Palpation simulator with stable haptic feedback.

PubMed

Kim, Sang-Youn; Ryu, Jee-Hwan; Lee, WooJeong

2015-01-01

The main difficulty in constructing palpation simulators is to compute and to generate stable and realistic haptic feedback without vibration. When a user haptically interacts with highly non-homogeneous soft tissues through a palpation simulator, a sudden change of stiffness in target tissues causes unstable interaction with the object. We propose a model consisting of a virtual adjustable damper and an energy measuring element. The energy measuring element gauges energy which is stored in a palpation simulator and the virtual adjustable damper dissipates the energy to achieve stable haptic interaction. To investigate the haptic behavior of the proposed method, impulse and continuous inputs are provided to target tissues. If a haptic interface point meets with the hardest portion in the target tissues modeled with a conventional method, we observe unstable motion and feedback force. However, when the target tissues are modeled with the proposed method, a palpation simulator provides stable interaction without vibration. The proposed method overcomes a problem in conventional haptic palpation simulators where unstable force or vibration can be generated if there is a big discrepancy in material property between an element and its neighboring elements in target tissues.

Improving the accuracy of Møller-Plesset perturbation theory with neural networks

NASA Astrophysics Data System (ADS)

McGibbon, Robert T.; Taube, Andrew G.; Donchev, Alexander G.; Siva, Karthik; Hernández, Felipe; Hargus, Cory; Law, Ka-Hei; Klepeis, John L.; Shaw, David E.

2017-10-01

Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when modeling van der Waals interactions and π-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interaction energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol-1 (root-mean-square error 0.09 kcal mol-1), a 6- to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory- and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Furthermore, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction energies, a feature not available from any alternative method.

Improving the accuracy of Møller-Plesset perturbation theory with neural networks.

PubMed

McGibbon, Robert T; Taube, Andrew G; Donchev, Alexander G; Siva, Karthik; Hernández, Felipe; Hargus, Cory; Law, Ka-Hei; Klepeis, John L; Shaw, David E

2017-10-28

Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when modeling van der Waals interactions and π-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interaction energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol -1 (root-mean-square error 0.09 kcal mol -1 ), a 6- to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory- and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Furthermore, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction energies, a feature not available from any alternative method.

Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-Hydrogen-Bond Datasets for Noncovalent Interactions.

PubMed

Suárez, Dimas; Díaz, Natalia; Francisco, Evelio; Martín Pendás, Angel

2018-04-17

The interacting quantum atoms (IQA) method can assess, systematically and in great detail, the strength and physics of both covalent and noncovalent interactions. The lack of a pair density in density functional theory (DFT), which precludes the direct IQA decomposition of the characteristic exchange-correlation energy, has been recently overcome by means of a scaling technique, which can largely expand the applicability of the method. To better assess the utility of the augmented IQA methodology to derive quantum chemical decompositions at the atomic and molecular levels, we report the results of Hartree-Fock (HF) and DFT calculations on the complexes included in the S66 and the ionic H-bond databases of benchmark geometry and binding energies. For all structures, we perform single-point and geometry optimizations using HF and selected DFT methods with triple-ζ basis sets followed by full IQA calculations. Pairwise dispersion energies are accounted for by the D3 method. We analyze the goodness of the HF-D3 and DFT-D3 binding energies, the magnitude of numerical errors, the fragment and atomic distribution of formation energies, etc. It is shown that fragment-based IQA decomposes the formation energies in comparable terms to those of perturbative approaches and that the atomic IQA energies hold the promise of rigorously quantifying atomic and group energy contributions in larger biomolecular systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

PubMed

Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

2014-11-18

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

A Prediction Method of Binding Free Energy of Protein and Ligand

NASA Astrophysics Data System (ADS)

Yang, Kun; Wang, Xicheng

2010-05-01

Predicting the binding free energy is an important problem in bimolecular simulation. Such prediction would be great benefit in understanding protein functions, and may be useful for computational prediction of ligand binding strengths, e.g., in discovering pharmaceutical drugs. Free energy perturbation (FEP)/thermodynamics integration (TI) is a classical method to explicitly predict free energy. However, this method need plenty of time to collect datum, and that attempts to deal with some simple systems and small changes of molecular structures. Another one for estimating ligand binding affinities is linear interaction energy (LIE) method. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. However, it also is time-consuming work. In this paper, a new prediction method based on steered molecular dynamics (SMD) with direction optimization is developed to compute binding free energy. Jarzynski's equality is used to derive the PMF or free-energy. The results for two numerical examples are presented, showing that the method has good accuracy and efficiency. The novel method can also simulate whole binding proceeding and give some important structural information about development of new drugs.

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.

Communication: Density functional theory overcomes the failure of predicting intermolecular interaction energies

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

Podeszwa, Rafal; Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716; Szalewicz, Krzysztof

2012-04-28

Density-functional theory (DFT) revolutionized the ability of computational quantum mechanics to describe properties of matter and is by far the most often used method. However, all the standard variants of DFT fail to predict intermolecular interaction energies. In recent years, a number of ways to go around this problem has been proposed. We show that some of these approaches can reproduce interaction energies with median errors of only about 5% in the complete range of intermolecular configurations. Such errors are comparable to typical uncertainties of wave-function-based methods in practical applications. Thus, these DFT methods are expected to find broad applicationsmore » in modelling of condensed phases and of biomolecules.« less

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Effects of an electric field on interaction of aromatic systems.

PubMed

Youn, Il Seung; Cho, Woo Jong; Kim, Kwang S

2016-04-30

The effect of uniform external electric field on the interactions between small aromatic compounds and an argon atom is investigated using post-HF (MP2, SCS-MP2, and CCSD(T)) and density functional (PBE0-D3, PBE0-TS, and vdW-DF2) methods. The electric field effect is quantified by the difference of interaction energy calculated in the presence and absence of the electric field. All the post-HF methods describe electric field effects accurately although the interaction energy itself is overestimated by MP2. The electric field effect is explained by classical electrostatic models, where the permanent dipole moment from mutual polarization mainly determines its sign. The size of π-conjugated system does not have significant effect on the electric field dependence. We found out that PBE0-based methods give reasonable interaction energies and electric field response in every case, while vdW-DF2 sometimes shows spurious artifact owing to its sensitivity toward the real space electron density. © 2015 Wiley Periodicals, Inc.

Fighting detection using interaction energy force

NASA Astrophysics Data System (ADS)

Wateosot, Chonthisa; Suvonvorn, Nikom

2017-02-01

Fighting detection is an important issue in security aimed to prevent criminal or undesirable events in public places. Many researches on computer vision techniques have studied to detect the specific event in crowded scenes. In this paper we focus on fighting detection using social-based Interaction Energy Force (IEF). The method uses low level features without object extraction and tracking. The interaction force is modeled using the magnitude and direction of optical flows. A fighting factor is developed under this model to detect fighting events using thresholding method. An energy map of interaction force is also presented to identify the corresponding events. The evaluation is performed using NUSHGA and BEHAVE datasets. The results show the efficiency with high accuracy regardless of various conditions.

CO oxidation reaction on Pt(111) studied by the dynamic Monte Carlo method including lateral interactions of adsorbates.

PubMed

Nagasaka, Masanari; Kondoh, Hiroshi; Nakai, Ikuyo; Ohta, Toshiaki

2007-01-28

The dynamics of adsorbate structures during CO oxidation on Pt(111) surfaces and its effects on the reaction were studied by the dynamic Monte Carlo method including lateral interactions of adsorbates. The lateral interaction energies between adsorbed species were calculated by the density functional theory method. Dynamic Monte Carlo simulations were performed for the oxidation reaction over a mesoscopic scale, where the experimentally determined activation energies of elementary paths were altered by the calculated lateral interaction energies. The simulated results reproduced the characteristics of the microscopic and mesoscopic scale adsorbate structures formed during the reaction, and revealed that the complicated reaction kinetics is comprehensively explained by a single reaction path affected by the surrounding adsorbates. We also propose from the simulations that weakly adsorbed CO molecules at domain boundaries promote the island-periphery specific reaction.

A theoretical approach for estimation of ultimate size of bimetallic nanocomposites synthesized in microemulsion systems

NASA Astrophysics Data System (ADS)

Salabat, Alireza; Saydi, Hassan

2012-12-01

In this research a new idea for prediction of ultimate sizes of bimetallic nanocomposites synthesized in water-in-oil microemulsion system is proposed. In this method, by modifying Tabor Winterton approximation equation, an effective Hamaker constant was introduced. This effective Hamaker constant was applied in the van der Waals attractive interaction energy. The obtained effective van der Waals interaction energy was used as attractive contribution in the total interaction energy. The modified interaction energy was applied successfully to predict some bimetallic nanoparticles, at different mass fraction, synthesized in microemulsion system of dioctyl sodium sulfosuccinate (AOT)/isooctane.

Interaction entropy for protein-protein binding

NASA Astrophysics Data System (ADS)

Sun, Zhaoxi; Yan, Yu N.; Yang, Maoyou; Zhang, John Z. H.

2017-03-01

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interaction entropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interaction entropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions.

PubMed

Vosmeer, C Ruben; Kooi, Derk P; Capoferri, Luigi; Terpstra, Margreet M; Vermeulen, Nico P E; Geerke, Daan P

2016-01-01

Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was shown to decrease the root-mean-square error and standard deviation of error prediction by combining interaction energies of simulations starting from different conformations. Thereby, different parts of protein-ligand conformational space are sampled in parallel simulations. The iterative LIE framework relies on the assumption that separate simulations explore different local parts of phase space, and do not show transitions to other parts of configurational space that are already covered in parallel simulations. In this work, a method is proposed to (automatically) detect such transitions during the simulations that are performed to construct LIE models and to predict binding affinities. Using noise-canceling techniques and splines to fit time series of the raw data for the interaction energies, transitions during simulation between different parts of phase space are identified. Boolean selection criteria are then applied to determine which parts of the interaction energy trajectories are to be used as input for the LIE calculations. Here we show that this filtering approach benefits the predictive quality of our previous CYP 2D6-aryloxypropanolamine LIE model. In addition, an analysis is performed of the gain in computational efficiency that can be obtained from monitoring simulations using the proposed filtering method and by prematurely terminating simulations accordingly.

Reconstructing the interaction between dark energy and dark matter using Gaussian processes

NASA Astrophysics Data System (ADS)

Yang, Tao; Guo, Zong-Kuan; Cai, Rong-Gen

2015-06-01

We present a nonparametric approach to reconstruct the interaction between dark energy and dark matter directly from SNIa Union 2.1 data using Gaussian processes, which is a fully Bayesian approach for smoothing data. In this method, once the equation of state (w ) of dark energy is specified, the interaction can be reconstructed as a function of redshift. For the decaying vacuum energy case with w =-1 , the reconstructed interaction is consistent with the standard Λ CDM model, namely, there is no evidence for the interaction. This also holds for the constant w cases from -0.9 to -1.1 and for the Chevallier-Polarski-Linder (CPL) parametrization case. If the equation of state deviates obviously from -1 , the reconstructed interaction exists at 95% confidence level. This shows the degeneracy between the interaction and the equation of state of dark energy when they get constraints from the observational data.

Energy Expenditure during Physically Interactive Video Game Playing in Male College Students with Different Playing Experience

ERIC Educational Resources Information Center

Sell, Katie; Lillie, Tia; Taylor, Julie

2008-01-01

Objective: Researchers have yet to explore the effect of physically interactive video game playing on energy expenditure, despite its potential for meeting current minimal daily activity and energy expenditure recommendations. Participants and Methods: Nineteen male college students-12 experienced "Dance Dance Revolution" (DDR) players and 7…

Non-expanded dispersion and induction energies, and damping functions, for molecular interactions with application to HF-He

NASA Astrophysics Data System (ADS)

Knowles, Peter J.; Meath, William J.

The evaluation of second order non-expanded dispersion and induction energies, and the associated damping functions, for interactions involving molecules is discussed with emphasis placed on using the time-dependent coupled Hartree-Fock method. Results are given for the HF-He interaction for all individual partial wave non-expanded dispersion and induction energies varying asymptotically for large R through O(R-8) and O(R-10) respectively and for most of the individual dispersion energies varying as R-9 and R-10. They are used to illustrate various features of charge overlap effects and the damping functions for molecular interactions, which are considerably more complicated than for atom-atom interactions.

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

NASA Astrophysics Data System (ADS)

Zoete, V.; Michielin, O.; Karplus, M.

2003-12-01

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SAS bur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, ΔGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC 50 without reparametrization.

Analysis of exergy efficiency of a super-critical compressed carbon dioxide energy-storage system based on the orthogonal method.

PubMed

He, Qing; Hao, Yinping; Liu, Hui; Liu, Wenyi

2018-01-01

Super-critical carbon dioxide energy-storage (SC-CCES) technology is a new type of gas energy-storage technology. This paper used orthogonal method and variance analysis to make significant analysis on the factors which would affect the thermodynamics characteristics of the SC-CCES system and obtained the significant factors and interactions in the energy-storage process, the energy-release process and the whole energy-storage system. Results have shown that the interactions in the components have little influence on the energy-storage process, the energy-release process and the whole energy-storage process of the SC-CCES system, the significant factors are mainly on the characteristics of the system component itself, which will provide reference for the optimization of the thermal properties of the energy-storage system.

Analysis of exergy efficiency of a super-critical compressed carbon dioxide energy-storage system based on the orthogonal method

PubMed Central

He, Qing; Liu, Hui; Liu, Wenyi

2018-01-01

Super-critical carbon dioxide energy-storage (SC-CCES) technology is a new type of gas energy-storage technology. This paper used orthogonal method and variance analysis to make significant analysis on the factors which would affect the thermodynamics characteristics of the SC-CCES system and obtained the significant factors and interactions in the energy-storage process, the energy-release process and the whole energy-storage system. Results have shown that the interactions in the components have little influence on the energy-storage process, the energy-release process and the whole energy-storage process of the SC-CCES system, the significant factors are mainly on the characteristics of the system component itself, which will provide reference for the optimization of the thermal properties of the energy-storage system. PMID:29634742

Symmetry-adapted perturbation theory interaction energy decomposition for some noble gas complexes

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Sadlej, Joanna

2008-06-01

This Letter contains a study of the interaction energy in HArF⋯N 2 and HArF⋯P 2 complexes. Symmetry-adapted perturbation theory (SAPT) has been applied to analyze the electrostatic, induction, dispersion and exchange contributions to the total interaction energy. The interaction energy has also been obtained by supermolecular method at the MP2, MP4, CCSD, CCSD(T) levels. The interaction energy for the studied complexes results from a partial cancelation of large attractive electrostatic, induction, dispersion terms by a strong repulsive exchange contribution. The induction and dispersion effects proved to be crucial in establishing the preference for the colinear HArF⋯N 2 and HArF⋯P 2 structures and shift direction of νHAr stretching vibrations.

Thick-target transmission method for excitation functions of interaction cross sections

NASA Astrophysics Data System (ADS)

Aikawa, M.; Ebata, S.; Imai, S.

2016-09-01

We propose a method, called as thick-target transmission (T3) method, to obtain an excitation function of interaction cross sections. In an ordinal experiment to measure the excitation function of interaction cross sections by the transmission method, we need to change the beam energy for each cross section. In the T3 method, the excitation function is derived from the beam attenuations measured at the targets of different thicknesses without changing the beam energy. The advantage of the T3 method is the simplicity and availability for radioactive beams. To confirm the availability, we perform a simulation for the 12C + 27Al system with the PHITS code instead of actual experiments. Our results have large uncertainties but well reproduce the tendency of the experimental data.

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

PubMed Central

2011-01-01

With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set. PMID:21836824

Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

PubMed

Bryce, Richard A

2011-04-01

The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

Molecular structure and interactions in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.

PubMed

Dhumal, Nilesh R; Noack, Kristina; Kiefer, Johannes; Kim, Hyung J

2014-04-03

Electronic structure theory (density functional and Møller-Plesset perturbation theory) and vibrational spectroscopy (FT-IR and Raman) are employed to study molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Different conformers of a cation-anion pair based on their molecular interactions are simulated in the gas phase and in a dielectric continuum solvent environment. Although the ordering of conformers in energy varies with theoretical methods, their predictions for three lowest energy conformers in the gas phase are similar. Strong C-H---N interactions between the acidic hydrogen atom of the cation imidazole ring and the nitrogen atom of the anion are predicted for either the lowest or second lowest energy conformer. In a continuum solvent, different theoretical methods yield the same ion-pair conformation for the lowest energy state. In both phases, the density functional method predicts that the anion is in a trans conformation in the lowest energy ion pair state. The theoretical results are compared with experimental observations from Raman scattering and IR absorption spectroscopies and manifestations of the molecular interactions in the vibrational spectra are discussed. The directions of the frequency shifts of the characteristic vibrations relative to the free anion and cation are explained by calculating the difference electron density coupled with electron density topography.

Intuitive Density Functional Theory-Based Energy Decomposition Analysis for Protein-Ligand Interactions.

PubMed

Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

2017-04-11

First-principles quantum mechanical calculations with methods such as density functional theory (DFT) allow the accurate calculation of interaction energies between molecules. These interaction energies can be dissected into chemically relevant components such as electrostatics, polarization, and charge transfer using energy decomposition analysis (EDA) approaches. Typically EDA has been used to study interactions between small molecules; however, it has great potential to be applied to large biomolecular assemblies such as protein-protein and protein-ligand interactions. We present an application of EDA calculations to the study of ligands that bind to the thrombin protein, using the ONETEP program for linear-scaling DFT calculations. Our approach goes beyond simply providing the components of the interaction energy; we are also able to provide visual representations of the changes in density that happen as a result of polarization and charge transfer, thus pinpointing the functional groups between the ligand and protein that participate in each kind of interaction. We also demonstrate with this approach that we can focus on studying parts (fragments) of ligands. The method is relatively insensitive to the protocol that is used to prepare the structures, and the results obtained are therefore robust. This is an application to a real protein drug target of a whole new capability where accurate DFT calculations can produce both energetic and visual descriptors of interactions. These descriptors can be used to provide insights for tailoring interactions, as needed for example in drug design.

Insights into the fold organization of TIM barrel from interaction energy based structure networks.

PubMed

Vijayabaskar, M S; Vishveshwara, Saraswathi

2012-01-01

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the "interaction conservation" viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Prediction of Ras-effector interactions using position energy matrices.

PubMed

Kiel, Christina; Serrano, Luis

2007-09-01

One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein-protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences. Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types. All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/). Supplementary data are available at Bioinformatics online.

Unraveling the role of secondary electrons upon their interaction with photoresist during EUV exposure

NASA Astrophysics Data System (ADS)

Pollentier, Ivan; Vesters, Yannick; Jiang, Jing; Vanelderen, Pieter; de Simone, Danilo

2017-10-01

The interaction of 91.6eV EUV photons with photoresist is very different to that of optical lithography at DUV wavelength. The latter is understood quite well and it is known that photons interact with the resist in a molecular way through the photoacid generator (PAG) of the chemically amplified resist (CAR). In EUV however, the high energy photons interact with the matter on atomic scale, resulting in the generation of secondary electrons. It is believed that these secondary electrons in their turn are responsible in chemical modification and lead to switching reactions that enable resist local dissolution. However, details of the interaction are still unclear, e.g. which reaction an electron with a given energy can initiate. In this work we have introduced a method to measure the chemical interaction of the secondary electrons with the EUV resist. The method is based on electron gun exposures of low energy electrons (range 1eV to 80eV) in the photoresist. The chemical interaction is then measured by Residual Gas Analysis (RGA), which can analyze out of the outgassing which and how much reaction products are generated. In this way a `chemical yield' can be quantified as function of electron energy. This method has been successfully applied to understand the interaction of secondary electrons on the traditional CAR materials. The understanding was facilitated by testing different compositions of an advanced EUV CAR, where resp. polymer only, polymer+PAG, and polymer+PAG+quencher are tested with the electron gun. It was found that low energy electrons down to 3-4eV can activate PAG dissociation, which can lead to polymer deprotection. However it was observed too that energy electrons of 12eV and higher can do direct deprotection even in absence of the PAG. In addition, testing suggests that electrons can generate also other chemical changes on the polymer chain that could lead to cross-linking.

