Yet, the delocalized nature of the plane wave basis set hinders the application of many powerful post-computation analysis approaches, many of which rely on localized atom-centered basis sets. Traditionally, this gap has been bridged via projection-based techniques from a plane wave to atom-centered basis. We instead propose an alternative projection-free approach utilizing direct calculation of matrix elements of the converged plane wave DFT Hamiltonian in an atom-centered basis. This projection-free approach yields a number of compelling advantages, including strictmore » orthonormality of the resulting bands without artificial band mixing and access to the Hamiltonian matrix elements, while faithfully preserving the underlying DFT band structure. The resulting atomic orbital representation of the Kohn-Sham wavefunction and Hamiltonian provides a gateway to a wide variety of analysis approaches. We demonstrate the utility of the approach for a diverse set of chemical systems and example analysis approaches.« less

Understanding the difference in cohesive energies between alpha and beta tin in DFT calculations

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

Legrain, Fleur; Manzhos, Sergei, E-mail: mpemanzh@nus.edu.sg

2016-04-15

The transition temperature between the low-temperature alpha phase of tin to beta tin is close to the room temperature (T{sub αβ} = 13{sup 0}C), and the difference in cohesive energy of the two phases at 0 K of about ΔE{sub coh} =0.02 eV/atom is at the limit of the accuracy of DFT (density functional theory) with available exchange-correlation functionals. It is however critically important to model the relative phase energies correctly for any reasonable description of phenomena and technologies involving these phases, for example, the performance of tin electrodes in electrochemical batteries. Here, we show that several commonly used andmore » converged DFT setups using the most practical and widely used PBE functional result in ΔE{sub coh} ≈0.04 eV/atom, with different types of basis sets and with different models of core electrons (all-electron or pseudopotentials of different types), which leads to a significant overestimation of T{sub αβ}. We show that this is due to the errors in relative positions of s and p –like bands, which, combined with different populations of these bands in α and β Sn, leads to overstabilization of alpha tin. We show that this error can be effectively corrected by applying a Hubbard +U correction to s –like states, whereby correct cohesive energies of both α and β Sn can be obtained with the same computational scheme. We quantify for the first time the effects of anharmonicity on ΔE{sub coh} and find that it is negligible.« less

A semi-blind logo watermarking scheme for color images by comparison and modification of DFT coefficients

NASA Astrophysics Data System (ADS)

Kusyk, Janusz; Eskicioglu, Ahmet M.

2005-10-01

Digital watermarking is considered to be a major technology for the protection of multimedia data. Some of the important applications are broadcast monitoring, copyright protection, and access control. In this paper, we present a semi-blind watermarking scheme for embedding a logo in color images using the DFT domain. After computing the DFT of the luminance layer of the cover image, the magnitudes of DFT coefficients are compared, and modified. A given watermark is embedded in three frequency bands: Low, middle, and high. Our experiments show that the watermarks extracted from the lower frequencies have the best visual quality for low pass filtering, adding Gaussian noise, JPEG compression, resizing, rotation, and scaling, and the watermarks extracted from the higher frequencies have the best visual quality for cropping, intensity adjustment, histogram equalization, and gamma correction. Extractions from the fragmented and translated image are identical to extractions from the unattacked watermarked image. The collusion and rewatermarking attacks do not provide the hacker with useful tools.

Simplified DFT methods for consistent structures and energies of large systems

NASA Astrophysics Data System (ADS)

Caldeweyher, Eike; Gerit Brandenburg, Jan

2018-05-01

Kohn–Sham density functional theory (DFT) is routinely used for the fast electronic structure computation of large systems and will most likely continue to be the method of choice for the generation of reliable geometries in the foreseeable future. Here, we present a hierarchy of simplified DFT methods designed for consistent structures and non-covalent interactions of large systems with particular focus on molecular crystals. The covered methods are a minimal basis set Hartree–Fock (HF-3c), a small basis set screened exchange hybrid functional (HSE-3c), and a generalized gradient approximated functional evaluated in a medium-sized basis set (B97-3c), all augmented with semi-classical correction potentials. We give an overview on the methods design, a comprehensive evaluation on established benchmark sets for geometries and lattice energies of molecular crystals, and highlight some realistic applications on large organic crystals with several hundreds of atoms in the primitive unit cell.

Quantitative 3D investigation of Neuronal network in mouse spinal cord model

NASA Astrophysics Data System (ADS)

Bukreeva, I.; Campi, G.; Fratini, M.; Spanò, R.; Bucci, D.; Battaglia, G.; Giove, F.; Bravin, A.; Uccelli, A.; Venturi, C.; Mastrogiacomo, M.; Cedola, A.

2017-01-01

The investigation of the neuronal network in mouse spinal cord models represents the basis for the research on neurodegenerative diseases. In this framework, the quantitative analysis of the single elements in different districts is a crucial task. However, conventional 3D imaging techniques do not have enough spatial resolution and contrast to allow for a quantitative investigation of the neuronal network. Exploiting the high coherence and the high flux of synchrotron sources, X-ray Phase-Contrast multiscale-Tomography allows for the 3D investigation of the neuronal microanatomy without any aggressive sample preparation or sectioning. We investigated healthy-mouse neuronal architecture by imaging the 3D distribution of the neuronal-network with a spatial resolution of 640 nm. The high quality of the obtained images enables a quantitative study of the neuronal structure on a subject-by-subject basis. We developed and applied a spatial statistical analysis on the motor neurons to obtain quantitative information on their 3D arrangement in the healthy-mice spinal cord. Then, we compared the obtained results with a mouse model of multiple sclerosis. Our approach paves the way to the creation of a “database” for the characterization of the neuronal network main features for a comparative investigation of neurodegenerative diseases and therapies.

Improved assignments of the vibrational fundamental modes of ortho -, meta -, and para -xylene using gas- and liquid-phase infrared and Raman spectra combined with ab initio calculations: Quantitative gas-phase infrared spectra for detection

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

Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.

Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, we report high quality quantitative vapor-phase infrared spectra of all three isomers over the 540-6500 cm -1 range. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C 2v symmetry for ortho-xylene, andmore » two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have C s and C 2 symmetry, and for para-xylene these conformers have C 2v or C 2h symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, we made an arbitrary choice to discuss the C s conformer for meta-xylene and the C 2v conformer for para-xylene. We report integrated band intensities for all isomers. Using the quantitative infrared data, we determine the global warming potential values of each isomer and discuss potential bands for atmospheric monitoring.« less

Improved assignments of the vibrational fundamental modes of ortho-, meta-, and para-xylene using gas- and liquid-phase infrared and Raman spectra combined with ab initio calculations: Quantitative gas-phase infrared spectra for detection

NASA Astrophysics Data System (ADS)

Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.; Nguyen, Kiet T.; Williams, Stephen D.; Johnson, Timothy J.

2017-12-01

Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, high quality quantitative vapor-phase infrared spectra of all three isomers over the 6500 - 540 cm-1 range are reported. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C2v symmetry for ortho-xylene, and two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have Cs and C2 symmetry, and for para-xylene these conformers have C2v or C2h symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, an arbitrary choice to discuss the Cs conformer for meta-xylene and the C2v conformer for para-xylene is made. Integrated band intensities for all isomers are reported. Using the quantitative infrared data, the global warming potential values of each isomer are determined. Potential bands for atmospheric monitoring are also discussed.

DFT/TD-DFT study on the electronic and spectroscopic properties of hollow cubic and hollow spherical (ZnO) m quantum dots interacting with CO, NO2 and SO3 molecules

NASA Astrophysics Data System (ADS)

Gopalakrishnan, Sankarasubramanian; Shankar, Ramasamy; Kolandaivel, Ponmalai

2018-03-01

Hollow spherical (HS) and hollow cubic (HC) (ZnO) m quantum dots (QDs) were constructed and optimized using density functional theory (DFT) method. CO, NO2 and SO3 molecules were used to interact with the HC and HS (ZnO) m QDs at the centre and on the surface of the QDs. The changes in the electronic energy levels of HC and HS (ZnO) m QDs due to the interactions of CO, NO2 and SO3 molecules have been studied. The electronic and spectroscopic properties, such as density of states, HOMO-LUMO energy gap, absorption spectra, IR and Raman spectra of HC and HS (ZnO) m QDs have been studied using DFT and Time dependent-DFT (TD-DFT) methods. The interaction energy values show that the SO3 molecule has strongly interacted with HC and HS (ZnO) m QDs than the CO and NO2 molecules. The results of the density of states show that the HC QDs have peaks that are very close to each other, whereas the same is found to be broad in the HS QDs. The HOMO-LUMO energy gap is more for the HS QDs than the HC QDs, and also it gets decreased, when the NO2 and SO3 molecules interact at the centre of the HC and HS (ZnO) m QDs. The blue and red shifts were observed in the absorption spectra of HS and HC QDs. The natural transition orbital (NTO) plot reveals that the interaction of the molecules on the surface of the QDs reduce the chance of electron-hole recombination; hence the energy gap increases for NO2 and SO3 molecular interactions on the surface of the HC and HS (ZnO) m QDs. The vibrational assignments have been made for HC and HS QDs interacting with CO, NO2 and SO3 molecules.

Neuroergonomics: Quantitative Modeling of Individual, Shared, and Team Neurodynamic Information.

PubMed

Stevens, Ronald H; Galloway, Trysha L; Willemsen-Dunlap, Ann

2018-06-01

The aim of this study was to use the same quantitative measure and scale to directly compare the neurodynamic information/organizations of individual team members with those of the team. Team processes are difficult to separate from those of individual team members due to the lack of quantitative measures that can be applied to both process sets. Second-by-second symbolic representations were created of each team member's electroencephalographic power, and quantitative estimates of their neurodynamic organizations were calculated from the Shannon entropy of the symbolic data streams. The information in the neurodynamic data streams of health care ( n = 24), submarine navigation ( n = 12), and high school problem-solving ( n = 13) dyads was separated into the information of each team member, the information shared by team members, and the overall team information. Most of the team information was the sum of each individual's neurodynamic information. The remaining team information was shared among the team members. This shared information averaged ~15% of the individual information, with momentary levels of 1% to 80%. Continuous quantitative estimates can be made from the shared, individual, and team neurodynamic information about the contributions of different team members to the overall neurodynamic organization of a team and the neurodynamic interdependencies among the team members. Information models provide a generalizable quantitative method for separating a team's neurodynamic organization into that of individual team members and that shared among team members.

A dynamic fault tree model of a propulsion system

NASA Technical Reports Server (NTRS)

Xu, Hong; Dugan, Joanne Bechta; Meshkat, Leila

2006-01-01

We present a dynamic fault tree model of the benchmark propulsion system, and solve it using Galileo. Dynamic fault trees (DFT) extend traditional static fault trees with special gates to model spares and other sequence dependencies. Galileo solves DFT models using a judicious combination of automatically generated Markov and Binary Decision Diagram models. Galileo easily handles the complexities exhibited by the benchmark problem. In particular, Galileo is designed to model phased mission systems.

Extinction coefficients of CC and CC bands in ethyne and ethene molecules interacting with Cu+ and Ag+ in zeolites--IR studies and quantumchemical DFT calculations.

PubMed

Kozyra, Paweł; Góra-Marek, Kinga; Datka, Jerzy

2015-02-05

The values of extinction coefficients of CC and CC IR bands of ethyne and ethene interacting with Cu+ and Ag+ in zeolites were determined in quantitative IR experiments and also by quantumchemical DFT calculations with QM/MM method. Both experimental and calculated values were in very good agreement validating the reliability of calculations. The values of extinction coefficients of ethyne and ethene interacting with bare cations and cations embedded in zeolite-like clusters were calculated. The interaction of organic molecules with Cu+ and Ag+ in zeolites ZSM-5 and especially charge transfers between molecule, cation and zeolite framework was also discussed in relation to the values of extinction coefficients. Copyright © 2014 Elsevier B.V. All rights reserved.

Framework for a Quantitative Systemic Toxicity Model (FutureToxII)

EPA Science Inventory

EPA’s ToxCast program profiles the bioactivity of chemicals in a diverse set of ~700 high throughput screening (HTS) assays. In collaboration with L’Oreal, a quantitative model of systemic toxicity was developed using no effect levels (NEL) from ToxRefDB for 633 chemicals with HT...

A quantitative risk-based model for reasoning over critical system properties

NASA Technical Reports Server (NTRS)

Feather, M. S.

2002-01-01

This position paper suggests the use of a quantitative risk-based model to help support reeasoning and decision making that spans many of the critical properties such as security, safety, survivability, fault tolerance, and real-time.

Predictive value of EEG in postanoxic encephalopathy: A quantitative model-based approach.

PubMed

Efthymiou, Evdokia; Renzel, Roland; Baumann, Christian R; Poryazova, Rositsa; Imbach, Lukas L

2017-10-01

The majority of comatose patients after cardiac arrest do not regain consciousness due to severe postanoxic encephalopathy. Early and accurate outcome prediction is therefore essential in determining further therapeutic interventions. The electroencephalogram is a standardized and commonly available tool used to estimate prognosis in postanoxic patients. The identification of pathological EEG patterns with poor prognosis relies however primarily on visual EEG scoring by experts. We introduced a model-based approach of EEG analysis (state space model) that allows for an objective and quantitative description of spectral EEG variability. We retrospectively analyzed standard EEG recordings in 83 comatose patients after cardiac arrest between 2005 and 2013 in the intensive care unit of the University Hospital Zürich. Neurological outcome was assessed one month after cardiac arrest using the Cerebral Performance Category. For a dynamic and quantitative EEG analysis, we implemented a model-based approach (state space analysis) to quantify EEG background variability independent from visual scoring of EEG epochs. Spectral variability was compared between groups and correlated with clinical outcome parameters and visual EEG patterns. Quantitative assessment of spectral EEG variability (state space velocity) revealed significant differences between patients with poor and good outcome after cardiac arrest: Lower mean velocity in temporal electrodes (T4 and T5) was significantly associated with poor prognostic outcome (p<0.005) and correlated with independently identified visual EEG patterns such as generalized periodic discharges (p<0.02). Receiver operating characteristic (ROC) analysis confirmed the predictive value of lower state space velocity for poor clinical outcome after cardiac arrest (AUC 80.8, 70% sensitivity, 15% false positive rate). Model-based quantitative EEG analysis (state space analysis) provides a novel, complementary marker for prognosis in postanoxic

Tip-Enhanced Raman Voltammetry: Coverage Dependence and Quantitative Modeling.

PubMed

Mattei, Michael; Kang, Gyeongwon; Goubert, Guillaume; Chulhai, Dhabih V; Schatz, George C; Jensen, Lasse; Van Duyne, Richard P

2017-01-11

Electrochemical atomic force microscopy tip-enhanced Raman spectroscopy (EC-AFM-TERS) was employed for the first time to observe nanoscale spatial variations in the formal potential, E 0' , of a surface-bound redox couple. TERS cyclic voltammograms (TERS CVs) of single Nile Blue (NB) molecules were acquired at different locations spaced 5-10 nm apart on an indium tin oxide (ITO) electrode. Analysis of TERS CVs at different coverages was used to verify the observation of single-molecule electrochemistry. The resulting TERS CVs were fit to the Laviron model for surface-bound electroactive species to quantitatively extract the formal potential E 0' at each spatial location. Histograms of single-molecule E 0' at each coverage indicate that the electrochemical behavior of the cationic oxidized species is less sensitive to local environment than the neutral reduced species. This information is not accessible using purely electrochemical methods or ensemble spectroelectrochemical measurements. We anticipate that quantitative modeling and measurement of site-specific electrochemistry with EC-AFM-TERS will have a profound impact on our understanding of the role of nanoscale electrode heterogeneity in applications such as electrocatalysis, biological electron transfer, and energy production and storage.

Quantitative detection of Streptococcus mutans in the dental plaque of Japanese preschool children by real-time PCR.

PubMed

Hata, S; Hata, H; Miyasawa-Hori, H; Kudo, A; Mayanagi, H

2006-02-01

To detect quantitatively the total bacteria and Streptococcus mutans in dental plaque by real-time PCR with prbac, Sm and GTF-B primers, and to compare their presence with the prevalence of dental caries in Japanese preschool children. Human dental plaque samples were collected from the labial surfaces of the upper primary central incisors of 107 children. The dental status was recorded as dft by WHO caries diagnostic criteria. Positive dt and dft scores by the Sm or GTF-B primer were significantly higher than negative scores (P < 0.01). The proportions of Strep. mutans to the total bacteria from sound, and sound and/or filled upper primary incisors were significantly lower than those from decayed or filled, and decayed incisors, respectively (P < 0.01). The ratios of Strep. mutans to total bacteria in plaque detected by real-time PCR with Sm and GTF-B primers were closely associated with the prevalence of dental caries in Japanese preschool children. These assays may be useful for the assessment of an individual's risk of dental caries.

[A quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse].

PubMed

Zhang, Yu; Chen, Yuzhen; Hu, Chunguang; Zhang, Huaning; Bi, Zhenwang; Bi, Zhenqiang

2015-05-01

To construct a quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse and to find out effective interventions to reduce salmonella contamination. We constructed a modular process risk model (MPRM) from evisceration to chilling in Excel Sheet using the data of the process parameters in poultry and the Salmomella concentration surveillance of Jinan in 2012. The MPRM was simulated by @ risk software. The concentration of salmonella on carcass after chilling was 1.96MPN/g which was calculated by model. The sensitive analysis indicated that the correlation coefficient of the concentration of salmonella after defeathering and in chilling pool were 0.84 and 0.34,which were the primary factors to the concentration of salmonella on carcass after chilling. The study provided a quantitative assessment model structure for salmonella on carcass in poultry slaughterhouse. The risk manager could control the contamination of salmonella on carcass after chilling by reducing the concentration of salmonella after defeathering and in chilling pool.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

Investigations of Topological Surface States in Sb (111) Ultrathin Films by STM/STS Experiments and DFT Calculations

NASA Astrophysics Data System (ADS)

Luo, Ziyu; Yao, Guanggeng; Xu, Wentao; Feng, Yuanping; Wang, Xue-Sen

2014-03-01

Bulk Sb was regarded as a semimetal with a nontrivial topological order. It is worth exploring whether the Sb ultrathin film has the potential to be an elementary topological insulator. In the presence of quantum confinement effect, we investigated the evolution of topological surface states in Sb (111) ultrathin films with different thickness by the scanning tunneling microscopy/ spectroscopy (STM/STS) experiments and density functional theory (DFT) calculations. By comparing the quasiparticle interference (QPI) patterns obtained from Fourier-transform scanning tunneling spectroscopy (FT-STS) and from DFT calculations, we successfully derive the spin properties of topological surface states on Sb (111) ultrathin films. In addition, based on the DFT calculations, the 8BL Sb (111) ultrathin film was proved to possess up to 30% spinseparated topological surface states within the bandgap. Therefore, the highquality 8BL Sb (111) ultrathin film could be regarded as an elementary topological insulator.

Combined multifrequency EPR and DFT study of dangling bonds in a-Si:H

NASA Astrophysics Data System (ADS)

Fehr, M.; Schnegg, A.; Rech, B.; Lips, K.; Astakhov, O.; Finger, F.; Pfanner, G.; Freysoldt, C.; Neugebauer, J.; Bittl, R.; Teutloff, C.

2011-12-01

Multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy using S-, X-, Q-, and W-band frequencies (3.6, 9.7, 34, and 94 GHz, respectively) was employed to study paramagnetic coordination defects in undoped hydrogenated amorphous silicon (a-Si:H). The improved spectral resolution at high magnetic field reveals a rhombic splitting of the g tensor with the following principal values: gx=2.0079, gy=2.0061, and gz=2.0034, and shows pronounced g strain, i.e., the principal values are widely distributed. The multifrequency approach furthermore yields precise 29Si hyperfine data. Density functional theory (DFT) calculations on 26 computer-generated a-Si:H dangling-bond models yielded g values close to the experimental data but deviating hyperfine interaction values. We show that paramagnetic coordination defects in a-Si:H are more delocalized than computer-generated dangling-bond defects and discuss models to explain this discrepancy.

A quantitative model to assess Social Responsibility in Environmental Science and Technology.

PubMed

Valcárcel, M; Lucena, R

2014-01-01

The awareness of the impact of human activities in society and environment is known as "Social Responsibility" (SR). It has been a topic of growing interest in many enterprises since the fifties of the past Century, and its implementation/assessment is nowadays supported by international standards. There is a tendency to amplify its scope of application to other areas of the human activities, such as Research, Development and Innovation (R + D + I). In this paper, a model of quantitative assessment of Social Responsibility in Environmental Science and Technology (SR EST) is described in detail. This model is based on well established written standards as the EFQM Excellence model and the ISO 26000:2010 Guidance on SR. The definition of five hierarchies of indicators, the transformation of qualitative information into quantitative data and the dual procedure of self-evaluation and external evaluation are the milestones of the proposed model, which can be applied to Environmental Research Centres and institutions. In addition, a simplified model that facilitates its implementation is presented in the article. © 2013 Elsevier B.V. All rights reserved.

Functional linear models for association analysis of quantitative traits.

PubMed

Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

2013-11-01

Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. © 2013 WILEY

Spectroscopic and molecular structure investigation of 2-furanacrylic acid monomer and dimer using HF and DFT methods

NASA Astrophysics Data System (ADS)

Ghalla, H.; Issaoui, N.; Govindarajan, M.; Flakus, H. T.; Jamroz, M. H.; Oujia, B.

2014-02-01

In the present work, we reported a combined experimental and theoretical study on molecular structure and vibrational spectra of 2-furanacrylic acid (abbreviated as 2FAA). The FT-IR and FT-Raman spectra of 2FAA have been recorded in the regions 4000-400 and 4000-100 cm-1. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The monomer and dimer structures of the title molecule have been obtained from Hartree-Fock (HF) and density functional theory (DFT) B3LYP methods with 6-311++G(d,p) as basis set calculations. The vibrational frequencies were calculated by DFT method and compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. Intermolecular OH⋯O hydrogen bonds are discussed in dimer structure of the molecule. The infrared and Raman spectra were also predicted from the calculated intensities. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. A study on the electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, are performed by time-dependent DFT (TD-DFT) approach. In addition, Milliken atomic charges, possible charge transfer, natural bond orbital (NBO) and AIM topological analysis were performed. Moreover, molecular electrostatic potential (MEP) and the thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

Spectral and magnetic properties of hematite Fe2O3 (001) surface: results from DFT+DMFT

NASA Astrophysics Data System (ADS)

Kabir, Alamgir; Turkowski, Volodymyr; Rahman, Talat S.

2015-03-01

It has been demonstrated that strong correlation effects may significantly modify the spectrum of a system, in particular leading to an increase of the bandgap and to a change in the orbital occupancies, which affects the magnetic properties of the system. With this in mind, we have examined the spectral and magnetic properties of the hematite Fe2O3 film system with (001) surface orientation by using the combined density functional theory (DFT) and dynamical mean-field theory (DMFT) approach. We pay special attention to the surface geometry and electronic structure, magnetization and magnetic anisotropy (MA) of the system by performing calculations at different values of the parameters for the local Coulomb repulsion and exchange energy. To calculate the MA of the system, we propose and apply a combined Bruno model within DMFT, and demonstrate that under-coordinated surface Fe atoms contribute significantly to the MA of the film. We also compare our results with the DFT+U solution and show that the dynamical effects taken into account by the DMFT significantly affect system properties, notably leading to a decrease of the atomic magnetic moments. Work supported in part by DOE Grant No. DOE-DE-FG02-07ER46354.

Blue M2: an intermediate melanoidin studied via conceptual DFT.

PubMed

Frau, Juan; Glossman-Mitnik, Daniel

2018-05-31

In this computational study, ten density functionals, viz. CAM-B3LYP, LC-ω PBE, M11, M11L, MN12L, MN12SX, N12, N12SX, ω B97X, and ω B97XD, related to the Def2TZVP basis sets, are assessed together with the SMD solvation model for calculation of the molecular properties and structure of blue-M2 intermediate melanoidin pigment. All the chemical reactivity descriptors for the system are calculated via conceptual density functional theory (DFT). The active sites suitable for nucleophilic, electrophilic, and radical attacks are selected by linking them with the Fukui function indices, electrophilic Parr functions, and condensed dual descriptors Δf(r), respectively. The prediction of the maximum absorption wavelength is considerably accurate relative to its experimental value. The study reveals that the MN12SX and N12SX density functionals are the most appropriate density functionals for predicting the chemical reactivity of the molecule under study.

Chemical Sensor Array Response Modeling Using Quantitative Structure-Activity Relationships Technique

NASA Astrophysics Data System (ADS)

Shevade, Abhijit V.; Ryan, Margaret A.; Homer, Margie L.; Zhou, Hanying; Manfreda, Allison M.; Lara, Liana M.; Yen, Shiao-Pin S.; Jewell, April D.; Manatt, Kenneth S.; Kisor, Adam K.

We have developed a Quantitative Structure-Activity Relationships (QSAR) based approach to correlate the response of chemical sensors in an array with molecular descriptors. A novel molecular descriptor set has been developed; this set combines descriptors of sensing film-analyte interactions, representing sensor response, with a basic analyte descriptor set commonly used in QSAR studies. The descriptors are obtained using a combination of molecular modeling tools and empirical and semi-empirical Quantitative Structure-Property Relationships (QSPR) methods. The sensors under investigation are polymer-carbon sensing films which have been exposed to analyte vapors at parts-per-million (ppm) concentrations; response is measured as change in film resistance. Statistically validated QSAR models have been developed using Genetic Function Approximations (GFA) for a sensor array for a given training data set. The applicability of the sensor response models has been tested by using it to predict the sensor activities for test analytes not considered in the training set for the model development. The validated QSAR sensor response models show good predictive ability. The QSAR approach is a promising computational tool for sensing materials evaluation and selection. It can also be used to predict response of an existing sensing film to new target analytes.

GW quasiparticle bandgaps of anatase TiO2 starting from DFT + U.

PubMed

Patrick, Christopher E; Giustino, Feliciano

2012-05-23

We investigate the quasiparticle band structure of anatase TiO(2), a wide gap semiconductor widely employed in photovoltaics and photocatalysis. We obtain GW quasiparticle energies starting from density-functional theory (DFT) calculations including Hubbard U corrections. Using a simple iterative procedure we determine the value of the Hubbard parameter yielding a vanishing quasiparticle correction to the fundamental bandgap of anatase TiO(2). The bandgap (3.3 eV) calculated using this optimal Hubbard parameter is smaller than the value obtained by applying many-body perturbation theory to standard DFT eigenstates and eigenvalues (3.7 eV). We extend our analysis to the rutile polymorph of TiO(2) and reach similar conclusions. Our work highlights the role of the starting non-interacting Hamiltonian in the calculation of GW quasiparticle energies in TiO(2) and suggests an optimal Hubbard parameter for future calculations.

Anisotropic lattice thermal expansion of PbFeBO 4: A study by X-ray and neutron diffraction, Raman spectroscopy and DFT calculations

DOE PAGES

Murshed, M. Mangir; Mendive, Cecilia B.; Curti, Mariano; ...

2014-11-01

We present the lattice thermal expansion of mullite-type PbFeBO 4 in this study. The thermal expansion coefficients of the metric parameters were obtained from composite data collected from temperature-dependent neutron and X-ray powder diffraction between 10 K and 700 K. The volume thermal expansion was modeled using extended Grüneisen first-order approximation to the zero-pressure equation of state. The additive frame of the model includes harmonic, quasi-harmonic and intrinsic anharmonic potentials to describe the change of the internal energy as a function of temperature. Moreover, the unit-cell volume at zero-pressure and 0 K was optimized during the DFT simulations. Harmonic frequenciesmore » of the optical Raman modes at the Γ-point of the Brillouin zone at 0 K were also calculated by DFT, which help to assign and crosscheck the experimental frequencies. The low-temperature Raman spectra showed significant anomaly in the antiferromagnetic regions, leading to softening or hardening of some phonons. Selected modes were analyzed using a modified Klemens model. The shift of the frequencies and the broadening of the line-widths helped to understand the anharmonic vibrational behaviors of the PbO4, FeO6 and BO3 polyhedra as a function of temperature.« less

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level.