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

PubMed

Comeau, Stephen R; Gatchell, David W; Vajda, Sandor; Camacho, Carlos J

2004-01-01

Predicting protein interactions is one of the most challenging problems in functional genomics. Given two proteins known to interact, current docking methods evaluate billions of docked conformations by simple scoring functions, and in addition to near-native structures yield many false positives, i.e. structures with good surface complementarity but far from the native. We have developed a fast algorithm for filtering docked conformations with good surface complementarity, and ranking them based on their clustering properties. The free energy filters select complexes with lowest desolvation and electrostatic energies. Clustering is then used to smooth the local minima and to select the ones with the broadest energy wells-a property associated with the free energy at the binding site. The robustness of the method was tested on sets of 2000 docked conformations generated for 48 pairs of interacting proteins. In 31 of these cases, the top 10 predictions include at least one near-native complex, with an average RMSD of 5 A from the native structure. The docking and discrimination method also provides good results for a number of complexes that were used as targets in the Critical Assessment of PRedictions of Interactions experiment. The fully automated docking and discrimination server ClusPro can be found at http://structure.bu.edu

Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method.

PubMed

Jara-Cortés, Jesús; Hernández-Trujillo, Jesús

2018-07-05

A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue

PubMed Central

Kjeldsen, Henrik D.; Kaiser, Marcus; Whittington, Miles A.

2015-01-01

Background Brain function is dependent upon the concerted, dynamical interactions between a great many neurons distributed over many cortical subregions. Current methods of quantifying such interactions are limited by consideration only of single direct or indirect measures of a subsample of all neuronal population activity. New method Here we present a new derivation of the electromagnetic analogy to near-field acoustic holography allowing high-resolution, vectored estimates of interactions between sources of electromagnetic activity that significantly improves this situation. In vitro voltage potential recordings were used to estimate pseudo-electromagnetic energy flow vector fields, current and energy source densities and energy dissipation in reconstruction planes at depth into the neural tissue parallel to the recording plane of the microelectrode array. Results The properties of the reconstructed near-field estimate allowed both the utilization of super-resolution techniques to increase the imaging resolution beyond that of the microelectrode array, and facilitated a novel approach to estimating causal relationships between activity in neocortical subregions. Comparison with existing methods The holographic nature of the reconstruction method allowed significantly better estimation of the fine spatiotemporal detail of neuronal population activity, compared with interpolation alone, beyond the spatial resolution of the electrode arrays used. Pseudo-energy flow vector mapping was possible with high temporal precision, allowing a near-realtime estimate of causal interaction dynamics. Conclusions Basic near-field electromagnetic holography provides a powerful means to increase spatial resolution from electrode array data with careful choice of spatial filters and distance to reconstruction plane. More detailed approaches may provide the ability to volumetrically reconstruct activity patterns on neuronal tissue, but the ability to extract vectored data with the method presented already permits the study of dynamic causal interactions without bias from any prior assumptions on anatomical connectivity. PMID:26026581

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer.

PubMed

Li, Jinshan; Zhao, Feng; Jing, Fuqian

2003-02-01

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 345-352, 2003

The multiple roles of histidine in protein interactions

PubMed Central

2013-01-01

Background Among the 20 natural amino acids histidine is the most active and versatile member that plays the multiple roles in protein interactions, often the key residue in enzyme catalytic reactions. A theoretical and comprehensive study on the structural features and interaction properties of histidine is certainly helpful. Results Four interaction types of histidine are quantitatively calculated, including: (1) Cation-π interactions, in which the histidine acts as the aromatic π-motif in neutral form (His), or plays the cation role in protonated form (His+); (2) π-π stacking interactions between histidine and other aromatic amino acids; (3) Hydrogen-π interactions between histidine and other aromatic amino acids; (4) Coordinate interactions between histidine and metallic cations. The energies of π-π stacking interactions and hydrogen-π interactions are calculated using CCSD/6-31+G(d,p). The energies of cation-π interactions and coordinate interactions are calculated using B3LYP/6-31+G(d,p) method and adjusted by empirical method for dispersion energy. Conclusions The coordinate interactions between histidine and metallic cations are the strongest one acting in broad range, followed by the cation-π, hydrogen-π, and π-π stacking interactions. When the histidine is in neutral form, the cation-π interactions are attractive; when it is protonated (His+), the interactions turn to repulsive. The two protonation forms (and pKa values) of histidine are reversibly switched by the attractive and repulsive cation-π interactions. In proteins the π-π stacking interaction between neutral histidine and aromatic amino acids (Phe, Tyr, Trp) are in the range from -3.0 to -4.0 kcal/mol, significantly larger than the van der Waals energies. PMID:23452343

Energetics of protein-DNA interactions.

PubMed

Donald, Jason E; Chen, William W; Shakhnovich, Eugene I

2007-01-01

Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that theoretical models describe the macromolecular interaction energetics accurately. While several methods have been proposed, there has not been a careful comparison of how well the different methods are able to predict biologically important quantities such as the correct DNA binding sequence, total binding free energy and free energy changes caused by DNA mutation. In addition to carrying out the comparison, we present two important theoretical models developed initially in protein folding that have not yet been tried on protein-DNA interactions. In the process, we find that the results of these knowledge-based potentials show a strong dependence on the interaction distance and the derivation method. Finally, we present a knowledge-based potential that gives comparable or superior results to the best of the other methods, including the molecular mechanics force field AMBER99.

New method to measure the attenuation of hadrons in extensive air showers

NASA Astrophysics Data System (ADS)

Apel, W. D.; Arteaga, J. C.; Badea, F.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Brüggemann, M.; Buchholz, P.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuhrmann, D.; Ghia, P. L.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hildebrand, D.; Hörandel, J. R.; Huege, T.; Isar, P. G.; Kampert, K.-H.; Kang, D.; Kickelbick, D.; Klages, H. O.; Kolotaev, Y.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Navarra, G.; Nehls, S.; Oehlschläger, J.; Ostapchenko, S.; Over, S.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schröder, F.; Sima, O.; Stümpert, M.; Toma, G.; Trinchero, G. C.; Ulrich, H.; van Buren, J.; Walkowiak, W.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.

2009-07-01

Extensive air showers are generated through interactions of high-energy cosmic rays impinging the Earth’s atmosphere. A new method is described to infer the attenuation of hadrons in air showers. The numbers of electrons and muons, registered with the scintillator array of the KASCADE experiment, are used to estimate the energy of the shower inducing primary particle. A large hadron calorimeter is used to measure the hadronic energy reaching observation level. The ratio of energy reaching ground level to the energy of the primary particle is used to derive an attenuation length of hadrons in air showers. In the energy range from 106 to 3×107GeV the attenuation length obtained increases from 170 to 210g/cm2. The experimental results are compared to predictions of simulations based on contemporary high-energy interaction models.

Nature of the water/aromatic parallel alignment interactions.

PubMed

Mitoraj, Mariusz P; Janjić, Goran V; Medaković, Vesna B; Veljković, Dušan Ž; Michalak, Artur; Zarić, Snežana D; Milčić, Miloš K

2015-01-30

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE(CCSD)(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O-H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.

Cluster approach to the prediction of thermodynamic and transport properties of ionic liquids

NASA Astrophysics Data System (ADS)

Seeger, Zoe L.; Kobayashi, Rika; Izgorodina, Ekaterina I.

2018-05-01

The prediction of physicochemical properties of ionic liquids such as conductivity and melting point would substantially aid the targeted design of ionic liquids for specific applications ranging from solvents for extraction of valuable chemicals to biowaste to electrolytes in alternative energy devices. The previously published study connecting the interaction energies of single ion pairs (1 IP) of ionic liquids to their thermodynamic and transport properties has been extended to larger systems consisting of two ion pairs (2 IPs), in which many-body and same-ion interactions are included. Routinely used cations, of the imidazolium and pyrrolidinium families, were selected in the study coupled with chloride, tetrafluoroborate, and dicyanamide. Their two ion pair clusters were subjected to extensive configuration screening to establish most stable structures. Interaction energies of these clusters were calculated at the spin-ratio scaled MP2 (SRS-MP2) level for the correlation interaction energy, and a newly developed scaled Hartree-Fock method for the rest of energetic contributions to interaction energy. A full geometry screening for each cation-anion combination resulted in 192 unique structures, whose stability was assessed using two criteria—widely used interaction energy and total electronic energy. Furthermore, the ratio of interaction energy to its dispersion component was correlated with experimentally observed melting points in 64 energetically favourable structures. These systems were also used to test the correlation of the dispersion contribution to interaction energy with measured conductivity.

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

PubMed

May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

2014-02-01

To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

Inclusion of Structural Flexibility in Design Load Analysis for Wave Energy Converters: Preprint

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

Guo, Yi; Yu, Yi-Hsiang; van Rij, Jennifer A

2017-08-14

Hydroelastic interactions, caused by ocean wave loading on wave energy devices with deformable structures, are studied in the time domain. A midfidelity, hybrid modeling approach of rigid-body and flexible-body dynamics is developed and implemented in an open-source simulation tool for wave energy converters (WEC-Sim) to simulate the dynamic responses of wave energy converter component structural deformations under wave loading. A generalized coordinate system, including degrees of freedom associated with rigid bodies, structural modes, and constraints connecting multiple bodies, is utilized. A simplified method of calculating stress loads and sectional bending moments is implemented, with the purpose of sizing and designingmore » wave energy converters. Results calculated using the method presented are verified with those of high-fidelity fluid-structure interaction simulations, as well as low-fidelity, frequency-domain, boundary element method analysis.« less

Correlation energy extrapolation by many-body expansion

DOE PAGES

Boschen, Jeffery S.; Theis, Daniel; Ruedenberg, Klaus; ...

2017-01-09

Accounting for electron correlation is required for high accuracy calculations of molecular energies. The full configuration interaction (CI) approach can fully capture the electron correlation within a given basis, but it does so at a computational expense that is impractical for all but the smallest chemical systems. In this work, a new methodology is presented to approximate configuration interaction calculations at a reduced computational expense and memory requirement, namely, the correlation energy extrapolation by many-body expansion (CEEMBE). This method combines a MBE approximation of the CI energy with an extrapolated correction obtained from CI calculations using subsets of the virtualmore » orbitals. The extrapolation approach is inspired by, and analogous to, the method of correlation energy extrapolation by intrinsic scaling. Benchmark calculations of the new method are performed on diatomic fluorine and ozone. Finally, the method consistently achieves agreement with CI calculations to within a few mhartree and often achieves agreement to within ~1 millihartree or less, while requiring significantly less computational resources.« less

Correlation energy extrapolation by many-body expansion

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

Boschen, Jeffery S.; Theis, Daniel; Ruedenberg, Klaus

Accounting for electron correlation is required for high accuracy calculations of molecular energies. The full configuration interaction (CI) approach can fully capture the electron correlation within a given basis, but it does so at a computational expense that is impractical for all but the smallest chemical systems. In this work, a new methodology is presented to approximate configuration interaction calculations at a reduced computational expense and memory requirement, namely, the correlation energy extrapolation by many-body expansion (CEEMBE). This method combines a MBE approximation of the CI energy with an extrapolated correction obtained from CI calculations using subsets of the virtualmore » orbitals. The extrapolation approach is inspired by, and analogous to, the method of correlation energy extrapolation by intrinsic scaling. Benchmark calculations of the new method are performed on diatomic fluorine and ozone. Finally, the method consistently achieves agreement with CI calculations to within a few mhartree and often achieves agreement to within ~1 millihartree or less, while requiring significantly less computational resources.« less

Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.

PubMed

Wei, Dongshan; Wang, Feng

2010-08-28

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

NASA Astrophysics Data System (ADS)

Wei, Dongshan; Wang, Feng

2010-08-01

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Calculating electronic correlation effects from densities of transitions

NASA Astrophysics Data System (ADS)

Haydock, Roger

Adding a localized electron to a system of interacting electrons induces a density of transitions described by the time-independent Heisenberg equation. Sequences of these transitions generate interacting states whose total energy is the sum of energies of the constituent transitions. A calculation of magnetic moments for itinerant electrons with Ising interactions illustrates this method. supported by the H. V. Snyder Gift to the University of Oregon.

Raman spectroscopy study and first-principles calculations of the interaction between nucleic acid bases and carbon nanotubes.

PubMed

Stepanian, Stepan G; Karachevtsev, Maksym V; Glamazda, Alexander Yu; Karachevtsev, Victor A; Adamowicz, L

2009-04-16

In this work, we have used Raman spectroscopy and quantum chemical methods (MP2 and DFT) to study the interactions between nucleic acid bases (NABs) and single-walled carbon nanotubes (SWCNT). We found that the appearance of the interaction between the nanotubes and the NABs is accompanied by a spectral shift of the high-frequency component of the SWCNT G band in the Raman spectrum to a lower frequency region. The value of this shift varies from 0.7 to 1.3 cm(-1) for the metallic nanotubes and from 2.1 to 3.2 cm(-1) for the semiconducting nanotubes. Calculations of the interaction energies between the NABs and a fragment of the zigzag(10,0) carbon nanotube performed at the MP2/6-31++G(d,p)[NABs atoms]|6-31G(d)[nanotube atoms] level of theory while accounting for the basis set superposition error during geometry optimization allowed us to order the NABs according to the increasing interaction energy value. The order is: guanine (-67.1 kJ mol(-1)) > adenine (-59.0 kJ mol(-1)) > cytosine (-50.3 kJ mol(-1)) approximately = thymine (-50.2 kJ mol(-1)) > uracil (-44.2 kJ mol(-1)). The MP2 equilibrium structures and the interaction energies were used as reference points in the evaluation of the ability of various functionals in the DFT method to predict those structures and energies. We showed that the M05, MPWB1K, and MPW1B95 density functionals are capable of correctly predicting the SWCNT-NAB geometries but not the interaction energies, while the M05-2X functional is capable of correctly predicting both the geometries and the interaction energies.

Effective fragment potential study of the interaction of DNA bases.

PubMed

Smith, Quentin A; Gordon, Mark S; Slipchenko, Lyudmila V

2011-10-20

Hydrogen-bonded and stacked structures of adenine-thymine and guanine-cytosine nucleotide base pairs, along with their methylated analogues, are examined with the ab inito based general effective fragment potential (EFP2) method. A comparison of coupled cluster with single, double, and perturbative triple (CCSD(T)) energies is presented, along with an EFP2 energy decomposition to illustrate the components of the interaction energy.

Probabilistic models for capturing more physicochemical properties on protein-protein interface.

PubMed

Guo, Fei; Li, Shuai Cheng; Du, Pufeng; Wang, Lusheng

2014-06-23

Protein-protein interactions play a key role in a multitude of biological processes, such as signal transduction, de novo drug design, immune responses, and enzymatic activities. It is of great interest to understand how proteins interact with each other. The general approach is to explore all possible poses and identify near-native ones with the energy function. The key issue here is to design an effective energy function, based on various physicochemical properties. In this paper, we first identify two new features, the coupled dihedral angles on the interfaces and the geometrical information on π-π interactions. We study these two features through statistical methods: a mixture of bivariate von Mises distributions is used to model the correlation of the coupled dihedral angles, while a mixture of bivariate normal distributions is used to model the orientation of the aromatic rings on π-π interactions. Using 6438 complexes, we parametrize the joint distribution of each new feature. Then, we propose a novel method to construct the energy function for protein-protein interface prediction, which includes the new features as well as the existing energy items such as dDFIRE energy, side-chain energy, atom contact energy, and amino acid energy. Experiments show that our method outperforms the state-of-the-art methods, ZRANK and ClusPro. We use the CAPRI evaluation criteria, Irmsd value, and Fnat value. On Benchmark v4.0, our method has an average Irmsd value of 3.39 Å and Fnat value of 62%, which improves upon the average Irmsd value of 3.89 Å and Fnat value of 49% for ZRANK, and the average Irmsd value of 3.99 Å and Fnat value of 46% for ClusPro. On the CAPRI targets, our method has an average Irmsd value of 3.56 Å and Fnat value of 42%, which improves upon the average Irmsd value of 4.27 Å and Fnat value of 39% for ZRANK, the average Irmsd value of 5.15 Å and Fnat value of 30% for ClusPro.

Cosmic rays energy determination by radio emission registration method at frequency 30-35 MHz

NASA Astrophysics Data System (ADS)

Knurenko, S. P.; Petrov, I. S.

2017-11-01

The study of cosmic rays (CR) of ultrahigh energies first of all requires an estimate of the energy, the spectrum in terms of energies, masses, and the anisotropy of the arrival of primary particles. This can only be done by calculating the energies of all the secondary particles formed during the interaction of the primary particle with the nuclei of the air atoms [1]. First of all, this is the registration of Cherenkov and ionization radiation [2, 3]. According to model calculations, the loss of ionization of air by particles is spent up to 80% of the total energy of the primary particle [4]. The rest of the energy is spent on nuclear interactions of hadrons (nucleons) and is carried away by high-energy muons at sea level. In the hybrid registration of air showers, i.e. electron, muon, and Cherenkov components, we can empirically estimate the energy of the primary CR particle. Such a method has been developed and is being used to this day at the Yakutsk complex installation of the EAS. A detailed description of this method is given in [5, 6]. As an alternative to the energy balance method, we describe below the method of independent estimation of E0 obtained by measuring the radio emission of EAS at the frequency of 30-35 MHz at the Yakutsk array.

A method for fast energy estimation and visualization of protein-ligand interaction

NASA Astrophysics Data System (ADS)

Tomioka, Nobuo; Itai, Akiko; Iitaka, Yoichi

1987-10-01

A new computational and graphical method for facilitating ligand-protein docking studies is developed on a three-dimensional computer graphics display. Various physical and chemical properties inside the ligand binding pocket of a receptor protein, whose structure is elucidated by X-ray crystal analysis, are calculated on three-dimensional grid points and are stored in advance. By utilizing those tabulated data, it is possible to estimate the non-bonded and electrostatic interaction energy and the number of possible hydrogen bonds between protein and ligand molecules in real time during an interactive docking operation. The method also provides a comprehensive visualization of the local environment inside the binding pocket. With this method, it becomes easier to find a roughly stable geometry of ligand molecules, and one can therefore make a rapid survey of the binding capability of many drug candidates. The method will be useful for drug design as well as for the examination of protein-ligand interactions.

Obtaining the lattice energy of the anthracene crystal by modern yet affordable first-principles methods

NASA Astrophysics Data System (ADS)

Sancho-García, J. C.; Aragó, J.; Ortí, E.; Olivier, Y.

2013-05-01

The non-covalent interactions in organic molecules are known to drive their self-assembly to form molecular crystals. We compare, in the case of anthracene and against experimental (electronic-only) sublimation energy, how modern quantum-chemical methods are able to calculate this cohesive energy taking into account all the interactions between occurring dimers in both first-and second-shells. These include both O(N6)- and O(N5)-scaling methods, Local Pair Natural Orbital-parameterized Coupled-Cluster Single and Double, and Spin-Component-Scaled-Møller-Plesset perturbation theory at second-order, respectively, as well as the most modern family of conceived density functionals: double-hybrid expressions in several variants (B2-PLYP, mPW2-PLYP, PWPB95) with customized dispersion corrections (-D3 and -NL). All-in-all, it is shown that these methods behave very accurately producing errors in the 1-2 kJ/mol range with respect to the experimental value taken into account the experimental uncertainty. These methods are thus confirmed as excellent tools for studying all kinds of interactions in chemical systems.

Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands.

PubMed

Deng, Nanjie; Cui, Di; Zhang, Bin W; Xia, Junchao; Cruz, Jeffrey; Levy, Ronald

2018-06-13

Accurately predicting absolute binding free energies of protein-ligand complexes is important as a fundamental problem in both computational biophysics and pharmaceutical discovery. Calculating binding free energies for charged ligands is generally considered to be challenging because of the strong electrostatic interactions between the ligand and its environment in aqueous solution. In this work, we compare the performance of the potential of mean force (PMF) method and the double decoupling method (DDM) for computing absolute binding free energies for charged ligands. We first clarify an unresolved issue concerning the explicit use of the binding site volume to define the complexed state in DDM together with the use of harmonic restraints. We also provide an alternative derivation for the formula for absolute binding free energy using the PMF approach. We use these formulas to compute the binding free energy of charged ligands at an allosteric site of HIV-1 integrase, which has emerged in recent years as a promising target for developing antiviral therapy. As compared with the experimental results, the absolute binding free energies obtained by using the PMF approach show unsigned errors of 1.5-3.4 kcal mol-1, which are somewhat better than the results from DDM (unsigned errors of 1.6-4.3 kcal mol-1) using the same amount of CPU time. According to the DDM decomposition of the binding free energy, the ligand binding appears to be dominated by nonpolar interactions despite the presence of very large and favorable intermolecular ligand-receptor electrostatic interactions, which are almost completely cancelled out by the equally large free energy cost of desolvation of the charged moiety of the ligands in solution. We discuss the relative strengths of computing absolute binding free energies using the alchemical and physical pathway methods.