PubMed

Mo, Yirong; Song, Lingchun; Lin, Yuchun

2007-08-30

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.

Methodologies for Quantitative Systems Pharmacology (QSP) Models: Design and Estimation.

PubMed

Ribba, B; Grimm, H P; Agoram, B; Davies, M R; Gadkar, K; Niederer, S; van Riel, N; Timmis, J; van der Graaf, P H

2017-08-01

With the increased interest in the application of quantitative systems pharmacology (QSP) models within medicine research and development, there is an increasing need to formalize model development and verification aspects. In February 2016, a workshop was held at Roche Pharma Research and Early Development to focus discussions on two critical methodological aspects of QSP model development: optimal structural granularity and parameter estimation. We here report in a perspective article a summary of presentations and discussions. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

SeO2 adsorption on CaO surface: DFT and experimental study on the adsorption of multiple SeO2 molecules

NASA Astrophysics Data System (ADS)

Fan, Yaming; Zhuo, Yuqun; Li, Liangliang

2017-10-01

SeO2 adsorption mechanisms on CaO surface were firstly investigated by both density functional theory (DFT) calculations and adsorption experiments. Adsorption of multiple SeO2 on the CaO (001) surface was investigated using slab model. Based on the results of adsorption energy and surface property, a double-layer adsorption mechanisms were proposed. In experiments, the SeO2 adsorption products were prepared in a U-shaped quartz reactor at 200 °C. The surface morphology was investigated by field emission scanning electron microscopy (FE-SEM). The superficial and total SeO2 mass fractions were measured by X-ray photoelectron spectroscopy (XPS) and inductively coupled plasma atomic emission spectroscopy (ICP-AES), respectively. The surface valence state and bulk structure are determined by XPS and X-Ray Diffraction (XRD). The experimental results are in good agreement with the DFT results. In conclusion, the fundamental SeO2 chemisorption mechanisms on CaO surface were suggested.

Dispersion interactions with linear scaling DFT: a study of planar molecules on charged polar surfaces

NASA Astrophysics Data System (ADS)

Andrinopoulos, Lampros; Hine, Nicholas; Haynes, Peter; Mostofi, Arash

2010-03-01

The placement of organic molecules such as CuPc (copper phthalocyanine) on wurtzite ZnO (zinc oxide) charged surfaces has been proposed as a way of creating photovoltaic solar cellsfootnotetextG.D. Sharma et al., Solar Energy Materials & Solar Cells 90, 933 (2006) ; optimising their performance may be aided by computational simulation. Electronic structure calculations provide high accuracy at modest computational cost but two challenges are encountered for such layered systems. First, the system size is at or beyond the limit of traditional cubic-scaling Density Functional Theory (DFT). Second, traditional exchange-correlation functionals do not account for van der Waals (vdW) interactions, crucial for determining the structure of weakly bonded systems. We present an implementation of recently developed approachesfootnotetextP.L. Silvestrelli, P.R.L. 100, 102 (2008) to include vdW in DFT within ONETEPfootnotetextC.-K. Skylaris, P.D. Haynes, A.A. Mostofi and M.C. Payne, J.C.P. 122, 084119 (2005) , a linear-scaling package for performing DFT calculations using a basis of localised functions. We have applied this methodology to simple planar organic molecules, such as benzene and pentacene, on ZnO surfaces.

76 FR 28819 - NUREG/CR-XXXX, Development of Quantitative Software Reliability Models for Digital Protection...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-18

... NUCLEAR REGULATORY COMMISSION [NRC-2011-0109] NUREG/CR-XXXX, Development of Quantitative Software..., ``Development of Quantitative Software Reliability Models for Digital Protection Systems of Nuclear Power Plants... of Risk Analysis, Office of Nuclear Regulatory Research, U.S. Nuclear Regulatory Commission...

Single metal catalysis: DFT and CAS modelling of species involved in the Fe cation assisted transformation of acetylene to benzene

NASA Astrophysics Data System (ADS)

Altun, Zikri; Bleda, Erdi; Trindle, Carl

2017-09-01

Gas phase conversion of acetylene to benzene, assisted by a single metal cation such as Fe(+), Ru(+) and Rh(+), offers an attractive prospect for application of computational modelling techniques to catalytic processes. Gas phase processes are not complicated by environmental effects and the participation of a single metal atom is a significant simplification. Still the process is complex, owing to the possibility of several low-energy spin states and the abundance of alternative structures. By density functional theory modelling using recently developed models with range and dispersion corrections, we locate and characterise a number of extreme points on the FeC6H6(+) surface, some of which have not been described previously. These include eta-1, eta-2 and eta-3 complexes of Fe(+) with the C4H4 ring. We identify new FeC6H6(+) structures as well, which may be landmarks for the Fe(+)-catalysed production of benzene from acetylene. The Fe(+) benzene complex is the most stable species on the FeC6H6 cation surface. With the abundant energy of complexation available in the isolated gas phase species, detachment of the Fe(+) and production of benzene can be efficient. We address the issue raised by other investigators whether multi-configurational self-consistent field methods are essential to the proper description of these systems. We find that the relative energy of intrinsically multi-determinant doublets is strongly affected, but judge that the density functional theory (DFT) description provides more accurate estimates of energetics and a more plausible reaction path.

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

PubMed

Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

2017-01-04

The structures of the mono- and the dihalogenated N -unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide ( ABB ) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer ( A ) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Additive effect of mesenchymal stem cells and defibrotide in an arterial rat thrombosis model.

PubMed

Dilli, Dilek; Kılıç, Emine; Yumuşak, Nihat; Beken, Serdar; Uçkan Çetinkaya, Duygu; Karabulut, Ramazan; Zenciroğlu, Ayşegu L

2017-06-01

In this study, we aimed to investigate the additive effect of mesenchymal stem cells (MSC) and defibrotide (DFT) in a rat model of femoral arterial thrombosis. Thirty Sprague Dawley rats were included. An arterial thrombosis model by ferric chloride (FeCl3) was developed in the left femoral artery. The rats were equally assigned to 5 groups: Group 1-Sham-operated (without arterial injury); Group 2-Phosphate buffered saline (PBS) injected; Group 3-MSC; Group 4-DFT; Group 5-MSC + DFT. All had two intraperitoneal injections of 0.5 ml: the 1st injection was 4 h after the procedure and the 2nd one 48 h after the 1st injection. The rats were sacrificed 7 days after the 2nd injection. Although the use of human bone marrow-derived (hBM) hBM-MSC or DFT alone enabled partial resolution of the thrombus, combining them resulted in near-complete resolution. Neovascularization was two-fold better in hBM-MSC + DFT treated rats (11.6 ± 2.4 channels) compared with the hBM-MSC (3.8 ± 2.7 channels) and DFT groups (5.5 ± 1.8 channels) (P < 0.0001 and P= 0.002, respectively). The combined use of hBM-MSC and DFT in a rat model of arterial thrombosis showed additive effect resulting in near-complete resolution of the thrombus.

Analyzing the errors of DFT approximations for compressed water systems

NASA Astrophysics Data System (ADS)

Alfè, D.; Bartók, A. P.; Csányi, G.; Gillan, M. J.

2014-07-01

We report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchange-correlation functionals, and we characterize their errors before and after correction for 1- and 2-body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm3 where the experimental pressure is 15 kilobars; second, thermal samples of compressed water clusters from the trimer to the 27-mer. For the liquid, we report four first-principles molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1- and 2-body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutron-diffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2-body and beyond-2-body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond-2-body errors of DFT make a substantial contribution to the overall errors, so that correction for 1- and 2-body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3-body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput. 9, 1103 (2013)] gives a reasonably good way of correcting for beyond-2-body errors, after which the remaining errors are typically 0.5 mEh ≃ 15 meV/monomer for the liquid and the

Analyzing the errors of DFT approximations for compressed water systems

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

Alfè, D.; London Centre for Nanotechnology, UCL, London WC1H 0AH; Thomas Young Centre, UCL, London WC1H 0AH

We report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchange-correlation functionals, and we characterize their errors before and after correction for 1- and 2-body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm{sup 3} where the experimental pressure is 15 kilobars; second, thermal samples of compressed watermore » clusters from the trimer to the 27-mer. For the liquid, we report four first-principles molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1- and 2-body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutron-diffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2-body and beyond-2-body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond-2-body errors of DFT make a substantial contribution to the overall errors, so that correction for 1- and 2-body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3-body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput. 9, 1103 (2013)] gives a reasonably good way of correcting for beyond-2-body errors, after which the remaining errors are typically 0.5 mE{sub h} ≃ 15 meV/monomer for the

Including crystal structure attributes in machine learning models of formation energies via Voronoi tessellations

NASA Astrophysics Data System (ADS)

Ward, Logan; Liu, Ruoqian; Krishna, Amar; Hegde, Vinay I.; Agrawal, Ankit; Choudhary, Alok; Wolverton, Chris

2017-07-01

While high-throughput density functional theory (DFT) has become a prevalent tool for materials discovery, it is limited by the relatively large computational cost. In this paper, we explore using DFT data from high-throughput calculations to create faster, surrogate models with machine learning (ML) that can be used to guide new searches. Our method works by using decision tree models to map DFT-calculated formation enthalpies to a set of attributes consisting of two distinct types: (i) composition-dependent attributes of elemental properties (as have been used in previous ML models of DFT formation energies), combined with (ii) attributes derived from the Voronoi tessellation of the compound's crystal structure. The ML models created using this method have half the cross-validation error and similar training and evaluation speeds to models created with the Coulomb matrix and partial radial distribution function methods. For a dataset of 435 000 formation energies taken from the Open Quantum Materials Database (OQMD), our model achieves a mean absolute error of 80 meV/atom in cross validation, which is lower than the approximate error between DFT-computed and experimentally measured formation enthalpies and below 15% of the mean absolute deviation of the training set. We also demonstrate that our method can accurately estimate the formation energy of materials outside of the training set and be used to identify materials with especially large formation enthalpies. We propose that our models can be used to accelerate the discovery of new materials by identifying the most promising materials to study with DFT at little additional computational cost.

Dissecting Embryonic Stem Cell Self-Renewal and Differentiation Commitment from Quantitative Models.

PubMed

Hu, Rong; Dai, Xianhua; Dai, Zhiming; Xiang, Qian; Cai, Yanning

2016-10-01

To model quantitatively embryonic stem cell (ESC) self-renewal and differentiation by computational approaches, we developed a unified mathematical model for gene expression involved in cell fate choices. Our quantitative model comprised ESC master regulators and lineage-specific pivotal genes. It took the factors of multiple pathways as input and computed expression as a function of intrinsic transcription factors, extrinsic cues, epigenetic modifications, and antagonism between ESC master regulators and lineage-specific pivotal genes. In the model, the differential equations of expression of genes involved in cell fate choices from regulation relationship were established according to the transcription and degradation rates. We applied this model to the Murine ESC self-renewal and differentiation commitment and found that it modeled the expression patterns with good accuracy. Our model analysis revealed that Murine ESC was an attractor state in culture and differentiation was predominantly caused by antagonism between ESC master regulators and lineage-specific pivotal genes. Moreover, antagonism among lineages played a critical role in lineage reprogramming. Our results also uncovered that the ordered expression alteration of ESC master regulators over time had a central role in ESC differentiation fates. Our computational framework was generally applicable to most cell-type maintenance and lineage reprogramming.

A quantitative quantum chemical model of the Dewar-Knott color rule for cationic diarylmethanes

NASA Astrophysics Data System (ADS)

Olsen, Seth

2012-04-01

We document the quantitative manifestation of the Dewar-Knott color rule in a four-electron, three-orbital state-averaged complete active space self-consistent field (SA-CASSCF) model of a series of bridge-substituted cationic diarylmethanes. We show that the lowest excitation energies calculated using multireference perturbation theory based on the model are linearly correlated with the development of hole density in an orbital localized on the bridge, and the depletion of pair density in the same orbital. We quantitatively express the correlation in the form of a generalized Hammett equation.

Anatase-rutile phase transformation of titanium dioxide bulk material: a DFT + U approach

NASA Astrophysics Data System (ADS)

Vu, Nam H.; Le, Hieu V.; Cao, Thi M.; Pham, Viet V.; Le, Hung M.; Nguyen-Manh, Duc

2012-10-01

The anatase-rutile phase transformation of TiO2 bulk material is investigated using a density functional theory (DFT) approach in this study. According to the calculations employing the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Vanderbilt ultrasoft pseudopotential, it is suggested that the anatase phase is more energetically stable than rutile, which is in variance with the experimental observations. Consequently, the DFT + U method is employed in order to predict the correct structural stability in titania from electronic-structure-based total energy calculations. The Hubbard U term is determined by examining the band structure of rutile with various values of U from 3 to 10 eV. At U = 5 eV, a theoretical bandgap for rutile is obtained as 3.12 eV, which is in very good agreement with the reported experimental bandgap. Hence, we choose the DFT + U method (with U = 5 eV) to investigate the transformation pathway using the newly-developed solid-state nudged elastic band (ss-NEB) method, and consequently obtain an intermediate transition structure that is 9.794 eV per four-TiO2 above the anatase phase. When the Ti-O bonds in the transition state are examined using charge density analysis, seven Ti-O bonds (out of 24 bonds in the anatase unit cell) are broken, and this result is in excellent agreement with a previous experimental study (Penn and Banfield 1999 Am. Miner. 84 871-6).

Wires in the soup: quantitative models of cell signaling

PubMed Central

Cheong, Raymond; Levchenko, Andre

2014-01-01

Living cells are capable of extracting information from their environments and mounting appropriate responses to a variety of associated challenges. The underlying signal transduction networks enabling this can be quite complex, necessitating for their unraveling by sophisticated computational modeling coupled with precise experimentation. Although we are still at the beginning of this process, some recent examples of integrative analysis of cell signaling are very encouraging. This review highlights the case of the NF-κB pathway in order to illustrate how a quantitative model of a signaling pathway can be gradually constructed through continuous experimental validation, and what lessons one might learn from such exercises. PMID:18291655

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

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

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

Using the DFT-D method to describe dispersion interactions in systems of weakly-bonded Xe-aromatic molecules

NASA Astrophysics Data System (ADS)

Andriichenko, N. N.; Ermilov, A. Yu.

2013-08-01

The optimum version of the DFT-D class of methods (BHHLYP-D2, 6-31G*) is chosen to describe binding in a Xe-phenol system with the aim of subsequent KM/MM calculations for complex Xe-containing protein systems. It is shown that the stability of the Xe-phenol system is due to weak dispersion interactions not described in conventional approaches using the density functional. The MP2 approach using the (aug)-cc-pVTZ basis and Stuttgart pseudopotential, which yield the best reproduction of the characteristics of a Xe2 xenon dimer, is chosen as the reference standard. It is noted that the 2010 DFT-D3 methods underestimate the binding energy by a factor of nearly three, while DFT methods without dispersion corrections do not reproduce the stability of Xe2 and Xe-phenol systems. It is found that in the best version of calculations, BHHLYP-D2, the binding energy in Xe-phenol complex is estimated to be 2.7 kcal/mol versus the 3.1 kcal/mol found using the comparative approach. It is concluded that BHHLYP-D2 adequately reproduces the difference between the two conformers of the Xe-phenol complex and trend toward an increase in binding energy in the series of aromatic amino acids (phenylalanine, tyrosine, and tryptophan). DFT-D can also indicate the existence of excess conformers that are missing in systems according to more precise descriptions (MP2/(aug)-cc-pVTZ).

The quantitative modelling of human spatial habitability

NASA Technical Reports Server (NTRS)

Wise, J. A.

1985-01-01

A model for the quantitative assessment of human spatial habitability is presented in the space station context. The visual aspect assesses how interior spaces appear to the inhabitants. This aspect concerns criteria such as sensed spaciousness and the affective (emotional) connotations of settings' appearances. The kinesthetic aspect evaluates the available space in terms of its suitability to accommodate human movement patterns, as well as the postural and anthrometric changes due to microgravity. Finally, social logic concerns how the volume and geometry of available space either affirms or contravenes established social and organizational expectations for spatial arrangements. Here, the criteria include privacy, status, social power, and proxemics (the uses of space as a medium of social communication).

General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters.

PubMed

Hadfield, J D; Nakagawa, S

2010-03-01

Although many of the statistical techniques used in comparative biology were originally developed in quantitative genetics, subsequent development of comparative techniques has progressed in relative isolation. Consequently, many of the new and planned developments in comparative analysis already have well-tested solutions in quantitative genetics. In this paper, we take three recent publications that develop phylogenetic meta-analysis, either implicitly or explicitly, and show how they can be considered as quantitative genetic models. We highlight some of the difficulties with the proposed solutions, and demonstrate that standard quantitative genetic theory and software offer solutions. We also show how results from Bayesian quantitative genetics can be used to create efficient Markov chain Monte Carlo algorithms for phylogenetic mixed models, thereby extending their generality to non-Gaussian data. Of particular utility is the development of multinomial models for analysing the evolution of discrete traits, and the development of multi-trait models in which traits can follow different distributions. Meta-analyses often include a nonrandom collection of species for which the full phylogenetic tree has only been partly resolved. Using missing data theory, we show how the presented models can be used to correct for nonrandom sampling and show how taxonomies and phylogenies can be combined to give a flexible framework with which to model dependence.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-01

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms.

PubMed

Mohamed, Gehad G; Hamed, Maher M; Zaki, Nadia G; Abdou, Mohamed M; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-05

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100μgmL -1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase. Copyright © 2017 Elsevier B.V. All rights reserved.

Generalizing the dynamic field theory of spatial cognition across real and developmental time scales

PubMed Central

Simmering, Vanessa R.; Spencer, John P.; Schutte, Anne R.

2008-01-01

Within cognitive neuroscience, computational models are designed to provide insights into the organization of behavior while adhering to neural principles. These models should provide sufficient specificity to generate novel predictions while maintaining the generality needed to capture behavior across tasks and/or time scales. This paper presents one such model, the Dynamic Field Theory (DFT) of spatial cognition, showing new simulations that provide a demonstration proof that the theory generalizes across developmental changes in performance in four tasks—the Piagetian A-not-B task, a sandbox version of the A-not-B task, a canonical spatial recall task, and a position discrimination task. Model simulations demonstrate that the DFT can accomplish both specificity—generating novel, testable predictions—and generality—spanning multiple tasks across development with a relatively simple developmental hypothesis. Critically, the DFT achieves generality across tasks and time scales with no modification to its basic structure and with a strong commitment to neural principles. The only change necessary to capture development in the model was an increase in the precision of the tuning of receptive fields as well as an increase in the precision of local excitatory interactions among neurons in the model. These small quantitative changes were sufficient to move the model through a set of quantitative and qualitative behavioral changes that span the age range from 8 months to 6 years and into adulthood. We conclude by considering how the DFT is positioned in the literature, the challenges on the horizon for our framework, and how a dynamic field approach can yield new insights into development from a computational cognitive neuroscience perspective. PMID:17716632

Relaxations of fluorouracil tautomers by decorations of fullerene-like SiCs: DFT studies

NASA Astrophysics Data System (ADS)

Kouchaki, Alireza; Gülseren, Oğuz; Hadipour, Nasser; Mirzaei, Mahmoud

2016-06-01

Decorations of silicon carbide (SiC) fullerene-like nanoparticles by fluorouracil (FU) and its tautomers are investigated through density functional theory (DFT) calculations. Two models of fullerene-like particles including Si12C8 and Si8C12 are constructed to be counterparts of decorated hybrid structures, FU@Si12C8 and FU@Si8C12, respectively. The initial models including original FU and tautomeric structures and SiC nanoparticles are individually optimized and then combined for further optimizations in the hybrid forms. Covalent bonds are observed for FU@Si12C8 hybrids, whereas non-covalent interactions are seen for FU@Si8C12 ones. The obtained properties indicated that Si12C8 model could be considered as a better counterpart for interactions with FU structures than Si8C12 model. The results also showed significant effects of interactions on the properties of atoms close to the interacting regions in nanoparticles. Finally, the tautomeric structures show different behaviors in interactions with SiC nanoparticles, in which the SiC nanoparticles could be employed to detect the situations of tautomeric processes for FU structures.

DFT and PCM-TD-DFT investigation of the electronic structures and spectra of 5-(3-phenyl-2-propenylidene)-2-thioxo-4-thiazolidinone derivatives

NASA Astrophysics Data System (ADS)

El-Taher, Sabry; Metwaly, Mohamed

2017-04-01

UV-Visible absorption spectra of 5-(3-phenyl-2-propenylidene)-2-thioxo-4-thiazolidinones (5pR-PPTT, R = H, CH3, CH3O, and N(CH3)2) were measured in different solvents and investigated using the theoretical PCM-TD-DFT scheme. A benchmark evaluation against experimental results on the accuracy of different DFT functionals has been performed. The best agreement with X-ray data is achieved by using the long-range corrected LC-wPBE functional, while the PBE0 functional provided the most accurate λmax for the studied compounds. The thionic forms of the ZE isomers of the studied compounds are found to be the most stable tautomers. The assignation debate of the second absorption band of rhodanine [2-thioxo-4-thiazolidinone (Rd)] has been solved by confirming on its π-π∗ nature. It was found that the expansion of the π-conjugation system at position 5 of Rd ring leads to significant bathochromic shift. The CT lengths (Δr) and dipole moment change (ΔμCT) indices showed that the charge transfer character of the electronic transitions is directly proportional to the electron-releasing strength of substituted phenyl ring. It was concluded that the red shifting of the maximum absorption is mainly regulated by the solvent polarizability and much less by solvent polarity.

From Mahan excitons to Landau levels at high magnetic fields: 2DFT spectroscopy reveals hidden quantum correlations (Conference Presentation)

NASA Astrophysics Data System (ADS)

Karaiskaj, Denis

2017-02-01

Two-dimensional electron gases have been the subject of research for decades. Modulation doped GaAs quantum wells in the absence of magnetic fields exhibit interesting many-body physics such as the Fermi edge singularity or Mahan exciton and can be regarded as a collective excitation of the system. Under high magnetic fields Landau levels form which have been studied using transport and optical measurements. Nonlinear coherent two-dimensional Fourier transform (2DFT) spectroscopy however provides new insights into these systems. We present the 2DFT spectra of Mahan Excitons associated with the heavy-hole and light-hole resonances observed in a modulation doped GaAs/AlGaAs single quantum well [1]. These resonances are observed to be strongly coupled through many-body interactions. The 2DFT spectra were measured using co-linear, cross-linear, and co-circular polarizations and reveal striking differences. Furthermore, 2DFT spectra at high magnetic fields performed at the National High Magnetic Field Lab (NHMFL) in Tallahassee, Florida will be discussed. The spectra exhibit new features and peculiar line shapes suggesting interesting underlying physics. [1] J. Paul, C. E. Stevens, C. Liu, P. Dey, C. McIntyre, V. Turkowski, J. L. Reno, D. J. Hilton, and D. Karaiskaj, Phys. Rev. Lett.116, 157401 (2016).

[Influence of sample surface roughness on mathematical model of NIR quantitative analysis of wood density].

PubMed

Huang, An-Min; Fei, Ben-Hua; Jiang, Ze-Hui; Hse, Chung-Yun

2007-09-01

Near infrared spectroscopy is widely used as a quantitative method, and the main multivariate techniques consist of regression methods used to build prediction models, however, the accuracy of analysis results will be affected by many factors. In the present paper, the influence of different sample roughness on the mathematical model of NIR quantitative analysis of wood density was studied. The result of experiments showed that if the roughness of predicted samples was consistent with that of calibrated samples, the result was good, otherwise the error would be much higher. The roughness-mixed model was more flexible and adaptable to different sample roughness. The prediction ability of the roughness-mixed model was much better than that of the single-roughness model.

A Quantitative Model of Early Atherosclerotic Plaques Parameterized Using In Vitro Experiments.

PubMed

Thon, Moritz P; Ford, Hugh Z; Gee, Michael W; Myerscough, Mary R

2018-01-01

There are a growing number of studies that model immunological processes in the artery wall that lead to the development of atherosclerotic plaques. However, few of these models use parameters that are obtained from experimental data even though data-driven models are vital if mathematical models are to become clinically relevant. We present the development and analysis of a quantitative mathematical model for the coupled inflammatory, lipid and macrophage dynamics in early atherosclerotic plaques. Our modeling approach is similar to the biologists' experimental approach where the bigger picture of atherosclerosis is put together from many smaller observations and findings from in vitro experiments. We first develop a series of three simpler submodels which are least-squares fitted to various in vitro experimental results from the literature. Subsequently, we use these three submodels to construct a quantitative model of the development of early atherosclerotic plaques. We perform a local sensitivity analysis of the model with respect to its parameters that identifies critical parameters and processes. Further, we present a systematic analysis of the long-term outcome of the model which produces a characterization of the stability of model plaques based on the rates of recruitment of low-density lipoproteins, high-density lipoproteins and macrophages. The analysis of the model suggests that further experimental work quantifying the different fates of macrophages as a function of cholesterol load and the balance between free cholesterol and cholesterol ester inside macrophages may give valuable insight into long-term atherosclerotic plaque outcomes. This model is an important step toward models applicable in a clinical setting.

Modeling logistic performance in quantitative microbial risk assessment.

PubMed

Rijgersberg, Hajo; Tromp, Seth; Jacxsens, Liesbeth; Uyttendaele, Mieke

2010-01-01

In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage times, temperatures, gas conditions, and their distributions) are determined. However, the logistic chain with its queues (storages, shelves) and mechanisms for ordering products is usually not taken into account. As a consequence, storage times-mutually dependent in successive steps in the chain-cannot be described adequately. This may have a great impact on the tails of risk distributions. Because food safety risks are generally very small, it is crucial to model the tails of (underlying) distributions as accurately as possible. Logistic performance can be modeled by describing the underlying planning and scheduling mechanisms in discrete-event modeling. This is common practice in operations research, specifically in supply chain management. In this article, we present the application of discrete-event modeling in the context of a QMRA for Listeria monocytogenes in fresh-cut iceberg lettuce. We show the potential value of discrete-event modeling in QMRA by calculating logistic interventions (modifications in the logistic chain) and determining their significance with respect to food safety.

Quantitative and Functional Requirements for Bioluminescent Cancer Models.

PubMed

Feys, Lynn; Descamps, Benedicte; Vanhove, Christian; Vermeulen, Stefan; Vandesompele, J O; Vanderheyden, Katrien; Messens, Kathy; Bracke, Marc; De Wever, Olivier

2016-01-01

Bioluminescent cancer models are widely used but detailed quantification of the luciferase signal and functional comparison with a non-transfected control cell line are generally lacking. In the present study, we provide quantitative and functional tests for luciferase-transfected cells. We quantified the luciferase expression in BLM and HCT8/E11 transfected cancer cells, and examined the effect of long-term luciferin exposure. The present study also investigated functional differences between parental and transfected cancer cells. Our results showed that quantification of different single-cell-derived populations are superior with droplet digital polymerase chain reaction. Quantification of luciferase protein level and luciferase bioluminescent activity is only useful when there is a significant difference in copy number. Continuous exposure of cell cultures to luciferin leads to inhibitory effects on mitochondrial activity, cell growth and bioluminescence. These inhibitory effects correlate with luciferase copy number. Cell culture and mouse xenograft assays showed no significant functional differences between luciferase-transfected and parental cells. Luciferase-transfected cells should be validated by quantitative and functional assays before starting large-scale experiments. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Ferrocene-isocoumarin conjugated molecules: synthesis, structural characterization, electronic properties, and DFT-TDDFT computational study.

PubMed

Peng, Ye-Dong; Zhou, Lin-Sen; Chen, Li-Li; Ma, Lu; Zhao, Yue; Zhang, Wen-Wei; Zuo, Jing-Lin

2015-08-28

Two ferrocene-isocoumarin conjugated molecules, methyl 3-ferrocenyl-1-oxo-1H-isochromene-6-carboxylate () and 3,8-bisferrocenylpyrano[3,4-g]isochromene-1,6-dione (), have been synthesized through the acid-prompted regioselective oxidative cyclization from dimethyl 2-(ferrocenylethynyl)terephthalate () and dimethyl 2,5-bis(ferrocenylethynyl)terephthalate (), respectively. Single-crystal X-ray diffraction, together with the density functional theory (DFT) calculations, shows that the ferrocene-isocoumarin conjugated compounds display better coplanarity than the corresponding ferrocenylethynyl terephthalates. All the compounds exhibit characteristic MLCT, ICT and π-π* transitions in the UV-visible range in solution, and and show higher oscillator strength of the absorption than and , which are verified by time-dependent DFT (TDDFT) theoretical calculations. The electrochemical properties are studied by cyclic voltammetry (CV), which are also in accord with the theoretical calculations.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 4-acetylpyridine

NASA Astrophysics Data System (ADS)

Atilgan, A.; Yurdakul, Ş.; Erdogdu, Y.; Güllüoğlu, M. T.

2018-06-01

The spectroscopic (UV-Vis and infrared), structural and some electronic property observations of the 4-acetylpyridine (4-AP) were reported, which are investigated by using some spectral methods and DFT calculations. FT-IR spectra were obtained for 4-AP at room temperature in the region 4000 cm-1- 400 cm-1. In the DFT calculations, the B3LYP functional with 6-311G++G(d,p) basis set was applied to carry out the quantum mechanical calculations. The Fourier Transform Infrared (FT-IR) and FT-Raman spectra were interpreted by using of normal coordinate analysis based on scaled quantum mechanical force field. The present work expands our understanding of the both the vibrational and structural properties as well as some electronic properties of the 4-AP by means of the theoretical and experimental methods.

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

PubMed

Cobbs, Gary

2012-08-16

Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of

Computational study of AuSi{sub n} (n=1-9) nanoalloy clusters invoking DFT based descriptors

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

Ranjan, Prabhat; Kumar, Ajay; Chakraborty, Tanmoy, E-mail: tanmoy.chakraborty@jaipur.manipal.edu, E-mail: tanmoychem@gmail.com

2016-04-13

Nanoalloy clusters formed between Au and Si are topics of great interest today from both scientific and technological point of view. Due to its remarkable catalytic, electronic, mechanical and magnetic properties Au-Si nanoalloy clusters have extensive applications in the field of microelectronics, catalysis, biomedicine, and jewelry industry. Density Functional Theory (DFT) is a new paradigm of quantum mechanics, which is very much popular to study the electronic properties of materials. Conceptual DFT based descriptors have been invoked to correlate the experimental properties of nanoalloy clusters. In this venture, we have systematically investigated AuSi{sub n} (n=1-9) nanoalloy clusters in the theoreticalmore » frame of the B3LYP exchange correlation. The experimental properties of AuSi{sub n} (n=1-9) nanoalloy clusters are correlated in terms of DFT based descriptors viz. HOMO-LUMO gap, Electronegativity (χ), Global Hardness (η), Global Softness (S) and Electrophilicity Index (ω). The calculated HOMO-LUMO gap exhibits interesting odd-even alteration behaviour, indicating that even numbered clusters possess higher stability as compare to their neighbour odd numbered clusters. This study also reflects a very well agreement between experimental bond length and computed data.« less

Computational prediction of the pKas of small peptides through Conceptual DFT descriptors

NASA Astrophysics Data System (ADS)

Frau, Juan; Hernández-Haro, Noemí; Glossman-Mitnik, Daniel

2017-03-01

The experimental pKa of a group of simple amines have been plotted against several Conceptual DFT descriptors calculated by means of different density functionals, basis sets and solvation schemes. It was found that the best fits are those that relate the pKa of the amines with the global hardness η through the MN12SX density functional in connection with the Def2TZVP basis set and the SMD solvation model, using water as a solvent. The parameterized equation resulting from the linear regression analysis has then been used for the prediction of the pKa of small peptides of interest in the study of diabetes and Alzheimer disease. The accuracy of the results is relatively good, with a MAD of 0.36 units of pKa.

ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling.

PubMed

Streif, Stefan; Savchenko, Anton; Rumschinski, Philipp; Borchers, Steffen; Findeisen, Rolf

2012-05-01

Often competing hypotheses for biochemical networks exist in the form of different mathematical models with unknown parameters. Considering available experimental data, it is then desired to reject model hypotheses that are inconsistent with the data, or to estimate the unknown parameters. However, these tasks are complicated because experimental data are typically sparse, uncertain, and are frequently only available in form of qualitative if-then observations. ADMIT (Analysis, Design and Model Invalidation Toolbox) is a MatLab(TM)-based tool for guaranteed model invalidation, state and parameter estimation. The toolbox allows the integration of quantitative measurement data, a priori knowledge of parameters and states, and qualitative information on the dynamic or steady-state behavior. A constraint satisfaction problem is automatically generated and algorithms are implemented for solving the desired estimation, invalidation or analysis tasks. The implemented methods built on convex relaxation and optimization and therefore provide guaranteed estimation results and certificates for invalidity. ADMIT, tutorials and illustrative examples are available free of charge for non-commercial use at http://ifatwww.et.uni-magdeburg.de/syst/ADMIT/

Charge Transfer Enhancement in the D-π-A Type Porphyrin Dyes: A Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) Study.

PubMed

Kang, Guo-Jun; Song, Chao; Ren, Xue-Feng

2016-11-25

The electronic geometries and optical properties of two D-π-A type zinc porphyrin dyes (NCH₃-YD2 and TPhe-YD) were systematically investigated by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) to reveal the origin of significantly altered charge transfer enhancement by changing the electron donor of the famous porphyrin-based sensitizer YD2-o-C8. The molecular geometries and photophysical properties of dyes before and after binding to the TiO₂ cluster were fully investigated. From the analyses of natural bond orbital (NBO), extended charge decomposition analysis (ECDA), and electron density variations (Δρ) between the excited state and ground state, it was found that the introduction of N(CH₃)₂ and 1,1,2-triphenylethene groups enhanced the intramolecular charge-transfer (ICT) character compared to YD2-o-C8. The absorption wavelength and transition possess character were significantly influenced by N(CH₃)₂ and 1,1,2-triphenylethene groups. NCH₃-YD2 with N(CH₃)₂ groups in the donor part is an effective way to improve the interactions between the dyes and TiO₂ surface, light having efficiency (LHE), and free energy change (ΔG inject ), which is expected to be an efficient dye for use in dye-sensitized solar cells (DSSCs).

FTIR and FT-Raman spectra and DFT vibrational analysis of phosphorus-containing dendrons

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukova, I. I.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2008-12-01

FTIR and FT-Raman spectra of four generations of phosphorus-containing dendrons with terminal aldehyde or P sbnd Cl groups have been recorded and analyzed. Their spectral patterns are determined by the ratio T/ R ( T, the number of terminal groups; R, the number of repeated units). Bands assigned to the core, repeated units and terminal groups were separated by the difference spectroscopy method. The optimized geometry, frequencies and intensity of IR bands of G1v generation dendron with terminal aldehyde groups were obtained by the density functional theory (DFT). It was found that the internal skeleton of molecules exists in a single stable conformation with planar sbnd O- C6H4- CHdbnd N- N( CH3)- P( dbnd S)< fragments, but terminal groups may adopt the t, g, g- and t,- g, g-rotational isomers. The t,- g, g-conformer is 0.74 kcal/mol less stable compared to the t, g, g-conformer. The bond length and bond angles obtained by DFT show the best agreement with experimental data. Relying on DFT calculations a complete assignment of vibrations is proposed for different parts of the studied dendrons. The calculated frequencies and intensity of IR bands of the t, g, g- and t,- g, g-conformers of G1v are found to be in reasonable agreement with the experimental results. The most reactive site in dendron is the core function and vinyl group is preferred for nucleophilic attack. In dendrimer the most reactive are the terminal groups.

Oxygenolysis of flavonoid compounds: DFT description of the mechanism for quercetin.

PubMed

Fiorucci, Sébastien; Golebiowski, Jerôme; Cabrol-Bass, Daniel; Antonczak, Serge

2004-11-12

Flavonoids are naturally occurring phenol derivatives present in substantial amounts in a large variety of plants, fruits and vegetables daily eaten by humans. Most of these compounds exhibit several interesting biological activities, such as antiradical and antioxidant actions. Indeed, by complexation with specific enzymes, flavonoids are notably liable to metabolize molecular dioxygen. On the basis of experimental results describing oxygenolysis of the flavonoid quercetin, activated by the enzyme quercetin 2,3-dioxygenase (2,3-QD),ur attention has focused on the role of metal center in the activation of the substrate quercetin. Thus, in the present study, by means of DFT calculations at the B3LYP/ 6-31(+)G* level on model molecular systems, we describe different mechanisms for dioxygen metabolization by quercetin. Stationary points are described, and energetic and structural analyses along the reaction paths are reported. Our calculations show that the copper cation must act as an oxidant towards the substrate and that the reaction proceeds through a 1,3-cycloaddition.

Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method.

PubMed

Xu, Zhongnan; Joshi, Yogesh V; Raman, Sumathy; Kitchin, John R

2015-04-14

We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

First-Principles DFT Studies of the Vibrational Properties of Germanene Nanoflakes

NASA Astrophysics Data System (ADS)

Richardson, Steven; Peroparde, Borja; Andrade, Xavier; Aspuru-Guzik, AláN.

The germanium analogue of graphene, germanene, is a potentially new atomically thin quantum material which theory predicts will possess unique transport and optoelectronic properties. Recently, there have been a number of experimental efforts to successfully grow two-dimensional films of germanene on noble metal substrates using molecular beam epitaxy. In addition to this top-down approach of synthesizing large scale films of germanene, we would like to focus on a bottom-up approach where nanoflakes of germanene could be used as molecular seeds or precursors to grow large films of two-dimensional germanene. A knowledge of their infrared and Raman spectra will be critical for characterizing these germanene nanoflakes in future experiments. In this work we used density-functional theory (DFT) to compute the vibrational spectra of a selected number of lower order germanene nanoflakes (e.g. hexagermabenzene, germa-naphthalene, germa-anthracene, germa-phenanthrene, germa-pyrene, germa-tetracene, and germa-pentacene). Our DFT studies also reveal that these germanene nanoflakes are vibrationally stable with buckling of these molecules from their normal two-dimensional planar forms which exist in graphene nanoflakes. This research is supported by NSF Grant No. DMR-1231319.

Quantitative computational models of molecular self-assembly in systems biology

PubMed Central

Thomas, Marcus; Schwartz, Russell

2017-01-01

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

Quantitative computational models of molecular self-assembly in systems biology.

PubMed

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Corequisite Model: An Effective Strategy for Remediation in Freshmen Level Quantitative Reasoning Course

ERIC Educational Resources Information Center

Kashyap, Upasana; Mathew, Santhosh

2017-01-01

The purpose of this study was to compare students' performances in a freshmen level quantitative reasoning course (QR) under three different instructional models. A cohort of 155 freshmen students was placed in one of the three models: needing a prerequisite course, corequisite (students enroll simultaneously in QR course and a course that…

Structure-activity relations of 2-(methylthio)benzimidazole by FTIR, FT-Raman, NMR, DFT and conceptual DFT methods.

PubMed

Arjunan, V; Raj, Arushma; Ravindran, P; Mohan, S

2014-01-24

The vibrational fundamental modes of 2-(methylthio)benzimidazole (2MTBI) have been analysed by combining FTIR, FT-Raman and quantum chemical calculations. The structural parameters of the compound are determined from the optimised geometry by B3LYP with 6-31G(∗∗), 6-311++G(∗∗) and cc-pVTZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra have been analysed and (1)H and (13)C nuclear magnetic resonance chemical shifts are calculated using the gauge independent atomic orbital (GIAO) method. The structure-activity relationship of the compound is also investigated by conceptual DFT methods. The chemical reactivity and site selectivity of the molecule has been determined with the help of global and local reactivity descriptors. Copyright © 2013 Elsevier B.V. All rights reserved.

Geometric structure of anatase Ti O2(101 )

NASA Astrophysics Data System (ADS)

Treacy, Jon P. W.; Hussain, Hadeel; Torrelles, Xavier; Grinter, David C.; Cabailh, Gregory; Bikondoa, Oier; Nicklin, Christopher; Selcuk, Sencer; Selloni, Annabella; Lindsay, Robert; Thornton, Geoff

2017-02-01

Surface x-ray diffraction has been used to determine the quantitative structure of the (101) termination of anatase Ti O2 . The atomic displacements from the bulk-terminated structure are significantly different from those previously calculated with density functional theory (DFT) methods with discrepancies for the Ti displacements in the [10 1 ¯] direction of up to 0.3 Å . DFT calculations carried out as part of the current paper provide a much better agreement through improved accuracy and thicker slab models.

A conceptual DFT study of the molecular properties of glycating carbonyl compounds.

PubMed

Frau, Juan; Glossman-Mitnik, Daniel

2017-01-01

Several glycating carbonyl compounds have been studied by resorting to the latest Minnesota family of density functional with the objective of determinating their molecular properties. In particular, the chemical reactivity descriptors that arise from conceptual density functional theory and chemical reactivity theory have been calculated through a [Formula: see text]SCF protocol. The validity of the KID (Koopmans' in DFT) procedure has been checked by comparing the reactivity descriptors obtained from the values of the HOMO and LUMO with those calculated through vertical energy values. The reactivity sites have been determined by means of the calculation of the Fukui function indices, the condensed dual descriptor [Formula: see text] and the electrophilic and nucleophilic Parr functions. The glycating power of the studied compounds have been compared with the same property for simple carbohydrates.Graphical abstractSeveral glycating carbonyl compounds have been studied by resorting to the latest Minnesota family of density functional with the objective of determinating their molecular properties, the chemical reactivity descriptors and the validity of the KID (Koopmans' in DFT) procedure.

Orientation of N-benzoyl glycine on silver nanoparticles: SERS and DFT studies

NASA Astrophysics Data System (ADS)

Parameswari, A.; Asath, R. Mohamed; Premkumar, R.; Benial, A. Milton Franklin

2017-05-01

Surface enhanced Raman scattering (SERS) studies of N-benzoyl glycine (NBG) adsorbed on silver nanoparticles (AgNPs) was studied by experimental and density functional theory (DFT) approach. Single crystals of NBG were prepared using slow evaporation method. The AgNPs were prepared and characterized. The DFT/ B3PW91 method with LanL2DZ basis set was used to optimize the molecular structure of NBG and NBG adsorbed on silver cluster. The calculated and observed vibrational frequencies were assingned on the basis of potential energy distribution calculation. The reduced band gap value was obtained for NBG adsorbed on silver nanoparticles from the frontier molecular orbitals analysis. Natural bond orbital analysis was carried out to inspect the intra-molecular stabilization interactions, which are responsible for the bio activity and nonlinear optical property of the molecule. The spectral analysis was also evidenced that NBG would adsorb tilted orientation on the silver surface over the binding sites such as lone pair electron of N atom in amine group and through phenyl ring π system.

NEGF-DFT characterization of diarylethene photoswitches: Impact of substituents

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

Van Dyck, Colin; Geskin, Victor; Cornil, Jérôme

2015-01-22

In this presentation we report a theoretical study on the performance of diarylethene photoswitches. We start with a comparison between the electronic structures of different substituted diarylethene cores. Using a NEGF-DFT formalism we compute self-consistently transmission and IV curves with a focus on the impact of the substituents usually introduced for various synthetic and functional reasons. We find that the conductance properties of the diarylethene photoswitches are rather insensitive to these substitutions in the core. In the interpretation of our results, we make a connection between transmission spectra and molecular electronic properties.

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

NTO-Picryl Constitutional Isomers—A DFT Study

NASA Astrophysics Data System (ADS)

Türker, Lemi; Çelik Bayar, Çağlar

2012-01-01

The quantum chemical properties and the detonation performance of some new explosives, 5-nitro-4-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class A) and 5-nitro-2-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class B), and their constitutional isomers have been investigated theoretically using the density functional theory (DFT) 6-31G(d,p) method. All of the constitutional isomers were found to be more sensitive than 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) and TNT but more insensitive than RDX and HMX. Their detonation performance is higher than that of NTO and TNT and all except two had lower detonation performance than RDX and HMX.

FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate

NASA Astrophysics Data System (ADS)

Chen, Yi; Zhang, Hui; Liu, Qing

The infrared vibration frequencies of vinyl acetate (VAc) in 18 different solvents were theoretically computed at Density Function Theory (DFT) B3LYP/6-311G* level based on Polarizable Continuum Model (PCM) and experimentally recorded by FT-IR spectroscopy. The solvent-induced long-range bulk electrostatic solvation free energies of VAc (ΔGelec) were calculated by the SMD model. The Cdbnd O stretching vibration frequencies of VAc were utilized as a measure of the chemical reactivities of the Cdbnd C group in VAc. The calculated and experimental Cdbnd O stretching vibration frequencies of VAc (νcal(Cdbnd O) and νexp(Cdbnd O)) were correlated with empirical solvent parameters including the KBM equation, the Swain equation and the linear solvation energy relationships (LSER). Through ab initio calculation, assignments of the two Cdbnd O absorption bands of VAc in alcohol solvents were achieved. The PCM, SMD and ab initio calculation offered supporting evidence to explain the FT-IR experimental observations from differing aspects.

Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT

NASA Astrophysics Data System (ADS)

Bardak, F.; Karaca, C.; Bilgili, S.; Atac, A.; Mavis, T.; Asiri, A. M.; Karabacak, M.; Kose, E.

2016-08-01

Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, 1H and 13C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts (1H and 13C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm- 1 and 3500-50 cm- 1, respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The 13C and 1H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained.

Establishment of quantitative retention-activity model by optimized microemulsion liquid chromatography.

PubMed

Xu, Liyuan; Gao, Haoshi; Li, Liangxing; Li, Yinnong; Wang, Liuyun; Gao, Chongkai; Li, Ning

2016-12-23

The effective permeability coefficient is of theoretical and practical importance in evaluation of the bioavailability of drug candidates. However, most methods currently used to measure this coefficient are expensive and time-consuming. In this paper, we addressed these problems by proposing a new measurement method which is based on the microemulsion liquid chromatography. First, the parallel artificial membrane permeability assays model was used to determine the effective permeability of drug so that quantitative retention-activity relationships could be established, which were used to optimize the microemulsion liquid chromatography. The most effective microemulsion system used a mobile phase of 6.0% (w/w) Brij35, 6.6% (w/w) butanol, 0.8% (w/w) octanol, and 86.6% (w/w) phosphate buffer (pH 7.4). Next, support vector machine and back-propagation neural networks are employed to develop a quantitative retention-activity relationships model associated with the optimal microemulsion system, and used to improve the prediction ability. Finally, an adequate correlation between experimental value and predicted value is computed to verify the performance of the optimal model. The results indicate that the microemulsion liquid chromatography can serve as a possible alternative to the PAMPA method for determination of high-throughput permeability and simulation of biological processes. Copyright © 2016. Published by Elsevier B.V.

Synthesis and DFT calculations of some 2-aminothiazoles

NASA Astrophysics Data System (ADS)

Rezania, Jafar; Behzadi, Hadi; Shockravi, Abbas; Ehsani, Morteza; Akbarzadeh, Elahe

2018-04-01

A series of 2-aminothiazole derivatives have been synthesized by the reaction of acetyl compounds with thiourea and iodine as catalyst under solvent-free condition, a green chemistry method. The quantum chemical calculations at the DFT/B3LYP level of theory in gas phase were carried out for starting acetyl derivatives. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and related reactivity descriptor of acetyl derivatives, as well as, enthalpy of reactions are calculated in order to investigate the reaction properties of acetyl compounds and yields of the reactions. The calculated reactivity descriptors are well correlated to activity of different acetyl derivatives.

Quantitative petri net model of gene regulated metabolic networks in the cell.

PubMed

Chen, Ming; Hofestädt, Ralf

2011-01-01

A method to exploit hybrid Petri nets (HPN) for quantitatively modeling and simulating gene regulated metabolic networks is demonstrated. A global kinetic modeling strategy and Petri net modeling algorithm are applied to perform the bioprocess functioning and model analysis. With the model, the interrelations between pathway analysis and metabolic control mechanism are outlined. Diagrammatical results of the dynamics of metabolites are simulated and observed by implementing a HPN tool, Visual Object Net ++. An explanation of the observed behavior of the urea cycle is proposed to indicate possibilities for metabolic engineering and medical care. Finally, the perspective of Petri nets on modeling and simulation of metabolic networks is discussed.

Electronic transport in VO 2 —Experimentally calibrated Boltzmann transport modeling

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

Kinaci, Alper; Kado, Motohisa; Rosenmann, Daniel

2015-12-28

Materials that undergo metal-insulator transitions (MITs) are under intense study because the transition is scientifically fascinating and technologically promising for various applications. Among these materials, VO2 has served as a prototype due to its favorable transition temperature. While the physical underpinnings of the transition have been heavily investigated experimentally and computationally, quantitative modeling of electronic transport in the two phases has yet to be undertaken. In this work, we establish a density-functional-theory (DFT)-based approach to model electronic transport properties in VO2 in the semiconducting and metallic regimes, focusing on band transport using the Boltzmann transport equations. We synthesized high qualitymore » VO2 films and measured the transport quantities across the transition, in order to calibrate the free parameters in the model. We find that the experimental calibration of the Hubbard correction term can efficiently and adequately model the metallic and semiconducting phases, allowing for further computational design of MIT materials for desirable transport properties.« less

DFT analysis of the structure and IR spectrum of potassium salt of diphenylsulfophthalide - A model compound for polydiphenylenesulfophthalide salts

NASA Astrophysics Data System (ADS)

Shishlov, N. M.; Akhmetzyanov, Sh S.; Khursan, S. L.

2017-02-01

Experimental IR spectra of crystalline dried and non-dried potassium diphenylsulfophthalide (TAC-K) as a model compound for polymeric salts are presented. DFT analysis (B3LYP/6-311G(d,p)) of the structure and IR spectra of a series of compounds similar in structure to TAC-K as well as their dimers indicates that the sulfonate group environment strongly affects the positions of absorption bands (ABs) of vibrations of Ssbnd O bonds and demonstrates that information on the exact structure of ion clusters is needed for reliable and unambiguous assignment of the ABs in experimental IR spectra of real sulfonate ion containing systems to particular vibrational modes. Various ways of metal ion coordination with sulfonate ion, as well as their reflection in IR spectra of model compounds, are considered and discussed. Using TAC-K as an example, the effect of an intramolecular hydrogen bond on the vibrational modes of sulfonate group and hydroxy group is considered. The effect of ion aggregation on the shape of the IR spectrum of TAC-K is analyzed for an energetically favorable dimer of this salt as an example. Based on a combination of calculated, literature and reference data, a number of ABs in the IR spectra of TAC-K have been tentatively assigned. In particular, the bands in the region of 3230-3180 cm-1 have been assigned to ν(Osbnd H); those at 1240-1160 cm-1, to νas(SO3-); the AB at 1080 cm-1, to νs(SO3-); that at 616 cm-1, to δ(oop)s(SO3-); and that at 570 cm-1, to δ(ip)as(SO3-).

A hybrid, coupled approach for modeling charged fluids from the nano to the mesoscale

NASA Astrophysics Data System (ADS)

Cheung, James; Frischknecht, Amalie L.; Perego, Mauro; Bochev, Pavel

2017-11-01

We develop and demonstrate a new, hybrid simulation approach for charged fluids, which combines the accuracy of the nonlocal, classical density functional theory (cDFT) with the efficiency of the Poisson-Nernst-Planck (PNP) equations. The approach is motivated by the fact that the more accurate description of the physics in the cDFT model is required only near the charged surfaces, while away from these regions the PNP equations provide an acceptable representation of the ionic system. We formulate the hybrid approach in two stages. The first stage defines a coupled hybrid model in which the PNP and cDFT equations act independently on two overlapping domains, subject to suitable interface coupling conditions. At the second stage we apply the principles of the alternating Schwarz method to the hybrid model by using the interface conditions to define the appropriate boundary conditions and volume constraints exchanged between the PNP and the cDFT subdomains. Numerical examples with two representative examples of ionic systems demonstrate the numerical properties of the method and its potential to reduce the computational cost of a full cDFT calculation, while retaining the accuracy of the latter near the charged surfaces.

A Team Mental Model Perspective of Pre-Quantitative Risk

NASA Technical Reports Server (NTRS)

Cooper, Lynne P.

2011-01-01

This study was conducted to better understand how teams conceptualize risk before it can be quantified, and the processes by which a team forms a shared mental model of this pre-quantitative risk. Using an extreme case, this study analyzes seven months of team meeting transcripts, covering the entire lifetime of the team. Through an analysis of team discussions, a rich and varied structural model of risk emerges that goes significantly beyond classical representations of risk as the product of a negative consequence and a probability. In addition to those two fundamental components, the team conceptualization includes the ability to influence outcomes and probabilities, networks of goals, interaction effects, and qualitative judgments about the acceptability of risk, all affected by associated uncertainties. In moving from individual to team mental models, team members employ a number of strategies to gain group recognition of risks and to resolve or accept differences.

Quantitative validation of an air-coupled ultrasonic probe model by Interferometric laser tomography

NASA Astrophysics Data System (ADS)

Revel, G. M.; Pandarese, G.; Cavuto, A.

2012-06-01

The present paper describes the quantitative validation of a finite element (FE) model of the ultrasound beam generated by an air coupled non-contact ultrasound transducer. The model boundary conditions are given by vibration velocities measured by laser vibrometry on the probe membrane. The proposed validation method is based on the comparison between the simulated 3D pressure field and the pressure data measured with interferometric laser tomography technique. The model details and the experimental techniques are described in paper. The analysis of results shows the effectiveness of the proposed approach and the possibility to quantitatively assess and predict the generated acoustic pressure field, with maximum discrepancies in the order of 20% due to uncertainty effects. This step is important for determining in complex problems the real applicability of air-coupled probes and for the simulation of the whole inspection procedure, also when the component is designed, so as to virtually verify its inspectability.

Quantitative Testing of Bedrock Incision Models, Clearwater River, WA

NASA Astrophysics Data System (ADS)

Tomkin, J. H.; Brandon, M.; Pazzaglia, F.; Barbour, J.; Willet, S.

2001-12-01

The topographic evolution of many active orogens is dominated by the process of bedrock channel incision. Several incision models based around the detachment limited shear-stress model (or stream power model) which employs an area (A) and slope (S) power law (E = K Sn Am) have been proposed to explain this process. They require quantitative assessment. We evaluate the proposed incision models by comparing their predictions with observations obtained from a river in a tectonically active mountain range: the Clearwater River in northwestern Washington State. Previous work on river terraces along the Clearwater have provided long-term incision rates for the river, and in conjunction with previous fission track studies it has also been determined that there is a long-term balance between river incision and rock uplift. This steady-state incision rate data allows us, through the use of inversion methods and statistical tests, to determine the applicability of the different incision models for the Clearwater. None of the models successfully explain the observations. This conclusion particularly applies to the commonly used detachment limited shear-stress model (or stream power model), which has a physically implausible best fit solution and systematic residuals for all the predicted combinations of m and n.

A Novel DFT-Based DOA Estimation by a Virtual Array Extension Using Simple Multiplications for FMCW Radar

PubMed Central

Kim, Bongseok; Kim, Sangdong; Lee, Jonghun

2018-01-01

We propose a novel discrete Fourier transform (DFT)-based direction of arrival (DOA) estimation by a virtual array extension using simple multiplications for frequency modulated continuous wave (FMCW) radar. DFT-based DOA estimation is usually employed in radar systems because it provides the advantage of low complexity for real-time signal processing. In order to enhance the resolution of DOA estimation or to decrease the missing detection probability, it is essential to have a considerable number of channel signals. However, due to constraints of space and cost, it is not easy to increase the number of channel signals. In order to address this issue, we increase the number of effective channel signals by generating virtual channel signals using simple multiplications of the given channel signals. The increase in channel signals allows the proposed scheme to detect DOA more accurately than the conventional scheme while using the same number of channel signals. Simulation results show that the proposed scheme achieves improved DOA estimation compared to the conventional DFT-based method. Furthermore, the effectiveness of the proposed scheme in a practical environment is verified through the experiment. PMID:29758016

Estimation of boiling points using density functional theory with polarized continuum model solvent corrections.