Configuration interaction singles natural orbitals: An orbital basis for an efficient and size intensive multireference description of electronic excited states

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

Shu, Yinan; Levine, Benjamin G., E-mail: levine@chemistry.msu.edu; Hohenstein, Edward G.

2015-01-14

Multireference quantum chemical methods, such as the complete active space self-consistent field (CASSCF) method, have long been the state of the art for computing regions of potential energy surfaces (PESs) where complex, multiconfigurational wavefunctions are required, such as near conical intersections. Herein, we present a computationally efficient alternative to the widely used CASSCF method based on a complete active space configuration interaction (CASCI) expansion built from the state-averaged natural orbitals of configuration interaction singles calculations (CISNOs). This CISNO-CASCI approach is shown to predict vertical excitation energies of molecules with closed-shell ground states similar to those predicted by state averaged (SA)-CASSCFmore » in many cases and to provide an excellent reference for a perturbative treatment of dynamic electron correlation. Absolute energies computed at the CISNO-CASCI level are found to be variationally superior, on average, to other CASCI methods. Unlike SA-CASSCF, CISNO-CASCI provides vertical excitation energies which are both size intensive and size consistent, thus suggesting that CISNO-CASCI would be preferable to SA-CASSCF for the study of systems with multiple excitable centers. The fact that SA-CASSCF and some other CASCI methods do not provide a size intensive/consistent description of excited states is attributed to changes in the orbitals that occur upon introduction of non-interacting subsystems. Finally, CISNO-CASCI is found to provide a suitable description of the PES surrounding a biradicaloid conical intersection in ethylene.« less

Δ isobars and nuclear saturation

NASA Astrophysics Data System (ADS)

Ekström, A.; Hagen, G.; Morris, T. D.; Papenbrock, T.; Schwartz, P. D.

2018-02-01

We construct a nuclear interaction in chiral effective field theory with explicit inclusion of the Δ -isobar Δ (1232 ) degree of freedom at all orders up to next-to-next-to-leading order (NNLO). We use pion-nucleon (π N ) low-energy constants (LECs) from a Roy-Steiner analysis of π N scattering data, optimize the LECs in the contact potentials up to NNLO to reproduce low-energy nucleon-nucleon scattering phase shifts, and constrain the three-nucleon interaction at NNLO to reproduce the binding energy and point-proton radius of 4He. For heavier nuclei we use the coupled-cluster method to compute binding energies, radii, and neutron skins. We find that radii and binding energies are much improved for interactions with explicit inclusion of Δ (1232 ) , while Δ -less interactions produce nuclei that are not bound with respect to breakup into α particles. The saturation of nuclear matter is significantly improved, and its symmetry energy is consistent with empirical estimates.

Interaction entropy for protein-protein binding.

PubMed

Sun, Zhaoxi; Yan, Yu N; Yang, Maoyou; Zhang, John Z H

2017-03-28

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interactionentropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interactionentropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

Many-body van der Waals interactions in molecules and condensed matter.

PubMed

DiStasio, Robert A; Gobre, Vivekanand V; Tkatchenko, Alexandre

2014-05-28

This work reviews the increasing evidence that many-body van der Waals (vdW) or dispersion interactions play a crucial role in the structure, stability and function of a wide variety of systems in biology, chemistry and physics. Starting with the exact expression for the electron correlation energy provided by the adiabatic connection fluctuation-dissipation theorem, we derive both pairwise and many-body interatomic methods for computing the long-range dispersion energy by considering a model system of coupled quantum harmonic oscillators within the random-phase approximation. By coupling this approach to density functional theory, the resulting many-body dispersion (MBD) method provides an accurate and efficient scheme for computing the frequency-dependent polarizability and many-body vdW energy in molecules and materials with a finite electronic gap. A select collection of applications are presented that ascertain the fundamental importance of these non-bonded interactions across the spectrum of intermolecular (the S22 and S66 benchmark databases), intramolecular (conformational energies of alanine tetrapeptide) and supramolecular (binding energy of the 'buckyball catcher') complexes, as well as molecular crystals (cohesive energies in oligoacenes). These applications demonstrate that electrodynamic response screening and beyond-pairwise many-body vdW interactions--both captured at the MBD level of theory--play a quantitative, and sometimes even qualitative, role in describing the properties considered herein. This work is then concluded with an in-depth discussion of the challenges that remain in the future development of reliable (accurate and efficient) methods for treating many-body vdW interactions in complex materials and provides a roadmap for navigating many of the research avenues that are yet to be explored.

Ionization energies and electron affinities from a random-phase-approximation many-body Green's-function method including exchange interactions

NASA Astrophysics Data System (ADS)

Heßelmann, Andreas

2017-06-01

A many-body Green's-function method employing an infinite order summation of ring and exchange-ring contributions to the self-energy is presented. The individual correlation and relaxation contributions to the quasiparticle energies are calculated using an iterative scheme which utilizes density fitting of the particle-hole, particle-particle and hole-hole densities. It is shown that the ionization energies and electron affinities of this approach agree better with highly accurate coupled-cluster singles and doubles with perturbative triples energy difference results than those obtained with second-order Green's-function approaches. An analysis of the correlation and relaxation terms of the self-energy for the direct- and exchange-random-phase-approximation (RPA) Green's-function methods shows that the inclusion of exchange interactions leads to a reduction of the two contributions in magnitude. These differences, however, strongly cancel each other when summing the individual terms to the quasiparticle energies. Due to this, the direct- and exchange-RPA methods perform similarly for the description of ionization energies (IPs) and electron affinities (EAs). The coupled-cluster reference IPs and EAs, if corrected to the adiabatic energy differences between the neutral and charged molecules, were shown to be in very good agreement with experimental measurements.

Intermolecular symmetry-adapted perturbation theory study of large organic complexes.

PubMed

Heßelmann, Andreas; Korona, Tatiana

2014-09-07

Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.

Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods

NASA Astrophysics Data System (ADS)

Sippl, Wolfgang

2000-08-01

One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient ( r 2 = 0.617, q 2 LOO = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained ( r 2 = 0.991, q 2 LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment ( r 2 = 0.951, q 2 LOO = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.

Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

PubMed

Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

2010-12-15

We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).

A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths.

PubMed

Olariu, Victor; Manesso, Erica; Peterson, Carsten

2017-06-01

Depicting developmental processes as movements in free energy genetic landscapes is an illustrative tool. However, exploring such landscapes to obtain quantitative or even qualitative predictions is hampered by the lack of free energy functions corresponding to the biochemical Michaelis-Menten or Hill rate equations for the dynamics. Being armed with energy landscapes defined by a network and its interactions would open up the possibility of swiftly identifying cell states and computing optimal paths, including those of cell reprogramming, thereby avoiding exhaustive trial-and-error simulations with rate equations for different parameter sets. It turns out that sigmoidal rate equations do have approximate free energy associations. With this replacement of rate equations, we develop a deterministic method for estimating the free energy surfaces of systems of interacting genes at different noise levels or temperatures. Once such free energy landscape estimates have been established, we adapt a shortest path algorithm to determine optimal routes in the landscapes. We explore the method on three circuits for haematopoiesis and embryonic stem cell development for commitment and reprogramming scenarios and illustrate how the method can be used to determine sequential steps for onsets of external factors, essential for efficient reprogramming.

A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths

PubMed Central

Olariu, Victor; Manesso, Erica

2017-01-01

Depicting developmental processes as movements in free energy genetic landscapes is an illustrative tool. However, exploring such landscapes to obtain quantitative or even qualitative predictions is hampered by the lack of free energy functions corresponding to the biochemical Michaelis–Menten or Hill rate equations for the dynamics. Being armed with energy landscapes defined by a network and its interactions would open up the possibility of swiftly identifying cell states and computing optimal paths, including those of cell reprogramming, thereby avoiding exhaustive trial-and-error simulations with rate equations for different parameter sets. It turns out that sigmoidal rate equations do have approximate free energy associations. With this replacement of rate equations, we develop a deterministic method for estimating the free energy surfaces of systems of interacting genes at different noise levels or temperatures. Once such free energy landscape estimates have been established, we adapt a shortest path algorithm to determine optimal routes in the landscapes. We explore the method on three circuits for haematopoiesis and embryonic stem cell development for commitment and reprogramming scenarios and illustrate how the method can be used to determine sequential steps for onsets of external factors, essential for efficient reprogramming. PMID:28680655

Dependence of the average spatial and energy characteristics of the hadron-lepton cascade on the strong interaction parameters at superhigh energies

NASA Technical Reports Server (NTRS)

Boyadjian, N. G.; Dallakyan, P. Y.; Garyaka, A. P.; Mamidjanian, E. A.

1985-01-01

A method for calculating the average spatial and energy characteristics of hadron-lepton cascades in the atmosphere is described. The results of calculations for various strong interaction models of primary protons and nuclei are presented. The sensitivity of the experimentally observed extensive air showers (EAS) characteristics to variations of the elementary act parameters is analyzed.

Feasibility of antihydrogen atom containment in helium: a problem of electron-positron correlation investigated by the Monte Carol method

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

Jackman, T.M.

1987-01-01

A theoretical investigation of the interaction potential between the helium atom and the antihydrogen atom was performed for the purpose of determining the feasibility of antihydrogen atom containment. The interaction potential showed an energy barrier to collapse of this system. A variational estimate of the height of this energy barrier and estimates of lifetime with respect to electron-positron annihilation were determined by the Variational Monte Carlo method. This calculation allowed for an improvement over an SCF result through the inclusion of explicit correlation factors in the trial wave function. An estimate of the correlation energy of this system was determinedmore » by the Green's Function Monte Carlo (GFMC) method.« less

Free energy calculation of single molecular interaction using Jarzynski's identity method: the case of HIV-1 protease inhibitor system

NASA Astrophysics Data System (ADS)

Li, De-Chang; Ji, Bao-Hua

2012-06-01

Jarzynski' identity (JI) method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and experiments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molecular dynamics (SMD) simulations to dissociate the protease of human immunodeficiency type I virus (HIV-1 protease) and its inhibitors. We showed that because of intrinsic complexity of the ligand-receptor system, the energy barrier predicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results suggested that the JI method is more appropriate for reconstructing free energy landscape using the data taken from experiments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distribution in SMD simulations.

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

PubMed Central

2011-01-01

Background The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. Results We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy. Conclusions Our results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone. PMID:21219630

On the Reliability of Pure and Hybrid DFT Methods for the Evaluation of Halogen, Chalcogen, and Pnicogen Bonds Involving Anionic and Neutral Electron Donors.

PubMed

Bauzá, Antonio; Alkorta, Ibon; Frontera, Antonio; Elguero, José

2013-11-12

In this article, we report a comprehensive theoretical study of halogen, chalcogen, and pnicogen bonding interactions using a large set of pure and hybrid functionals and some ab initio methods. We have observed that the pure and some hybrid functionals largely overestimate the interaction energies when the donor atom is anionic (Cl(-) or Br(-)), especially in the halogen bonding complexes. To evaluate the reliability of the different DFT (BP86, BP86-D3, BLYP, BLYP-D3, B3LYP, B97-D, B97-D3, PBE0, HSE06, APFD, and M06-2X) and ab initio (MP2, RI-MP2, and HF) methods, we have compared the binding energies and equilibrium distances to those obtained using the CCSD(T)/aug-cc-pVTZ level of theory, as reference. The addition of the latest available correction for dispersion (D3) to pure functionals is not recommended for the calculation of halogen, chalcogen, and pnicogen complexes with anions, since it further contributes to the overestimation of the binding energies. In addition, in chalcogen bonding interactions, we have studied how the hybridization of the chalcogen atom influences the interaction energies.

Transition-density-fragment interaction combined with transfer integral approach for excitation-energy transfer via charge-transfer states

NASA Astrophysics Data System (ADS)

Fujimoto, Kazuhiro J.

2012-07-01

A transition-density-fragment interaction (TDFI) combined with a transfer integral (TI) method is proposed. The TDFI method was previously developed for describing electronic Coulomb interaction, which was applied to excitation-energy transfer (EET) [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc. 131, 14152 (2009)] and exciton-coupled circular dichroism spectra [K. J. Fujimoto, J. Chem. Phys. 133, 124101 (2010)]. In the present study, the TDFI method is extended to the exchange interaction, and hence it is combined with the TI method for applying to the EET via charge-transfer (CT) states. In this scheme, the overlap correction is also taken into account. To check the TDFI-TI accuracy, several test calculations are performed to an ethylene dimer. As a result, the TDFI-TI method gives a much improved description of the electronic coupling, compared with the previous TDFI method. Based on the successful description of the electronic coupling, the decomposition analysis is also performed with the TDFI-TI method. The present analysis clearly shows a large contribution from the Coulomb interaction in most of the cases, and a significant influence of the CT states at the small separation. In addition, the exchange interaction is found to be small in this system. The present approach is useful for analyzing and understanding the mechanism of EET.

Electron Capture in Slow Collisions of Si4+ With Atomic Hydrogen

NASA Astrophysics Data System (ADS)

Joseph, D. C.; Gu, J. P.; Saha, B. C.

2009-10-01

In recent years the charge transfer involving Si4+ and H at low energies has drawn considerable attention both theoretically and experimentally due to its importance not only in astronomical environments but also in modern semiconductor industries. Accurate information regarding its molecular structures and interactions are essential to understand the low energy collision dynamics. Ab initio calculations are performed using the multireference single- and double-excitation configuration-interaction (MRD-CI) method to evaluate potential energies. State selective cross sections are calculate using fully quantum and semi-classical molecular-orbital close coupling (MOCC) methods in the adiabatic representation. Detail results will be presented in the conference.

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

PubMed Central

Christensen, Anders S.; Elstner, Marcus; Cui, Qiang

2015-01-01

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets. PMID:26328834

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

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

Christensen, Anders S., E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Cui, Qiang, E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Elstner, Marcus

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculatedmore » at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.« less

Computational active site analysis of molecular pathways to improve functional classification of enzymes.

PubMed

Ozyurt, A Sinem; Selby, Thomas L

2008-07-01

This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined X-ray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility; (b) low homology enzymes; and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis. 2008 Wiley-Liss, Inc.

Scale transition using dislocation dynamics and the nudged elastic band method

DOE PAGES

Sobie, Cameron; Capolungo, Laurent; McDowell, David L.; ...

2017-08-01

Microstructural features such as precipitates or irradiation-induced defects impede dislocation motion and directly influence macroscopic mechanical properties such as yield point and ductility. In dislocation-defect interactions both atomic scale and long range elastic interactions are involved. Thermally assisted dislocation bypass of obstacles occurs when thermal fluctuations and driving stresses contribute sufficient energy to overcome the energy barrier. The Nudged Elastic Band (NEB) method is typically used in the context of atomistic simulations to quantify the activation barriers for a given reaction. In this work, the NEB method is generalized to coarse-grain continuum representations of evolving microstructure states beyond the discretemore » particle descriptions of first principles and atomistics. The method we employed enables the calculation of activation energies for a View the MathML source glide dislocation bypassing a [001] self-interstitial atom loop of size in the range of 4-10 nm with a spacing larger than 150nm in α-iron for a range of applied stresses and interaction geometries. This study is complemented by a comparison between atomistic and continuum based prediction of barriers.« less

Theoretical study on the polar hydrogen-π (Hp-π) interactions between protein side chains

PubMed Central

2013-01-01

Background In the study of biomolecular structures and interactions the polar hydrogen-π bonds (Hp-π) are an extensive molecular interaction type. In proteins 11 of 20 natural amino acids and in DNA (or RNA) all four nucleic acids are involved in this type interaction. Results The Hp-π in proteins are studied using high level QM method CCSD/6-311 + G(d,p) + H-Bq (ghost hydrogen basis functions) in vacuum and in solutions (water, acetonitrile, and cyclohexane). Three quantum chemical methods (B3LYP, CCSD, and CCSD(T)) and three basis sets (6-311 + G(d,p), TZVP, and cc-pVTZ) are compared. The Hp-π donors include R2NH, RNH2, ROH, and C6H5OH; and the acceptors are aromatic amino acids, peptide bond unit, and small conjugate π-groups. The Hp-π interaction energies of four amino acid pairs (Ser-Phe, Lys-Phe, His-Phe, and Tyr-Phe) are quantitatively calculated. Conclusions Five conclusion points are abstracted from the calculation results. (1) The common DFT method B3LYP fails in describing the Hp-π interactions. On the other hand, CCSD/6-311 + G(d,p) plus ghost atom H-Bq can yield better results, very close to the state-of-the-art method CCSD(T)/cc-pVTZ. (2) The Hp-π interactions are point to π-plane interactions, possessing much more interaction conformations and broader energy range than other interaction types, such as common hydrogen bond and electrostatic interactions. (3) In proteins the Hp-π interaction energies are in the range 10 to 30 kJ/mol, comparable or even larger than common hydrogen bond interactions. (4) The bond length of Hp-π interactions are in the region from 2.30 to 3.00 Å at the perpendicular direction to the π-plane, much longer than the common hydrogen bonds (~1.9 Å). (5) Like common hydrogen bond interactions, the Hp-π interactions are less affected by solvation effects. PMID:23705926

Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody.

PubMed

Laitinen, Tuomo; Kankare, Jussi A; Peräkylä, Mikael

2004-04-01

Antiestradiol antibody 57-2 binds 17beta-estradiol (E2) with moderately high affinity (K(a) = 5 x 10(8) M(-1)). The structurally related natural estrogens estrone and estriol as well synthetic 17-deoxy-estradiol and 17alpha-estradiol are bound to the antibody with 3.7-4.9 kcal mol(-1) lower binding free energies than E2. Free energy perturbation (FEP) simulations and the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method were applied to investigate the factors responsible for the relatively low cross-reactivity of the antibody with these four steroids, differing from E2 by the substituents of the steroid D-ring. In addition, computational alanine scanning of the binding site residues was carried out with the MM-PBSA method. Both the FEP and MM-PBSA methods reproduced the experimental relative affinities of the five steroids in good agreement with experiment. On the basis of FEP simulations, the number of hydrogen bonds formed between the antibody and steroids, which varied from 0 to 3 in the steroids studied, determined directly the magnitude of the steroid-antibody interaction free energies. One hydrogen bond was calculated to contribute about 3 kcal mol(-1) to the interaction energy. Because the relative binding free energies of estrone (two antibody-steroid hydrogen bonds), estriol (three hydrogen bonds), 17-deoxy-estradiol (no hydrogen bonds), and 17alpha-estradiol (two hydrogen bonds) are close to each other and clearly lower than that of E2 (three hydrogen bonds), the water-steroid interactions lost upon binding to the antibody make an important contribution to the binding free energies. The MM-PBSA calculations showed that the binding of steroids to the antiestradiol antibody is driven by van der Waals interactions, whereas specificity is solely due to electrostatic interactions. In addition, binding of steroids to the antiestradiol antibody 57-2 was compared to the binding to the antiprogesterone antibody DB3 and antitestosterone antibody 3-C4F5, studied earlier with the MM-PBSA method. Copyright 2004 Wiley-Liss, Inc.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

A method to explore the quantitative interactions between metal and ceria for M/CeO2 catalysts

NASA Astrophysics Data System (ADS)

Zhu, Kong-Jie; Liu, Jie; Yang, Yan-Ju; Xu, Yu-Xing; Teng, Bo-Tao; Wen, Xiao-Dong; Fan, Maohong

2018-03-01

To explore the quantitative relationship of metal interaction with ceria plays a key role in the theoretical design of M/CeO2 catalysts, especially for the new hot topic of atomically dispersed catalysts. A method to quantitatively explore the interactions between metal and ceria is proposed in the present work on the basis of the qualitative analysis of the effects of different factors on metal adsorption at different ceria surfaces by using Ag/CeO2 as a case. Two parameters are firstly presented, Ep which converts the total adsorption energy into the interaction energy per Agsbnd O bond, and θdiff which measures the deviation of Agsbnd Osbnd Ce bond angle from the angle of the sp3 orbital hybridization of O atom. Using the two parameters, the quantitative relationship of the interaction energy between Ag and ceria is established. There is a linear correlation between Ep and dAgsbndO with θdiff. The higher θdiff, the weaker Ep, and the longer Agsbnd O bond. This method is also suitable for other metals (Cu, Ni, Pd, and Rh, etc.) on ceria. It is the first time to establish the quantitative relationship for the interaction between metal and ceria, and sheds light into the theoretical design of M/CeO2 catalysts.