PubMed

Chan, Poh Yin; Tong, Chi Ming; Durrant, Marcus C

2011-09-01

An empirical method for estimation of the boiling points of organic molecules based on density functional theory (DFT) calculations with polarized continuum model (PCM) solvent corrections has been developed. The boiling points are calculated as the sum of three contributions. The first term is calculated directly from the structural formula of the molecule, and is related to its effective surface area. The second is a measure of the electronic interactions between molecules, based on the DFT-PCM solvation energy, and the third is employed only for planar aromatic molecules. The method is applicable to a very diverse range of organic molecules, with normal boiling points in the range of -50 to 500 °C, and includes ten different elements (C, H, Br, Cl, F, N, O, P, S and Si). Plots of observed versus calculated boiling points gave R²=0.980 for a training set of 317 molecules, and R²=0.979 for a test set of 74 molecules. The role of intramolecular hydrogen bonding in lowering the boiling points of certain molecules is quantitatively discussed. Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.

Molecular Reactivity and Absorption Properties of Melanoidin Blue-G1 through Conceptual DFT.

PubMed

Frau, Juan; Glossman-Mitnik, Daniel

2018-03-02

This computational study presents the assessment of eleven density functionals that include CAM-B3LYP, LC-wPBE, M11, M11L, MN12L, MN12SX, N12, N12SX, wB97, wB97X and wB97XD related to the Def2TZVP basis sets together with the Solvation Model Density (SMD) solvation model in calculating the molecular properties and structure of the Blue-G1 intermediate melanoidin pigment. The chemical reactivity descriptors for the system are calculated via the conceptual Density Functional Theory (DFT). The choice of the active sites related to the nucleophilic, electrophilic, as well as radical attacks is made by linking them with the Fukui function indices, the electrophilic Parr functions and the condensed dual descriptor Δ f ( r ) . The prediction of the maximum absorption wavelength tends to be considerably accurate relative to its experimental value. The study found the MN12SX and N12SX density functionals to be the most appropriate density functionals in predicting the chemical reactivity of the studied molecule.

Quantitative modeling of multiscale neural activity

NASA Astrophysics Data System (ADS)

Robinson, Peter A.; Rennie, Christopher J.

2007-01-01

The electrical activity of the brain has been observed for over a century and is widely used to probe brain function and disorders, chiefly through the electroencephalogram (EEG) recorded by electrodes on the scalp. However, the connections between physiology and EEGs have been chiefly qualitative until recently, and most uses of the EEG have been based on phenomenological correlations. A quantitative mean-field model of brain electrical activity is described that spans the range of physiological and anatomical scales from microscopic synapses to the whole brain. Its parameters measure quantities such as synaptic strengths, signal delays, cellular time constants, and neural ranges, and are all constrained by independent physiological measurements. Application of standard techniques from wave physics allows successful predictions to be made of a wide range of EEG phenomena, including time series and spectra, evoked responses to stimuli, dependence on arousal state, seizure dynamics, and relationships to functional magnetic resonance imaging (fMRI). Fitting to experimental data also enables physiological parameters to be infered, giving a new noninvasive window into brain function, especially when referenced to a standardized database of subjects. Modifications of the core model to treat mm-scale patchy interconnections in the visual cortex are also described, and it is shown that resulting waves obey the Schroedinger equation. This opens the possibility of classical cortical analogs of quantum phenomena.

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative–quantitative modeling

PubMed Central

Streif, Stefan; Savchenko, Anton; Rumschinski, Philipp; Borchers, Steffen; Findeisen, Rolf

2012-01-01

Summary: Often competing hypotheses for biochemical networks exist in the form of different mathematical models with unknown parameters. Considering available experimental data, it is then desired to reject model hypotheses that are inconsistent with the data, or to estimate the unknown parameters. However, these tasks are complicated because experimental data are typically sparse, uncertain, and are frequently only available in form of qualitative if–then observations. ADMIT (Analysis, Design and Model Invalidation Toolbox) is a MatLabTM-based tool for guaranteed model invalidation, state and parameter estimation. The toolbox allows the integration of quantitative measurement data, a priori knowledge of parameters and states, and qualitative information on the dynamic or steady-state behavior. A constraint satisfaction problem is automatically generated and algorithms are implemented for solving the desired estimation, invalidation or analysis tasks. The implemented methods built on convex relaxation and optimization and therefore provide guaranteed estimation results and certificates for invalidity. Availability: ADMIT, tutorials and illustrative examples are available free of charge for non-commercial use at http://ifatwww.et.uni-magdeburg.de/syst/ADMIT/ Contact: stefan.streif@ovgu.de PMID:22451270

Spectroscopic (FT-IR and UV-Vis) and theoretical (HF and DFT) investigation of 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline

NASA Astrophysics Data System (ADS)

Ceylan, Ümit; Tarı, Gonca Özdemir; Gökce, Halil; Ağar, Erbil

2016-04-01

Crystal structure of the title compound, 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline, C13H12N2O2S, has been synthesized and characterized by FT-IR and UV-Vis spectrum. The compound crystallized in the monoclinic space group P 21/c with a = 11.3578 (4) Å, b = 7.4923 (2) Å, c = 14.9676 (6) Å and β = 99.589 (3)° and Z = 4 in the unit cell. The molecular geometry was also calculated using the Gaussian 03 software and structure was optimized using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set in ground state. Using the TD-DFT method, the electronic absorption spectra of the title compound was computed in both the gas phase and ethanol solvent. The harmonic vibrational frequencies of the title compound were calculated using the same methods with the 6-311++G(d,p) basis set. The calculated results were compared with the experimental determination results of the compound. It was seen that the optimized structure was in excellent agreement with the X-ray crystal structure. The energetic behaviors of the title compound in solvent media were examined using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set applying the polarizable continuum model (PCM). In addition, the molecular orbitals (FMOs) analysis, molecular electrostatic potential (MEP), nonlinear optical and thermodynamic properties of the title compound were performed using the same methods with the 6-311++G(d,p) basis set.

Model-based functional neuroimaging using dynamic neural fields: An integrative cognitive neuroscience approach

PubMed Central

Wijeakumar, Sobanawartiny; Ambrose, Joseph P.; Spencer, John P.; Curtu, Rodica

2017-01-01

A fundamental challenge in cognitive neuroscience is to develop theoretical frameworks that effectively span the gap between brain and behavior, between neuroscience and psychology. Here, we attempt to bridge this divide by formalizing an integrative cognitive neuroscience approach using dynamic field theory (DFT). We begin by providing an overview of how DFT seeks to understand the neural population dynamics that underlie cognitive processes through previous applications and comparisons to other modeling approaches. We then use previously published behavioral and neural data from a response selection Go/Nogo task as a case study for model simulations. Results from this study served as the ‘standard’ for comparisons with a model-based fMRI approach using dynamic neural fields (DNF). The tutorial explains the rationale and hypotheses involved in the process of creating the DNF architecture and fitting model parameters. Two DNF models, with similar structure and parameter sets, are then compared. Both models effectively simulated reaction times from the task as we varied the number of stimulus-response mappings and the proportion of Go trials. Next, we directly simulated hemodynamic predictions from the neural activation patterns from each model. These predictions were tested using general linear models (GLMs). Results showed that the DNF model that was created by tuning parameters to capture simultaneously trends in neural activation and behavioral data quantitatively outperformed a Standard GLM analysis of the same dataset. Further, by using the GLM results to assign functional roles to particular clusters in the brain, we illustrate how DNF models shed new light on the neural populations’ dynamics within particular brain regions. Thus, the present study illustrates how an interactive cognitive neuroscience model can be used in practice to bridge the gap between brain and behavior. PMID:29118459

Synthesis, characterization, and DFT studies of a new chiral ionic liquid from (S)-1-phenylethylamine

NASA Astrophysics Data System (ADS)

Cui, Shuya; Wang, Tao; Hu, Xiaoli

2014-12-01

A new chiral ionic liquid was synthesized from (S)-1-phenylethylamine and it was studied by IR, Raman, polarimetry, NMR and X-ray crystal diffraction. Its vibrational spectral bands are precisely ascribed to the studied structure with the aid of DFT theoretical calculations. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from IR and Raman spectra are assigned based on the results of the theoretical calculations by the DFT-B3LYP method at 6-311G(d,p) level. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The vibrational modes assignments were performed by using the animation option of GaussView5.0 graphical interface for Gaussian program.

A generalised individual-based algorithm for modelling the evolution of quantitative herbicide resistance in arable weed populations.

PubMed

Liu, Chun; Bridges, Melissa E; Kaundun, Shiv S; Glasgow, Les; Owen, Micheal Dk; Neve, Paul

2017-02-01

Simulation models are useful tools for predicting and comparing the risk of herbicide resistance in weed populations under different management strategies. Most existing models assume a monogenic mechanism governing herbicide resistance evolution. However, growing evidence suggests that herbicide resistance is often inherited in a polygenic or quantitative fashion. Therefore, we constructed a generalised modelling framework to simulate the evolution of quantitative herbicide resistance in summer annual weeds. Real-field management parameters based on Amaranthus tuberculatus (Moq.) Sauer (syn. rudis) control with glyphosate and mesotrione in Midwestern US maize-soybean agroecosystems demonstrated that the model can represent evolved herbicide resistance in realistic timescales. Sensitivity analyses showed that genetic and management parameters were impactful on the rate of quantitative herbicide resistance evolution, whilst biological parameters such as emergence and seed bank mortality were less important. The simulation model provides a robust and widely applicable framework for predicting the evolution of quantitative herbicide resistance in summer annual weed populations. The sensitivity analyses identified weed characteristics that would favour herbicide resistance evolution, including high annual fecundity, large resistance phenotypic variance and pre-existing herbicide resistance. Implications for herbicide resistance management and potential use of the model are discussed. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Comparison of DFT-S-orthogonal frequency division multiplexing and single-carrier in a radio-over-fiber system

NASA Astrophysics Data System (ADS)

Wang, Kaihui; Li, Xinying; Yu, Jianjun

2017-09-01

DFT-S-orthogonal frequency division multiplexing (OFDM) and single-carrier (SC) modulation are two typical modulation formats in radio-over-fiber (RoF) systems. They may have respective advantages and disadvantages in different scenarios. Therefore, bit error ratio comparison results of these two modulation formats will be useful for designing and optimizing the practical RoF system. We experimentally compare these two modulation formats in a long wireless distance RoF system at W-band. It can be concluded that DFT-S-OFDM and SC modulation have similar performances in a RoF system with transmission distance over 80-km fiber and 224-m wireless link.

Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.

PubMed

Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang

2013-01-15

Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (ωB97X, ωB97, LC-ωPBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ωB97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ωB97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ωB97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

Extreme Basicity of Biguanide Drugs in Aqueous Solutions: Ion Transfer Voltammetry and DFT Calculations.

PubMed

Langmaier, Jan; Pižl, Martin; Samec, Zdeněk; Záliš, Stanislav

2016-09-22

Ion transfer voltammetry is used to estimate the acid dissociation constants Ka1 and Ka2 of the mono- and diprotonated forms of the biguanide drugs metformin (MF), phenformin (PF), and 1-phenylbiguanide (PB) in an aqueous solution. Measurements gave the pKa1 values for MFH(+), PFH(+), and PBH(+) characterizing the basicity of MF, PF, and PB, which are significantly higher than those reported in the literature. As a result, the monoprotonated forms of these biguanides should prevail in a considerably broader range of pH 1-15 (MFH(+), PFH(+)) and 2-13 (PBH(+)). DFT calculations with solvent correction were performed for possible tautomeric forms of neutral, monoprotonated, and diprotonated species. Extreme basicity of all drugs is confirmed by DFT calculations of pKa1 for the most stable tautomers of the neutral and protonated forms with explicit water molecules in the first solvation sphere included.

A Quantitative Geochemical Target for Modeling the Formation of the Earth and Moon

NASA Technical Reports Server (NTRS)

Boyce, Jeremy W.; Barnes, Jessica J.; McCubbin, Francis M.

2017-01-01

The past decade has been one of geochemical, isotopic, and computational advances that are bringing the laboratory measurements and computational modeling neighborhoods of the Earth-Moon community to ever closer proximity. We are now however in the position to become even better neighbors: modelers can generate testable hypthotheses for geochemists; and geochemists can provide quantitive targets for modelers. Here we present a robust example of the latter based on Cl isotope measurements of mare basalts.

Computational modeling approaches to quantitative structure-binding kinetics relationships in drug discovery.

PubMed

De Benedetti, Pier G; Fanelli, Francesca

2018-03-21

Simple comparative correlation analyses and quantitative structure-kinetics relationship (QSKR) models highlight the interplay of kinetic rates and binding affinity as an essential feature in drug design and discovery. The choice of the molecular series, and their structural variations, used in QSKR modeling is fundamental to understanding the mechanistic implications of ligand and/or drug-target binding and/or unbinding processes. Here, we discuss the implications of linear correlations between kinetic rates and binding affinity constants and the relevance of the computational approaches to QSKR modeling. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Quantitative-MFG Test: A Linear Mixed Effect Model to Detect Maternal-Offspring Gene Interactions.

PubMed

Clark, Michelle M; Blangero, John; Dyer, Thomas D; Sobel, Eric M; Sinsheimer, Janet S

2016-01-01

Maternal-offspring gene interactions, aka maternal-fetal genotype (MFG) incompatibilities, are neglected in complex diseases and quantitative trait studies. They are implicated in birth to adult onset diseases but there are limited ways to investigate their influence on quantitative traits. We present the quantitative-MFG (QMFG) test, a linear mixed model where maternal and offspring genotypes are fixed effects and residual correlations between family members are random effects. The QMFG handles families of any size, common or general scenarios of MFG incompatibility, and additional covariates. We develop likelihood ratio tests (LRTs) and rapid score tests and show they provide correct inference. In addition, the LRT's alternative model provides unbiased parameter estimates. We show that testing the association of SNPs by fitting a standard model, which only considers the offspring genotypes, has very low power or can lead to incorrect conclusions. We also show that offspring genetic effects are missed if the MFG modeling assumptions are too restrictive. With genome-wide association study data from the San Antonio Family Heart Study, we demonstrate that the QMFG score test is an effective and rapid screening tool. The QMFG test therefore has important potential to identify pathways of complex diseases for which the genetic etiology remains to be discovered. © 2015 John Wiley & Sons Ltd/University College London.

Three models intercomparison for Quantitative Precipitation Forecast over Calabria

NASA Astrophysics Data System (ADS)

Federico, S.; Avolio, E.; Bellecci, C.; Colacino, M.; Lavagnini, A.; Accadia, C.; Mariani, S.; Casaioli, M.

2004-11-01

In the framework of the National Project “Sviluppo di distretti industriali per le Osservazioni della Terra” (Development of Industrial Districts for Earth Observations) funded by MIUR (Ministero dell'Università e della Ricerca Scientifica --Italian Ministry of the University and Scientific Research) two operational mesoscale models were set-up for Calabria, the southernmost tip of the Italian peninsula. Models are RAMS (Regional Atmospheric Modeling System) and MM5 (Mesoscale Modeling 5) that are run every day at Crati scrl to produce weather forecast over Calabria (http://www.crati.it). This paper reports model intercomparison for Quantitative Precipitation Forecast evaluated for a 20 month period from 1th October 2000 to 31th May 2002. In addition to RAMS and MM5 outputs, QBOLAM rainfall fields are available for the period selected and included in the comparison. This model runs operationally at “Agenzia per la Protezione dell'Ambiente e per i Servizi Tecnici”. Forecasts are verified comparing models outputs with raingauge data recorded by the regional meteorological network, which has 75 raingauges. Large-scale forcing is the same for all models considered and differences are due to physical/numerical parameterizations and horizontal resolutions. QPFs show differences between models. Largest differences are for BIA compared to the other considered scores. Performances decrease with increasing forecast time for RAMS and MM5, whilst QBOLAM scores better for second day forecast.

Comparison of semi-quantitative and quantitative dynamic contrast-enhanced MRI evaluations of vertebral marrow perfusion in a rat osteoporosis model.

PubMed

Zhu, Jingqi; Xiong, Zuogang; Zhang, Jiulong; Qiu, Yuyou; Hua, Ting; Tang, Guangyu

2017-11-14

This study aims to investigate the technical feasibility of semi-quantitative and quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in the assessment of longitudinal changes of marrow perfusion in a rat osteoporosis model, using bone mineral density (BMD) measured by micro-computed tomography (micro-CT) and histopathology as the gold standards. Fifty rats were randomly assigned to the control group (n=25) and ovariectomy (OVX) group whose bilateral ovaries were excised (n=25). Semi-quantitative and quantitative DCE-MRI, micro-CT, and histopathological examinations were performed on lumbar vertebrae at baseline and 3, 6, 9, and 12 weeks after operation. The differences between the two groups in terms of semi-quantitative DCE-MRI parameter (maximum enhancement, E max ), quantitative DCE-MRI parameters (volume transfer constant, K trans ; interstitial volume, V e ; and efflux rate constant, K ep ), micro-CT parameter (BMD), and histopathological parameter (microvessel density, MVD) were compared at each of the time points using an independent-sample t test. The differences in these parameters between baseline and other time points in each group were assessed via Bonferroni's multiple comparison test. A Pearson correlation analysis was applied to assess the relationships between DCE-MRI, micro-CT, and histopathological parameters. In the OVX group, the E max values decreased significantly compared with those of the control group at weeks 6 and 9 (p=0.003 and 0.004, respectively). The K trans values decreased significantly compared with those of the control group from week 3 (p<0.05). However, the V e values decreased significantly only at week 9 (p=0.032), and no difference in the K ep was found between two groups. The BMD values of the OVX group decreased significantly compared with those of the control group from week 3 (p<0.05). Transmission electron microscopy showed tighter gaps between vascular endothelial cells with swollen mitochondria

High-Frequency Fe-H Vibrations in a Bridging Hydride Complex Characterized by NRVS and DFT.

PubMed

Pelmenschikov, Vladimir; Gee, Leland B; Wang, Hongxin; MacLeod, K Cory; McWilliams, Sean F; Skubi, Kazimer L; Cramer, Stephen P; Holland, Patrick L

2018-05-30

High-spin iron species with bridging hydrides have been detected in species trapped during nitrogenase catalysis, but there are few general methods of evaluating Fe-H bonds in high-spin multinuclear iron systems. An 57 Fe nuclear resonance vibrational spectroscopy (NRVS) study on an Fe(μ-H) 2 Fe model complex reveals Fe-H stretching vibrations for bridging hydrides at frequencies greater than 1200 cm -1 . These isotope-sensitive vibrational bands are not evident in infrared (IR) spectra, showing the power of NRVS for identifying hydrides in this high-spin iron system. Complementary density functional theory (DFT) calculations elucidate the normal modes of the rhomboidal iron hydride core. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Wannier-function-based constrained DFT with nonorthogonality-correcting Pulay forces in application to the reorganization effects in graphene-adsorbed pentacene

NASA Astrophysics Data System (ADS)

Roychoudhury, Subhayan; O'Regan, David D.; Sanvito, Stefano

2018-05-01

Pulay terms arise in the Hellmann-Feynman forces in electronic-structure calculations when one employs a basis set made of localized orbitals that move with their host atoms. If the total energy of the system depends on a subspace population defined in terms of the localized orbitals across multiple atoms, then unconventional Pulay terms will emerge due to the variation of the orbital nonorthogonality with ionic translation. Here, we derive the required exact expressions for such terms, which cannot be eliminated by orbital orthonormalization. We have implemented these corrected ionic forces within the linear-scaling density functional theory (DFT) package onetep, and we have used constrained DFT to calculate the reorganization energy of a pentacene molecule adsorbed on a graphene flake. The calculations are performed by including ensemble DFT, corrections for periodic boundary conditions, and empirical Van der Waals interactions. For this system we find that tensorially invariant population analysis yields an adsorbate subspace population that is very close to integer-valued when based upon nonorthogonal Wannier functions, and also but less precisely so when using pseudoatomic functions. Thus, orbitals can provide a very effective population analysis for constrained DFT. Our calculations show that the reorganization energy of the adsorbed pentacene is typically lower than that of pentacene in the gas phase. We attribute this effect to steric hindrance.

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

USDA-ARS?s Scientific Manuscript database

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and human health effect...

Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

PubMed

Han, Lide; Yang, Jian; Zhu, Jun

2007-06-01

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

A chaotic modified-DFT encryption scheme for physical layer security and PAPR reduction in OFDM-PON

NASA Astrophysics Data System (ADS)

Fu, Xiaosong; Bi, Meihua; Zhou, Xuefang; Yang, Guowei; Li, Qiliang; Zhou, Zhao; Yang, Xuelin

2018-05-01

This letter proposes a modified discrete Fourier transform (DFT) encryption scheme with multi-dimensional chaos for the physical layer security and peak-to-average power ratio (PAPR) reduction in orthogonal frequency division multiplexing passive optical network (OFDM-PON) system. This multiple-fold encryption algorithm is mainly composed by using the column vectors permutation and the random phase encryption in the standard DFT matrix, which can create ∼10551 key space. The transmission of ∼10 Gb/s encrypted OFDM signal is verified over 20-km standard single mode fiber (SMF). Moreover, experimental results show that, the proposed scheme can achieve ∼2.6-dB PAPR reduction and ∼1-dB improvement of receiver sensitivity if compared with the common OFDM-PON.

Spectroscopic and DFT study of atenolol and metoprolol and their copper complexes

NASA Astrophysics Data System (ADS)

Cozar, O.; Szabó, L.; Cozar, I. B.; Leopold, N.; David, L.; Căinap, C.; Chiş, V.

2011-05-01

IR, Raman and surface-enhanced Raman scattering (SERS) spectra of atenolol (ATE) and metoprolol (MET) were recorded and assigned on the basis of density functional theory (DFT) calculations. A reliable assignment of vibrational IR and Raman bands of the two compounds was possible by a proper choice of models used in quantum chemical calculations. Both molecules are adsorbed to the silver surface mainly through the oxygen atoms and π-electrons of the phenyl ring. The coordination mode of the metal ions in Cu(II)-ATE and -MET compounds was also derived from IR and EPR spectra. EPR spectra give evidence for a square-planar arrangement around the copper (II) ion in the case of Cu-ATE complex, with a N 2O 2 chromophore. Only oxygen atoms are involved in the cooper coordination for Cu-MET complex, and two types of local symmetries with d and d as ground states for paramagnetic electron coexist.

Functionalization of ( n, 0) CNTs ( n = 3-16) by uracil: DFT studies

NASA Astrophysics Data System (ADS)

Mirzaei, Mahmoud; Harismah, Kun; Jafari, Elham; Gülseren, Oğuz; Rad, Ali Shokuhi

2018-01-01

Density functional theory (DFT) calculations were performed to investigate stabilities and properties for uracil (U)-functionalized carbon nanotubes (CNTs). To this aim, the optimized molecular properties were evaluated for ( n, 0) models of CNTs ( n = 3-16) in the original and U-functionalized forms. The results indicated that the dipole moments and energy gaps were independent of tubular diameters whereas the binding energies showed that the U-functionalization could be better achieved for n = 8-11 curvatures of ( n, 0) CNTs. Further studies based on the evaluated atomic-scale properties, including quadrupole coupling constants ( C Q ), indicated that the electronic properties of atoms could detect the effects of diameters variations of ( n, 0) CNTs, in which the effects were very much significant for the atoms around the U-functionalization regions. Finally, the achieved results of singular U, original CNTs, and CNT-U hybrids were compared to each other to demonstrate the stabilities and properties for the U-functionalized ( n, 0) CNTs.

Predicting Catalytic Activity of Nanoparticles by a DFT-Aided Machine-Learning Algorithm.

PubMed

Jinnouchi, Ryosuke; Asahi, Ryoji

2017-09-07

Catalytic activities are often dominated by a few specific surface sites, and designing active sites is the key to realize high-performance heterogeneous catalysts. The great triumphs of modern surface science lead to reproduce catalytic reaction rates by modeling the arrangement of surface atoms with well-defined single-crystal surfaces. However, this method has limitations in the case for highly inhomogeneous atomic configurations such as on alloy nanoparticles with atomic-scale defects, where the arrangement cannot be decomposed into single crystals. Here, we propose a universal machine-learning scheme using a local similarity kernel, which allows interrogation of catalytic activities based on local atomic configurations. We then apply it to direct NO decomposition on RhAu alloy nanoparticles. The proposed method can efficiently predict energetics of catalytic reactions on nanoparticles using DFT data on single crystals, and its combination with kinetic analysis can provide detailed information on structures of active sites and size- and composition-dependent catalytic activities.

DFT investigation on the electronic structure of Faujasite

NASA Astrophysics Data System (ADS)

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza

2013-11-01

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

NASA Astrophysics Data System (ADS)

Cai, Kaicong; Zheng, Xuan; Du, Fenfen

2017-08-01

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

Quantitative stress measurement of elastic deformation using mechanoluminescent sensor: An intensity ratio model

NASA Astrophysics Data System (ADS)

Cai, Tao; Guo, Songtao; Li, Yongzeng; Peng, Di; Zhao, Xiaofeng; Liu, Yingzheng

2018-04-01

The mechanoluminescent (ML) sensor is a newly developed non-invasive technique for stress/strain measurement. However, its application has been mostly restricted to qualitative measurement due to the lack of a well-defined relationship between ML intensity and stress. To achieve accurate stress measurement, an intensity ratio model was proposed in this study to establish a quantitative relationship between the stress condition and its ML intensity in elastic deformation. To verify the proposed model, experiments were carried out on a ML measurement system using resin samples mixed with the sensor material SrAl2O4:Eu2+, Dy3+. The ML intensity ratio was found to be dependent on the applied stress and strain rate, and the relationship acquired from the experimental results agreed well with the proposed model. The current study provided a physical explanation for the relationship between ML intensity and its stress condition. The proposed model was applicable in various SrAl2O4:Eu2+, Dy3+-based ML measurement in elastic deformation, and could provide a useful reference for quantitative stress measurement using the ML sensor in general.

Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl Methylphosphonate (DMMP)/TiO2 (110) Intermolecular Interaction

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

Yang, Li; Tunega, Daniel; Xu, Lai

2013-08-29

In a previous study (J. Phys. Chem. C 2011, 115, 12403) cluster models for the TiO2 rutile (110) surface and MP2 calculations were used to develop an analytic potential energy function for dimethyl methylphosphonate (DMMP) interacting with this surface. In the work presented here, this analytic potential and MP2 cluster models are compared with DFT "slab" calculations for DMMP interacting with the TiO2 (110) surface and with DFT cluster models for the TiO2 (110) surface. The DFT slab calculations were performed with the PW91 and PBE functionals. The analytic potential gives DMMP/ TiO2 (110) potential energy curves in excellent agreementmore » with those obtained from the slab calculations. The cluster models for the TiO2 (110) surface, used for the MP2 calculations, were extended to DFT calculations with the B3LYP, PW91, and PBE functional. These DFT calculations do not give DMMP/TiO2 (110) interaction energies which agree with those from the DFT slab calculations. Analyses of the wave functions for these cluster models show that they do not accurately represent the HOMO and LUMO for the surface, which should be 2p and 3d orbitals, respectively, and the models also do not give an accurate band gap. The MP2 cluster models do not accurately represent the LUMO and that they give accurate DMMP/TiO2 (110) interaction energies is apparently fortuitous, arising from their highly inaccurate band gaps. Accurate cluster models, consisting of 7, 10, and 15 Ti-atoms and which have the correct HOMO and LUMO properties, are proposed. The work presented here illustrates the care that must be taken in "constructing" cluster models which accurately model surfaces.« less

Synthesis, characterization, and DFT studies of a new chiral ionic liquid from (S)-1-phenylethylamine.

PubMed

Cui, Shuya; Wang, Tao; Hu, Xiaoli

2014-12-10

A new chiral ionic liquid was synthesized from (S)-1-phenylethylamine and it was studied by IR, Raman, polarimetry, NMR and X-ray crystal diffraction. Its vibrational spectral bands are precisely ascribed to the studied structure with the aid of DFT theoretical calculations. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from IR and Raman spectra are assigned based on the results of the theoretical calculations by the DFT-B3LYP method at 6-311G(d,p) level. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies.The vibrational modes assignments were performed by using the animation option of GaussView5.0 graphical interface for Gaussian program. Copyright © 2014 Elsevier B.V. All rights reserved.

Computing sextic centrifugal distortion constants by DFT: A benchmark analysis on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi

2017-05-01

This work presents a benchmark study on the calculation of the sextic centrifugal distortion constants employing cubic force fields computed by means of density functional theory (DFT). For a set of semi-rigid halogenated organic compounds several functionals (B2PLYP, B3LYP, B3PW91, M06, M06-2X, O3LYP, X3LYP, ωB97XD, CAM-B3LYP, LC-ωPBE, PBE0, B97-1 and B97-D) were used for computing the sextic centrifugal distortion constants. The effects related to the size of basis sets and the performances of hybrid approaches, where the harmonic data obtained at higher level of electronic correlation are coupled with cubic force constants yielded by DFT functionals, are presented and discussed. The predicted values were compared to both the available data published in the literature and those obtained by calculations carried out at increasing level of electronic correlation: Hartree-Fock Self Consistent Field (HF-SCF), second order Møller-Plesset perturbation theory (MP2), and coupled-cluster single and double (CCSD) level of theory. Different hybrid approaches, having the cubic force field computed at DFT level of theory coupled to harmonic data computed at increasing level of electronic correlation (up to CCSD level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T)) were considered. The obtained results demonstrate that they can represent reliable and computationally affordable methods to predict sextic centrifugal terms with an accuracy almost comparable to that yielded by the more expensive anharmonic force fields fully computed at MP2 and CCSD levels of theory. In view of their reduced computational cost, these hybrid approaches pave the route to the study of more complex systems.

Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si Maps: Beta-cellobiose

USDA-ARS?s Scientific Manuscript database

New cellobiose Phi-H/Si-H maps are rapidly generated using a mixed basis set DFT method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are made for different conformational states of cellobiose, showing how glycosidic bond dihe...

A hybrid, coupled approach for modeling charged fluids from the nano to the mesoscale

DOE PAGES

Cheung, James; Frischknecht, Amalie L.; Perego, Mauro; ...

2017-07-20

Here, we develop and demonstrate a new, hybrid simulation approach for charged fluids, which combines the accuracy of the nonlocal, classical density functional theory (cDFT) with the efficiency of the Poisson–Nernst–Planck (PNP) equations. The approach is motivated by the fact that the more accurate description of the physics in the cDFT model is required only near the charged surfaces, while away from these regions the PNP equations provide an acceptable representation of the ionic system. We formulate the hybrid approach in two stages. The first stage defines a coupled hybrid model in which the PNP and cDFT equations act independentlymore » on two overlapping domains, subject to suitable interface coupling conditions. At the second stage we apply the principles of the alternating Schwarz method to the hybrid model by using the interface conditions to define the appropriate boundary conditions and volume constraints exchanged between the PNP and the cDFT subdomains. Numerical examples with two representative examples of ionic systems demonstrate the numerical properties of the method and its potential to reduce the computational cost of a full cDFT calculation, while retaining the accuracy of the latter near the charged surfaces.« less

A hybrid, coupled approach for modeling charged fluids from the nano to the mesoscale

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

Cheung, James; Frischknecht, Amalie L.; Perego, Mauro

Here, we develop and demonstrate a new, hybrid simulation approach for charged fluids, which combines the accuracy of the nonlocal, classical density functional theory (cDFT) with the efficiency of the Poisson–Nernst–Planck (PNP) equations. The approach is motivated by the fact that the more accurate description of the physics in the cDFT model is required only near the charged surfaces, while away from these regions the PNP equations provide an acceptable representation of the ionic system. We formulate the hybrid approach in two stages. The first stage defines a coupled hybrid model in which the PNP and cDFT equations act independentlymore » on two overlapping domains, subject to suitable interface coupling conditions. At the second stage we apply the principles of the alternating Schwarz method to the hybrid model by using the interface conditions to define the appropriate boundary conditions and volume constraints exchanged between the PNP and the cDFT subdomains. Numerical examples with two representative examples of ionic systems demonstrate the numerical properties of the method and its potential to reduce the computational cost of a full cDFT calculation, while retaining the accuracy of the latter near the charged surfaces.« less

Phenothiazine-anthraquinone donor-acceptor molecules: synthesis, electronic properties and DFT-TDDFT computational study.

PubMed

Zhang, Wen-Wei; Mao, Wei-Li; Hu, Yun-Xia; Tian, Zi-Qi; Wang, Zhi-Lin; Meng, Qing-Jin

2009-09-17

Two donor-acceptor molecules with different pi-electron conjugative units, 1-((10-methyl-10H-phenothiazin-3-yl)ethynyl)anthracene-9,10-dione (AqMp) and 1,1'-(10-methyl-10H-phenothiazine-3,7-diyl)bis(ethyne-2,1-diyl)dianthracene-9,10-dione (Aq2Mp), have been synthesized and investigated for their photochemical and electrochemical properties. Density functional theory (DFT) calculations provide insights into their molecular geometry, electronic structures, and properties. These studies satisfactorily explain the electrochemistry of the two compounds and indicate that larger conjugative effect leads to smaller HOMO-LUMO gap (Eg) in Aq2Mp. Both compounds show ICT and pi --> pi* transitions in the UV-visible range in solution, and Aq2Mp has a bathochromic shift and shows higher oscillator strength of the absorption, which has been verified by time-dependent DFT (TDDFT) calculations. The differences between AqMp and Aq2Mp indicate that the structural and conjugative effects have great influence on the electronic properties of the molecules.

Probing the (110)-Oriented plane of rutile ZnF2: A DFT investigation

NASA Astrophysics Data System (ADS)

Tamijani, Ali Abbaspour; Ebrahimiaqda, Elham

2017-12-01

For many years, rutile-like crystals have given rise to pronounced enthusiasm amongst mineralogists. In this context, rutile-type ZnF2 has found numerous applications across a variety of disciplines, ranging from material sciences to optoelectronics. Surprisingly, very limited literature is concerned with the molecular adsorption on ZnF2 surfaces and related energetics. Additionally, surface probing with small particles is a well-entrenched technique to analyze the interfacial properties. In this regard, small organic species are valuable picks. In the present work, we have employed electronic structure calculations to simulate the adsorption of methane, chloroform, pyrrole, benzene, naphthalene, anthracene, tetracene and pentacene at the (110) plane of rutile ZnF2. Dispersion-corrected DFT method was chosen to predict the binding energies and structures of molecule-adsorbed surfaces. Interestingly, a linear proportionality relationship was found between the binding energies of aromatic adsorbates and their respective molecular lengths. By applying this relationship, we were able to predict the adsorption energy of pentacene on ZnF2 to within 2% of our DFT-based result.

DFT-based molecular modeling and vibrational study of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin).

PubMed

Mihaylov, Tzvetan; Trendafilova, Natasha; Georgieva, Ivelina

2008-05-01

Molecular modeling of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density distribution and the nucleophilic centers of the deprotonated ligand PhDC(2-) in a solvent environment were estimated on the basis of Hirshfeld atomic charges, electrostatic potential values at the nuclei, and Nalewajski-Mrozek bond orders. In accordance with the empirical formula La(PhDC)(OH)(H(2)O), a chain structure of the complex was simulated by means of two types of molecular fragment: (1) two La(III) cations bound to one PhDC(2-) ligand, and (2) two PhDC(2-) ligands bound to one La(III) cation. Different orientations of PhDC(2-), OH(-) and H(2)O ligands in the La(III) complexes were investigated using 20 possible [La(PhDC(2-))(2)(OH)(H(2)O)](2-) fragments. Energy calculations predicted that the prism-like structure based on "tail-head" cis-LML2 type binding and stabilized via HO...HOH intramolecular hydrogen bonds is the most probable structure for the La(III) complex. The calculated vibrational spectrum of the lowest energy La(III) model fragment is in very good agreement with the experimental IR spectrum of the complex, supporting the suggested ligand binding mode to La(III) in a chain structure, namely, every PhDC(2-) interacts with two La(III) cations through both carbonylic and both hydroxylic oxygens, and every La(III) cation binds four oxygen atoms of two different PhDC(2-).

Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model

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

Solovyeva, Alisa; Technical University Braunschweig, Institute for Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig; Pavanello, Michele

2012-05-21

Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn-Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a {pi}-stacked guanine-thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn-Sham DFT calculations.more » In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn-Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.« less

Applying quantitative adiposity feature analysis models to predict benefit of bevacizumab-based chemotherapy in ovarian cancer patients

NASA Astrophysics Data System (ADS)

Wang, Yunzhi; Qiu, Yuchen; Thai, Theresa; More, Kathleen; Ding, Kai; Liu, Hong; Zheng, Bin

2016-03-01

How to rationally identify epithelial ovarian cancer (EOC) patients who will benefit from bevacizumab or other antiangiogenic therapies is a critical issue in EOC treatments. The motivation of this study is to quantitatively measure adiposity features from CT images and investigate the feasibility of predicting potential benefit of EOC patients with or without receiving bevacizumab-based chemotherapy treatment using multivariate statistical models built based on quantitative adiposity image features. A dataset involving CT images from 59 advanced EOC patients were included. Among them, 32 patients received maintenance bevacizumab after primary chemotherapy and the remaining 27 patients did not. We developed a computer-aided detection (CAD) scheme to automatically segment subcutaneous fat areas (VFA) and visceral fat areas (SFA) and then extracted 7 adiposity-related quantitative features. Three multivariate data analysis models (linear regression, logistic regression and Cox proportional hazards regression) were performed respectively to investigate the potential association between the model-generated prediction results and the patients' progression-free survival (PFS) and overall survival (OS). The results show that using all 3 statistical models, a statistically significant association was detected between the model-generated results and both of the two clinical outcomes in the group of patients receiving maintenance bevacizumab (p<0.01), while there were no significant association for both PFS and OS in the group of patients without receiving maintenance bevacizumab. Therefore, this study demonstrated the feasibility of using quantitative adiposity-related CT image features based statistical prediction models to generate a new clinical marker and predict the clinical outcome of EOC patients receiving maintenance bevacizumab-based chemotherapy.

Quantitative structure-property relationship (QSPR) modeling of drug-loaded polymeric micelles via genetic function approximation.

PubMed

Wu, Wensheng; Zhang, Canyang; Lin, Wenjing; Chen, Quan; Guo, Xindong; Qian, Yu; Zhang, Lijuan

2015-01-01

Self-assembled nano-micelles of amphiphilic polymers represent a novel anticancer drug delivery system. However, their full clinical utilization remains challenging because the quantitative structure-property relationship (QSPR) between the polymer structure and the efficacy of micelles as a drug carrier is poorly understood. Here, we developed a series of QSPR models to account for the drug loading capacity of polymeric micelles using the genetic function approximation (GFA) algorithm. These models were further evaluated by internal and external validation and a Y-randomization test in terms of stability and generalization, yielding an optimization model that is applicable to an expanded materials regime. As confirmed by experimental data, the relationship between microstructure and drug loading capacity can be well-simulated, suggesting that our models are readily applicable to the quantitative evaluation of the drug-loading capacity of polymeric micelles. Our work may offer a pathway to the design of formulation experiments.

Anti-inflammatory drugs interacting with Zn (II) metal ion based on thiocyanate and azide ligands: synthesis, spectroscopic studies, DFT calculations and antibacterial assays.

PubMed

Chiniforoshan, Hossein; Tabrizi, Leila; Hadizade, Morteza; Sabzalian, Mohammad R; Chermahini, Alireza Najafi; Rezapour, Mehdi

2014-07-15

Zinc (II) complexes with non-steroidal anti-inflammatory drugs (NSAIDs) naproxen (nap) and ibuprofen (ibu) were synthesized in the presence of nitrogen donor ligands (thiocyanate or azide). The complexes were characterized by elemental analysis, FT-IR, (1)H NMR and UV-Vis spectroscopes. The binding modes of the ligands in complexes were established by means of molecular modeling of the complexes, and calculation of their IR, NMR and absorption spectra at DFT (TDDFT)/B3LYP level were studied. The experimental and calculated data verified monodentate binding through the carboxylic oxygen atoms of anti-inflammatory drugs in the zinc complexes. The calculated (1)H, FT-IR and UV-Vis data are in better agreement with the experimental results, and confirm the predicted tetrahedral structures for the Zn (II) complexes. In addition to DFT calculations of complexes, natural bond orbital (NBO) was performed at B3LYP/6-31+G(d,p) level of theory. Biological studies showed the antibacterial activity of zinc complexes against Gram-positive and Gram-negative bacterial strains. Copyright © 2014 Elsevier B.V. All rights reserved.

DFT, NBO and molecular docking studies of the adsorption of fluoxetine into and on the surface of simple and sulfur-doped carbon nanotubes

NASA Astrophysics Data System (ADS)

Shahabi, Dana; Tavakol, Hossein

2017-10-01

In this study, noncovalent interactions between Fluoxetine (FX) and different carbon nanotubes (CNTs) or sulfur doped carbon nanotubes (SCNTs) were fully considered using DFT, natural bond orbital (NBO) and molecular docking calculations. Two different CNTs (and SCNTs) with 7,7 and 8,8 chiralities were considered as the adsorbents and the adsorption of FX by these adsorbents were studied in two cases: into the nanotubes and on their surfaces. The results of DFT and NBO calculations proposed that the 8,8 nanotubes are more suitable adsorbents for FX because the energies of their adsorptions are minimum. Population: analyses were also proposed that the adsorption of FX by SCNTs lead to more changes in electronic and sensing properties than the adsorption by CNTs. Moreover, the adsorption energies, obtained from molecular docking calculations (using 94 different models), proposed that the adsorption of FX into (versus out of) the nanotubes, adsorption processes by double-walled or triple-walled (versus single-walled) nanotubes and the adsorption by nanotubes with 8,8 chiralities are the most favorable adsorption processes.

Quantitative determination of Auramine O by terahertz spectroscopy with 2DCOS-PLSR model

NASA Astrophysics Data System (ADS)

Zhang, Huo; Li, Zhi; Chen, Tao; Qin, Binyi

2017-09-01

Residues of harmful dyes such as Auramine O (AO) in herb and food products threaten the health of people. So, fast and sensitive detection techniques of the residues are needed. As a powerful tool for substance detection, terahertz (THz) spectroscopy was used for the quantitative determination of AO by combining with an improved partial least-squares regression (PLSR) model in this paper. Absorbance of herbal samples with different concentrations was obtained by THz-TDS in the band between 0.2THz and 1.6THz. We applied two-dimensional correlation spectroscopy (2DCOS) to improve the PLSR model. This method highlighted the spectral differences of different concentrations, provided a clear criterion of the input interval selection, and improved the accuracy of detection result. The experimental result indicated that the combination of the THz spectroscopy and 2DCOS-PLSR is an excellent quantitative analysis method.

Optimization of training sequence for DFT-spread DMT signal in optical access network with direct detection utilizing DML.

PubMed

Li, Fan; Li, Xinying; Yu, Jianjun; Chen, Lin

2014-09-22

We experimentally demonstrated the transmission of 79.86-Gb/s discrete-Fourier-transform spread 32 QAM discrete multi-tone (DFT-spread 32 QAM-DMT) signal over 20-km standard single-mode fiber (SSMF) utilizing directly modulated laser (DML). The experimental results show DFT-spread effectively reduces Peak-to-Average Power Ratio (PAPR) of DMT signal, and also well overcomes narrowband interference and high frequencies power attenuation. We compared different types of training sequence (TS) symbols and found that the optimized TS for channel estimation is the symbol with digital BPSK/QPSK modulation format due to its best performance against optical link noise during channel estimation.

Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches

NASA Astrophysics Data System (ADS)

Choubey, Sanjay K.; Mariadasse, Richard; Rajendran, Santhosh; Jeyaraman, Jeyakanthan

2016-12-01

Overexpression of HDAC1, a member of Class I histone deacetylase is reported to be implicated in breast cancer. Epigenetic alteration in carcinogenesis has been the thrust of research for few decades. Increased deacetylation leads to accelerated cell proliferation, cell migration, angiogenesis and invasion. HDAC1 is pronounced as the potential drug target towards the treatment of breast cancer. In this study, the biochemical potential of 6-aminonicotinamide derivatives was rationalized. Five point pharmacophore model with one hydrogen-bond acceptor (A3), two hydrogen-bond donors (D5, D6), one ring (R12) and one hydrophobic group (H8) was developed using 6-aminonicotinamide derivatives. The pharmacophore hypothesis yielded a 3D-QSAR model with correlation-coefficient (r2 = 0.977, q2 = 0.801) and it was externally validated with (r2pred = 0.929, r2cv = 0.850 and r2m = 0.856) which reveals the statistical significance of the model having high predictive power. The model was then employed as 3D search query for virtual screening against compound libraries (Zinc, Maybridge, Enamine, Asinex, Toslab, LifeChem and Specs) in order to identify novel scaffolds which can be experimentally validated to design future drug molecule. Density Functional Theory (DFT) at B3LYP/6-31G* level was employed to explore the electronic features of the ligands involved in charge transfer reaction during receptor ligand interaction. Binding free energy (ΔGbind) calculation was done using MM/GBSA which defines the affinity of ligands towards the receptor.

Molecular structure, nonlinear optical studies and spectroscopic analysis of chalcone derivative (2E)-3-[4-(methylsulfanyl) phenyl]-1-(3-bromophenyl) prop-2-en-1-one by DFT calculations

NASA Astrophysics Data System (ADS)

Kumar, Amit; Kumar, Rajesh; Gupta, Archana; Tandon, Poonam; D'silva, E. Deepak

2017-12-01

A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of nonlinear optical chalcone derivative (2E)-3-[4-(methylsulfanyl) phenyl]-1-(3-bromophenyl) prop-2-en-1-one (3Br4MSP). The FT-IR and FT-Raman spectra of the molecule in the solid phase have been recorded. Density functional theory (DFT) calculations at B3LYP level with 6-311++G (d,p) basis set have been carried out to derive useful information about the molecular structure and to assign the relevant electronic and vibrational features. These calculations reveal that the optimized geometry closely resembles the experimental XRD data. The vibrational spectra were analyzed on the basis of the potential energy distribution (PED) of each vibrational mode, which allowed us to obtain a quantitative as well as qualitative interpretation of FT-IR and FT-Raman spectra. The UV-vis spectrum was recorded in methanol solution. The excited state properties have been determined by TD-DFT method and the effect of solvent was analyzed by PCM model. The most prominent transition corresponds to π→π∗. The reactivity parameters as chemical potential, global hardness, and electrophilicity index have also been calculated. To provide an explicit assignment and analysis of 13C and 1H NMR spectra, theoretical calculations on chemical shift of the title compound were done through GIAO method at B3LYP/6-311++G (d,p) level. The Mulliken's population analysis shows one of the simplest pictures of charge distribution. The standard statistical thermodynamic functions like heat capacity at constant pressure (Cop,m), entropy (Som) and enthalpy (Hom) were obtained from the theoretical harmonic frequencies for the optimized molecule. The nonlinear optical properties of title molecule are also addressed theoretically. Two contributions, vibrational and electronic, to the electrical properties polarizability and first order hyperpolarizability of 3Br4MSP have been evaluated using the

DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

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

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

DOE PAGES

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin; ...

2017-01-26

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

DOSIMETRY MODELING OF INHALED FORMALDEHYDE: BINNING NASAL FLUX PREDICTIONS FOR QUANTITATIVE RISK ASSESSMENT

EPA Science Inventory

Dosimetry Modeling of Inhaled Formaldehyde: Binning Nasal Flux Predictions for Quantitative Risk Assessment. Kimbell, J.S., Overton, J.H., Subramaniam, R.P., Schlosser, P.M., Morgan, K.T., Conolly, R.B., and Miller, F.J. (2001). Toxicol. Sci. 000, 000:000.

Interspecies e...

Synthesis, fungicidal activity, structure-activity relationships (SARs) and density functional theory (DFT) studies of novel strobilurin analogues containing arylpyrazole rings.

PubMed

Liu, Yuanyuan; Lv, Kunzhi; Li, Yi; Nan, Qiuli; Xu, Jinyuan

2018-05-18

A series of novel strobilurin analogues (1a-1f, 2a-2e, 3a-3e) containing arylpyrazole rings were synthesized and characterized by NMR spectroscopy. The structures of 1f, 2b and 3b were also determined by single crystal X-ray diffraction analysis. These analogues were collected together with other twenty-eight similar compounds 4a-4f, 5a-5h, 6a-6h and 7a-7f from our previous studies, for in vitro bioassays and thorough structure-activity relationships (SARs) studies. Most compounds exhibited excellent-to-good fungicidal activity against Rhizoctonia solani, especially 5c, 7a, 6c, and 3b with 98.94%, 83.40%, 71.40% and 65.87% inhibition rates at 0.1 μg mL -1 , respectively, better than commercial pyraclostrobin. Comparative molecular field analysis (CoMFA) was employed to study three-dimensional quantitative structure-activity relationships (3D-QSARs). Density functional theory (DFT) calculation was also carried out to provide more information regarding SARs. The present work provided some hints for developing novel strobilurin fungicides.

Gene Level Meta-Analysis of Quantitative Traits by Functional Linear Models.

PubMed

Fan, Ruzong; Wang, Yifan; Boehnke, Michael; Chen, Wei; Li, Yun; Ren, Haobo; Lobach, Iryna; Xiong, Momiao

2015-08-01

Meta-analysis of genetic data must account for differences among studies including study designs, markers genotyped, and covariates. The effects of genetic variants may differ from population to population, i.e., heterogeneity. Thus, meta-analysis of combining data of multiple studies is difficult. Novel statistical methods for meta-analysis are needed. In this article, functional linear models are developed for meta-analyses that connect genetic data to quantitative traits, adjusting for covariates. The models can be used to analyze rare variants, common variants, or a combination of the two. Both likelihood-ratio test (LRT) and F-distributed statistics are introduced to test association between quantitative traits and multiple variants in one genetic region. Extensive simulations are performed to evaluate empirical type I error rates and power performance of the proposed tests. The proposed LRT and F-distributed statistics control the type I error very well and have higher power than the existing methods of the meta-analysis sequence kernel association test (MetaSKAT). We analyze four blood lipid levels in data from a meta-analysis of eight European studies. The proposed methods detect more significant associations than MetaSKAT and the P-values of the proposed LRT and F-distributed statistics are usually much smaller than those of MetaSKAT. The functional linear models and related test statistics can be useful in whole-genome and whole-exome association studies. Copyright © 2015 by the Genetics Society of America.

Quantitative Finance

NASA Astrophysics Data System (ADS)

James, Jessica

2017-01-01

Quantitative finance is a field that has risen to prominence over the last few decades. It encompasses the complex models and calculations that value financial contracts, particularly those which reference events in the future, and apply probabilities to these events. While adding greatly to the flexibility of the market available to corporations and investors, it has also been blamed for worsening the impact of financial crises. But what exactly does quantitative finance encompass, and where did these ideas and models originate? We show that the mathematics behind finance and behind games of chance have tracked each other closely over the centuries and that many well-known physicists and mathematicians have contributed to the field.

Equations of State for Mixtures: Results from DFT Simulations of Xenon/Ethane Mixtures Compared to High Accuracy Validation Experiments on Z

NASA Astrophysics Data System (ADS)

Magyar, Rudolph

2013-06-01

We report a computational and validation study of equation of state (EOS) properties of liquid / dense plasma mixtures of xenon and ethane to explore and to illustrate the physics of the molecular scale mixing of light elements with heavy elements. Accurate EOS models are crucial to achieve high-fidelity hydrodynamics simulations of many high-energy-density phenomena such as inertial confinement fusion and strong shock waves. While the EOS is often tabulated for separate species, the equation of state for arbitrary mixtures is generally not available, requiring properties of the mixture to be approximated by combining physical properties of the pure systems. The main goal of this study is to access how accurate this approximation is under shock conditions. Density functional theory molecular dynamics (DFT-MD) at elevated-temperature and pressure is used to assess the thermodynamics of the xenon-ethane mixture. The simulations are unbiased as to elemental species and therefore provide comparable accuracy when describing total energies, pressures, and other physical properties of mixtures as they do for pure systems. In addition, we have performed shock compression experiments using the Sandia Z-accelerator on pure xenon, ethane, and various mixture ratios thereof. The Hugoniot results are compared to the DFT-MD results and the predictions of different rules for combing EOS tables. The DFT-based simulation results compare well with the experimental points, and it is found that a mixing rule based on pressure equilibration performs reliably well for the mixtures considered. 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.

DFT investigation on the electronic structure of Faujasite

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

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian

2013-11-13

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed formore » describing atomic charge distribution in the chosen systems.« less

Using Integrated Environmental Modeling to Automate a Process-Based Quantitative Microbial Risk Assessment (presentation)

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and...

Electron affinity of perhalogenated benzenes: A theoretical DFT study

NASA Astrophysics Data System (ADS)

Volatron, François; Roche, Cécile

2007-10-01

The potential energy surfaces (PES) of unsubstituted and perhalogenated benzene anions ( CX6-, X = F, Cl, Br, and I) were explored by means of DFT-B3LYP calculations. In the F and Cl cases seven extrema were located and characterized. In the Br and I cases only one minimum and two extrema were found. In each case the minimum was recomputed at the CCSD(T) level. The electron affinities of C 6X 6 were calculated (ZPE included). The results obtained agree well with the experimental determinations when available. The values obtained in the X = Br and the X = I cases are expected to be valuable predictions.

A new quantitative model of ecological compensation based on ecosystem capital in Zhejiang Province, China*

PubMed Central

Jin, Yan; Huang, Jing-feng; Peng, Dai-liang

2009-01-01

Ecological compensation is becoming one of key and multidiscipline issues in the field of resources and environmental management. Considering the change relation between gross domestic product (GDP) and ecological capital (EC) based on remote sensing estimation, we construct a new quantitative estimate model for ecological compensation, using county as study unit, and determine standard value so as to evaluate ecological compensation from 2001 to 2004 in Zhejiang Province, China. Spatial differences of the ecological compensation were significant among all the counties or districts. This model fills up the gap in the field of quantitative evaluation of regional ecological compensation and provides a feasible way to reconcile the conflicts among benefits in the economic, social, and ecological sectors. PMID:19353749

A new quantitative model of ecological compensation based on ecosystem capital in Zhejiang Province, China.

PubMed

Jin, Yan; Huang, Jing-feng; Peng, Dai-liang

2009-04-01

Ecological compensation is becoming one of key and multidiscipline issues in the field of resources and environmental management. Considering the change relation between gross domestic product (GDP) and ecological capital (EC) based on remote sensing estimation, we construct a new quantitative estimate model for ecological compensation, using county as study unit, and determine standard value so as to evaluate ecological compensation from 2001 to 2004 in Zhejiang Province, China. Spatial differences of the ecological compensation were significant among all the counties or districts. This model fills up the gap in the field of quantitative evaluation of regional ecological compensation and provides a feasible way to reconcile the conflicts among benefits in the economic, social, and ecological sectors.

Quantitative Structure-Property Relationship (QSPR) Modeling of Drug-Loaded Polymeric Micelles via Genetic Function Approximation

PubMed Central

Lin, Wenjing; Chen, Quan; Guo, Xindong; Qian, Yu; Zhang, Lijuan

2015-01-01

Self-assembled nano-micelles of amphiphilic polymers represent a novel anticancer drug delivery system. However, their full clinical utilization remains challenging because the quantitative structure-property relationship (QSPR) between the polymer structure and the efficacy of micelles as a drug carrier is poorly understood. Here, we developed a series of QSPR models to account for the drug loading capacity of polymeric micelles using the genetic function approximation (GFA) algorithm. These models were further evaluated by internal and external validation and a Y-randomization test in terms of stability and generalization, yielding an optimization model that is applicable to an expanded materials regime. As confirmed by experimental data, the relationship between microstructure and drug loading capacity can be well-simulated, suggesting that our models are readily applicable to the quantitative evaluation of the drug-loading capacity of polymeric micelles. Our work may offer a pathway to the design of formulation experiments. PMID:25780923

Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

NASA Technical Reports Server (NTRS)

Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

2006-01-01

A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

Quantitative model for the blood pressure-lowering interaction of valsartan and amlodipine.