Tertiary structure-based analysis of microRNA–target interactions

PubMed Central

Gan, Hin Hark; Gunsalus, Kristin C.

2013-01-01

Current computational analysis of microRNA interactions is based largely on primary and secondary structure analysis. Computationally efficient tertiary structure-based methods are needed to enable more realistic modeling of the molecular interactions underlying miRNA-mediated translational repression. We incorporate algorithms for predicting duplex RNA structures, ionic strength effects, duplex entropy and free energy, and docking of duplex–Argonaute protein complexes into a pipeline to model and predict miRNA–target duplex binding energies. To ensure modeling accuracy and computational efficiency, we use an all-atom description of RNA and a continuum description of ionic interactions using the Poisson–Boltzmann equation. Our method predicts the conformations of two constructs of Caenorhabditis elegans let-7 miRNA–target duplexes to an accuracy of ∼3.8 Å root mean square distance of their NMR structures. We also show that the computed duplex formation enthalpies, entropies, and free energies for eight miRNA–target duplexes agree with titration calorimetry data. Analysis of duplex–Argonaute docking shows that structural distortions arising from single-base-pair mismatches in the seed region influence the activity of the complex by destabilizing both duplex hybridization and its association with Argonaute. Collectively, these results demonstrate that tertiary structure-based modeling of miRNA interactions can reveal structural mechanisms not accessible with current secondary structure-based methods. PMID:23417009

Investigation of the effective atomic numbers of dosimetric materials for electrons, protons and alpha particles using a direct method in the energy region 10 keV-1 GeV: a comparative study.

PubMed

Kurudirek, Murat; Aksakal, Oğuz; Akkuş, Tuba

2015-11-01

A direct method has been used for the first time, to compute effective atomic numbers (Z eff) of water, air, human tissues, and some organic and inorganic compounds, for total electron proton and alpha particle interaction in the energy region 10 keV-1 GeV. The obtained values for Z eff were then compared to those obtained using an interpolation procedure. In general, good agreement has been observed for electrons, and the difference (%) in Z eff between the results of the direct and the interpolation method was found to be <10 % for all materials, in the energy range from 10 keV to 1 MeV. More specifically, results of the two methods were found to agree well (Dif. <10 %) for air, calcium fluoride, kapton polyimide film, paraffin wax and plastic scintillator in the entire energy region with respect to the total electron interaction. On the other hand, values for Z eff calculated using both methods for protons and alpha particles generally agree with each other in the high-energy region above 10 MeV.

Comparison of photon attenuation coefficients (2-150 KeV) for diagnostic imaging simulations

NASA Astrophysics Data System (ADS)

Dodge, Charles W., III; Flynn, Michael J.

2004-05-01

The Radiology Research Laboratory at the Henry Ford Hospital has been involved in modeling x-ray units in order to predict image quality. A critical part of that modeling process is the accurate choice of interaction coefficients. This paper serves as a review and comparison of existing interaction models. Our objective was to obtain accurate and easily calculated interaction coefficients, at diagnostically relevant energies. We obtained data from: McMaster, Lawrence Berkeley Lab data (LBL), XCOM and FFAST Data from NIST, and the EPDL-97 database via LLNL. Our studies involve low energy photons; therefore, comparisons were limited to Coherent (Rayleigh), Incoherent (Compton) and Photoelectric effects, which were summed to determine a total interaction cross section. Without measured data, it becomes difficult to definitively choose the most accurate method. However, known limitations in the McMaster data and smoothing of photo-edge transitions can be used as a guide to establish more valid approaches. Each method was compared to one another graphically and at individual points. We found that agreement between all methods was excellent when away from photo-edges. Near photo-edges and at low energies, most methods were less accurate. Only the Chanter (FFAST) data seems to have consistently and accurately predicted the placement of edges (through M-shell), while minimizing smoothing errors. The EPDL-97 data by LLNL was the best over method in predicting coherent and incoherent cross sections.

Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model.

PubMed

Warwicker, J

1989-03-20

A method of calculating the electrostatic potential energy between two molecules, using finite difference potential, is presented. A reduced charge set is used so that the interaction energy can be calculated as the two static molecules explore their full six-dimensional configurational space. The energies are contoured over surfaces fixed to each molecule with an interactive computer graphics program. For two crystal structures (trypsin-trypsin inhibitor and anti-lysozyme Fab-lysozyme), it is found that the complex corresponds to highly favourable interacting regions in the contour plots. These matches arise from a small number of protruding basic residues interacting with enhanced negative potential in each case. The redox pair cytochrome c peroxidase-cytochrome c exhibits an extensive favourably interacting surface within which a possible electron transfer complex may be defined by an increased electrostatic complementarity, but a decreased electrostatic energy. A possible substrate transfer configuration for the glycolytic enzyme pair glyceraldehyde phosphate dehydrogenase-phosphoglycerate kinase is presented.

Interaction between alkaline earth cations and oxo-ligands. DFT study of the affinity of the Ca2+ cation for carbonyl ligands.

PubMed

da Costa, Leonardo Moreira; Carneiro, José Walkimar de Mesquita; Romeiro, Gilberto Alves; Paes, Lilian Weitzel Coelho

2011-02-01

The affinity of the Ca(2+) ion for a set of substituted carbonyl ligands was analyzed with both the DFT (B3LYP/6-31+G(d)) and semi-empirical (PM6) methods. Two types of ligands were studied: a set of monosubstituted [O=CH(R)] and a set of disubstituted ligands [O=C(R)(2)] (R=H, F, Cl, Br, OH, OCH(3), CH(3), CN, NH(2) and NO(2)), with R either directly bound to the carbonyl carbon atom or to the para position of a phenyl ring. The interaction energy was calculated to quantify the affinity of the Ca(2+) cation for the ligands. Geometric and electronic parameters were correlated with the intensity of the metal-ligand interaction. The electronic nature of the substituent is the main parameter that determines the interaction energy. Donor groups make the interaction energy more negative (stabilizing the complex formed), while acceptor groups make the interaction energy less negative (destabilizing the complex formed).

Phase diagrams and free-energy landscapes for model spin-crossover materials with antiferromagnetic-like nearest-neighbor and ferromagnetic-like long-range interactions

NASA Astrophysics Data System (ADS)

Chan, C. H.; Brown, G.; Rikvold, P. A.

2017-11-01

We present phase diagrams, free-energy landscapes, and order-parameter distributions for a model spin-crossover material with a two-step transition between the high-spin and low-spin states (a square-lattice Ising model with antiferromagnetic-like nearest-neighbor and ferromagnetic-like long-range interactions) [P. A. Rikvold et al., Phys. Rev. B 93, 064109 (2016), 10.1103/PhysRevB.93.064109]. The results are obtained by a recently introduced, macroscopically constrained Wang-Landau Monte Carlo simulation method [Phys. Rev. E 95, 053302 (2017), 10.1103/PhysRevE.95.053302]. The method's computational efficiency enables calculation of thermodynamic quantities for a wide range of temperatures, applied fields, and long-range interaction strengths. For long-range interactions of intermediate strength, tricritical points in the phase diagrams are replaced by pairs of critical end points and mean-field critical points that give rise to horn-shaped regions of metastability. The corresponding free-energy landscapes offer insights into the nature of asymmetric, multiple hysteresis loops that have been experimentally observed in spin-crossover materials characterized by competing short-range interactions and long-range elastic interactions.

Optimizing energy functions for protein-protein interface design.

PubMed

Sharabi, Oz; Yanover, Chen; Dekel, Ayelet; Shifman, Julia M

2011-01-15

Protein design methods have been originally developed for the design of monomeric proteins. When applied to the more challenging task of protein–protein complex design, these methods yield suboptimal results. In particular, they often fail to recapitulate favorable hydrogen bonds and electrostatic interactions across the interface. In this work, we aim to improve the energy function of the protein design program ORBIT to better account for binding interactions between proteins. By using the advanced machine learning framework of conditional random fields, we optimize the relative importance of all the terms in the energy function, attempting to reproduce the native side-chain conformations in protein–protein interfaces. We evaluate the performance of several optimized energy functions, each describes the van der Waals interactions using a different potential. In comparison with the original energy function, our best energy function (a) incorporates a much “softer” repulsive van der Waals potential, suitable for the discrete rotameric representation of amino acid side chains; (b) does not penalize burial of polar atoms, reflecting the frequent occurrence of polar buried residues in protein–protein interfaces; and (c) significantly up-weights the electrostatic term, attesting to the high importance of these interactions for protein–protein complex formation. Using this energy function considerably improves side chain placement accuracy for interface residues in a large test set of protein–protein complexes. Moreover, the optimized energy function recovers the native sequences of protein–protein interface at a higher rate than the default function and performs substantially better in predicting changes in free energy of binding due to mutations.

The validity of a structured interactive 24-hour recall in estimating energy and nutrient intakes in 15-month-old rural Malawian children.

PubMed

Thakwalakwa, Chrissie M; Kuusipalo, Heli M; Maleta, Kenneth M; Phuka, John C; Ashorn, Per; Cheung, Yin Bun

2012-07-01

This study aimed to compare the nutritional intake values among 15-month-old rural Malawian children obtained by weighed food record (WFR) with those obtained by modified 24-hour recall (mod 24-HR), and to develop algorithm for adjusting mod 24-HR values so as to predict mean intake based on WFRs. The study participants were 169 15-month-old children who participated in a clinical trial. Food consumption on one day was observed and weighed (established criterion) by a research assistant to provide the estimates of energy and nutrient intakes. On the following day, another research assistant, blinded to the direct observation, conducted the structured interactive 24-hour recall (24-HR) interview (test method). Paired t-tests and scatter-plots were used to compare intake values of the two methods. The structured interactive 24-HR method tended to overestimate energy and nutrient intakes (each P < 0.001). The regression-through-the-origin method was used to develop adjustment algorithms. Results showed that multiplying the mean energy, protein, fat, iron, zinc and vitamin A intake estimates based on the test method by 0.86, 0.80, 0.68, 0.69, 0.72 and 0.76, respectively, provides an approximation of the mean values based on WFRs. © 2011 Blackwell Publishing Ltd.

Which Density Functional Should Be Used to Describe Protonated Water Clusters?

PubMed

Shi, Ruili; Huang, Xiaoming; Su, Yan; Lu, Hai-Gang; Li, Si-Dian; Tang, Lingli; Zhao, Jijun

2017-04-27

Protonated water cluster is one of the most important hydrogen-bond network systems. Finding an appropriate DFT method to study the properties of protonated water clusters can substantially improve the economy in computational resources without sacrificing the accuracy compared to high-level methods. Using high-level MP2 and CCSD(T) methods as well as experimental results as benchmark, we systematically examined the effect of seven exchange-correlation GGA functionals (with BLYP, B3LYP, X3LYP, PBE0, PBE1W, M05-2X, and B97-D parametrizations) in describing the geometric parameters, interaction energies, dipole moments, and vibrational properties of protonated water clusters H + (H 2 O) 2-9,12 . The overall performance of all these functionals is acceptable, and each of them has its advantage in certain aspects. X3LYP is the best to describe the interaction energies, and PBE0 and M05-2X are also recommended to investigate interaction energies. PBE0 gives the best anharmonic frequencies, followed by PBE1W, B97-D and BLYP methods. PBE1W, B3LYP, B97-D, and X3LYP can yield better geometries. The capability of B97-D to distinguish the relative energies between isomers is the best among all the seven methods, followed by M05-2X and PBE0.

Third-order interelectronic-interaction correction to the 2 p1/2-2 s transition energy in lithiumlike ions

NASA Astrophysics Data System (ADS)

Zherebtsov, O. M.; Shabaev, V. M.; Yerokhin, V. A.

2000-12-01

Third-order interelectronic-interaction correction to the energies of (1 s) 22 s and (1 s) 22 p1/2 states of high- Z lithiumlike ions is evaluated within the Breit approximation in the range 20⩽ Z⩽100. The calculation is carried out using both the relativistic configuration-interaction method and perturbation theory. The correction is shown to be important for the comparison of theory and experiment.

Bioluminescence resonance energy transfer system for measuring dynamic protein-protein interactions in bacteria.

PubMed

Cui, Boyu; Wang, Yao; Song, Yunhong; Wang, Tietao; Li, Changfu; Wei, Yahong; Luo, Zhao-Qing; Shen, Xihui

2014-05-20

Protein-protein interactions are important for virtually every biological process, and a number of elegant approaches have been designed to detect and evaluate such interactions. However, few of these methods allow the detection of dynamic and real-time protein-protein interactions in bacteria. Here we describe a bioluminescence resonance energy transfer (BRET) system based on the bacterial luciferase LuxAB. We found that enhanced yellow fluorescent protein (eYFP) accepts the emission from LuxAB and emits yellow fluorescence. Importantly, BRET occurred when LuxAB and eYFP were fused, respectively, to the interacting protein pair FlgM and FliA. Furthermore, we observed sirolimus (i.e., rapamycin)-inducible interactions between FRB and FKBP12 and a dose-dependent abolishment of such interactions by FK506, the ligand of FKBP12. Using this system, we showed that osmotic stress or low pH efficiently induced multimerization of the regulatory protein OmpR and that the multimerization induced by low pH can be reversed by a neutralizing agent, further indicating the usefulness of this system in the measurement of dynamic interactions. This method can be adapted to analyze dynamic protein-protein interactions and the importance of such interactions in bacterial processes such as development and pathogenicity. Real-time measurement of protein-protein interactions in prokaryotes is highly desirable for determining the roles of protein complex in the development or virulence of bacteria, but methods that allow such measurement are not available. Here we describe the development of a bioluminescence resonance energy transfer (BRET) technology that meets this need. The use of endogenous excitation light in this strategy circumvents the requirement for the sophisticated instrument demanded by standard fluorescence resonance energy transfer (FRET). Furthermore, because the LuxAB substrate decanal is membrane permeable, the assay can be performed without lysing the bacterial cells, thus allowing the detection of protein-protein interactions in live bacterial cells. This BRET system added another useful tool to address important questions in microbiological studies. Copyright © 2014 Cui et al.

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

PubMed

Copeland, Kari L; Anderson, Julie A; Farley, Adam R; Cox, James R; Tschumper, Gregory S

2008-11-13

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo

2013-08-01

A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

[A graph cuts-based interactive method for segmentation of magnetic resonance images of meningioma].

PubMed

Li, Shuan-qiang; Feng, Qian-jin; Chen, Wu-fan; Lin, Ya-zhong

2011-06-01

For accurate segmentation of the magnetic resonance (MR) images of meningioma, we propose a novel interactive segmentation method based on graph cuts. The high dimensional image features was extracted, and for each pixel, the probabilities of its origin, either the tumor or the background regions, were estimated by exploiting the weighted K-nearest neighborhood classifier. Based on these probabilities, a new energy function was proposed. Finally, a graph cut optimal framework was used for the solution of the energy function. The proposed method was evaluated by application in the segmentation of MR images of meningioma, and the results showed that the method significantly improved the segmentation accuracy compared with the gray level information-based graph cut method.

Monitoring Ligand-Activated Protein-Protein Interactions Using Bioluminescent Resonance Energy Transfer (BRET) Assay.

PubMed

Coriano, Carlos; Powell, Emily; Xu, Wei

2016-01-01

The bioluminescent resonance energy transfer (BRET) assay has been extensively used in cell-based and in vivo imaging systems for detecting protein-protein interactions in the native environment of living cells. These protein-protein interactions are essential for the functional response of many signaling pathways to environmental chemicals. BRET has been used as a toxicological tool for identifying chemicals that either induce or inhibit these protein-protein interactions. This chapter focuses on describing the toxicological applications of BRET and its optimization as a high-throughput detection system in live cells. Here we review the construction of BRET fusion proteins, describe the BRET methodology, and outline strategies to overcome obstacles that may arise. Furthermore, we describe the advantage of BRET over other resonance energy transfer methods for monitoring protein-protein interactions.

Positioning true coincidences that undergo inter-and intra-crystal scatter for a sub-mm resolution cadmium zinc telluride-based PET system

NASA Astrophysics Data System (ADS)

Abbaszadeh, Shiva; Chinn, Garry; Levin, Craig S.

2018-01-01

The kinematics of Compton scatter can be used to estimate the interaction sequence of inter-crystal scatter interactions in 3D position-sensitive cadmium zinc telluride (CZT) detectors. However, in the case of intra-crystal scatter in a ‘cross-strip’ CZT detector slab, multiple anode and cathode strips may be triggered, creating position ambiguity due to uncertainty in possible combinations of anode-cathode pairings. As a consequence, methods such as energy-weighted centroid are not applicable to position the interactions. In practice, since the event position is uncertain, these intra-crystal scatters events are discarded. In this work, we studied using Compton kinematics and a ‘direction difference angle’ to provide a method to correctly identify the anode-cathode pair corresponding to the first interaction position in an intra-crystal scatter event. GATE simulation studies of a NEMA NU4 image quality phantom in a small animal positron emission tomography under development composed of 192, 40~mm×40~mm×5 mm CZT crystals shows that 47% of total numbers of multiple-interaction photon events (MIPEs) are intra-crystal scatter with a 100 keV lower energy threshold per interaction. The sensitivity of the system increases from 0.6 to 4.10 (using 10 keV as system lower energy threshold) by including rather than discarding inter- and intra-crystal scatter. The contrast-to-noise ratio (CNR) also increases from 5.81+/-0.3 to 12.53+/-0.37 . It was shown that a higher energy threshold limits the capability of the system to detect MIPEs and reduces CNR. Results indicate a sensitivity increase (4.1 to 5.88) when raising the lower energy threshold (10 keV to 100 keV) for the case of only two-interaction events. In order to detect MIPEs accurately, a low noise system capable of a low energy threshold (10 keV) per interaction is desired.

Properties of the water to boron nitride interaction: From zero to two dimensions with benchmark accuracy.

PubMed

Al-Hamdani, Yasmine S; Rossi, Mariana; Alfè, Dario; Tsatsoulis, Theodoros; Ramberger, Benjamin; Brandenburg, Jan Gerit; Zen, Andrea; Kresse, Georg; Grüneis, Andreas; Tkatchenko, Alexandre; Michaelides, Angelos

2017-07-28

Molecular adsorption on surfaces plays an important part in catalysis, corrosion, desalination, and various other processes that are relevant to industry and in nature. As a complement to experiments, accurate adsorption energies can be obtained using various sophisticated electronic structure methods that can now be applied to periodic systems. The adsorption energy of water on boron nitride substrates, going from zero to 2-dimensional periodicity, is particularly interesting as it calls for an accurate treatment of polarizable electrostatics and dispersion interactions, as well as posing a practical challenge to experiments and electronic structure methods. Here, we present reference adsorption energies, static polarizabilities, and dynamic polarizabilities, for water on BN substrates of varying size and dimension. Adsorption energies are computed with coupled cluster theory, fixed-node quantum Monte Carlo (FNQMC), the random phase approximation, and second order Møller-Plesset theory. These wavefunction based correlated methods are found to agree in molecular as well as periodic systems. The best estimate of the water/h-BN adsorption energy is -107±7 meV from FNQMC. In addition, the water adsorption energy on the BN substrates could be expected to grow monotonically with the size of the substrate due to increased dispersion interactions, but interestingly, this is not the case here. This peculiar finding is explained using the static polarizabilities and molecular dispersion coefficients of the systems, as computed from time-dependent density functional theory (DFT). Dynamic as well as static polarizabilities are found to be highly anisotropic in these systems. In addition, the many-body dispersion method in DFT emerges as a particularly useful estimation of finite size effects for other expensive, many-body wavefunction based methods.