PubMed

Heo, Young-A; Holford, Nick; Kim, Yukyung; Son, Mijeong; Park, Kyungsoo

2016-12-01

The objective of this study was to develop a population pharmacokinetic (PK) and pharmacodynamic (PD) model to quantitatively describe the antihypertensive effect of combined therapy with amlodipine and valsartan. PK modelling was used with data collected from 48 healthy volunteers receiving a single dose of combined formulation of 10 mg amlodipine and 160 mg valsartan. Systolic (SBP) and diastolic blood pressure (DBP) were recorded during combined administration. SBP and DBP data for each drug alone were gathered from the literature. PKPD models of each drug and for combined administration were built with NONMEM 7.3. A two-compartment model with zero order absorption best described the PK data of both drugs. Amlodipine and valsartan monotherapy effects on SBP and DBP were best described by an I max model with an effect compartment delay. Combined therapy was described using a proportional interaction term as follows: (D 1  + D 2 ) +ALPHA×(D 1 × D 2 ). D 1 and D 2 are the predicted drug effects of amlodipine and valsartan monotherapy respectively. ALPHA is the interaction term for combined therapy. Quantitative estimates of ALPHA were -0.171 (95% CI: -0.218, -0.143) for SBP and -0.0312 (95% CI: -0.07739, -0.00283) for DBP. These infra-additive interaction terms for both SBP and DBP were consistent with literature results for combined administration of drugs in these classes. PKPD models for SBP and DBP successfully described the time course of the antihypertensive effects of amlodipine and valsartan. An infra-additive interaction between amlodipine and valsartan when used in combined administration was confirmed and quantified. © 2016 The British Pharmacological Society.

Quantitative model for the blood pressure‐lowering interaction of valsartan and amlodipine

PubMed Central

Heo, Young‐A; Holford, Nick; Kim, Yukyung; Son, Mijeong

2016-01-01

Aims The objective of this study was to develop a population pharmacokinetic (PK) and pharmacodynamic (PD) model to quantitatively describe the antihypertensive effect of combined therapy with amlodipine and valsartan. Methods PK modelling was used with data collected from 48 healthy volunteers receiving a single dose of combined formulation of 10 mg amlodipine and 160 mg valsartan. Systolic (SBP) and diastolic blood pressure (DBP) were recorded during combined administration. SBP and DBP data for each drug alone were gathered from the literature. PKPD models of each drug and for combined administration were built with NONMEM 7.3. Results A two‐compartment model with zero order absorption best described the PK data of both drugs. Amlodipine and valsartan monotherapy effects on SBP and DBP were best described by an I max model with an effect compartment delay. Combined therapy was described using a proportional interaction term as follows: (D1 + D2) +ALPHA×(D1 × D2). D1 and D2 are the predicted drug effects of amlodipine and valsartan monotherapy respectively. ALPHA is the interaction term for combined therapy. Quantitative estimates of ALPHA were −0.171 (95% CI: −0.218, −0.143) for SBP and −0.0312 (95% CI: −0.07739, −0.00283) for DBP. These infra‐additive interaction terms for both SBP and DBP were consistent with literature results for combined administration of drugs in these classes. Conclusion PKPD models for SBP and DBP successfully described the time course of the antihypertensive effects of amlodipine and valsartan. An infra‐additive interaction between amlodipine and valsartan when used in combined administration was confirmed and quantified. PMID:27504853

Tannin structural elucidation and quantitative ³¹P NMR analysis. 1. Model compounds.

PubMed

Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

2013-10-02

Tannins and flavonoids are secondary metabolites of plants that display a wide array of biological activities. This peculiarity is related to the inhibition of extracellular enzymes that occurs through the complexation of peptides by tannins. Not only the nature of these interactions, but more fundamentally also the structure of these heterogeneous polyphenolic molecules are not completely clear. This first paper describes the development of a new analytical method for the structural characterization of tannins on the basis of tannin model compounds employing an in situ labeling of all labile H groups (aliphatic OH, phenolic OH, and carboxylic acids) with a phosphorus reagent. The ³¹P NMR analysis of ³¹P-labeled samples allowed the unprecedented quantitative and qualitative structural characterization of hydrolyzable tannins, proanthocyanidins, and catechin tannin model compounds, forming the foundations for the quantitative structural elucidation of a variety of actual tannin samples described in part 2 of this series.

The Structure of Psychopathology: Toward an Expanded Quantitative Empirical Model

PubMed Central

Wright, Aidan G.C.; Krueger, Robert F.; Hobbs, Megan J.; Markon, Kristian E.; Eaton, Nicholas R.; Slade, Tim

2013-01-01

There has been substantial recent interest in the development of a quantitative, empirically based model of psychopathology. However, the majority of pertinent research has focused on analyses of diagnoses, as described in current official nosologies. This is a significant limitation because existing diagnostic categories are often heterogeneous. In the current research, we aimed to redress this limitation of the existing literature, and to directly compare the fit of categorical, continuous, and hybrid (i.e., combined categorical and continuous) models of syndromes derived from indicators more fine-grained than diagnoses. We analyzed data from a large representative epidemiologic sample (the 2007 Australian National Survey of Mental Health and Wellbeing; N = 8,841). Continuous models provided the best fit for each syndrome we observed (Distress, Obsessive Compulsivity, Fear, Alcohol Problems, Drug Problems, and Psychotic Experiences). In addition, the best fitting higher-order model of these syndromes grouped them into three broad spectra: Internalizing, Externalizing, and Psychotic Experiences. We discuss these results in terms of future efforts to refine emerging empirically based, dimensional-spectrum model of psychopathology, and to use the model to frame psychopathology research more broadly. PMID:23067258

Electromagnetic braking: A simple quantitative model

NASA Astrophysics Data System (ADS)

Levin, Yan; da Silveira, Fernando L.; Rizzato, Felipe B.

2006-09-01

A calculation is presented that quantitatively accounts for the terminal velocity of a cylindrical magnet falling through a long copper or aluminum pipe. The experiment and the theory are a dramatic illustration of Faraday's and Lenz's laws.

Quantitation of active pharmaceutical ingredients and excipients in powder blends using designed multivariate calibration models by near-infrared spectroscopy.

PubMed

Li, Weiyong; Worosila, Gregory D

2005-05-13

This research note demonstrates the simultaneous quantitation of a pharmaceutical active ingredient and three excipients in a simulated powder blend containing acetaminophen, Prosolv and Crospovidone. An experimental design approach was used in generating a 5-level (%, w/w) calibration sample set that included 125 samples. The samples were prepared by weighing suitable amount of powders into separate 20-mL scintillation vials and were mixed manually. Partial least squares (PLS) regression was used in calibration model development. The models generated accurate results for quantitation of Crospovidone (at 5%, w/w) and magnesium stearate (at 0.5%, w/w). Further testing of the models demonstrated that the 2-level models were as effective as the 5-level ones, which reduced the calibration sample number to 50. The models had a small bias for quantitation of acetaminophen (at 30%, w/w) and Prosolv (at 64.5%, w/w) in the blend. The implication of the bias is discussed.

27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

USDA-ARS?s Scientific Manuscript database

DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

A classical density functional theory for the asymmetric restricted primitive model of ionic liquids

NASA Astrophysics Data System (ADS)

Lu, Hongduo; Nordholm, Sture; Woodward, Clifford E.; Forsman, Jan

2018-05-01

A new three-parameter (valency, ion size, and charge asymmetry) model, the asymmetric restricted primitive model (ARPM) of ionic liquids, has recently been proposed. Given that ionic liquids generally are composed of monovalent species, the ARPM effectively reduces to a two-parameter model. Monte Carlo (MC) simulations have demonstrated that the ARPM is able to reproduce key properties of room temperature ionic liquids (RTILs) in bulk and at charged surfaces. The relatively modest complexity of the model raises the possibility, which is explored here, that a classical density functional theory (DFT) could resolve its properties. This is relevant because it might generate great improvements in terms of both numerical efficiency and understanding in the continued research of RTILs and their applications. In this report, a DFT for rod-like molecules is proposed as an approximate theoretical tool for an ARPM fluid. Borrowing data on the ion pair fraction from a single bulk simulation, the ARPM is modelled as a mixture of dissociated ions and connected ion pairs. We have specifically studied an ARPM where the hard-sphere diameter is 5 Å, with the charge located 1 Å from the hard-sphere centre. We focus on fluid structure and electrochemical behaviour of this ARPM fluid, into which a model electrode is immersed. The latter is modelled as a perfect conductor, and surface polarization is handled by the method of image charges. Approximate methods, which were developed in an earlier study, to take image interactions into account, are also incorporated in the DFT. We make direct numerical comparisons between DFT predictions and corresponding simulation data. The DFT theory is implemented both in the normal mean field form with respect to the electrostatic interactions and in a correlated form based on hole formation by both steric repulsions and ion-ion Coulomb interactions. The results clearly show that ion-ion correlations play a very important role in the screening of

Quantitative first-principles theory of interface absorption in multilayer heterostructures

DOE PAGES

Hachtel, Jordan A.; Sachan, Ritesh; Mishra, Rohan; ...

2015-09-03

The unique chemical bonds and electronic states of interfaces result in optical properties that are different from those of the constituting bulk materials. In the nanoscale regime, the interface effects can be dominant and impact the optical response of devices. Using density functional theory (DFT), the interface effects can be calculated, but DFT is computationally limited to small systems. In this paper, we describe a method to combine DFT with macroscopic methodologies to extract the interface effect on absorption in a consistent and quantifiable manner. The extracted interface effects are an independent parameter and can be applied to more complicatedmore » systems. Finally, we demonstrate, using NiSi 2/Si heterostructures, that by varying the relative volume fractions of interface and bulk, we can tune the spectral range of the heterostructure absorption.« less

Raman spectra and DFT calculations for botryococcene and methylsqualene hydrocarbons from the B race of the green microalga Botryococcus braunii

NASA Astrophysics Data System (ADS)

Tatli, Mehmet; Chun, Hye Jin; Camp, Charles H.; Li, Jingting; Cicerone, Marcus T.; Shih, Wei-Chuan; Laane, Jaan; Devarenne, Timothy P.

2017-11-01

Botryococcus braunii, a green colonial microalga, is a prodigious producer of liquid hydrocarbon oils that can be used as renewable feedstocks for producing combustion engine fuels. The B race of B. braunii mainly produces the triterpene hydrocarbons known as botryococcenes, which have over twenty known structures. Minor hydrocarbons in the B race include the triterpene methylsqualenes. Here we report an examination of the molecular structure for ten botryococcenes and five methylsqualenes using Raman spectroscopy and density functional theory (DFT) calculations in an effort to distinguish between these structurally similar molecules by spectroscopic approaches. The DFT calculations show that these molecules have between 243 and 271 vibrational frequencies. A comparison of the experimental Raman spectroscopy and DFT calculations indicates several spectral regions such as those for ν(Cdbnd C) stretching, CH2/CH3 bending, and ring bending can be used to distinguish between these molecules. In an extension of this analysis, a broadband coherent anti-Stokes Raman spectroscopy (BCARS) analysis was used to clearly distinguish between several botryococcenes isomers.

Quantitative Model of Systemic Toxicity Using ToxCast and ToxRefDB (SOT)

EPA Science Inventory

EPA’s ToxCast program profiles the bioactivity of chemicals in a diverse set of ~700 high throughput screening (HTS) assays. In collaboration with L’Oreal, a quantitative model of systemic toxicity was developed using no effect levels (NEL) from ToxRefDB for 633 chemicals with HT...

DFT simulation on H2 adsorption over Ni-decorated defective h-BN nanosheets

NASA Astrophysics Data System (ADS)

Zhou, Xuan; Chu, Wei; Zhou, Yanan; Sun, Wenjing; Xue, Ying

2018-05-01

Nickel doped defective h-BN nanosheets and their potential application on hydrogen storage were explored by density functional theory (DFT) calculation. Three types of defective h-BN (SW defect, VB and VN substrates) were modeled. In comparison with the SW defect, the B or N vacancy can improve the interaction between Ni atom and h-BN nanosheet strikingly. Furthermore, the Ni-doped SW defect sheet shows chemisorption on H2 molecules, and the Hsbnd H bond is partially dissociated. While on the VB sheet, Ni adatom interacts with H2 in the range of physisorption. However, the Ni-functionalized VN sheet exhibits a desirable adsorption on H2, and the corresponding energy varies from -0.40 to -0.51 eV, which is favorable for H2 adsorption and release at ambient conditions. As a result, the VN substrate is expected to a desirable support for H2 storage. Our work provides an insight into H2 storage on Ni-functionalized defective h-BN monolayer.

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations.

PubMed

Cai, Kaicong; Zheng, Xuan; Du, Fenfen

2017-08-05

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models.

PubMed

Liu, Junting; Wang, Yabin; Qu, Xiaochao; Li, Xiangsi; Ma, Xiaopeng; Han, Runqiang; Hu, Zhenhua; Chen, Xueli; Sun, Dongdong; Zhang, Rongqing; Chen, Duofang; Chen, Dan; Chen, Xiaoyuan; Liang, Jimin; Cao, Feng; Tian, Jie

2010-06-07

Bioluminescence tomography (BLT) is a new optical molecular imaging modality, which can monitor both physiological and pathological processes by using bioluminescent light-emitting probes in small living animal. Especially, this technology possesses great potential in drug development, early detection, and therapy monitoring in preclinical settings. In the present study, we developed a dual modality BLT prototype system with Micro-computed tomography (MicroCT) registration approach, and improved the quantitative reconstruction algorithm based on adaptive hp finite element method (hp-FEM). Detailed comparisons of source reconstruction between the heterogeneous and homogeneous mouse models were performed. The models include mice with implanted luminescence source and tumor-bearing mice with firefly luciferase report gene. Our data suggest that the reconstruction based on heterogeneous mouse model is more accurate in localization and quantification than the homogeneous mouse model with appropriate optical parameters and that BLT allows super-early tumor detection in vivo based on tomographic reconstruction of heterogeneous mouse model signal.

Flow assignment model for quantitative analysis of diverting bulk freight from road to railway

PubMed Central

Liu, Chang; Wang, Jiaxi; Xiao, Jie; Liu, Siqi; Wu, Jianping; Li, Jian

2017-01-01

Since railway transport possesses the advantage of high volume and low carbon emissions, diverting some freight from road to railway will help reduce the negative environmental impacts associated with transport. This paper develops a flow assignment model for quantitative analysis of diverting truck freight to railway. First, a general network which considers road transportation, railway transportation, handling and transferring is established according to all the steps in the whole transportation process. Then general functions which embody the factors which the shippers will pay attention to when choosing mode and path are formulated. The general functions contain the congestion cost on road, the capacity constraints of railways and freight stations. Based on the general network and general cost function, a user equilibrium flow assignment model is developed to simulate the flow distribution on the general network under the condition that all shippers choose transportation mode and path independently. Since the model is nonlinear and challenging, we adopt a method that uses tangent lines to constitute envelope curve to linearize it. Finally, a numerical example is presented to test the model and show the method of making quantitative analysis of bulk freight modal shift between road and railway. PMID:28771536

Synthesis, structural, DFT studies, docking and antibacterial activity of a xanthene based hydrazone ligand

NASA Astrophysics Data System (ADS)

Naseem, Saira; Khalid, Muhammad; Tahir, Muhammad Nawaz; Halim, Mohammad A.; Braga, Ataualpa A. C.; Naseer, Muhammad Moazzam; Shafiq, Zahid

2017-09-01

Herein, we present the synthesis of novel xanthene-based hydrazone (1). The chemical structure of 1 was resolved using spectroscopic techniques such as NMR, FT-IR, UV-VIS and X-ray crystallographic approaches. X-ray diffraction analysis shows that the compound (1) crystallizes in triclinic crystal lattice with the Pbar1 space group and diffused to form multi-layered structure due to non-covalent interactions such as intramolecular hydrogen bonding (H.B). In addition to experimental investigation, density functional theory (DFT) calculation with M06-2X/6-31G(d,p) and B3LYP/6-31G(d,p) level of theories was performed on compound (1) to obtain optimized geometry, spectroscopic and electronic properties. DFT optimized geometry shows good agreement with the experimental XRD structure. The hyper conjugative interactions and hydrogen bonding network are responsible for the stability of compound (1) as revealed by natural bond orbital (NBO) calculation. Moreover, hydrogen bonding network in the dimer is confirmed by FT-IR and thermodynamic studies showing excellent agreement with XRD and NBO findings. TD-DFT/UV-VIS analysis provides insight that maximum excitation is found in 1 which shows good agreement with experimental UV-VIS result. The global reactivity parameters are calculated using the energies of frontier molecular orbitals also disclosed that the compound is more stable might be due to hydrogen bonding network. Experimental and molecular docking studies indicated that this compound has anti-bacterial and anti-diabetic properties. The binding affinity of this compound against the multidrug efflux pump subunit AcrB OS=Escherichia coli (strain K12) and Human Pancreatic Alpha-Amylase is -9.2 and -10.00 kcal/mol which are higher than the control drugs. Pi-Pi, Pi-anaion, amide-pi and pi-alkyl bonds play key role in drug-protein complexes.

Adsorption of alanine with heteroatom substituted fullerene for solar cell application: A DFT study.

PubMed

Dheivamalar, S; Sugi, L; Ravichandran, K; Sriram, S

2018-09-05

C 20 is the most important fullerene cage and alanine is the simplest representation of a backbone unit of the protein. The absorption feasibility of alanine molecule in the Si-doped C 20 and B-doped C 20 fullerenes has been studied based on calculated electronic properties of fullerenes using density functional theory (DFT). In this work, we explore the ability of Si-doped C 20 , B-doped C 20 fullerene to interact with alanine at the DFT-B3LYP/6-31G, RHF level of theory. We find that noticeable structural change takes place in C 20 when one of its carbon is substituted with Si or B. The molecular geometry, electronic properties and vibrational analysis have also been performed on the title compounds. The NMR study reveals the aromaticity of the pure and doped fullerene compounds. Stability of the doped fullerene - alanine compound arises from hyper conjugative interactions. It leads to one of the major property of bioactivity, charge transfer and delocalization of charge and this properties has been analyzed using Natural Bond Orbital (NBO) analysis. The energy gap of the doped fullerene reveals that there is a decrease in the size of energy gap significantly, making them more reactive as compared to C 20 fullerene. Theoretical studies of the electronic spectra by using time - dependent density functional theory (TD-DFT) method were helpful to interpret the observed electronic transition state. We aim to optimize the performance of the solar cells by altering the frontier orbital energy gaps. Considering all studied properties, it may be inferred that the applicability of C 20 fullerene as the non-linear optical (NLO) material and its NLO property would increase on doping fullerene with Si and B atom. Specifically C 19 Si would be better among them. Copyright © 2018. Published by Elsevier B.V.

Experimental investigation and DFT calculation of different amine/ammonium salts adsorption on kaolinite

NASA Astrophysics Data System (ADS)

Chen, Jun; Min, Fan-fei; Liu, Lingyun; Liu, Chunfu; Lu, Fangqin

2017-10-01

The adsorption of four different amine/ammonium salts of DDA (Dodecyl amine), MDA (N-methyldodecyl amine), DMDA (N,N-dimethyldodecyl amine) and DTAC (Dodecyl trimethyl ammonium chloride) on kaolinite particles was investigated in the study through the measurement of contact angles, zeta potentials, aggregation observation, adsorption and sedimentation. The results show that different amine/ammonium salts can adsorb on the kaolinite surface to enhance the hydrophobicity and reduce the electronegativity of kaolinite particle surface, and thus induce a strong hydrophobic aggregation of kaolinite particles which promotes the settlement of kaolinite. To explore the adsorption mechanism of these four amine/ammonium salts on kaolinite surfaces, the adsorptions of DDA+, MDA+, DMDA+ and DTAC+ on kaolinite (001) surface and (00 1 bar) surface are calculated with DFT (Density functional theory). The DFT calculation results indicate that different amine/ammonium cations can strongly adsorbed on kaolinite (001) surface and (00 1 bar) surface by forming Nsbnd H⋯O strong hydrogen bonds or Csbnd H⋯O weak hydrogen bonds, and there are strongly electrostatic attractions between different amine/ammonium cations and kaolinite surfaces. The main adsorption mechanism of amine/ammonium cations on kaolinite is hydrogen-bond interaction and electrostatic attraction.

Synthesis, FTIR, FT-Raman, UV-visible, ab initio and DFT studies on benzohydrazide.

PubMed

Arjunan, V; Rani, T; Mythili, C V; Mohan, S

2011-08-01

A systematic vibrational spectroscopic assignment and analysis of benzohydrazide (BH) has been carried out by using FTIR and FT-Raman spectral data. The vibrational analysis were aided by electronic structure calculations--ab initio (RHF) and hybrid density functional methods (B3LYP and B3PW91) performed with 6-31G(d,p) and 6-311++G(d,p) basis sets. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed and complete assignment of the observed spectra have been proposed. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λ(max) were determined by time-dependent DFT (TD-DFT) method. The geometrical, thermodynamical parameters and absorption wavelengths were compared with the experimental data. The interactions of carbonyl and hydrazide groups on the benzene ring skeletal modes were investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride.

PubMed

Grosjean, Benoit; Pean, Clarisse; Siria, Alessandro; Bocquet, Lydéric; Vuilleumier, Rodolphe; Bocquet, Marie-Laure

2016-11-17

Recent nanofluidic experiments revealed strongly different surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013, 494, 455-458; Phys. Rev. Lett. 2016, 116, 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials-chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pK a ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario.

Chemisorption of Hydroxide on 2D Materials From DFT Calculations: Graphene Versus Hexagonal Boron Nitride

PubMed Central

Grosjean, Benoit; Pean, Clarisse; Siria, Alessandro; Bocquet, Lyderic; Vuilleumier, Rodolphe; Bocquet, Marie-Laure

2017-01-01

Recent nanofluidic measurements revealed strongly different surface charge measurements for boron-nitride and graphitic nanotubes when in contact with saline and alkaline water. 1,2 These observations contrast with the similar reactivity of a graphene layer and its boron nitride counterpart, using Density Functional Theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here, we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials – chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values resulting in a favorable (non-favorable) adsorption on BN (graphene). We also calculate a pKa ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echoes the weaker surface charge measurements, but points to an alternative scenario. PMID:27809540

Quantitative Hydraulic Models Of Early Land Plants Provide Insight Into Middle Paleozoic Terrestrial Paleoenvironmental Conditions

NASA Astrophysics Data System (ADS)

Wilson, J. P.; Fischer, W. W.

2010-12-01

Fossil plants provide useful proxies of Earth’s climate because plants are closely connected, through physiology and morphology, to the environments in which they lived. Recent advances in quantitative hydraulic models of plant water transport provide new insight into the history of climate by allowing fossils to speak directly to environmental conditions based on preserved internal anatomy. We report results of a quantitative hydraulic model applied to one of the earliest terrestrial plants preserved in three dimensions, the ~396 million-year-old vascular plant Asteroxylon mackei. This model combines equations describing the rate of fluid flow through plant tissues with detailed observations of plant anatomy; this allows quantitative estimates of two critical aspects of plant function. First and foremost, results from these models quantify the supply of water to evaporative surfaces; second, results describe the ability of plant vascular systems to resist tensile damage from extreme environmental events, such as drought or frost. This approach permits quantitative comparisons of functional aspects of Asteroxylon with other extinct and extant plants, informs the quality of plant-based environmental proxies, and provides concrete data that can be input into climate models. Results indicate that despite their small size, water transport cells in Asteroxylon could supply a large volume of water to the plant's leaves--even greater than cells from some later-evolved seed plants. The smallest Asteroxylon tracheids have conductivities exceeding 0.015 m^2 / MPa * s, whereas Paleozoic conifer tracheids do not reach this threshold until they are three times wider. However, this increase in conductivity came at the cost of little to no adaptations for transport safety, placing the plant’s vegetative organs in jeopardy during drought events. Analysis of the thickness-to-span ratio of Asteroxylon’s tracheids suggests that environmental conditions of reduced relative

AUTOMATED ANALYSIS OF QUANTITATIVE IMAGE DATA USING ISOMORPHIC FUNCTIONAL MIXED MODELS, WITH APPLICATION TO PROTEOMICS DATA.

PubMed

Morris, Jeffrey S; Baladandayuthapani, Veerabhadran; Herrick, Richard C; Sanna, Pietro; Gutstein, Howard

2011-01-01

Image data are increasingly encountered and are of growing importance in many areas of science. Much of these data are quantitative image data, which are characterized by intensities that represent some measurement of interest in the scanned images. The data typically consist of multiple images on the same domain and the goal of the research is to combine the quantitative information across images to make inference about populations or interventions. In this paper, we present a unified analysis framework for the analysis of quantitative image data using a Bayesian functional mixed model approach. This framework is flexible enough to handle complex, irregular images with many local features, and can model the simultaneous effects of multiple factors on the image intensities and account for the correlation between images induced by the design. We introduce a general isomorphic modeling approach to fitting the functional mixed model, of which the wavelet-based functional mixed model is one special case. With suitable modeling choices, this approach leads to efficient calculations and can result in flexible modeling and adaptive smoothing of the salient features in the data. The proposed method has the following advantages: it can be run automatically, it produces inferential plots indicating which regions of the image are associated with each factor, it simultaneously considers the practical and statistical significance of findings, and it controls the false discovery rate. Although the method we present is general and can be applied to quantitative image data from any application, in this paper we focus on image-based proteomic data. We apply our method to an animal study investigating the effects of opiate addiction on the brain proteome. Our image-based functional mixed model approach finds results that are missed with conventional spot-based analysis approaches. In particular, we find that the significant regions of the image identified by the proposed method

Conformational stability, vibrational spectra, molecular structure, NBO and HOMO-LUMO analysis of 5-nitro-2-furaldehyde oxime based on DFT calculations.

PubMed

Arivazhagan, M; Jeyavijayan, S; Geethapriya, J

2013-03-01

The FTIR and FT-Raman spectra of 5-nitro-2-furaldehyde oxime (NFAO) have been recorded in the regions 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The total energies of different conformations have been obtained from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The computational results identify the most stable conformer of NFAO as the C1 form. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of NFAO is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. Besides, molecular electrostatic potential (MEP), HOMO and LUMO analysis, and several thermodynamic properties were performed by the DFT method. Mulliken's net charges have been calculated and compared with the natural atomic charges. Ultraviolet-visible spectrum of the title molecule has also been calculated using TD-DFT method. Copyright © 2012 Elsevier B.V. All rights reserved.

Study of gas-phase O-H bond dissociation enthalpies and ionization potentials of substituted phenols - Applicability of ab initio and DFT/B3LYP methods

NASA Astrophysics Data System (ADS)

Klein, Erik; Lukeš, Vladimír

2006-11-01

In this paper, the study of phenol and 37 compounds representing various ortho-, para-, and meta-substituted phenols is presented. Molecules and their radical structures were studied using ab initio methods with inclusion of correlation energy and DFT in order to calculate the O-H bond dissociation enthalpies (BDEs) and vertical ionization potentials (IPs). Calculated BDEs and IPs were compared with available experimental values to ascertain the suitability of used methods, especially for the description of the substituent induced changes in BDE and IP. MP2, MP3, and MP4 methods do not give reliable results, since they significantly underestimate substituent induced changes in BDE and do not reflect distinct effect of substituents related to para and meta position correctly. DFT/B3LYP method reflects the effect of substituents on BDE satisfactorily, though ΔBDEs are in narrower range than experimental values. BDE of phenol was calculated also using CCSD(T) method in various basis sets. Both, DFT and HF methods describe the effect of substituents on IP identically. However, DFT considerably underestimates individual values. HF method gives IPs in very good agreement with experimental data. Obtained results show that dependences of BDEs and IPs on Hammett constants of the substituents are linear. Linearity of DFT BDE vs. IP dependence is even better than the dependences on Hammett constants and obtained equations allow estimating of O-H BDEs of meta- and para-substituted phenols from calculated IPs.

FT IR spectral investigations of toxic material dibrom using DFT

NASA Astrophysics Data System (ADS)

Parvathy, M.; Gopika, M. S.; Mary, B. L. Bincy; Nimmi, D. E.; Praveen, S. G.; Binoy, J.

2018-05-01

Since, dibrom is widely used organophosphate pesticide, the exploration of its structural features is of immense research interest, and can be effectively carried out using infrared spectroscopy aided by DFT simulation. The present work aims to investigate the interrelation between carbon-halogen bond strength and electronegativity halogen. The resonance of phosphate in dibrom and the deviation from resonant structure due to bridging of oxygen by electron donating methyl group has been investigated in detail. The molecular docking study has been performed to explore the bioactivity of dibrom and to assess the strength of interaction of dibrom towards DNA and BSA.

Quantifying Zika: Advancing the Epidemiology of Zika With Quantitative Models.

PubMed

Keegan, Lindsay T; Lessler, Justin; Johansson, Michael A

2017-12-16

When Zika virus (ZIKV) emerged in the Americas, little was known about its biology, pathogenesis, and transmission potential, and the scope of the epidemic was largely hidden, owing to generally mild infections and no established surveillance systems. Surges in congenital defects and Guillain-Barré syndrome alerted the world to the danger of ZIKV. In the context of limited data, quantitative models were critical in reducing uncertainties and guiding the global ZIKV response. Here, we review some of the models used to assess the risk of ZIKV-associated severe outcomes, the potential speed and size of ZIKV epidemics, and the geographic distribution of ZIKV risk. These models provide important insights and highlight significant unresolved questions related to ZIKV and other emerging pathogens. Published by Oxford University Press for the Infectious Diseases Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Properties of MgO to 1.2 TPa from high-precision experiments on Sandia's Z machine and first-principles simulations using QMC and DFT

NASA Astrophysics Data System (ADS)

Shulenburger, Luke

2015-11-01

MgO is a major constituent of Earth's mantle, the rocky cores of gas giants and is a likely component of the interiors of many exoplanets. The high pressure - high temperature behavior of MgO directly affects equation of state models for planetary structure and formation. In this work, we examine MgO under extreme conditions using experimental and theoretical methods to determine the phase diagram and transport properties. Using plate impact experiments on Sandia's Z facility a low entropy solid-solid phase transition from B1 to B2 is clearly determined. The melting transition, on the other hand, is subtle, involving little to no signal in us-up space. Theoretical work utilizing density functional theory (DFT) provides a complementary picture of the phase diagram. The solid-solid phase transition is identified through a series of quasi-harmonic phonon calculations and thermodynamic integration, while the melt boundary is found using phase coexistence calculations. The calculation of reflectivity along the Hugoniot and the influence of the ionic structure on the transport properties requires particular care because of the underestimation of the band gap and attendant overestimation of transport properties due to the use of semi-local density functional theory. We will explore the impact of this theoretical challenge and its potential solutions in this talk. Finally, understanding the behavior of MgO as the pressure releases from the Hugoniot state is a key ingredient to modeling giant impact events. We explore this regime both through additional DFT calculations and by observing the release state of the MgO into lower impedance materials. The integrated use of DFT simulations and high-accuracy shock experiments together provide a comprehensive understanding of MgO under extreme conditions. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U

Direct modeling of the electrochemistry in the three-phase boundary of solid oxide fuel cell anodes by density functional theory: a critical overview.

PubMed

Shishkin, M; Ziegler, T

2014-02-07

The first principles modeling of electrochemical reactions has proven useful for the development of efficient, durable and low cost solid oxide full cells (SOFCs). In this account we focus on recent advances in modeling of structural, electronic and catalytic properties of the SOFC anodes based on density functional theory (DFT) first principle calculations. As a starting point, we highlight that the adequate analysis of cell electrochemistry generally requires modeling of chemical reactions at the metal/oxide interface rather than on individual metal or oxide surfaces. The atomic models of Ni/YSZ and Ni/CeO2 interfaces, required for DFT simulations of reactions on SOFC anodes are discussed next, together with the analysis of the electronic structure of these interfaces. Then we proceed to DFT-based findings on charge transfer mechanisms during redox reactions on these two anodes. We provide a comparison of the electronic properties of Ni/YSZ and Ni/CeO2 interfaces and present an interpretation of their different chemical performances. Subsequently we discuss the computed energy pathways of fuel oxidation mechanisms, obtained by various groups to date. We also discuss the results of DFT studies combined with microkinetic modeling as well as the results of kinetic Monte Carlo simulations. In conclusion we summarize the key findings of DFT modeling of metal/oxide interfaces to date and highlight possible directions in the future modeling of SOFC anodes.

SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

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

Khabibullin, A.R.; Woods, L.M.; Karolak, A.

2016-06-15

Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis setmore » in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA

Quantitative comparison between crowd models for evacuation planning and evaluation

NASA Astrophysics Data System (ADS)

Viswanathan, Vaisagh; Lee, Chong Eu; Lees, Michael Harold; Cheong, Siew Ann; Sloot, Peter M. A.

2014-02-01

Crowd simulation is rapidly becoming a standard tool for evacuation planning and evaluation. However, the many crowd models in the literature are structurally different, and few have been rigorously calibrated against real-world egress data, especially in emergency situations. In this paper we describe a procedure to quantitatively compare different crowd models or between models and real-world data. We simulated three models: (1) the lattice gas model, (2) the social force model, and (3) the RVO2 model, and obtained the distributions of six observables: (1) evacuation time, (2) zoned evacuation time, (3) passage density, (4) total distance traveled, (5) inconvenience, and (6) flow rate. We then used the DISTATIS procedure to compute the compromise matrix of statistical distances between the three models. Projecting the three models onto the first two principal components of the compromise matrix, we find the lattice gas and RVO2 models are similar in terms of the evacuation time, passage density, and flow rates, whereas the social force and RVO2 models are similar in terms of the total distance traveled. Most importantly, we find that the zoned evacuation times of the three models to be very different from each other. Thus we propose to use this variable, if it can be measured, as the key test between different models, and also between models and the real world. Finally, we compared the model flow rates against the flow rate of an emergency evacuation during the May 2008 Sichuan earthquake, and found the social force model agrees best with this real data.

Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models.

PubMed

Fu, Guifang; Dai, Xiaotian; Symanzik, Jürgen; Bushman, Shaun

2017-01-01

Leaf shape traits have long been a focus of many disciplines, but the complex genetic and environmental interactive mechanisms regulating leaf shape variation have not yet been investigated in detail. The question of the respective roles of genes and environment and how they interact to modulate leaf shape is a thorny evolutionary problem, and sophisticated methodology is needed to address it. In this study, we investigated a framework-level approach that inputs shape image photographs and genetic and environmental data, and then outputs the relative importance ranks of all variables after integrating shape feature extraction, dimension reduction, and tree-based statistical models. The power of the proposed framework was confirmed by simulation and a Populus szechuanica var. tibetica data set. This new methodology resulted in the detection of novel shape characteristics, and also confirmed some previous findings. The quantitative modeling of a combination of polygenetic, plastic, epistatic, and gene-environment interactive effects, as investigated in this study, will improve the discernment of quantitative leaf shape characteristics, and the methods are ready to be applied to other leaf morphology data sets. Unlike the majority of approaches in the quantitative leaf shape literature, this framework-level approach is data-driven, without assuming any pre-known shape attributes, landmarks, or model structures. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Quantitative rubber sheet models of gravitation wells using Spandex

NASA Astrophysics Data System (ADS)

White, Gary

2008-04-01

Long a staple of introductory treatments of general relativity, the rubber sheet model exhibits Wheeler's concise summary---``Matter tells space-time how to curve and space-time tells matter how to move''---very nicely. But what of the quantitative aspects of the rubber sheet model: how far can the analogy be pushed? We show^1 that when a mass M is suspended from the center of an otherwise unstretched elastic sheet affixed to a circular boundary it exhibits a distortion far from the center given by h = A*(M*r^2)^1/3 . Here, as might be expected, h and r are the vertical and axial distances from the center, but this result is not the expected logarithmic form of 2-D solutions to LaPlace's equation (the stretched drumhead). This surprise has a natural explanation and is confirmed experimentally with Spandex as the medium, and its consequences for general rubber sheet models are pursued. ^1``The shape of `the Spandex' and orbits upon its surface'', American Journal of Physics, 70, 48-52 (2002), G. D. White and M. Walker. See also the comment by Don S. Lemons and T. C. Lipscombe, also in AJP, 70, 1056-1058 (2002).

Quantitative Modelling of Trace Elements in Hard Coal.

PubMed

Smoliński, Adam; Howaniec, Natalia

2016-01-01

The significance of coal in the world economy remains unquestionable for decades. It is also expected to be the dominant fossil fuel in the foreseeable future. The increased awareness of sustainable development reflected in the relevant regulations implies, however, the need for the development and implementation of clean coal technologies on the one hand, and adequate analytical tools on the other. The paper presents the application of the quantitative Partial Least Squares method in modeling the concentrations of trace elements (As, Ba, Cd, Co, Cr, Cu, Mn, Ni, Pb, Rb, Sr, V and Zn) in hard coal based on the physical and chemical parameters of coal, and coal ash components. The study was focused on trace elements potentially hazardous to the environment when emitted from coal processing systems. The studied data included 24 parameters determined for 132 coal samples provided by 17 coal mines of the Upper Silesian Coal Basin, Poland. Since the data set contained outliers, the construction of robust Partial Least Squares models for contaminated data set and the correct identification of outlying objects based on the robust scales were required. These enabled the development of the correct Partial Least Squares models, characterized by good fit and prediction abilities. The root mean square error was below 10% for all except for one the final Partial Least Squares models constructed, and the prediction error (root mean square error of cross-validation) exceeded 10% only for three models constructed. The study is of both cognitive and applicative importance. It presents the unique application of the chemometric methods of data exploration in modeling the content of trace elements in coal. In this way it contributes to the development of useful tools of coal quality assessment.

Quantitative Modelling of Trace Elements in Hard Coal

PubMed Central

Smoliński, Adam; Howaniec, Natalia

2016-01-01

The significance of coal in the world economy remains unquestionable for decades. It is also expected to be the dominant fossil fuel in the foreseeable future. The increased awareness of sustainable development reflected in the relevant regulations implies, however, the need for the development and implementation of clean coal technologies on the one hand, and adequate analytical tools on the other. The paper presents the application of the quantitative Partial Least Squares method in modeling the concentrations of trace elements (As, Ba, Cd, Co, Cr, Cu, Mn, Ni, Pb, Rb, Sr, V and Zn) in hard coal based on the physical and chemical parameters of coal, and coal ash components. The study was focused on trace elements potentially hazardous to the environment when emitted from coal processing systems. The studied data included 24 parameters determined for 132 coal samples provided by 17 coal mines of the Upper Silesian Coal Basin, Poland. Since the data set contained outliers, the construction of robust Partial Least Squares models for contaminated data set and the correct identification of outlying objects based on the robust scales were required. These enabled the development of the correct Partial Least Squares models, characterized by good fit and prediction abilities. The root mean square error was below 10% for all except for one the final Partial Least Squares models constructed, and the prediction error (root mean square error of cross–validation) exceeded 10% only for three models constructed. The study is of both cognitive and applicative importance. It presents the unique application of the chemometric methods of data exploration in modeling the content of trace elements in coal. In this way it contributes to the development of useful tools of coal quality assessment. PMID:27438794

Monitoring with Trackers Based on Semi-Quantitative Models

NASA Technical Reports Server (NTRS)

Kuipers, Benjamin

1997-01-01

In three years of NASA-sponsored research preceding this project, we successfully developed a technology for: (1) building qualitative and semi-quantitative models from libraries of model-fragments, (2) simulating these models to predict future behaviors with the guarantee that all possible behaviors are covered, (3) assimilating observations into behaviors, shrinking uncertainty so that incorrect models are eventually refuted and correct models make stronger predictions for the future. In our object-oriented framework, a tracker is an object which embodies the hypothesis that the available observation stream is consistent with a particular behavior of a particular model. The tracker maintains its own status (consistent, superceded, or refuted), and answers questions about its explanation for past observations and its predictions for the future. In the MIMIC approach to monitoring of continuous systems, a number of trackers are active in parallel, representing alternate hypotheses about the behavior of a system. This approach is motivated by the need to avoid 'system accidents' [Perrow, 1985] due to operator fixation on a single hypothesis, as for example at Three Mile Island. As we began to address these issues, we focused on three major research directions that we planned to pursue over a three-year project: (1) tractable qualitative simulation, (2) semiquantitative inference, and (3) tracking set management. Unfortunately, funding limitations made it impossible to continue past year one. Nonetheless, we made major progress in the first two of these areas. Progress in the third area as slower because the graduate student working on that aspect of the project decided to leave school and take a job in industry. I enclosed a set of abstract of selected papers on the work describe below. Several papers that draw on the research supported during this period appeared in print after the grant period ended.

Synthesis and spectral properties of Methyl-Phenyl pyrazoloquinoxaline fluorescence emitters: Experiment and DFT/TDDFT calculations

NASA Astrophysics Data System (ADS)

Gąsiorski, P.; Matusiewicz, M.; Gondek, E.; Uchacz, T.; Wojtasik, K.; Danel, A.; Shchur, Ya.; Kityk, A. V.

2018-01-01

Paper reports the synthesis and spectroscopic studies of two novel 1-Methyl-3-phenyl-1H-pyrazolo[3,4-b]quinoxaline (PQX) derivatives with 6-substituted methyl (MeMPPQX) or methoxy (MeOMPPQX) side groups. The optical absorption and fluorescence emission spectra are recorded in solvents of different polarity. Steady state and time-resolved spectroscopy provide photophysical characterization of MeMPPQX and MeOMPPQX dyes as materials for potential luminescence or electroluminescence applications. Measured optical absorption and fluorescence emission spectra are compared with quantum-chemical DFT/TDDFT calculations using long-range corrected xc-functionals, LRC-BLYP and CAM-B3LYP in combination with self-consistent reaction field model based on linear response (LR), state specific (SS) or corrected linear response (CLR) solvations. Performances of relevant theoretical models and approaches are compared. The reparameterized LRC-BLYP functional (ω = 0.231 Bohr-1) in combination with CLR solvation provides most accurate prediction of both excitation and emission energies. The MeMPPQX and MeOMPPQX dyes represent efficient fluorescence emitters in blue-green region of the visible spectra.

The importance of topography-controlled sub-grid process heterogeneity and semi-quantitative prior constraints in distributed hydrological models

NASA Astrophysics Data System (ADS)

Nijzink, Remko C.; Samaniego, Luis; Mai, Juliane; Kumar, Rohini; Thober, Stephan; Zink, Matthias; Schäfer, David; Savenije, Hubert H. G.; Hrachowitz, Markus

2016-03-01

Heterogeneity of landscape features like terrain, soil, and vegetation properties affects the partitioning of water and energy. However, it remains unclear to what extent an explicit representation of this heterogeneity at the sub-grid scale of distributed hydrological models can improve the hydrological consistency and the robustness of such models. In this study, hydrological process complexity arising from sub-grid topography heterogeneity was incorporated into the distributed mesoscale Hydrologic Model (mHM). Seven study catchments across Europe were used to test whether (1) the incorporation of additional sub-grid variability on the basis of landscape-derived response units improves model internal dynamics, (2) the application of semi-quantitative, expert-knowledge-based model constraints reduces model uncertainty, and whether (3) the combined use of sub-grid response units and model constraints improves the spatial transferability of the model. Unconstrained and constrained versions of both the original mHM and mHMtopo, which allows for topography-based sub-grid heterogeneity, were calibrated for each catchment individually following a multi-objective calibration strategy. In addition, four of the study catchments were simultaneously calibrated and their feasible parameter sets were transferred to the remaining three receiver catchments. In a post-calibration evaluation procedure the probabilities of model and transferability improvement, when accounting for sub-grid variability and/or applying expert-knowledge-based model constraints, were assessed on the basis of a set of hydrological signatures. In terms of the Euclidian distance to the optimal model, used as an overall measure of model performance with respect to the individual signatures, the model improvement achieved by introducing sub-grid heterogeneity to mHM in mHMtopo was on average 13 %. The addition of semi-quantitative constraints to mHM and mHMtopo resulted in improvements of 13 and 19

Experimentally validated quantitative linear model for the device physics of elastomeric microfluidic valves

NASA Astrophysics Data System (ADS)

Kartalov, Emil P.; Scherer, Axel; Quake, Stephen R.; Taylor, Clive R.; Anderson, W. French

2007-03-01

A systematic experimental study and theoretical modeling of the device physics of polydimethylsiloxane "pushdown" microfluidic valves are presented. The phase space is charted by 1587 dimension combinations and encompasses 45-295μm lateral dimensions, 16-39μm membrane thickness, and 1-28psi closing pressure. Three linear models are developed and tested against the empirical data, and then combined into a fourth-power-polynomial superposition. The experimentally validated final model offers a useful quantitative prediction for a valve's properties as a function of its dimensions. Typical valves (80-150μm width) are shown to behave like thin springs.

Quantitative structure-activity relationship (QSAR) for insecticides: development of predictive in vivo insecticide activity models.

PubMed

Naik, P K; Singh, T; Singh, H

2009-07-01

Quantitative structure-activity relationship (QSAR) analyses were performed independently on data sets belonging to two groups of insecticides, namely the organophosphates and carbamates. Several types of descriptors including topological, spatial, thermodynamic, information content, lead likeness and E-state indices were used to derive quantitative relationships between insecticide activities and structural properties of chemicals. A systematic search approach based on missing value, zero value, simple correlation and multi-collinearity tests as well as the use of a genetic algorithm allowed the optimal selection of the descriptors used to generate the models. The QSAR models developed for both organophosphate and carbamate groups revealed good predictability with r(2) values of 0.949 and 0.838 as well as [image omitted] values of 0.890 and 0.765, respectively. In addition, a linear correlation was observed between the predicted and experimental LD(50) values for the test set data with r(2) of 0.871 and 0.788 for both the organophosphate and carbamate groups, indicating that the prediction accuracy of the QSAR models was acceptable. The models were also tested successfully from external validation criteria. QSAR models developed in this study should help further design of novel potent insecticides.

Polymorphism and Elastic Response of Molecular Materials from First Principles: How Hard Can it Be?

NASA Astrophysics Data System (ADS)

Reilly, Anthony; Tkatchenko, Alexandre

2014-03-01

Molecular materials are of great fundamental and applied importance in science and industry, with numerous applications in pharmaceuticals, electronics, sensing, and catalysis. A key challenge for theory has been the prediction of their stability, polymorphism and response to perturbations. While pairwise models of van der Waals (vdW) interactions have improved the ability of density functional theory (DFT) to model these systems, substantial quantitative and even qualitative failures remain. In this contribution we show how a many-body description of vdW interactions can dramatically improve the accuracy of DFT for molecular materials, yielding quantitative description of stabilities and polymorphism for these challenging systems. Moreover, the role of many-body vdW interactions goes beyond stabilities to response properties. In particular, we have studied the elastic properties of a series of molecular crystals, finding that many-body vdW interactions can account for up to 30% of the elastic response, leading to quantitative and qualitative changes in elastic behavior. We will illustrate these crucial effects with the challenging case of the polymorphs of aspirin, leading to a better understanding of the conflicting experimental and theoretical studies of this system.

Quantitative structure-activity relationship analysis of substituted arylazo pyridone dyes in photocatalytic system: Experimental and theoretical study.

PubMed

Dostanić, J; Lončarević, D; Zlatar, M; Vlahović, F; Jovanović, D M

2016-10-05

A series of arylazo pyridone dyes was synthesized by changing the type of the substituent group in the diazo moiety, ranging from strong electron-donating to strong electron-withdrawing groups. The structural and electronic properties of the investigated dyes was calculated at the M062X/6-31+G(d,p) level of theory. The observed good linear correlations between atomic charges and Hammett σp constants provided a basis to discuss the transmission of electronic substituent effects through a dye framework. The reactivity of synthesized dyes was tested through their decolorization efficiency in TiO2 photocatalytic system (Degussa P-25). Quantitative structure-activity relationship analysis revealed a strong correlation between reactivity of investigated dyes and Hammett substituent constants. The reaction was facilitated by electron-withdrawing groups, and retarded by electron-donating ones. Quantum mechanical calculations was used in order to describe the mechanism of the photocatalytic oxidation reactions of investigated dyes and interpret their reactivities within the framework of the Density Functional Theory (DFT). According to DFT based reactivity descriptors, i.e. Fukui functions and local softness, the active site moves from azo nitrogen atom linked to benzene ring to pyridone carbon atom linked to azo bond, going from dyes with electron-donating groups to dyes with electron-withdrawing groups. Copyright © 2016 Elsevier B.V. All rights reserved.

Maximal Predictability Approach for Identifying the Right Descriptors for Electrocatalytic Reactions.

PubMed

Krishnamurthy, Dilip; Sumaria, Vaidish; Viswanathan, Venkatasubramanian

2018-02-01

Density functional theory (DFT) calculations are being routinely used to identify new material candidates that approach activity near fundamental limits imposed by thermodynamics or scaling relations. DFT calculations are associated with inherent uncertainty, which limits the ability to delineate materials (distinguishability) that possess high activity. Development of error-estimation capabilities in DFT has enabled uncertainty propagation through activity-prediction models. In this work, we demonstrate an approach to propagating uncertainty through thermodynamic activity models leading to a probability distribution of the computed activity and thereby its expectation value. A new metric, prediction efficiency, is defined, which provides a quantitative measure of the ability to distinguish activity of materials and can be used to identify the optimal descriptor(s) ΔG opt . We demonstrate the framework for four important electrochemical reactions: hydrogen evolution, chlorine evolution, oxygen reduction and oxygen evolution. Future studies could utilize expected activity and prediction efficiency to significantly improve the prediction accuracy of highly active material candidates.

Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models.

PubMed

Allen, R J; Rieger, T R; Musante, C J

2016-03-01

Quantitative systems pharmacology models mechanistically describe a biological system and the effect of drug treatment on system behavior. Because these models rarely are identifiable from the available data, the uncertainty in physiological parameters may be sampled to create alternative parameterizations of the model, sometimes termed "virtual patients." In order to reproduce the statistics of a clinical population, virtual patients are often weighted to form a virtual population that reflects the baseline characteristics of the clinical cohort. Here we introduce a novel technique to efficiently generate virtual patients and, from this ensemble, demonstrate how to select a virtual population that matches the observed data without the need for weighting. This approach improves confidence in model predictions by mitigating the risk that spurious virtual patients become overrepresented in virtual populations.

Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models

PubMed Central

Rieger, TR; Musante, CJ

2016-01-01

Quantitative systems pharmacology models mechanistically describe a biological system and the effect of drug treatment on system behavior. Because these models rarely are identifiable from the available data, the uncertainty in physiological parameters may be sampled to create alternative parameterizations of the model, sometimes termed “virtual patients.” In order to reproduce the statistics of a clinical population, virtual patients are often weighted to form a virtual population that reflects the baseline characteristics of the clinical cohort. Here we introduce a novel technique to efficiently generate virtual patients and, from this ensemble, demonstrate how to select a virtual population that matches the observed data without the need for weighting. This approach improves confidence in model predictions by mitigating the risk that spurious virtual patients become overrepresented in virtual populations. PMID:27069777

DFT computations on: Crystal structure, vibrational studies and optical investigations of a luminescent self-assembled material

NASA Astrophysics Data System (ADS)

Kessentini, A.; Ben Ahmed, A.; Dammak, T.; Belhouchet, M.

2018-02-01

The current work undertakes the growth and the physicochemical properties of a novel green-yellow luminescence semi-organic material, the 3-picolylammonium bromide abbreviated (Pico-Br). In this paper, we report the X-ray diffraction measurements which show that the crystal lattice consists of distinct 3-picolylammonium cations and free bromide anions connected via Nsbnd H ⋯ Br and Nsbnd H ⋯ N hydrogen bonds leading to form a two dimensional frameworks. Molecular geometry compared with its optimized counterpart shows that the quantum chemical calculations carried out with density functional method (DFT) well produce the perceived structure by X-ray resolution of the studied material. To provide further insight into the spectroscopic properties, additional characterization of this material have been performed with Raman and infrared studies at room temperature. Theoretical computations have been computed using the (DFT) method at B3LYP/LanL2DZ level of theory implemented within Gaussian 03 program to study the vibrational spectra of the investigated molecule in the ground state. Optical absorption spectrum inspected by UV-visible absorption reveals the appearance of sharp optical gap of 280 nm (4.42 eV) as well as a strong green photoluminescence emission at 550 nm (2.25 eV) is detected on the photoluminescence (PL) spectrum at room temperature. Using the TD/DFT method, HOMO-LUMO energy gap and the Mulliken atomic charges were calculated in order to get an insight into the material. Good agreement between the theoretical results and the experimental ones was predicted.

A quantitative speciation model for the adsorption of organic pollutants on activated carbon.

PubMed

Grivé, M; García, D; Domènech, C; Richard, L; Rojo, I; Martínez, X; Rovira, M

2013-01-01

Granular activated carbon (GAC) is commonly used as adsorbent in water treatment plants given its high capacity for retaining organic pollutants in aqueous phase. The current knowledge on GAC behaviour is essentially empirical, and no quantitative description of the chemical relationships between GAC surface groups and pollutants has been proposed. In this paper, we describe a quantitative model for the adsorption of atrazine onto GAC surface. The model is based on results of potentiometric titrations and three types of adsorption experiments which have been carried out in order to determine the nature and distribution of the functional groups on the GAC surface, and evaluate the adsorption characteristics of GAC towards atrazine. Potentiometric titrations have indicated the existence of at least two different families of chemical groups on the GAC surface, including phenolic- and benzoic-type surface groups. Adsorption experiments with atrazine have been satisfactorily modelled with the geochemical code PhreeqC, assuming that atrazine is sorbed onto the GAC surface in equilibrium (log Ks = 5.1 ± 0.5). Independent thermodynamic calculations suggest a possible adsorption of atrazine on a benzoic derivative. The present work opens a new approach for improving the adsorption capabilities of GAC towards organic pollutants by modifying its chemical properties.

SOME USES OF MODELS OF QUANTITATIVE GENETIC SELECTION IN SOCIAL SCIENCE.

PubMed

Weight, Michael D; Harpending, Henry

2017-01-01

The theory of selection of quantitative traits is widely used in evolutionary biology, agriculture and other related fields. The fundamental model known as the breeder's equation is simple, robust over short time scales, and it is often possible to estimate plausible parameters. In this paper it is suggested that the results of this model provide useful yardsticks for the description of social traits and the evaluation of transmission models. The differences on a standard personality test between samples of Old Order Amish and Indiana rural young men from the same county and the decline of homicide in Medieval Europe are used as illustrative examples of the overall approach. It is shown that the decline of homicide is unremarkable under a threshold model while the differences between rural Amish and non-Amish young men are too large to be a plausible outcome of simple genetic selection in which assortative mating by affiliation is equivalent to truncation selection.

Quantitative assessment of computational models for retinotopic map formation

PubMed Central

Sterratt, David C; Cutts, Catherine S; Willshaw, David J; Eglen, Stephen J

2014-01-01

ABSTRACT Molecular and activity‐based cues acting together are thought to guide retinal axons to their terminal sites in vertebrate optic tectum or superior colliculus (SC) to form an ordered map of connections. The details of mechanisms involved, and the degree to which they might interact, are still not well understood. We have developed a framework within which existing computational models can be assessed in an unbiased and quantitative manner against a set of experimental data curated from the mouse retinocollicular system. Our framework facilitates comparison between models, testing new models against known phenotypes and simulating new phenotypes in existing models. We have used this framework to assess four representative models that combine Eph/ephrin gradients and/or activity‐based mechanisms and competition. Two of the models were updated from their original form to fit into our framework. The models were tested against five different phenotypes: wild type, Isl2‐EphA3 ki/ki, Isl2‐EphA3 ki/+, ephrin‐A2,A3,A5 triple knock‐out (TKO), and Math5 −/− (Atoh7). Two models successfully reproduced the extent of the Math5 −/− anteromedial projection, but only one of those could account for the collapse point in Isl2‐EphA3 ki/+. The models needed a weak anteroposterior gradient in the SC to reproduce the residual order in the ephrin‐A2,A3,A5 TKO phenotype, suggesting either an incomplete knock‐out or the presence of another guidance molecule. Our article demonstrates the importance of testing retinotopic models against as full a range of phenotypes as possible, and we have made available MATLAB software, we wrote to facilitate this process. © 2014 Wiley Periodicals, Inc. Develop Neurobiol 75: 641–666, 2015 PMID:25367067

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

PubMed Central

Zhu, Hao; Sun, Yan; Rajagopal, Gunaretnam; Mondry, Adrian; Dhar, Pawan

2004-01-01

Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described. PMID:15339335

FT-IR, FT-Raman, UV spectra and DFT calculations on monomeric and dimeric structure of 2-amino-5-bromobenzoic acid.