Van der Waals Interactions of Organic Molecules on Semiconductor and Metal Surfaces: a Comparative Study

NASA Astrophysics Data System (ADS)

Li, Guo; Cooper, Valentino; Cho, Jun-Hyung; Tamblyn, Isaac; Du, Shixuan; Neaton, Jeffrey; Gao, Hong-Jun; Zhang, Zhenyu

2012-02-01

We present a comparative investigation of vdW interactions of the organic molecules on semiconductor and metal surfaces using the DFT method implemented with vdW-DF. For styrene/H-Si(100), the vdW interactions reverse the effective intermolecular interaction from repulsive to attractive, ensuring preferred growth of long wires as observed experimentally. We further propose that an external E field and the selective creation of Si dangling bonds can drastically improve the ordered arrangement of the molecular nanowires [1]. For BDA/Au(111), the vdW interactions not only dramatically enhances the adsorption energies, but also significantly changes the molecular configurations. In the azobenzene/Ag(111) system, vdW-DF produces superior predictions for the adsorption energy than those obtained with other vdW corrected DFT approaches, providing evidence for the applicability of the vdW-DF method [2].

Lattice quantum chromodynamical approach to nuclear physics

NASA Astrophysics Data System (ADS)

Aoki, Sinya; Doi, Takumi; Hatsuda, Tetsuo; Ikeda, Yoichi; Inoue, Takashi; Ishii, Noriyoshi; Murano, Keiko; Nemura, Hidekatsu; Sasaki, Kenji; HAL QCD Collaboration

2012-09-01

We review recent progress in the HAL QCD method, which was recently proposed to investigate hadron interactions in lattice quantum chromodynamics (QCD). The strategy to extract the energy-independent non-local potential in lattice QCD is explained in detail. The method is applied to study nucleon-nucleon, nucleon-hyperon, hyperon-hyperon, and meson-baryon interactions. Several extensions of the method are also discussed.

Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

PubMed

Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

2016-01-01

We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

Self-interaction corrections applied to Mg-porphyrin, C60, and pentacene molecules

NASA Astrophysics Data System (ADS)

Pederson, Mark R.; Baruah, Tunna; Kao, Der-you; Basurto, Luis

2016-04-01

We have applied a recently developed method to incorporate the self-interaction correction through Fermi orbitals to Mg-porphyrin, C60, and pentacene molecules. The Fermi-Löwdin orbitals are localized and unitarily invariant to the Kohn-Sham orbitals from which they are constructed. The self-interaction-corrected energy is obtained variationally leading to an optimum set of Fermi-Löwdin orbitals (orthonormalized Fermi orbitals) that gives the minimum energy. A Fermi orbital, by definition, is dependent on a certain point which is referred to as the descriptor position. The degree to which the initial choice of descriptor positions influences the variational approach to the minimum and the complexity of the energy landscape as a function of Fermi-orbital descriptors is examined in detail for Mg-porphyrin. The applications presented here also demonstrate that the method can be applied to larger molecular systems containing a few hundred electrons. The atomization energy of the C60 molecule within the Fermi-Löwdin-orbital self-interaction-correction approach is significantly improved compared to local density approximation in the Perdew-Wang 92 functional and generalized gradient approximation of Perdew-Burke-Ernzerhof functionals. The eigenvalues of the highest occupied molecular orbitals show qualitative improvement.

Calculation of effective atomic number and electron density of essential biomolecules for electron, proton, alpha particle and multi-energetic photon interactions

NASA Astrophysics Data System (ADS)

Kurudirek, Murat; Onaran, Tayfur

2015-07-01

Effective atomic numbers (Zeff) and electron densities (Ne) of some essential biomolecules have been calculated for total electron interaction, total proton interaction and total alpha particle interaction using an interpolation method in the energy region 10 keV-1 GeV. Also, the spectrum weighted Zeff for multi-energetic photons has been calculated using Auto-Zeff program. Biomolecules consist of fatty acids, amino acids, carbohydrates and basic nucleotides of DNA and RNA. Variations of Zeff and Ne with kinetic energy of ionizing charged particles and effective photon energies of heterogeneous sources have been studied for the given materials. Significant variations in Zeff and Ne have been observed through the entire energy region for electron, proton and alpha particle interactions. Non-uniform variation has been observed for protons and alpha particles in low and intermediate energy regions, respectively. The maximum values of Zeff have found to be in higher energies for total electron interaction whereas maximum values have found to be in relatively low energies for total proton and total alpha particle interactions. When it comes to the multi-energetic photon sources, it has to be noted that the highest Zeff values were found at low energy region where photoelectric absorption is the pre-dominant interaction process. The lowest values of Zeff have been shown in biomolecules such as stearic acid, leucine, mannitol and thymine, which have highest H content in their groups. Variation in Ne seems to be more or less the same with the variation in Zeff for the given materials as expected.

Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies.

PubMed

Gnanasekaran, Ramachandran

2017-11-08

We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein. This approach locates energy transport channels from the dTTP to remote regions of the protein via residues and water molecules. We examine the water dynamics near the catalytic site of HIV-1 RT by molecular dynamics (MD) simulations. We find that, within the catalytic site, the relaxation of water molecules is similar to that of the hydration water molecules present in other proteins and the relaxation time scale is fast enough to transport energy and helps in communication between dTTP and other residues in the system. To quantify energy transfer, we also calculate the interaction energies of dTTP, 2Mg 2+ , doxy-guanosine nucleotide (DG22) with their surrounding residues by using the B3LYP-D3 method. The results, from classical vibrational energy diffusivity and QM interaction energy, are complementary to identify the important residues involved in the process of polymerization. The positive and negative interactions by dTTP with different types of residues in the catalytic region make the residues transfer energy through vibrational communication.

Method, apparatus and system for low-energy beta particle detection

DOEpatents

Akers, Douglas W.; Drigert, Mark W.

2012-09-25

An apparatus, method, and system relating to radiation detection of low-energy beta particles are disclosed. An embodiment includes a radiation detector with a first scintillator and a second scintillator operably coupled to each other. The first scintillator and the second scintillator are each structured to generate a light pulse responsive to interaction with beta particles. The first scintillator is structured to experience full energy deposition of low-energy beta particles, and permit a higher-energy beta particle to pass therethrough and interact with the second scintillator. The radiation detector further includes a light-to-electrical converter operably coupled to the second scintillator and configured to convert light pulses generated by the first scintillator and the second scintillator into electrical signals. The first scintillator and the second scintillator have at least one mutually different characteristic to enable an electronic system to determine whether a given light pulse is generated in the first scintillator or the second scintillator.

Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue.

PubMed

Kjeldsen, Henrik D; Kaiser, Marcus; Whittington, Miles A

2015-09-30

Brain function is dependent upon the concerted, dynamical interactions between a great many neurons distributed over many cortical subregions. Current methods of quantifying such interactions are limited by consideration only of single direct or indirect measures of a subsample of all neuronal population activity. Here we present a new derivation of the electromagnetic analogy to near-field acoustic holography allowing high-resolution, vectored estimates of interactions between sources of electromagnetic activity that significantly improves this situation. In vitro voltage potential recordings were used to estimate pseudo-electromagnetic energy flow vector fields, current and energy source densities and energy dissipation in reconstruction planes at depth into the neural tissue parallel to the recording plane of the microelectrode array. The properties of the reconstructed near-field estimate allowed both the utilization of super-resolution techniques to increase the imaging resolution beyond that of the microelectrode array, and facilitated a novel approach to estimating causal relationships between activity in neocortical subregions. The holographic nature of the reconstruction method allowed significantly better estimation of the fine spatiotemporal detail of neuronal population activity, compared with interpolation alone, beyond the spatial resolution of the electrode arrays used. Pseudo-energy flow vector mapping was possible with high temporal precision, allowing a near-realtime estimate of causal interaction dynamics. Basic near-field electromagnetic holography provides a powerful means to increase spatial resolution from electrode array data with careful choice of spatial filters and distance to reconstruction plane. More detailed approaches may provide the ability to volumetrically reconstruct activity patterns on neuronal tissue, but the ability to extract vectored data with the method presented already permits the study of dynamic causal interactions without bias from any prior assumptions on anatomical connectivity. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Spherical and hyperspherical harmonics representation of van der Waals aggregates

NASA Astrophysics Data System (ADS)

Lombardi, Andrea; Palazzetti, Federico; Aquilanti, Vincenzo; Grossi, Gaia; Albernaz, Alessandra F.; Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.

2016-12-01

The representation of the potential energy surfaces of atom-molecule or molecular dimers interactions should account faithfully for the symmetry properties of the systems, preserving at the same time a compact analytical form. To this aim, the choice of a proper set of coordinates is a necessary precondition. Here we illustrate a description in terms of hyperspherical coordinates and the expansion of the intermolecular interaction energy in terms of hypersherical harmonics, as a general method for building potential energy surfaces suitable for molecular dynamics simulations of van der Waals aggregates. Examples for the prototypical case diatomic-molecule-diatomic-molecule interactions are shown.

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.

Noncovalent π⋅⋅⋅π interaction between graphene and aromatic molecule: Structure, energy, and nature

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

Wang, Weizhou, E-mail: wzw@lynu.edu.cn, E-mail: ybw@gzu.edu.cn; Zhang, Yu; Wang, Yi-Bo, E-mail: wzw@lynu.edu.cn, E-mail: ybw@gzu.edu.cn

2014-03-07

Noncovalent π⋅⋅⋅π interactions between graphene and aromatic molecules have been studied by using density functional theory with empirical dispersion correction (ωB97X-D) combined with zeroth-order symmetry adapted perturbation theory (SAPT0). Excellent agreement of the interaction energies computed by means of ωB97X-D and spin component scaled (SCS) SAPT0 methods, respectively, shows great promise for the two methods in the study of the adsorption of aromatic molecules on graphene. The other important finding in this study is that, according to SCS-SAPT0 analyses, π⋅⋅⋅π interactions between graphene and aromatic molecules are largely dependent on both dispersion and electrostatic type interactions. It is also noticedmore » that π⋅⋅⋅π interactions become stronger and more dispersive (less electrostatic) upon substitution of the very electronegative fluorine atoms onto the aromatic molecules.« less

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

Quantum Monte Carlo methods for nuclear physics

DOE PAGES

Carlson, J.; Gandolfi, S.; Pederiva, F.; ...

2015-09-09

Quantum Monte Carlo methods have proved valuable to study the structure and reactions of light nuclei and nucleonic matter starting from realistic nuclear interactions and currents. These ab-initio calculations reproduce many low-lying states, moments, and transitions in light nuclei, and simultaneously predict many properties of light nuclei and neutron matter over a rather wide range of energy and momenta. The nuclear interactions and currents are reviewed along with a description of the continuum quantum Monte Carlo methods used in nuclear physics. These methods are similar to those used in condensed matter and electronic structure but naturally include spin-isospin, tensor, spin-orbit,more » and three-body interactions. A variety of results are presented, including the low-lying spectra of light nuclei, nuclear form factors, and transition matrix elements. Low-energy scattering techniques, studies of the electroweak response of nuclei relevant in electron and neutrino scattering, and the properties of dense nucleonic matter as found in neutron stars are also described. Furthermore, a coherent picture of nuclear structure and dynamics emerges based upon rather simple but realistic interactions and currents.« less

Quantum Monte Carlo methods for nuclear physics

DOE PAGES

Carlson, Joseph A.; Gandolfi, Stefano; Pederiva, Francesco; ...

2014-10-19

Quantum Monte Carlo methods have proved very valuable to study the structure and reactions of light nuclei and nucleonic matter starting from realistic nuclear interactions and currents. These ab-initio calculations reproduce many low-lying states, moments and transitions in light nuclei, and simultaneously predict many properties of light nuclei and neutron matter over a rather wide range of energy and momenta. We review the nuclear interactions and currents, and describe the continuum Quantum Monte Carlo methods used in nuclear physics. These methods are similar to those used in condensed matter and electronic structure but naturally include spin-isospin, tensor, spin-orbit, and three-bodymore » interactions. We present a variety of results including the low-lying spectra of light nuclei, nuclear form factors, and transition matrix elements. We also describe low-energy scattering techniques, studies of the electroweak response of nuclei relevant in electron and neutrino scattering, and the properties of dense nucleonic matter as found in neutron stars. A coherent picture of nuclear structure and dynamics emerges based upon rather simple but realistic interactions and currents.« less

Testing Hadronic Interactions at Ultrahigh Energies with Air Showers Measured by the Pierre Auger Observatory

NASA Astrophysics Data System (ADS)

Aab, A.; Abreu, P.; Aglietta, M.; Ahn, E. J.; Al Samarai, I.; Albuquerque, I. F. M.; Allekotte, I.; Allen, J. D.; Allison, P.; Almela, A.; Alvarez Castillo, J.; Alvarez-Muñiz, J.; Ambrosio, M.; Anastasi, G. A.; Anchordoqui, L.; Andrada, B.; Andringa, S.; Aramo, C.; Arqueros, F.; Arsene, N.; Asorey, H.; Assis, P.; Aublin, J.; Avila, G.; Badescu, A. M.; Baus, C.; Beatty, J. J.; Becker, K. H.; Bellido, J. A.; Berat, C.; Bertaina, M. E.; Bertou, X.; Biermann, P. L.; Billoir, P.; Biteau, J.; Blaess, S. G.; Blanco, A.; Blazek, J.; Bleve, C.; Blümer, H.; Boháčová, M.; Boncioli, D.; Bonifazi, C.; Borodai, N.; Botti, A. M.; Brack, J.; Brancus, I.; Bretz, T.; Bridgeman, A.; Briechle, F. L.; Buchholz, P.; Bueno, A.; Buitink, S.; Buscemi, M.; Caballero-Mora, K. S.; Caccianiga, B.; Caccianiga, L.; Cancio, A.; Canfora, F.; Caramete, L.; Caruso, R.; Castellina, A.; Cataldi, G.; Cazon, L.; Cester, R.; Chavez, A. G.; Chiavassa, A.; Chinellato, J. A.; Chirinos Diaz, J. C.; Chudoba, J.; Clay, R. W.; Colalillo, R.; Coleman, A.; Collica, L.; Coluccia, M. R.; Conceição, R.; Contreras, F.; Cooper, M. J.; Coutu, S.; Covault, C. E.; Cronin, J.; Dallier, R.; D'Amico, S.; Daniel, B.; Dasso, S.; Daumiller, K.; Dawson, B. R.; de Almeida, R. M.; de Jong, S. J.; De Mauro, G.; de Mello Neto, J. R. T.; De Mitri, I.; de Oliveira, J.; de Souza, V.; Debatin, J.; del Peral, L.; Deligny, O.; Dhital, N.; Di Giulio, C.; Di Matteo, A.; Díaz Castro, M. L.; Diogo, F.; Dobrigkeit, C.; D'Olivo, J. C.; Dorofeev, A.; dos Anjos, R. C.; Dova, M. T.; Dundovic, A.; Ebr, J.; Engel, R.; Erdmann, M.; Erfani, M.; Escobar, C. O.; Espadanal, J.; Etchegoyen, A.; Falcke, H.; Fang, K.; Farrar, G. R.; Fauth, A. C.; Fazzini, N.; Ferguson, A. P.; Fick, B.; Figueira, J. M.; Filevich, A.; Filipčič, A.; Fratu, O.; Freire, M. M.; Fujii, T.; Fuster, A.; Gallo, F.; García, B.; Garcia-Pinto, D.; Gate, F.; Gemmeke, H.; Gherghel-Lascu, A.; Ghia, P. L.; Giaccari, U.; Giammarchi, M.; Giller, M.; Głas, D.; Glaser, C.; Glass, H.; Golup, G.; Gómez Berisso, M.; Gómez Vitale, P. F.; González, N.; Gookin, B.; Gordon, J.; Gorgi, A.; Gorham, P.; Gouffon, P.; Griffith, N.; Grillo, A. F.; Grubb, T. D.; Guarino, F.; Guedes, G. P.; Hampel, M. R.; Hansen, P.; Harari, D.; Harrison, T. A.; Harton, J. L.; Hasankiadeh, Q.; Haungs, A.; Hebbeker, T.; Heck, D.; Heimann, P.; Herve, A. E.; Hill, G. C.; Hojvat, C.; Hollon, N.; Holt, E.; Homola, P.; Hörandel, J. R.; Horvath, P.; Hrabovský, M.; Huege, T.; Hulsman, J.; Insolia, A.; Isar, P. G.; Jandt, I.; Jansen, S.; Jarne, C.; Johnsen, J. A.; Josebachuili, M.; Kääpä, A.; Kambeitz, O.; Kampert, K. H.; Kasper, P.; Katkov, I.; Keilhauer, B.; Kemp, E.; Kieckhafer, R. M.; Klages, H. O.; Kleifges, M.; Kleinfeller, J.; Krause, R.; Krohm, N.; Kuempel, D.; Kukec Mezek, G.; Kunka, N.; Kuotb Awad, A.; LaHurd, D.; Latronico, L.; Lauscher, M.; Lautridou, P.; Lebrun, P.; Legumina, R.; Leigui de Oliveira, M. A.; Letessier-Selvon, A.; Lhenry-Yvon, I.; Link, K.; Lopes, L.; López, R.; López Casado, A.; Lucero, A.; Malacari, M.; Mallamaci, M.; Mandat, D.; Mantsch, P.; Mariazzi, A. G.; Marin, V.; Mariş, I. C.; Marsella, G.; Martello, D.; Martinez, H.; Martínez Bravo, O.; Masías Meza, J. J.; Mathes, H. J.; Mathys, S.; Matthews, J.; Matthews, J. A. J.; Matthiae, G.; Maurizio, D.; Mayotte, E.; Mazur, P. O.; Medina, C.; Medina-Tanco, G.; Mello, V. B. B.; Melo, D.; Menshikov, A.; Messina, S.; Micheletti, M. I.; Middendorf, L.; Minaya, I. A.; Miramonti, L.; Mitrica, B.; Molina-Bueno, L.; Mollerach, S.; Montanet, F.; Morello, C.; Mostafá, M.; Moura, C. A.; Müller, G.; Muller, M. A.; Müller, S.; Naranjo, I.; Navas, S.; Necesal, P.; Nellen, L.; Nelles, A.; Neuser, J.; Nguyen, P. H.; Niculescu-Oglinzanu, M.; Niechciol, M.; Niemietz, L.; Niggemann, T.; Nitz, D.; Nosek, D.; Novotny, V.; Nožka, H.; Núñez, L. A.; Ochilo, L.; Oikonomou, F.; Olinto, A.; Pakk Selmi-Dei, D.; Palatka, M.; Pallotta, J.; Papenbreer, P.; Parente, G.; Parra, A.; Paul, T.; Pech, M.; Pedreira, F.; Pekala, J.; Pelayo, R.; Peña-Rodriguez, J.; Pepe, I. M.; Pereira, L. A. S.; Perrone, L.; Petermann, E.; Peters, C.; Petrera, S.; Phuntsok, J.; Piegaia, R.; Pierog, T.; Pieroni, P.; Pimenta, M.; Pirronello, V.; Platino, M.; Plum, M.; Porowski, C.; Prado, R. R.; Privitera, P.; Prouza, M.; Quel, E. J.; Querchfeld, S.; Quinn, S.; Rautenberg, J.; Ravel, O.; Ravignani, D.; Revenu, B.; Ridky, J.; Risse, M.; Ristori, P.; Rizi, V.; Rodrigues de Carvalho, W.; Rodriguez Rojo, J.; Rodríguez-Frías, M. D.; Rogozin, D.; Rosado, J.; Roth, M.; Roulet, E.; Rovero, A. C.; Saffi, S. J.; Saftoiu, A.; Salazar, H.; Saleh, A.; Salesa Greus, F.; Salina, G.; Sanabria Gomez, J. D.; Sánchez, F.; Sanchez-Lucas, P.; Santos, E. M.; Santos, E.; Sarazin, F.; Sarkar, B.; Sarmento, R.; Sarmiento-Cano, C.; Sato, R.; Scarso, C.; Schauer, M.; Scherini, V.; Schieler, H.; Schmidt, D.; Scholten, O.; Schoorlemmer, H.; Schovánek, P.; Schröder, F. G.; Schulz, A.; Schulz, J.; Schumacher, J.; Sciutto, S. J.; Segreto, A.; Settimo, M.; Shadkam, A.; Shellard, R. C.; Sigl, G.; Sima, O.; Śmiałkowski, A.; Šmída, R.; Snow, G. R.; Sommers, P.; Sonntag, S.; Sorokin, J.; Squartini, R.; Stanca, D.; Stanič, S.; Stapleton, J.; Stasielak, J.; Strafella, F.; Stutz, A.; Suarez, F.; Suarez Durán, M.; Sudholz, T.; Suomijärvi, T.; Supanitsky, A. D.; Sutherland, M. S.; Swain, J.; Szadkowski, Z.; Taborda, O. A.; Tapia, A.; Tepe, A.; Theodoro, V. M.; Timmermans, C.; Todero Peixoto, C. J.; Tomankova, L.; Tomé, B.; Tonachini, A.; Torralba Elipe, G.; Torres Machado, D.; Travnicek, P.; Trini, M.; Ulrich, R.; Unger, M.; Urban, M.; Valbuena-Delgado, A.; Valdés Galicia, J. F.; Valiño, I.; Valore, L.; van Aar, G.; van Bodegom, P.; van den Berg, A. M.; van Vliet, A.; Varela, E.; Vargas Cárdenas, B.; Varner, G.; Vázquez, J. R.; Vázquez, R. A.; Veberič, D.; Verzi, V.; Vicha, J.; Videla, M.; Villaseñor, L.; Vorobiov, S.; Wahlberg, H.; Wainberg, O.; Walz, D.; Watson, A. A.; Weber, M.; Weindl, A.; Wiencke, L.; Wilczyński, H.; Winchen, T.; Wittkowski, D.; Wundheiler, B.; Wykes, S.; Yang, L.; Yapici, T.; Yelos, D.; Zas, E.; Zavrtanik, D.; Zavrtanik, M.; Zepeda, A.; Zimmermann, B.; Ziolkowski, M.; Zong, Z.; Zuccarello, F.; Pierre Auger Collaboration

2016-11-01

Ultrahigh energy cosmic ray air showers probe particle physics at energies beyond the reach of accelerators. Here we introduce a new method to test hadronic interaction models without relying on the absolute energy calibration, and apply it to events with primary energy 6-16 EeV (ECM=110 - 170 TeV ), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory. The average hadronic shower is 1.33 ±0.16 (1.61 ±0.21 ) times larger than predicted using the leading LHC-tuned models EPOS-LHC (QGSJetII-04), with a corresponding excess of muons.