PubMed

Karabacak, Mehmet; Cinar, Mehmet

2012-02-01

In this work, the molecular conformation, vibrational and electronic transition analysis of 2-amino-5-bromobenzoic acid (2A5BrBA) were presented for the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the regions of 400-4000 cm(-1) and 50-4000 cm(-1), respectively. There are four conformers, C1, C2, C3 and C4 for this molecule. The geometrical parameters, energies and wavenumbers have been obtained for all four conformers. The computational results diagnose the most stable conformer of 2A5BrBA as the C1 form. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Raman activities calculated by DFT method have been converted to the corresponding Raman intensities using Raman scattering theory. The UV spectra of investigated compound were recorded in the region of 200-400 nm for ethanol and water solutions. The electronic properties were evaluated with help of time-dependent DFT (TD-DFT) theoretically and results were compared with experimental observations. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. The observed and the calculated geometric parameters, vibrational wavenumbers and electronic transitions were compared with observed data and found to be in good agreement. Copyright © 2011 Elsevier B.V. All rights reserved.

A Predictive Model for Chemically-Induced Fracture

NASA Astrophysics Data System (ADS)

Carter, Emily

2004-03-01

Mechanical properties of bulk solids are affected not only by macroscopic external loads, but also by chemical reactions, typically at surfaces and interfaces. For example, impurities in metals often coalesce at grain boundaries, leading to weakening of the sample under stress. Atmospheric corrosion is another example that, when combined with external loads, leads to stress-corrosion cracking. These are inherently multiscale phenomena, where the chemistry occurring at the atomic scale profoundly affects the mechanical properties at the micron to millimeter scale. Here we discuss a multiscale model of environmentally-assisted fracture. This involves coupling periodic density functional theory (DFT) at the atomic scale to a finite element continuum mechanics description of the coarser scale. A key component is the cohesive law, which we have shown takes on a universal form distinct from the generally used UBER model. Further, we propose a scheme to calculate physically realistic cohesive laws in the presence of mobile impurities. This cohesive law is then used to in a continuum model that couples stress-assisted diffusion with cohesive zone models of fracture to describe hydrogen embrittlement in metals. We show that this model, with a first principles-based cohesive law, provides insight into the observed intermittent cracking in steel, as well as good quantitative agreement with experiment.

Photoinduced dynamics to photoluminescence in Ln3+ (Ln = Ce, Pr) doped β-NaYF4 nanocrystals computed in basis of non-collinear spin DFT with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Han, Yulun; Vogel, Dayton J.; Inerbaev, Talgat M.; May, P. Stanley; Berry, Mary T.; Kilin, Dmitri S.

2018-03-01

In this work, non-collinear spin DFT + U approaches with spin-orbit coupling (SOC) are applied to Ln3+ doped β-NaYF4 (Ln = Ce, Pr) nanocrystals in Vienna ab initio Simulation Package taking into account unpaired spin configurations using the Perdew-Burke-Ernzerhof functional in a plane wave basis set. The calculated absorption spectra from non-collinear spin DFT + U approaches are compared with that from spin-polarised DFT + U approaches. The spectral difference indicates the importance of spin-flip transitions of Ln3+ ions. Suite of codes for nonadiabatic dynamics has been developed for 2-component spinor orbitals. On-the-fly nonadiabatic coupling calculations provide transition probabilities facilitated by nuclear motion. Relaxation rates of electrons and holes are calculated using Redfield theory in the reduced density matrix formalism cast in the basis of non-collinear spin DFT + U with SOC. The emission spectra are calculated using the time-integrated method along the excited state trajectories based on nonadiabatic couplings.

Compilation of a near-infrared library for the construction of quantitative models of amoxicillin and potassium clavulanate oral dosage forms

NASA Astrophysics Data System (ADS)

Zou, Wen-bo; Chong, Xiao-meng; Wang, Yan; Hu, Chang-qin

2018-05-01

The accuracy of NIR quantitative models depends on calibration samples with concentration variability. Conventional sample collecting methods have some shortcomings especially the time-consuming which remains a bottleneck in the application of NIR models for Process Analytical Technology (PAT) control. A study was performed to solve the problem of sample selection collection for construction of NIR quantitative models. Amoxicillin and potassium clavulanate oral dosage forms were used as examples. The aim was to find a normal approach to rapidly construct NIR quantitative models using an NIR spectral library based on the idea of a universal model [2021]. The NIR spectral library of amoxicillin and potassium clavulanate oral dosage forms was defined and consisted of spectra of 377 batches of samples produced by 26 domestic pharmaceutical companies, including tablets, dispersible tablets, chewable tablets, oral suspensions, and granules. The correlation coefficient (rT) was used to indicate the similarities of the spectra. The samples’ calibration sets were selected from a spectral library according to the median rT of the samples to be analyzed. The rT of the samples selected was close to the median rT. The difference in rT of those samples was 1.0% to 1.5%. We concluded that sample selection is not a problem when constructing NIR quantitative models using a spectral library versus conventional methods of determining universal models. The sample spectra with a suitable concentration range in the NIR models were collected quickly. In addition, the models constructed through this method were more easily targeted.

Spin–orbit DFT with Analytic Gradients and Applications to Heavy Element Compounds

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

Zhang, Zhiyong

We have implemented the unrestricted DFT approach with one-electron spin–orbit operators in the massively parallel NWChem program. Also implemented is the analytic gradient in the DFT approach with spin–orbit interactions. The current capabilities include single-point calculations and geometry optimization. Vibrational frequencies can be calculated numerically from the analytically calculated gradients. The implementation is based on the spin–orbit interaction operator derived from the effective core potential approach. The exchange functionals used in the implementation are functionals derived for non-spin–orbit calculations, including GGA as well as hybrid functionals. Spin–orbit Hartree–Fock calculations can also be carried out. We have applied the spin–orbit DFTmore » methods to the Uranyl aqua complexes. We have optimized the structures and calculated the vibrational frequencies of both (UO2 2+)aq and (UO2 +)aq with and without spin–orbit effects. The effects of the spin–orbit interaction on the structures and frequencies of these two complexes are discussed. We also carried out calculations for Th2, and several low-lying electronic states are calculated. Our results indicate that, for open-shell systems, there are significant effects due to the spin–orbit effects and the electronic configurations with and without spin–orbit interactions could change due to the occupation of orbitals of larger spin–orbit interactions.« less

Molecular structure, vibrational spectral assignments (FT-IR and FT-RAMAN), NMR, NBO, HOMO-LUMO and NLO properties of O-methoxybenzaldehyde based on DFT calculations

NASA Astrophysics Data System (ADS)

Vennila, P.; Govindaraju, M.; Venkatesh, G.; Kamal, C.

2016-05-01

Fourier transform - Infra red (FT-IR) and Fourier transform - Raman (FT-Raman) spectroscopic techniques have been carried out to analyze O-methoxy benzaldehyde (OMB) molecule. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT). The vibrational analysis of stable isomer of OMB has been carried out by FT-IR and FT-Raman in combination with theoretical method simultaneously. The first-order hyperpolarizability and the anisotropy polarizability invariant were computed by DFT method. The atomic charges, hardness, softness, ionization potential, electronegativity, HOMO-LUMO energies, and electrophilicity index have been calculated. The 13C and 1H Nuclear magnetic resonance (NMR) have also been obtained by GIAO method. Molecular electronic potential (MEP) has been calculated by the DFT calculation method. Electronic excitation energies, oscillator strength and excited states characteristics were computed by the closed-shell singlet calculation method.

Downscaling SSPs in Bangladesh - Integrating Science, Modelling and Stakeholders Through Qualitative and Quantitative Scenarios

NASA Astrophysics Data System (ADS)

Allan, A.; Barbour, E.; Salehin, M.; Hutton, C.; Lázár, A. N.; Nicholls, R. J.; Rahman, M. M.

2015-12-01

A downscaled scenario development process was adopted in the context of a project seeking to understand relationships between ecosystem services and human well-being in the Ganges-Brahmaputra delta. The aim was to link the concerns and priorities of relevant stakeholders with the integrated biophysical and poverty models used in the project. A 2-stage process was used to facilitate the connection between stakeholders concerns and available modelling capacity: the first to qualitatively describe what the future might look like in 2050; the second to translate these qualitative descriptions into the quantitative form required by the numerical models. An extended, modified SSP approach was adopted, with stakeholders downscaling issues identified through interviews as being priorities for the southwest of Bangladesh. Detailed qualitative futures were produced, before modellable elements were quantified in conjunction with an expert stakeholder cadre. Stakeholder input, using the methods adopted here, allows the top-down focus of the RCPs to be aligned with the bottom-up approach needed to make the SSPs appropriate at the more local scale, and also facilitates the translation of qualitative narrative scenarios into a quantitative form that lends itself to incorporation of biophysical and socio-economic indicators. The presentation will describe the downscaling process in detail, and conclude with findings regarding the importance of stakeholder involvement (and logistical considerations), balancing model capacity with expectations and recommendations on SSP refinement at local levels.

Synthesis, crystal structure and DFT studies of a dual fluorescent ketamine: Structural changes in the ground and excited states

NASA Astrophysics Data System (ADS)

Latha, V.; Balakrishnan, C.; Neelakantan, M. A.

2015-07-01

A fluorescent probe 2Z,2‧Z-3,3‧-(4,4‧-methylenebis(4,1-phenylene) bis(azanediyl))bis (1,3-diphenylprop-2-en-1-one) (L) was synthesized and characterized by IR, 1H NMR, ESI-mass, UV-visible and fluorescence spectral techniques. The single crystal analysis illustrates the existence of L in ketamine form. The crystal structure is stabilized by intramolecular and intermolecular hydrogen bonding. The thermal stability of L was studied by TG analysis. The fluorescence spectrum of L shows dual emission, and is due to excited state intramolecular proton transfer (ESIPT) process. This is supported by the high Stokes shift value. Electronic structure calculations of L in the ground and excited state have been carried out using DFT and TD-DFT at B3LYP/6-31G (d,p) level, respectively. The vibrational spectrum was computed at this level and compared with experimental values. Major orbital contributions for the electronic transitions were assigned with the help of TD-DFT. The changes in the Mulliken charge, bond lengths and bond angles between the ground and excited states of the tautomers demonstrate that twisted intramolecular charge transfer (TICT) process occurs along with ESIPT in the excited state.

Highly efficient regioselective synthesis, spectroscopic characterizations and DFT calculations of novel hydroxymethylated 1,4-disubstituted-1,2,3-triazole-based sulfonamides

NASA Astrophysics Data System (ADS)

Taheri, Elmira; Mirjafary, Zohreh; Saeidian, Hamid

2018-04-01

The novel hydroxymethylated 1,4-disubstituted-1,2,3-triazole-based sulfonamides were synthesized in excellent yields and high regioselectivity via a one-pot, two-step, three-component reaction of N-propargylsulfonamides, sodium azide, and epoxide derivatives under green conditions. Green and mild reaction condition, commercially readily available and inexpensive starting materials, wide scope and easy work-up are the key features of the present method. The Li+ and Na+ ion affinities of the model structure have been also investigated by density functional theory (DFT) studies to find the applicability of these products as ligand in coordination chemistry.

Aconitum and Delphinium sp. Alkaloids as Antagonist Modulators of Voltage-Gated Na+ Channels. AM1/DFT Electronic Structure Investigations and QSAR Studies

PubMed Central

Turabekova, Malakhat A.; Rasulev, Bakhtiyor F.; Levkovich, Mikhail G.; Abdullaev, Nasrulla D.; Leszczynski, Jerzy

2015-01-01

Early pharmacological studies of Aconitum and Delphinium sp. alkaloids suggested that these neurotoxins act at site 2 of voltage-gated Na+ channel and allosterically modulate its function. Understanding structural requirements for these compounds to exhibit binding activity at voltage-gated Na+ channel has been important in various fields. This paper reports quantum-chemical studies and quantitative structure-activity relationships (QSARs) based on a total of 65 natural alkaloids from two plant species, which includes both blockers and openers of sodium ion channel. A series of 18 antagonist alkaloids (9 blockers and 9 openers) have been studied using AM1 and DFT computational methods in order to reveal their structure-activity (structure-toxicity) relationship at electronic level. An examination of frontier orbitals obtained for ground and protonated forms of the compounds revealed that HOMOs and LUMOs were mainly represented by nitrogen atom and benzyl/benzoylester orbitals with –OH and –OCOCH3 contributions. The results obtained from this research have confirmed the experimental findings suggesting that neurotoxins acting at type 2 receptor site of voltage-dependent sodium channel are activators and blockers with common structural features and differ only in efficacy. The energetic tendency of HOMO-LUMO energy gap can probably distinguish activators and blockers that have been observed. Genetic Algorithm with Multiple Linear Regression Analysis (GA-MLRA) technique was also applied for the generation of two-descriptor QSAR models for the set of 65 blockers. Additionally to the computational studies, the HOMO-LUMO gap descriptor in each obtained QSAR model has confirmed the crucial role of charge transfer in receptor-ligand interactions. A number of other descriptors such as logP, IBEG, nNH2, nHDon, nCO have been selected as complementary ones to LUMO and their role in activity alteration has also been discussed. PMID:18201930

Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

PubMed

Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

2013-11-14

We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

Synthesis, crystal structure investigation, spectroscopic characterizations and DFT computations on a novel 1-(2-chloro-4-phenylquinolin-3-yl)ethanone

NASA Astrophysics Data System (ADS)

Murugavel, S.; Stephen, C. S. Jacob Prasanna; Subashini, R.; Reddy, H. Raveendranatha; AnanthaKrishnan, Dhanabalan

2016-10-01

The title compound 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE) was synthesised effectively by chlorination of 3-acetyl-4-phenylquinolin-2(1H)-one (APQ) using POCl3 reagent. Structural and vibrational spectroscopic studies were performed by utilizing single crystal X-ray diffraction, FTIR and NMR spectral analysis along with DFT method utilizing GAUSSIAN‧ 03 software. Veda program has been employed to perform a detailed interpretation of vibrational spectra. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NBO, Global chemical reactivity descriptors and thermodynamic properties have been examined by (DFT/B3LYP) method with the 6-311G(d,p) basis set level.

Spontaneous Symmetry Breaking Facilitates Metal-to-Ligand Charge Transfer: A Quantitative Two-Photon Absorption Study of Ferrocene-phenyleneethynylene Oligomers.

PubMed

Mikhaylov, Alexander; Uudsemaa, Merle; Trummal, Aleksander; Arias, Eduardo; Moggio, Ivana; Ziolo, Ronald; Cooper, Thomas M; Rebane, Aleksander

2018-04-19

Change of the permanent molecular electric dipole moment, Δμ, in a series of nominally centrosymmetric and noncentrosymmteric ferrocene-phenyleneethynylene oligomers was estimated by measuring the two-photon absorption cross-section spectra of the lower energy metal-to-ligand charge-transfer transitions using femtosecond nonlinear transmission method and was found to vary in the range up to 12 D, with the highest value corresponding to the most nonsymmetric system. Calculations of the Δμ performed by the TD-DFT method show quantitative agreement with the experimental values and reveal that facile rotation of the ferrocene moieties relative to the organic ligand breaks the ground-state inversion symmetry in the nominally symmetric structures.

Quantitative structure-property relationship modeling of remote liposome loading of drugs.

PubMed

Cern, Ahuva; Golbraikh, Alexander; Sedykh, Aleck; Tropsha, Alexander; Barenholz, Yechezkel; Goldblum, Amiram

2012-06-10

Remote loading of liposomes by trans-membrane gradients is used to achieve therapeutically efficacious intra-liposome concentrations of drugs. We have developed Quantitative Structure Property Relationship (QSPR) models of remote liposome loading for a data set including 60 drugs studied in 366 loading experiments internally or elsewhere. Both experimental conditions and computed chemical descriptors were employed as independent variables to predict the initial drug/lipid ratio (D/L) required to achieve high loading efficiency. Both binary (to distinguish high vs. low initial D/L) and continuous (to predict real D/L values) models were generated using advanced machine learning approaches and 5-fold external validation. The external prediction accuracy for binary models was as high as 91-96%; for continuous models the mean coefficient R(2) for regression between predicted versus observed values was 0.76-0.79. We conclude that QSPR models can be used to identify candidate drugs expected to have high remote loading capacity while simultaneously optimizing the design of formulation experiments. Copyright © 2011 Elsevier B.V. All rights reserved.

A quantitative dynamic systems model of health-related quality of life among older adults

PubMed Central

Roppolo, Mattia; Kunnen, E Saskia; van Geert, Paul L; Mulasso, Anna; Rabaglietti, Emanuela

2015-01-01

Health-related quality of life (HRQOL) is a person-centered concept. The analysis of HRQOL is highly relevant in the aged population, which is generally suffering from health decline. Starting from a conceptual dynamic systems model that describes the development of HRQOL in individuals over time, this study aims to develop and test a quantitative dynamic systems model, in order to reveal the possible dynamic trends of HRQOL among older adults. The model is tested in different ways: first, with a calibration procedure to test whether the model produces theoretically plausible results, and second, with a preliminary validation procedure using empirical data of 194 older adults. This first validation tested the prediction that given a particular starting point (first empirical data point), the model will generate dynamic trajectories that lead to the observed endpoint (second empirical data point). The analyses reveal that the quantitative model produces theoretically plausible trajectories, thus providing support for the calibration procedure. Furthermore, the analyses of validation show a good fit between empirical and simulated data. In fact, no differences were found in the comparison between empirical and simulated final data for the same subgroup of participants, whereas the comparison between different subgroups of people resulted in significant differences. These data provide an initial basis of evidence for the dynamic nature of HRQOL during the aging process. Therefore, these data may give new theoretical and applied insights into the study of HRQOL and its development with time in the aging population. PMID:26604722

Novel mathematic models for quantitative transitivity of quality-markers in extraction process of the Buyanghuanwu decoction.

PubMed

Zhang, Yu-Tian; Xiao, Mei-Feng; Deng, Kai-Wen; Yang, Yan-Tao; Zhou, Yi-Qun; Zhou, Jin; He, Fu-Yuan; Liu, Wen-Long

2018-06-01

Nowadays, to research and formulate an efficiency extraction system for Chinese herbal medicine, scientists have always been facing a great challenge for quality management, so that the transitivity of Q-markers in quantitative analysis of TCM was proposed by Prof. Liu recently. In order to improve the quality of extraction from raw medicinal materials for clinical preparations, a series of integrated mathematic models for transitivity of Q-markers in quantitative analysis of TCM were established. Buyanghuanwu decoction (BYHWD) was a commonly TCMs prescription, which was used to prevent and treat the ischemic heart and brain diseases. In this paper, we selected BYHWD as an extraction experimental subject to study the quantitative transitivity of TCM. Based on theory of Fick's Rule and Noyes-Whitney equation, novel kinetic models were established for extraction of active components. Meanwhile, fitting out kinetic equations of extracted models and then calculating the inherent parameters in material piece and Q-marker quantitative transfer coefficients, which were considered as indexes to evaluate transitivity of Q-markers in quantitative analysis of the extraction process of BYHWD. HPLC was applied to screen and analyze the potential Q-markers in the extraction process. Fick's Rule and Noyes-Whitney equation were adopted for mathematically modeling extraction process. Kinetic parameters were fitted and calculated by the Statistical Program for Social Sciences 20.0 software. The transferable efficiency was described and evaluated by potential Q-markers transfer trajectory via transitivity availability AUC, extraction ratio P, and decomposition ratio D respectively. The Q-marker was identified with AUC, P, D. Astragaloside IV, laetrile, paeoniflorin, and ferulic acid were studied as potential Q-markers from BYHWD. The relative technologic parameters were presented by mathematic models, which could adequately illustrate the inherent properties of raw materials

Building Quantitative Hydrologic Storylines from Process-based Models for Managing Water Resources in the U.S. Under Climate-changed Futures

NASA Astrophysics Data System (ADS)

Arnold, J.; Gutmann, E. D.; Clark, M. P.; Nijssen, B.; Vano, J. A.; Addor, N.; Wood, A.; Newman, A. J.; Mizukami, N.; Brekke, L. D.; Rasmussen, R.; Mendoza, P. A.

2016-12-01

Climate change narratives for water-resource applications must represent the change signals contextualized by hydroclimatic process variability and uncertainty at multiple scales. Building narratives of plausible change includes assessing uncertainties across GCM structure, internal climate variability, climate downscaling methods, and hydrologic models. Work with this linked modeling chain has dealt mostly with GCM sampling directed separately to either model fidelity (does the model correctly reproduce the physical processes in the world?) or sensitivity (of different model responses to CO2 forcings) or diversity (of model type, structure, and complexity). This leaves unaddressed any interactions among those measures and with other components in the modeling chain used to identify water-resource vulnerabilities to specific climate threats. However, time-sensitive, real-world vulnerability studies typically cannot accommodate a full uncertainty ensemble across the whole modeling chain, so a gap has opened between current scientific knowledge and most routine applications for climate-changed hydrology. To close that gap, the US Army Corps of Engineers, the Bureau of Reclamation, and the National Center for Atmospheric Research are working on techniques to subsample uncertainties objectively across modeling chain components and to integrate results into quantitative hydrologic storylines of climate-changed futures. Importantly, these quantitative storylines are not drawn from a small sample of models or components. Rather, they stem from the more comprehensive characterization of the full uncertainty space for each component. Equally important from the perspective of water-resource practitioners, these quantitative hydrologic storylines are anchored in actual design and operations decisions potentially affected by climate change. This talk will describe part of our work characterizing variability and uncertainty across modeling chain components and their

Quantitative Decision Support Requires Quantitative User Guidance

NASA Astrophysics Data System (ADS)

Smith, L. A.

2009-12-01

Is it conceivable that models run on 2007 computer hardware could provide robust and credible probabilistic information for decision support and user guidance at the ZIP code level for sub-daily meteorological events in 2060? In 2090? Retrospectively, how informative would output from today’s models have proven in 2003? or the 1930’s? Consultancies in the United Kingdom, including the Met Office, are offering services to “future-proof” their customers from climate change. How is a US or European based user or policy maker to determine the extent to which exciting new Bayesian methods are relevant here? or when a commercial supplier is vastly overselling the insights of today’s climate science? How are policy makers and academic economists to make the closely related decisions facing them? How can we communicate deep uncertainty in the future at small length-scales without undermining the firm foundation established by climate science regarding global trends? Three distinct aspects of the communication of the uses of climate model output targeting users and policy makers, as well as other specialist adaptation scientists, are discussed. First, a brief scientific evaluation of the length and time scales at which climate model output is likely to become uninformative is provided, including a note on the applicability the latest Bayesian methodology to current state-of-the-art general circulation models output. Second, a critical evaluation of the language often employed in communication of climate model output, a language which accurately states that models are “better”, have “improved” and now “include” and “simulate” relevant meteorological processed, without clearly identifying where the current information is thought to be uninformative and misleads, both for the current climate and as a function of the state of the (each) climate simulation. And thirdly, a general approach for evaluating the relevance of quantitative climate model output

Quantitative model of the growth of floodplains by vertical accretion

USGS Publications Warehouse

Moody, J.A.; Troutman, B.M.

2000-01-01

A simple one-dimensional model is developed to quantitatively predict the change in elevation, over a period of decades, for vertically accreting floodplains. This unsteady model approximates the monotonic growth of a floodplain as an incremental but constant increase of net sediment deposition per flood for those floods of a partial duration series that exceed a threshold discharge corresponding to the elevation of the floodplain. Sediment deposition from each flood increases the elevation of the floodplain and consequently the magnitude of the threshold discharge resulting in a decrease in the number of floods and growth rate of the floodplain. Floodplain growth curves predicted by this model are compared to empirical growth curves based on dendrochronology and to direct field measurements at five floodplain sites. The model was used to predict the value of net sediment deposition per flood which best fits (in a least squares sense) the empirical and field measurements; these values fall within the range of independent estimates of the net sediment deposition per flood based on empirical equations. These empirical equations permit the application of the model to estimate of floodplain growth for other floodplains throughout the world which do not have detailed data of sediment deposition during individual floods. Copyright (C) 2000 John Wiley and Sons, Ltd.

Quantitative model of super-Arrhenian behavior in glass forming materials

NASA Astrophysics Data System (ADS)

Caruthers, J. M.; Medvedev, G. A.

2018-05-01

The key feature of glass forming liquids is the super-Arrhenian temperature dependence of the mobility, where the mobility can increase by ten orders of magnitude or more as the temperature is decreased if crystallization does not intervene. A fundamental description of the super-Arrhenian behavior has been developed; specifically, the logarithm of the relaxation time is a linear function of 1 /U¯x , where U¯x is the independently determined excess molar internal energy and B is a material constant. This one-parameter mobility model quantitatively describes data for 21 glass forming materials, which are all the materials where there are sufficient experimental data for analysis. The effect of pressure on the loga mobility is also described using the same U¯x(T ,p ) function determined from the difference between the liquid and crystalline internal energies. It is also shown that B is well correlated with the heat of fusion. The prediction of the B /U¯x model is compared to the Adam and Gibbs 1 /T S¯x model, where the B /U¯x model is significantly better in unifying the full complement of mobility data. The implications of the B /U¯x model for the development of a fundamental description of glass are discussed.

Crystal growth, spectroscopic, DFT computational and third harmonic generation studies of nicotinic acid

NASA Astrophysics Data System (ADS)

Thaya Kumari, C. Rathika; Nageshwari, M.; Raman, R. Ganapathi; Caroline, M. Lydia

2018-07-01

An organic centrosymmetric nicotinic acid (NA) single crystal has been grown employing slow evaporation method in water. NA crystallizes in monoclinic system with centric space group P21/C. The experimental and theoretical investigation includes vibrational spectra based on Hartree - Fock (HF) and density functional theory (DFT) has been applied using different function at B3LYP level of theory using 6-311G++(d,p) basis set. The optical transparency of the title molecule was examined by TD- DFT analysis and for comparison basis experimental UV-Vis spectrum was recorded. The interaction of charge within the molecule was analyzed and the HOMO - LUMO energy gap was evaluated. The value of dipole moment, Mulliken charge and molecular electrostatic potential were estimated at the same level of theory. Also the first order hyper polarizability for NA was calculated. The dielectric behavior of the grown crystal was determined for few selected temperatures. The third order nonlinear response of NA has been examined using Z-scan technique and nonlinear susceptibility (χ3), nonlinear refraction (n2) and nonlinear absorption coefficient (β) has been calculated. The current results clearly indicate that the title compound is an excellent applicant in the domain of opto - electronic applications.

DFT Studies of SN2 Dechlorination of Polychlorinated Biphenyls.

PubMed

Krzemińska, Agnieszka; Paneth, Piotr

2016-06-21

Nucleophilic dechlorination of all 209 PCBs congeners by ethylene glycol anion has been studied theoretically at the DFT level. The obtained Gibbs free energies of activation are in the range 7-22 kcal/mol. The reaction Gibbs free energies indicate that all reactions are virtually irreversible. Due to geometric constrains these reactions undergo rather untypical attack with attacking oxygen atom being nearly perpendicular to the attacked C-Cl bond. The most prone to substitution are chlorine atoms that occupy ortho- (2, 2', 6, 6') positions. These results provide extensive information on the PEG/KOH dependent PCBs degradation. They can also be used in further developments of reaction class transition state theory (RC-TST) for description of complex reactive systems encountered for example in combustion processes.

Quantitative Acoustic Model for Adhesion Evaluation of Pmma/silicon Film Structures

NASA Astrophysics Data System (ADS)