Testing Hadronic Interactions at Ultrahigh Energies with Air Showers Measured by the Pierre Auger Observatory.

PubMed

Aab, A; Abreu, P; Aglietta, M; Ahn, E J; Al Samarai, I; Albuquerque, I F M; Allekotte, I; Allen, J D; Allison, P; Almela, A; Alvarez Castillo, J; Alvarez-Muñiz, J; Ambrosio, M; Anastasi, G A; Anchordoqui, L; Andrada, B; Andringa, S; Aramo, C; Arqueros, F; Arsene, N; Asorey, H; Assis, P; Aublin, J; Avila, G; Badescu, A M; Baus, C; Beatty, J J; Becker, K H; Bellido, J A; Berat, C; Bertaina, M E; Bertou, X; Biermann, P L; Billoir, P; Biteau, J; Blaess, S G; Blanco, A; Blazek, J; Bleve, C; Blümer, H; Boháčová, M; Boncioli, D; Bonifazi, C; Borodai, N; Botti, A M; Brack, J; Brancus, I; Bretz, T; Bridgeman, A; Briechle, F L; Buchholz, P; Bueno, A; Buitink, S; Buscemi, M; Caballero-Mora, K S; Caccianiga, B; Caccianiga, L; Cancio, A; Canfora, F; Caramete, L; Caruso, R; Castellina, A; Cataldi, G; Cazon, L; Cester, R; Chavez, A G; Chiavassa, A; Chinellato, J A; Chirinos Diaz, J C; Chudoba, J; Clay, R W; Colalillo, R; Coleman, A; Collica, L; Coluccia, M R; Conceição, R; Contreras, F; Cooper, M J; Coutu, S; Covault, C E; Cronin, J; Dallier, R; D'Amico, S; Daniel, B; Dasso, S; Daumiller, K; Dawson, B R; de Almeida, R M; de Jong, S J; De Mauro, G; de Mello Neto, J R T; De Mitri, I; de Oliveira, J; de Souza, V; Debatin, J; Del Peral, L; Deligny, O; Dhital, N; Di Giulio, C; Di Matteo, A; Díaz Castro, M L; Diogo, F; Dobrigkeit, C; D'Olivo, J C; Dorofeev, A; Dos Anjos, R C; Dova, M T; Dundovic, A; Ebr, J; Engel, R; Erdmann, M; Erfani, M; Escobar, C O; Espadanal, J; Etchegoyen, A; Falcke, H; Fang, K; Farrar, G R; Fauth, A C; Fazzini, N; Ferguson, A P; Fick, B; Figueira, J M; Filevich, A; Filipčič, A; Fratu, O; Freire, M M; Fujii, T; Fuster, A; Gallo, F; García, B; Garcia-Pinto, D; Gate, F; Gemmeke, H; Gherghel-Lascu, A; Ghia, P L; Giaccari, U; Giammarchi, M; Giller, M; Głas, D; Glaser, C; Glass, H; Golup, G; Gómez Berisso, M; Gómez Vitale, P F; González, N; Gookin, B; Gordon, J; Gorgi, A; Gorham, P; Gouffon, P; Griffith, N; Grillo, A F; Grubb, T D; Guarino, F; Guedes, G P; Hampel, M R; Hansen, P; Harari, D; Harrison, T A; Harton, J L; Hasankiadeh, Q; Haungs, A; Hebbeker, T; Heck, D; Heimann, P; Herve, A E; Hill, G C; Hojvat, C; Hollon, N; Holt, E; Homola, P; Hörandel, J R; Horvath, P; Hrabovský, M; Huege, T; Hulsman, J; Insolia, A; Isar, P G; Jandt, I; Jansen, S; Jarne, C; Johnsen, J A; Josebachuili, M; Kääpä, A; Kambeitz, O; Kampert, K H; Kasper, P; Katkov, I; Keilhauer, B; Kemp, E; Kieckhafer, R M; Klages, H O; Kleifges, M; Kleinfeller, J; Krause, R; Krohm, N; Kuempel, D; Kukec Mezek, G; Kunka, N; Kuotb Awad, A; LaHurd, D; Latronico, L; Lauscher, M; Lautridou, P; Lebrun, P; Legumina, R; Leigui de Oliveira, M A; Letessier-Selvon, A; Lhenry-Yvon, I; Link, K; Lopes, L; López, R; López Casado, A; Lucero, A; Malacari, M; Mallamaci, M; Mandat, D; Mantsch, P; Mariazzi, A G; Marin, V; Mariş, I C; Marsella, G; Martello, D; Martinez, H; Martínez Bravo, O; Masías Meza, J J; Mathes, H J; Mathys, S; Matthews, J; Matthews, J A J; Matthiae, G; Maurizio, D; Mayotte, E; Mazur, P O; Medina, C; Medina-Tanco, G; Mello, V B B; Melo, D; Menshikov, A; Messina, S; Micheletti, M I; Middendorf, L; Minaya, I A; Miramonti, L; Mitrica, B; Molina-Bueno, L; Mollerach, S; Montanet, F; Morello, C; Mostafá, M; Moura, C A; Müller, G; Muller, M A; Müller, S; Naranjo, I; Navas, S; Necesal, P; Nellen, L; Nelles, A; Neuser, J; Nguyen, P H; Niculescu-Oglinzanu, M; Niechciol, M; Niemietz, L; Niggemann, T; Nitz, D; Nosek, D; Novotny, V; Nožka, H; Núñez, L A; Ochilo, L; Oikonomou, F; Olinto, A; Pakk Selmi-Dei, D; Palatka, M; Pallotta, J; Papenbreer, P; Parente, G; Parra, A; Paul, T; Pech, M; Pedreira, F; Pękala, J; Pelayo, R; Peña-Rodriguez, J; Pepe, I M; Pereira, L A S; Perrone, L; Petermann, E; Peters, C; Petrera, S; Phuntsok, J; Piegaia, R; Pierog, T; Pieroni, P; Pimenta, M; Pirronello, V; Platino, M; Plum, M; Porowski, C; Prado, R R; Privitera, P; Prouza, M; Quel, E J; Querchfeld, S; Quinn, S; Rautenberg, J; Ravel, O; Ravignani, D; Revenu, B; Ridky, J; Risse, M; Ristori, P; Rizi, V; Rodrigues de Carvalho, W; Rodriguez Rojo, J; Rodríguez-Frías, M D; Rogozin, D; Rosado, J; Roth, M; Roulet, E; Rovero, A C; Saffi, S J; Saftoiu, A; Salazar, H; Saleh, A; Salesa Greus, F; Salina, G; Sanabria Gomez, J D; Sánchez, F; Sanchez-Lucas, P; Santos, E M; Santos, E; Sarazin, F; Sarkar, B; Sarmento, R; Sarmiento-Cano, C; Sato, R; Scarso, C; Schauer, M; Scherini, V; Schieler, H; Schmidt, D; Scholten, O; Schoorlemmer, H; Schovánek, P; Schröder, F G; Schulz, A; Schulz, J; Schumacher, J; Sciutto, S J; Segreto, A; Settimo, M; Shadkam, A; Shellard, R C; Sigl, G; Sima, O; Śmiałkowski, A; Šmída, R; Snow, G R; Sommers, P; Sonntag, S; Sorokin, J; Squartini, R; Stanca, D; Stanič, S; Stapleton, J; Stasielak, J; Strafella, F; Stutz, A; Suarez, F; Suarez Durán, M; Sudholz, T; Suomijärvi, T; Supanitsky, A D; Sutherland, M S; Swain, J; Szadkowski, Z; Taborda, O A; Tapia, A; Tepe, A; Theodoro, V M; Timmermans, C; Todero Peixoto, C J; Tomankova, L; Tomé, B; Tonachini, A; Torralba Elipe, G; Torres Machado, D; Travnicek, P; Trini, M; Ulrich, R; Unger, M; Urban, M; Valbuena-Delgado, A; Valdés Galicia, J F; Valiño, I; Valore, L; van Aar, G; van Bodegom, P; van den Berg, A M; van Vliet, A; Varela, E; Vargas Cárdenas, B; Varner, G; Vázquez, J R; Vázquez, R A; Veberič, D; Verzi, V; Vicha, J; Videla, M; Villaseñor, L; Vorobiov, S; Wahlberg, H; Wainberg, O; Walz, D; Watson, A A; Weber, M; Weindl, A; Wiencke, L; Wilczyński, H; Winchen, T; Wittkowski, D; Wundheiler, B; Wykes, S; Yang, L; Yapici, T; Yelos, D; Zas, E; Zavrtanik, D; Zavrtanik, M; Zepeda, A; Zimmermann, B; Ziolkowski, M; Zong, Z; Zuccarello, F

2016-11-04

Ultrahigh energy cosmic ray air showers probe particle physics at energies beyond the reach of accelerators. Here we introduce a new method to test hadronic interaction models without relying on the absolute energy calibration, and apply it to events with primary energy 6-16 EeV (E_{CM}=110-170  TeV), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory. The average hadronic shower is 1.33±0.16 (1.61±0.21) times larger than predicted using the leading LHC-tuned models EPOS-LHC (QGSJetII-04), with a corresponding excess of muons.

Ion-dipole interactions in concentrated organic electrolytes.

PubMed

Chagnes, Alexandre; Nicolis, Stamatios; Carré, Bernard; Willmann, Patrick; Lemordant, Daniel

2003-06-16

An algorithm is proposed for calculating the energy of ion-dipole interactions in concentrated organic electrolytes. The ion-dipole interactions increase with increasing salt concentration and must be taken into account when the activation energy for the conductivity is calculated. In this case, the contribution of ion-dipole interactions to the activation energy for this transport process is of the same order of magnitude as the contribution of ion-ion interactions. The ion-dipole interaction energy was calculated for a cell of eight ions, alternatingly anions and cations, placed on the vertices of an expanded cubic lattice whose parameter is related to the mean interionic distance (pseudolattice theory). The solvent dipoles were introduced randomly into the cell by assuming a randomness compacity of 0.58. The energy of the dipole assembly in the cell was minimized by using a Newton-Raphson numerical method. The dielectric field gradient around ions was taken into account by a distance parameter and a dielectric constant of epsilon = 3 at the surfaces of the ions. A fair agreement between experimental and calculated activation energy has been found for systems composed of gamma-butyrolactone (BL) as solvent and lithium perchlorate (LiClO4), lithium tetrafluoroborate (LiBF4), lithium hexafluorophosphate (LiPF6), lithium hexafluoroarsenate (LiAsF6), and lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) as salts.

Quantitative assessment of interfacial interactions with rough membrane surface and its implications for membrane selection and fabrication in a MBR.

PubMed

Chen, Jianrong; Mei, Rongwu; Shen, Liguo; Ding, Linxian; He, Yiming; Lin, Hongjun; Hong, Huachang

2015-03-01

The interfacial interactions between a foulant particle and rough membrane surface in a submerged membrane bioreactor (MBR) were quantitatively assessed by using a new-developed method. It was found that the profile of total interaction versus separation distance was complicated. There were an energy barrier and two negative energy ranges in the profile. Further analysis showed that roughness scale significantly affected the strength and properties of interfacial interactions. It was revealed that there existed a critical range of roughness scale within which the total energy in the separation distance ranged from 0 to several nanometers was continually repulsive. Decrease in foulant size would increase the strength of specific interaction energy, but did not change the existence of a critical roughness scale range. These findings suggested the possibility to "tailor" membrane surface morphology for membrane fouling mitigation, and thus gave significant implications for membrane selection and fabrication in MBRs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular simulations of the pairwise interaction of monoclonal antibodies.

PubMed

Lapelosa, Mauro; Patapoff, Thomas W; Zarraga, Isidro E

2014-11-20

Molecular simulations are employed to compute the free energy of pairwise monoclonal antibodies (mAbs) association using a conformational sampling algorithm with a scoring function. The work reported here is aimed at investigating the mAb-mAb association driven by weak interactions with a computational method capable of predicting experimental observations of low binding affinity. The simulations are able to explore the free energy landscape. A steric interaction component, electrostatic interactions, and a nonpolar component of the free energy form the energy scoring function. Electrostatic interactions are calculated by solving the Poisson-Boltzmann equation. The nonpolar component is derived from the van der Waals interactions upon close contact of the protein surfaces. Two mAbs with similar IgG1 framework but with small sequence differences, mAb1 and mAb2, are considered for their different viscosity and propensity to form a weak interacting dimer. mAb1 presents favorable free energy of association at pH 6 with 15 mM of ion concentration reproducing experimental trends of high viscosity and dimer formation at high concentration. Free energy landscape and minimum free energy configurations of the dimer, as well as the second virial coefficient (B22) values are calculated. The energy distributions for mAb1 are obtained, and the most probable configurations are seen to be consistent with experimental measurements. In contrast, mAb2 shows an unfavorable average free energy at the same buffer conditions due to poor electrostatic complementarity, and reversible dimer configurations with favorable free energy are found to be unlikely. Finally, the simulations of the mAb association dynamics provide insights on the self-association responsible for bulk solution behavior and aggregation, which are important to the processing and the quality of biopharmaceuticals.

Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals

NASA Astrophysics Data System (ADS)

Ge, Qinghui; Mao, Yuezhi; Head-Gordon, Martin

2018-02-01

An energy decomposition analysis (EDA) scheme is developed for understanding the intermolecular interaction involving molecules in their excited states. The EDA utilizes absolutely localized molecular orbitals to define intermediate states and is compatible with excited state methods based on linear response theory such as configuration interaction singles and time-dependent density functional theory. The shift in excitation energy when an excited molecule interacts with the environment is decomposed into frozen, polarization, and charge transfer contributions, and the frozen term can be further separated into Pauli repulsion and electrostatics. These terms can be added to their counterparts obtained from the ground state EDA to form a decomposition of the total interaction energy. The EDA scheme is applied to study a variety of systems, including some model systems to demonstrate the correct behavior of all the proposed energy components as well as more realistic systems such as hydrogen-bonding complexes (e.g., formamide-water, pyridine/pyrimidine-water) and halide (F-, Cl-)-water clusters that involve charge-transfer-to-solvent excitations.

Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions

NASA Technical Reports Server (NTRS)

Stallcop, James R.; Partridge, Harry; Levin, Eugene

1996-01-01

Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes.

PubMed

Uchikoga, Nobuyuki; Hirokawa, Takatsugu

2010-05-11

Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG), CaM kinase kinase (CaMKK) and the plasma membrane Ca2+ ATPase pump (PMCA), and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

A variation-perturbation method for atomic and molecular interactions. I - Theory. II - The interaction potential and van der Waals molecule for Ne-HF

NASA Astrophysics Data System (ADS)

Gallup, G. A.; Gerratt, J.

1985-09-01

The van der Waals energy between the two parts of a system is a very small fraction of the total electronic energy. In such cases, calculations have been based on perturbation theory. However, such an approach involves certain difficulties. For this reason, van der Waals energies have also been directly calculated from total energies. But such a method has definite limitations as to the size of systems which can be treated, and recently ab initio calculations have been combined with damped semiempirical long-range dispersion potentials to treat larger systems. In this procedure, large basis set superposition errors occur, which must be removed by the counterpoise method. The present investigation is concerned with an approach which is intermediate between the previously considered procedures. The first step in the new approach involves a variational calculation based upon valence bond functions. The procedure includes also the optimization of excited orbitals, and an approximation of atomic integrals and Hamiltonian matrix elements.

Three-dimensional potential energy surface of selected carbohydrates' CH/π dispersion interactions calculated by high-level quantum mechanical methods.

PubMed

Kozmon, Stanislav; Matuška, Radek; Spiwok, Vojtěch; Koča, Jaroslav

2011-05-09

In this study we present the first systematic computational three-dimensional scan of carbohydrate hydrophobic patches for the ability to interact through CH/π dispersion interactions. The carbohydrates β-d-glucopyranose, β-d-mannopyranose and α-l-fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/π interaction in carbohydrate/protein complexes. The 3D relaxed scans were performed at the SCC-DFTB-D level with 3 757 grid points for both carbohydrate hydrophobic sides. The interaction energy of all grid points was recalculated at the DFT-D BP/def2-TZVPP level. The results obtained clearly show highly delimited and separated areas around each CH group, with an interaction energy up to -5.40 kcal mol(-1) . The results also show that with increasing H⋅⋅⋅π distance these delimited areas merge and form one larger region, which covers all hydrogen atoms on that specific carbohydrate side. Simultaneously, the interaction becomes weaker with an energy of -2.5 kcal mol(-1) . All local energy minima were optimized at the DFT-D BP/def2-TZVPP level and the interaction energies of these complexes were refined by use of the high-level ab initio computation at the CCSD(T)/CBS level. Results obtained from the optimization suggest that the CH group hydrogen atoms are not equivalent and the interaction energy at the CCSD(T)/CBS level range from -3.54 to -5.40 kcal mol(-1) . These results also reveal that the optimal H⋅⋅⋅π distance for the CH/π dispersion interaction is approximately (2.310±0.030) Å, and the angle defined as carbon-hydrogen-benzene geometrical centre is (180±30)°. These results reveal that whereas the dispersion interactions with the lowest interaction energies are quite strictly located in space, the slightly higher interaction energy regions adopt a much larger space. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods.

PubMed

Lise, Stefano; Archambeau, Cedric; Pontil, Massimiliano; Jones, David T

2009-10-30

Alanine scanning mutagenesis is a powerful experimental methodology for investigating the structural and energetic characteristics of protein complexes. Individual amino-acids are systematically mutated to alanine and changes in free energy of binding (DeltaDeltaG) measured. Several experiments have shown that protein-protein interactions are critically dependent on just a few residues ("hot spots") at the interface. Hot spots make a dominant contribution to the free energy of binding and if mutated they can disrupt the interaction. As mutagenesis studies require significant experimental efforts, there is a need for accurate and reliable computational methods. Such methods would also add to our understanding of the determinants of affinity and specificity in protein-protein recognition. We present a novel computational strategy to identify hot spot residues, given the structure of a complex. We consider the basic energetic terms that contribute to hot spot interactions, i.e. van der Waals potentials, solvation energy, hydrogen bonds and Coulomb electrostatics. We treat them as input features and use machine learning algorithms such as Support Vector Machines and Gaussian Processes to optimally combine and integrate them, based on a set of training examples of alanine mutations. We show that our approach is effective in predicting hot spots and it compares favourably to other available methods. In particular we find the best performances using Transductive Support Vector Machines, a semi-supervised learning scheme. When hot spots are defined as those residues for which DeltaDeltaG >or= 2 kcal/mol, our method achieves a precision and a recall respectively of 56% and 65%. We have developed an hybrid scheme in which energy terms are used as input features of machine learning models. This strategy combines the strengths of machine learning and energy-based methods. Although so far these two types of approaches have mainly been applied separately to biomolecular problems, the results of our investigation indicate that there are substantial benefits to be gained by their integration.

A low noise discrete velocity method for the Boltzmann equation with quantized rotational and vibrational energy

NASA Astrophysics Data System (ADS)

Clarke, Peter; Varghese, Philip; Goldstein, David

2018-01-01

A discrete velocity method is developed for gas mixtures of diatomic molecules with both rotational and vibrational energy states. A full quantized model is described, and rotation-translation and vibration-translation energy exchanges are simulated using a Larsen-Borgnakke exchange model. Elastic and inelastic molecular interactions are modeled during every simulated collision to help produce smooth internal energy distributions. The method is verified by comparing simulations of homogeneous relaxation by our discrete velocity method to numerical solutions of the Jeans and Landau-Teller equations, and to direct simulation Monte Carlo. We compute the structure of a 1D shock using this method, and determine how the rotational energy distribution varies with spatial location in the shock and with position in velocity space.

Imaging Galactic Dark Matter with High-Energy Cosmic Neutrinos

NASA Astrophysics Data System (ADS)

Argüelles, Carlos A.; Kheirandish, Ali; Vincent, Aaron C.

2017-11-01

We show that the high-energy cosmic neutrinos seen by the IceCube Neutrino Observatory can be used to probe interactions between neutrinos and the dark sector that cannot be reached by current cosmological methods. The origin of the observed neutrinos is still unknown, and their arrival directions are compatible with an isotropic distribution. This observation, together with dedicated studies of Galactic plane correlations, suggests a predominantly extragalactic origin. Interactions between this isotropic extragalactic flux and the dense dark matter (DM) bulge of the Milky Way would thus lead to an observable imprint on the distribution, which would be seen by IceCube as (i) slightly suppressed fluxes at energies below a PeV and (ii) a deficit of events in the direction of the Galactic center. We perform an extended unbinned likelihood analysis using the four-year high-energy starting event data set to constrain the strength of DM-neutrino interactions for two model classes. We find that, in spite of low statistics, IceCube can probe regions of the parameter space inaccessible to current cosmological methods.

Interactive Marine Spatial Planning: Siting Tidal Energy Arrays around the Mull of Kintyre

PubMed Central

Alexander, Karen A.; Janssen, Ron; Arciniegas, Gustavo; O'Higgins, Timothy G.; Eikelboom, Tessa; Wilding, Thomas A.

2012-01-01

The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the ‘ecosystem approach’ (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP. PMID:22253865

Imaging Galactic Dark Matter with High-Energy Cosmic Neutrinos.

PubMed

Argüelles, Carlos A; Kheirandish, Ali; Vincent, Aaron C

2017-11-17

We show that the high-energy cosmic neutrinos seen by the IceCube Neutrino Observatory can be used to probe interactions between neutrinos and the dark sector that cannot be reached by current cosmological methods. The origin of the observed neutrinos is still unknown, and their arrival directions are compatible with an isotropic distribution. This observation, together with dedicated studies of Galactic plane correlations, suggests a predominantly extragalactic origin. Interactions between this isotropic extragalactic flux and the dense dark matter (DM) bulge of the Milky Way would thus lead to an observable imprint on the distribution, which would be seen by IceCube as (i) slightly suppressed fluxes at energies below a PeV and (ii) a deficit of events in the direction of the Galactic center. We perform an extended unbinned likelihood analysis using the four-year high-energy starting event data set to constrain the strength of DM-neutrino interactions for two model classes. We find that, in spite of low statistics, IceCube can probe regions of the parameter space inaccessible to current cosmological methods.

Calculations of the excitation energies of all-trans and 11,12s-dicis retinals using localized molecular orbitals obtained by the elongation method

NASA Astrophysics Data System (ADS)

Kurihara, Youji; Aoki, Yuriko; Imamura, Akira

1997-09-01

In the present article, the excitation energies of the all-trans and the 11,12s-dicis retinals were calculated by using the elongation method. The geometries of these molecules were optimized with the 4-31G basis set by using the GAUSSIAN 92 program. The wave functions for the calculation of the excitation energies were obtained with CNDO/S approximation by the elongation method, which enables us to analyze electronic structures of aperiodic polymers in terms of the exciton-type local excitation and the charge transfer-type excitation. The excitation energies were calculated by using the single excitation configuration interaction (SECI) on the basis of localized molecular orbitals (LMOs). The LMOs were obtained in the process of the elongation method. The configuration interaction (CI) matrices were diagonalized by Davidson's method. The calculated results were in good agreement with the experimental data for absorption spectra. In order to consider the isomerization path from 11,12s-dicis to all-trans retinals, the barriers to the rotations about C11-C12 double and C12-C13 single bonds were evaluated.

Exciplex-exciplex energy transfer and annihilation in solid films of porphyrin-fullerene dyads.

PubMed

Lehtivuori, Heli; Lemmetyinen, Helge; Tkachenko, Nikolai V

2006-12-20

Exciplex-exciplex annihilation was observed for the first time in porphyrin-fullerene molecular films. The films were prepared using Langmuir-Blodgett and drop casting methods. The exciplex-exciplex interactions were studied using femtosecond pump-probe method. The exciplex-exciplex annihilation can be seen as a fast (within few picoseconds) decay of the transient absorption at excitation densities higher than 0.4 mJ/cm2. Analysis of the excitation density dependences indicates that in average four dyads are involved in the exciplex-exciplex interaction, suggesting that an exciplex-exciplex energy transfer may precede the annihilation.

Theoretical investigation of the weak interaction between graphene and alcohol solvents

NASA Astrophysics Data System (ADS)

Wang, Haining; Chen, Sian; Lu, Shanfu; Xiang, Yan

2017-05-01

The dispersion of graphene in five different alcohol solvents was investigated by evaluating the binding energy between graphene and alcohol molecules using DFT-D method. The calculation showed the most stable binding energy appeared at the distance of ∼3.5 Å between graphene and alcohol molecules and increased linearly as changing the alcohol from methanol to 1-pentanol. The weak interaction was further graphically illustrated using the reduced density gradient method. The theoretical study revealed alcohols with more carbon atoms could be a good starting point for screening suitable solvents for graphene dispersion.

Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

PubMed Central

Gargallo, Raimundo; Hünenberger, Philippe H.; Avilés, Francesc X.; Oliva, Baldomero

2003-01-01

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method. PMID:14500874

Thin Film Evaporation Model with Retarded Van Der Waals Interaction (Postprint)

DTIC Science & Technology

2013-11-01

Waals interaction. The retarded van der Waals interaction is derived from Hamaker theory, the summation of retarded pair potentials for all molecules...interaction is derived from Hamaker theory, the summation of retarded pair potentials for all molecules for a given geometry. When combined, the governing...interaction force is the negative derivative with respect to distance of the interaction energy. The method due to Hamaker essentially sums all pair

Charged nanoparticle attraction in multivalent salt solution: A classical-fluids density functional theory and molecular dynamics study

DOE PAGES

Salerno, K. Michael; Frischknecht, Amalie L.; Stevens, Mark J.

2016-04-08

Here, negatively charged nanoparticles (NPs) in 1:1, 1:2, and 1:3 electrolyte solutions are studied in a primitive ion model using molecular dynamics (MD) simulations and classical density functional theory (DFT). We determine the conditions for attractive interactions between the like-charged NPs. Ion density profiles and NP–NP interaction free energies are compared between the two methods and are found to be in qualitative agreement. The NP interaction free energy is purely repulsive for monovalent counterions, but can be attractive for divalent and trivalent counterions. Using DFT, the NP interaction free energy for different NP diameters and charges is calculated. The depthmore » and location of the minimum in the interaction depend strongly on the NPs’ charge. For certain parameters, the depth of the attractive well can reach 8–10 k BT, indicating that kinetic arrest and aggregation of the NPs due to electrostatic interactions is possible. Rich behavior arises from the geometric constraints of counterion packing at the NP surface. Layering of counterions around the NPs is observed and, as secondary counterion layers form the minimum of the NP–NP interaction free energy shifts to larger separation, and the depth of the free energy minimum varies dramatically. We find that attractive interactions occur with and without NP overcharging.« less

When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms.

PubMed

Petković, Milena; Nakarada, Đura; Etinski, Mihajlo

2018-05-25

Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Calculation of the Coulomb Fission Cross Sections for Pb-Pb and Bi-Pb Interactions at 158 A GeV

NASA Technical Reports Server (NTRS)

Poyser, William J.; Ahern, Sean C.; Norbury, John W.; Tripathi, R. K.

2002-01-01

The Weizsacker-Williams (WW) method of virtual quanta is used to make approximate cross section calculations for peripheral relativistic heavy-ion collisions. We calculated the Coulomb fission cross sections for projectile ions of Pb-208 and Bi-209 with energies of 158 A GeV interacting with a Pb-208 target. We also calculated the electromagnetic absorption cross section for Pb-208 ion interacting as described. For comparison we use both the full WW method and a standard approximate WW method. The approximate WW method in larger cross sections compared to the more accurate full WW method.

Quantum dynamics modeled by interacting trajectories

NASA Astrophysics Data System (ADS)

Cruz-Rodríguez, L.; Uranga-Piña, L.; Martínez-Mesa, A.; Meier, C.

2018-03-01

We present quantum dynamical simulations based on the propagation of interacting trajectories where the effect of the quantum potential is mimicked by effective pseudo-particle interactions. The method is applied to several quantum systems, both for bound and scattering problems. For the bound systems, the quantum ground state density and zero point energy are shown to be perfectly obtained by the interacting trajectories. In the case of time-dependent quantum scattering, the Eckart barrier and uphill ramp are considered, with transmission coefficients in very good agreement with standard quantum calculations. Finally, we show that via wave function synthesis along the trajectories, correlation functions and energy spectra can be obtained based on the dynamics of interacting trajectories.

Radiative interactions in transient energy transfer in gaseous systems

NASA Technical Reports Server (NTRS)

Tiwari, S. N.

1985-01-01

Analyses and numerical procedures are presented to investigate the radiative interactions in transient energy transfer processes in gaseous systems. The nongray radiative formulations are based on the wide-band model correlations for molecular absorption. Various relations for the radiative flux are developed; these are useful for different flow conditions and physical problems. Specific plans for obtaining extensive results for different cases are presented. The methods presented in this study can be extended easily to investigate the radiative interactions in realistic flows of hydrogen-air species in the scramjet engine.

The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of the XD programming package to several solids including a pentapeptide.

PubMed

Abramov, Y A; Volkov, A; Wu, G; Coppens, P

2000-11-01

A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, L-asparagine monohydrate and the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol). The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM (kappa'-restricted multipole model) refinements, using the Buckingham expression for non-overlapping charge densities. Results for p-nitroaniline are compared with Hartree-Fock (HF), density functional (DFT) and Moller-Plesset (MP2) supermolecular calculations and with HF and DFT periodic calculations. The HF and DFT methods fail to predict the stability of the p-nitroaniline crystal but the results of the experimental charge-density approach (ECDA) are in good agreement with both MP2 interaction energies and the experimental lattice energy. ECDA results for L-asparagine monohydrate compare well with those from DFT supermolecular and periodic HF calculations. The disorder of the terminal group in the pentapeptide, which persists at the experimental temperature of 20 K, corresponds to an energy difference of only 0.35 kJ mol(-1), which is too small to be reproduced with current methods.

A machine learning approach to graph-theoretical cluster expansions of the energy of adsorbate layers

NASA Astrophysics Data System (ADS)

Vignola, Emanuele; Steinmann, Stephan N.; Vandegehuchte, Bart D.; Curulla, Daniel; Stamatakis, Michail; Sautet, Philippe

2017-08-01

The accurate description of the energy of adsorbate layers is crucial for the understanding of chemistry at interfaces. For heterogeneous catalysis, not only the interaction of the adsorbate with the surface but also the adsorbate-adsorbate lateral interactions significantly affect the activation energies of reactions. Modeling the interactions of the adsorbates with the catalyst surface and with each other can be efficiently achieved in the cluster expansion Hamiltonian formalism, which has recently been implemented in a graph-theoretical kinetic Monte Carlo (kMC) scheme to describe multi-dentate species. Automating the development of the cluster expansion Hamiltonians for catalytic systems is challenging and requires the mapping of adsorbate configurations for extended adsorbates onto a graphical lattice. The current work adopts machine learning methods to reach this goal. Clusters are automatically detected based on formalized, but intuitive chemical concepts. The corresponding energy coefficients for the cluster expansion are calculated by an inversion scheme. The potential of this method is demonstrated for the example of ethylene adsorption on Pd(111), for which we propose several expansions, depending on the graphical lattice. It turns out that for this system, the best description is obtained as a combination of single molecule patterns and a few coupling terms accounting for lateral interactions.

Evaluating effective pair and multisite interactions for Ni-Mo system

NASA Astrophysics Data System (ADS)

Banerjee, Rumu H.; Arya, A.; Banerjee, S.

2018-04-01

Cluster expansion (CE) method was used to calculate the energies of various Ni-Mo phases. The clusters comprising of few nearest neighbours can describe any phase of Ni-Mo system by suitable choice of effective pair and multisite interaction parameters (ECI). The ECIs were evaluated in present study by fitting the ground state energies obtained by first principle calculations. The ECIs evaluated for Ni-Mo system were mostly pair clusters followed by triplets and quadruplet clusters with cluster diameters in the range 2.54 - 10.20 Å. The ECI values diminished for multi-body (triplets and quadruplets) clusters as compared to 2-point or pair clusters indicating a good convergence of CE model. With these ECIs the predicted energies of all the Ni-Mo structures across the Mo concentration range 0-100 at% were obtained. The quantitative error in the energies calculated by CE approach and first principle is very small (< 0.026 meV/atom). The appreciable values of 2-point ECIs upto 4th nearest neighbour reveal that two body interactions are dominant in the case of Ni-Mo system. These ECIs are compared with the reported values of compositional dependent effective pair interactions evaluated by first principle as well as by Monte Carlo method.

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects.

PubMed

Zuo, Zhili; Gandhi, Neha S; Mancera, Ricardo L

2010-12-27

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Solving the Schroedinger Equation of Atoms and Molecules without Analytical Integration Based on the Free Iterative-Complement-Interaction Wave Function

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

Nakatsuji, H.; Nakashima, H.; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510

2007-12-14

A local Schroedinger equation (LSE) method is proposed for solving the Schroedinger equation (SE) of general atoms and molecules without doing analytic integrations over the complement functions of the free ICI (iterative-complement-interaction) wave functions. Since the free ICI wave function is potentially exact, we can assume a flatness of its local energy. The variational principle is not applicable because the analytic integrations over the free ICI complement functions are very difficult for general atoms and molecules. The LSE method is applied to several 2 to 5 electron atoms and molecules, giving an accuracy of 10{sup -5} Hartree in total energy.more » The potential energy curves of H{sub 2} and LiH molecules are calculated precisely with the free ICI LSE method. The results show the high potentiality of the free ICI LSE method for developing accurate predictive quantum chemistry with the solutions of the SE.« less

Experiment in multiple-criteria energy policy analysis

NASA Astrophysics Data System (ADS)

Ho, J. K.

1980-07-01

An international panel of energy analysts participated in an experiment to use HOPE (holistic preference evaluation): an interactive parametric linear programming method for multiple criteria optimization. The criteria of cost, environmental effect, crude oil, and nuclear fuel were considered, according to BESOM: an energy model for the US in the year 2000.

Testing hadronic interactions at ultrahigh energies with air showers measured by the Pierre Auger Observatory

DOE PAGES

Aab, A.; Abreu, P.; Aglietta, M.; ...

2016-10-31

Ultrahigh energy cosmic ray air showers probe particle physics at energies beyond the reach of accelerators. Here we introduce a new method to test hadronic interaction models without relying on the absolute energy calibration, and apply it to events with primary energy 6–16 EeV (E CM = 110–170 TeV), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory. As a result, the average hadronic shower is 1.33±0.16 (1.61±0.21) times larger than predicted using the leading LHC-tuned models EPOS-LHC (QGSJetII-04), with a corresponding excess of muons.

Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors.

PubMed

Xu, Fengqi; Tanaka, Shigenori; Watanabe, Hirofumi; Shimane, Yasuhiro; Iwasawa, Misako; Ohishi, Kazue; Maruyama, Tadashi

2018-05-03

Measles virus (MV) causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM), CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH), we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO) method. The calculated inter-fragment interaction energies (IFIEs) revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar) hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4). In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy.

Extended methods using thick-targets for nuclear reaction data of radioactive isotopes

NASA Astrophysics Data System (ADS)

Ebata, Shuichiro; Aikawa, Masayuki; Imai, Shotaro

2017-09-01

The nuclear transmutation is a technology to dispose of radioactive wastes. However, we do not have enough basic data for its developments, such as thick-target yields (TTY) and the interaction cross sections for radioactive material. We suggest two methods to estimate the TTY using inverse kinematics and to obtain the excitation function of the interaction cross sections which is named the thick-target transmission (T3) method. We deduce the energy-dependent conversion relation between the TTYs of the original system and its inverse kinematics, which can be replaced to a constant coefficient in the high energy region. Furthermore we show the usefulness of the T3 method to investigate the excitation function of the 12C + 27Al reaction in the simulation.

Direct computation of general chemical energy differences: Application to ionization potentials, excitation, and bond energies.

PubMed

Beste, A; Harrison, R J; Yanai, T

2006-08-21

Chemists are mainly interested in energy differences. In contrast, most quantum chemical methods yield the total energy which is a large number compared to the difference and has therefore to be computed to a higher relative precision than would be necessary for the difference alone. Hence, it is desirable to compute energy differences directly, thereby avoiding the precision problem. Whenever it is possible to find a parameter which transforms smoothly from an initial to a final state, the energy difference can be obtained by integrating the energy derivative with respect to that parameter (cf. thermodynamic integration or adiabatic connection methods). If the dependence on the parameter is predominantly linear, accurate results can be obtained by single-point integration. In density functional theory and Hartree-Fock, we applied the formalism to ionization potentials, excitation energies, and chemical bond breaking. Example calculations for ionization potentials and excitation energies showed that accurate results could be obtained with a linear estimate. For breaking bonds, we introduce a nongeometrical parameter which gradually turns the interaction between two fragments of a molecule on. The interaction changes the potentials used to determine the orbitals as well as the constraint on the orbitals to be orthogonal.

Orbital-optimized MP2.5 and its analytic gradients: Approaching CCSD(T) quality for noncovalent interactions

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

Bozkaya, Uğur, E-mail: ugur.bozkaya@atauni.edu.tr; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332; Sherrill, C. David

2014-11-28

Orbital-optimized MP2.5 [or simply “optimized MP2.5,” OMP2.5, for short] and its analytic energy gradients are presented. The cost of the presented method is as much as that of coupled-cluster singles and doubles (CCSD) [O(N{sup 6}) scaling] for energy computations. However, for analytic gradient computations the OMP2.5 method is only half as expensive as CCSD because there is no need to solve λ{sub 2}-amplitude equations for OMP2.5. The performance of the OMP2.5 method is compared with that of the standard second-order Møller–Plesset perturbation theory (MP2), MP2.5, CCSD, and coupled-cluster singles and doubles with perturbative triples (CCSD(T)) methods for equilibrium geometries, hydrogenmore » transfer reactions between radicals, and noncovalent interactions. For bond lengths of both closed and open-shell molecules, the OMP2.5 method improves upon MP2.5 and CCSD by 38%–43% and 31%–28%, respectively, with Dunning's cc-pCVQZ basis set. For complete basis set (CBS) predictions of hydrogen transfer reaction energies, the OMP2.5 method exhibits a substantially better performance than MP2.5, providing a mean absolute error of 1.1 kcal mol{sup −1}, which is more than 10 times lower than that of MP2.5 (11.8 kcal mol{sup −1}), and comparing to MP2 (14.6 kcal mol{sup −1}) there is a more than 12-fold reduction in errors. For noncovalent interaction energies (at CBS limits), the OMP2.5 method maintains the very good performance of MP2.5 for closed-shell systems, and for open-shell systems it significantly outperforms MP2.5 and CCSD, and approaches CCSD(T) quality. The MP2.5 errors decrease by a factor of 5 when the optimized orbitals are used for open-shell noncovalent interactions, and comparing to CCSD there is a more than 3-fold reduction in errors. Overall, the present application results indicate that the OMP2.5 method is very promising for open-shell noncovalent interactions and other chemical systems with difficult electronic structures.« less

Vibronic coupling effect on circular dichroism spectrum: Carotenoid-retinal interaction in xanthorhodopsin

NASA Astrophysics Data System (ADS)

Fujimoto, Kazuhiro J.; Balashov, Sergei P.

2017-03-01

The role of vibronic coupling of antenna carotenoid and retinal in xanthorhodopsin (XR) in its circular dichroism (CD) spectrum is examined computationally. A vibronic exciton model combined with a transition-density-fragment interaction (TDFI) method is developed, and applied to absorption and CD spectral calculations of XR. The TDFI method is based on the electronic Coulomb and exchange interactions between transition densities for individual chromophores [K. J. Fujimoto, J. Chem. Phys. 137, 034101 (2012)], which provides a quantitative description of electronic coupling energy. The TDFI calculation reveals a dominant contribution of the Coulomb interaction to the electronic coupling energy and a negligible contribution of the exchange interaction, indicating that the antenna function of carotenoid results from the Förster type of excitation-energy transfer, not from the Dexter one. The calculated absorption and CD spectra successfully reproduce the main features of the experimental results, which allow us to investigate the mechanism of biphasic CD spectrum observed in XR. The results indicate that vibronic coupling between carotenoid and retinal plays a significant role in the shape of the CD spectrum. Further analysis reveals that the negative value of electronic coupling directly contributes to the biphasic shape of CD spectrum. This study also reveals that the C6—C7 bond rotation of salinixanthin is not the main factor for the biphasic CD spectrum although it gives a non-negligible contribution to the spectral shift. The present method is useful for analyzing the molecular mechanisms underlying the chromophore-chromophore interactions in biological systems.

Energy exchange between a laser beam and charged particles using inverse transition radiation and method for its use

DOEpatents

Kimura, Wayne D.; Romea, Richard D.; Steinhauer, Loren C.

1998-01-01

A method and apparatus for exchanging energy between relativistic charged particles and laser radiation using inverse diffraction radiation or inverse transition radiation. The beam of laser light is directed onto a particle beam by means of two optical elements which have apertures or foils through which the particle beam passes. The two apertures or foils are spaced by a predetermined distance of separation and the angle of interaction between the laser beam and the particle beam is set at a specific angle. The separation and angle are a function of the wavelength of the laser light and the relativistic energy of the particle beam. In a diffraction embodiment, the interaction between the laser and particle beams is determined by the diffraction effect due to the apertures in the optical elements. In a transition embodiment, the interaction between the laser and particle beams is determined by the transition effect due to pieces of foil placed in the particle beam path.

Electric-field-induced modification in Dzyaloshinskii-Moriya interaction of Co monolayer on Pt(111)

NASA Astrophysics Data System (ADS)

Nakamura, Kohji; Akiyama, Toru; Ito, Tomonori; Ono, Teruo; Weinert, Michael

Magnetism induced by an external electric field (E-field) has received much attention as a potential approach for controlling magnetism at the nano-scale with the promise of ultra-low energy power consumption. Here, the E-field-induced modification of the Dzyaloshinskii-Moriya interaction (DMI) for a prototypical transition-metal thin layer of a Co monolayer on Pt(111) is investigated by first-principles calculations by using the full-potential linearized augmented plane wave method that treats spin-spiral structures in an E-field. With inclusion of the spin-orbit coupling (SOC) by the second variational method for commensurate spin-spiral structures, the DMI constants were estimated from an asymmetric contribution in the total energy with respect to the spin-spiral wavevector. The results predicted that the DMI is modified by the E-field, but the change is found to be small compared to that in the exchange interaction (a symmetric contribution in the total energy) by a factor of ten.

High-spin level structure and Ground-state phase transition in the odd-mass 103-109Rh isotopes in the framework of exactly solvable sdg interacting boson-fermion model

NASA Astrophysics Data System (ADS)

Ghapanvari, M.; Ghorashi, A. H.; Ranjbar, Z.; Jafarizadeh, M. A.

2018-03-01

In this article, the negative-parity states in the odd-mass 103 - 109Rh isotopes in terms of the sd and sdg interacting-boson fermion models were studied. The transitional interacting boson-fermion model Hamiltonians in sd and sdg-IBFM versions based on affine SU (1 , 1) Lie Algebra were employed to describe the evolution from the spherical to deformed gamma unstable shapes along with the chain of Rh isotopes. In this method, sdg-IBFM Hamiltonian, which is a three level pairing Hamiltonian was determined easily via the exactly solvable method. Some observables of the shape phase transitions such as energy levels, the two neutron separation energies, signature splitting of the γ-vibrational band, the α-decay and double β--decay energies were calculated and examined for these isotopes. The present calculation correctly reproduces the spherical to gamma-soft phase transition in the Rh isotopes. Some comparisons were made with sd-IBFM.

Applications of the Trojan Horse method in nuclear astrophysics

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

Spitaleri, Claudio, E-mail: spitaleri@lns.infn.it

2015-02-24

The study of the energy production in stars and related nucleosyntesis processes requires increasingly precise knowledge of the nuclear reaction cross section and reaction rates at interaction energy. In order to overcome the experimental difficulties, arising from small cross-sections involved in charge particle induced reactions at astrophysical energies, and from the presence of electron screening, it was necessary to introduce indirect methods. Trough these methods it is possible to measure cross sections at very small energies and retrieve information on electron screening effect when ultra-low energy direct measurements are available. The Trojan Horse Method (THM) represents the indirect technique tomore » determine the bare nucleus astrophysical S-factor for reactions between charged particles at astrophysical energies. The basic theory of the THM is discussed in the case of non-resonant.« less

Classical field configurations and infrared slavery

NASA Astrophysics Data System (ADS)

Swanson, Mark S.

1987-09-01

The problem of determining the energy of two spinor particles interacting through massless-particle exchange is analyzed using the path-integral method. A form for the long-range interaction energy is obtained by analyzing an abridged vertex derived from the parent theory. This abridged vertex describes the radiation of zero-momentum particles by pointlike sources. A path-integral formalism for calculating the energy of the radiation field associated with this abridged vertex is developed and applications are made to determine the energy necessary for adiabatic separation of two sources in quantum electrodynamics and for an SU(2) Yang-Mills theory. The latter theory is shown to be consistent with confinement via infrared slavery.

Interlayer interactions in graphites.

PubMed

Chen, Xiaobin; Tian, Fuyang; Persson, Clas; Duan, Wenhui; Chen, Nan-xian

2013-11-06

Based on ab initio calculations of both the ABC- and AB-stacked graphites, interlayer potentials (i.e., graphene-graphene interaction) are obtained as a function of the interlayer spacing using a modified Möbius inversion method, and are used to calculate basic physical properties of graphite. Excellent consistency is observed between the calculated and experimental phonon dispersions of AB-stacked graphite, showing the validity of the interlayer potentials. More importantly, layer-related properties for nonideal structures (e.g., the exfoliation energy, cleave energy, stacking fault energy, surface energy, etc.) can be easily predicted from the interlayer potentials, which promise to be extremely efficient and helpful in studying van der Waals structures.

The Self-Association of Graphane Is Driven by London Dispersion and Enhanced Orbital Interactions.

PubMed

Wang, Changwei; Mo, Yirong; Wagner, J Philipp; Schreiner, Peter R; Jemmis, Eluvathingal D; Danovich, David; Shaik, Sason

2015-04-14

We investigated the nature of the cohesive energy between graphane sheets via multiple CH···HC interactions, using density functional theory (DFT) including dispersion correction (Grimme's D3 approach) computations of [n]graphane σ dimers (n = 6-73). For comparison, we also evaluated the binding between graphene sheets that display prototypical π/π interactions. The results were analyzed using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory. BLW interprets the intermolecular interactions in terms of frozen interaction energy (ΔE(F)) composed of electrostatic and Pauli repulsion interactions, polarization (ΔE(pol)), charge-transfer interaction (ΔE(CT)), and dispersion effects (ΔE(disp)). The BLW analysis reveals that the cohesive energy between graphane sheets is dominated by two stabilizing effects, namely intermolecular London dispersion and two-way charge transfer energy due to the σ(CH) → σ*(HC) interactions. The shift of the electron density around the nonpolar covalent C-H bonds involved in the intermolecular interaction decreases the C-H bond lengths uniformly by 0.001 Å. The ΔE(CT) term, which accounts for ∼15% of the total binding energy, results in the accumulation of electron density in the interface area between two layers. This accumulated electron density thus acts as an electronic "glue" for the graphane layers and constitutes an important driving force in the self-association and stability of graphane under ambient conditions. Similarly, the "double faced adhesive tape" style of charge transfer interactions was also observed among graphene sheets in which it accounts for ∼18% of the total binding energy. The binding energy between graphane sheets is additive and can be expressed as a sum of CH···HC interactions, or as a function of the number of C-H bonds.

Impact of the Fano Factor on Position and Energy Estimation in Scintillation Detectors.

PubMed

Bora, Vaibhav; Barrett, Harrison H; Jha, Abhinav K; Clarkson, Eric

2015-02-01

The Fano factor for an integer-valued random variable is defined as the ratio of its variance to its mean. Light from various scintillation crystals have been reported to have Fano factors from sub-Poisson (Fano factor < 1) to super-Poisson (Fano factor > 1). For a given mean, a smaller Fano factor implies a smaller variance and thus less noise. We investigated if lower noise in the scintillation light will result in better spatial and energy resolutions. The impact of Fano factor on the estimation of position of interaction and energy deposited in simple gamma-camera geometries is estimated by two methods - calculating the Cramér-Rao bound and estimating the variance of a maximum likelihood estimator. The methods are consistent with each other and indicate that when estimating the position of interaction and energy deposited by a gamma-ray photon, the Fano factor of a scintillator does not affect the spatial resolution. A smaller Fano factor results in a better energy resolution.

A Multi-Variate Fit to the Chemical Composition of the Cosmic-Ray Spectrum

NASA Astrophysics Data System (ADS)

Eisch, Jonathan

Since the discovery of cosmic rays over a century ago, evidence of their origins has remained elusive. Deflected by galactic magnetic fields, the only direct evidence of their origin and propagation remain encoded in their energy distribution and chemical composition. Current models of galactic cosmic rays predict variations of the energy distribution of individual elements in an energy region around 3x1015 eV known as the knee. This work presents a method to measure the energy distribution of individual elemental groups in the knee region and its application to a year of data from the IceCube detector. The method uses cosmic rays detected by both IceTop, the surface-array component, and the deep-ice component of IceCube during the 2009-2010 operation of the IC-59 detector. IceTop is used to measure the energy and the relative likelihood of the mass composition using the signal from the cosmic-ray induced extensive air shower reaching the surface. IceCube, 1.5 km below the surface, measures the energy of the high-energy bundle of muons created in the very first interactions after the cosmic ray enters the atmosphere. These event distributions are fit by a constrained model derived from detailed simulations of cosmic rays representing five chemical elements. The results of this analysis are evaluated in terms of the theoretical uncertainties in cosmic-ray interactions and seasonal variations in the atmosphere. The improvements in high-energy cosmic ray hadronic-interaction models informed by this analysis, combined with increased data from subsequent operation of the IceCube detector, could provide crucial limits on the origin of cosmic rays and their propagation through the galaxy. In the course of developing this method, a number of analysis and statistical techniques were developed to deal with the difficulties inherent in this type of measurement. These include a composition-sensitive air shower reconstruction technique, a method to model simulated event distributions with limited statistics, and a method to optimize and estimate the error on a regularized fit.

Energy of adhesion of human T cells to adsorption layers of monoclonal antibodies measured by a film trapping technique.

PubMed Central

Ivanov, I B; Hadjiiski, A; Denkov, N D; Gurkov, T D; Kralchevsky, P A; Koyasu, S

1998-01-01

A novel method for studying the interaction of biological cells with interfaces (e.g., adsorption monolayers of antibodies) is developed. The method is called the film trapping technique because the cell is trapped within an aqueous film of equilibrium thickness smaller than the cell diameter. A liquid film of uneven thickness is formed around the trapped cell. When observed in reflected monochromatic light, this film exhibits an interference pattern of concentric bright and dark fringes. From the radii of the fringes one can restore the shape of interfaces and the cell. Furthermore, one can calculate the adhesive energy between the cell membrane and the aqueous film surface (which is covered by a layer of adsorbed proteins and/or specific ligands), as well as the disjoining pressure, representing the force of interaction per unit area of the latter film. The method is applied to two human T cell lines: Jurkat and its T cell receptor negative (TCR-) derivative. The interaction of these cells with monolayers of three different monoclonal antibodies adsorbed at a water-air interface is studied. The results show that the adhesive energy is considerable (above 0.5 mJ/m2) when the adsorption monolayer contains antibodies acting as specific ligands for the receptors expressed on the cell surface. In contrast, the adhesive energy is close to zero in the absence of such a specific ligand-receptor interaction. In principle, the method can be applied to the study of the interaction of a variety of biological cells (B cells, natural killer cells, red blood cells, etc.) with adsorption monolayers of various biologically active molecules. In particular, film trapping provides a tool for the gentle micromanipulation of cells and for monitoring of processes (say the activation of a T lymphocyte) occurring at the single-cell level. PMID:9649417

A non-oscillatory energy-splitting method for the computation of compressible multi-fluid flows

NASA Astrophysics Data System (ADS)

Lei, Xin; Li, Jiequan

2018-04-01

This paper proposes a new non-oscillatory energy-splitting conservative algorithm for computing multi-fluid flows in the Eulerian framework. In comparison with existing multi-fluid algorithms in the literature, it is shown that the mass fraction model with isobaric hypothesis is a plausible choice for designing numerical methods for multi-fluid flows. Then we construct a conservative Godunov-based scheme with the high order accurate extension by using the generalized Riemann problem solver, through the detailed analysis of kinetic energy exchange when fluids are mixed under the hypothesis of isobaric equilibrium. Numerical experiments are carried out for the shock-interface interaction and shock-bubble interaction problems, which display the excellent performance of this type of schemes and demonstrate that nonphysical oscillations are suppressed around material interfaces substantially.

Two methods for estimating limits to large-scale wind power generation

PubMed Central

Miller, Lee M.; Brunsell, Nathaniel A.; Mechem, David B.; Gans, Fabian; Monaghan, Andrew J.; Vautard, Robert; Keith, David W.; Kleidon, Axel

2015-01-01

Wind turbines remove kinetic energy from the atmospheric flow, which reduces wind speeds and limits generation rates of large wind farms. These interactions can be approximated using a vertical kinetic energy (VKE) flux method, which predicts that the maximum power generation potential is 26% of the instantaneous downward transport of kinetic energy using the preturbine climatology. We compare the energy flux method to the Weather Research and Forecasting (WRF) regional atmospheric model equipped with a wind turbine parameterization over a 105 km2 region in the central United States. The WRF simulations yield a maximum generation of 1.1 We⋅m−2, whereas the VKE method predicts the time series while underestimating the maximum generation rate by about 50%. Because VKE derives the generation limit from the preturbine climatology, potential changes in the vertical kinetic energy flux from the free atmosphere are not considered. Such changes are important at night when WRF estimates are about twice the VKE value because wind turbines interact with the decoupled nocturnal low-level jet in this region. Daytime estimates agree better to 20% because the wind turbines induce comparatively small changes to the downward kinetic energy flux. This combination of downward transport limits and wind speed reductions explains why large-scale wind power generation in windy regions is limited to about 1 We⋅m−2, with VKE capturing this combination in a comparatively simple way. PMID:26305925

Determination of primary energy in nucleus-nucleus collisions and the high P(sub)T tail of alpha-particles

NASA Technical Reports Server (NTRS)

Freier, P. S.; Atwater, T. W.

1985-01-01

A determination of primary energy is required in order to study the energy dependence of meson multiplicity in A-A collisions in cosmic rays. Various procedures which estimate the energy of a primary nucleus from its interaction were investigated. An average of two methods were used, one using the pions and wounded protons and the other using spectator protons and alpha particles. The high P sub T tail observed for Z = 2 fragments requires a modification of the latter method.

Analytical RISM-MP2 free energy gradient method: Application to the Schlenk equilibrium of Grignard reagent

NASA Astrophysics Data System (ADS)

Mori, Toshifumi; Kato, Shigeki

2007-03-01

We present a method to evaluate the analytical gradient of reference interaction site model Møller-Plesset second order free energy with respect to solute nuclear coordinates. It is applied to calculate the geometries and energies in the equilibria of the Grignard reagent (CH 3MgCl) in dimethylether solvent. The Mg-Mg and Mg-Cl distances as well as the binding energies of solvents are largely affected by the dynamical electron correlation. The solvent effect on the Schlenk equilibrium is examined.

Cation-π Interactions: Computational Analyses of the Aromatic Box Motif and the Fluorination Strategy for Experimental Evaluation

PubMed Central

Davis, Matthew R.; Dougherty, Dennis A.

2015-01-01

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4+ and NMe4+ to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the “fluorination strategy” to study cation-π interactions in vivo. PMID:26467787

Cation-π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation.

PubMed

Davis, Matthew R; Dougherty, Dennis A

2015-11-21

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4(+) and NMe4(+) to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the "fluorination strategy" to study cation-π interactions in vivo.

An ab initio study of the C3(+) cation using multireference methods

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Martin, J. M. L.; Francois, J. P.; Gijbels, R.

1991-01-01

The energy difference between the linear 2 sigma(sup +, sub u) and cyclic 2B(sub 2) structures of C3(+) has been investigated using large (5s3p2d1f) basis sets and multireference electron correlation treatments, including complete active space self consistent fields (CASSCF), multireference configuration interaction (MRCI), and averaged coupled-pair functional (ACPF) methods, as well as the single-reference quadratic configuration interaction (QCISD(T)) method. Our best estimate, including a correction for basis set incompleteness, is that the linear form lies above the cyclic from by 5.2(+1.5 to -1.0) kcal/mol. The 2 sigma(sup +, sub u) state is probably not a transition state, but a local minimum. Reliable computation of the cyclic/linear energy difference in C3(+) is extremely demanding of the electron correlation treatment used: of the single-reference methods previously considered, CCSD(T) and QCISD(T) perform best. The MRCI + Q(0.01)/(4s2p1d) energy separation of 1.68 kcal/mol should provide a comparison standard for other electron correlation methods applied to this system.

Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane

NASA Astrophysics Data System (ADS)

Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S.; Gray, C. G.

2008-03-01

Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05±0.39kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.

Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane.

PubMed

Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S; Gray, C G

2008-03-01

Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05+/-0.39 kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors

PubMed Central

2017-01-01

Cytochrome P450 aromatase (CYP19A1) plays a key role in the development of estrogen dependent breast cancer, and aromatase inhibitors have been at the front line of treatment for the past three decades. The development of potent, selective and safer inhibitors is ongoing with in silico screening methods playing a more prominent role in the search for promising lead compounds in bioactivity-relevant chemical space. Here we present a set of comprehensive binding affinity prediction models for CYP19A1 using our automated Linear Interaction Energy (LIE) based workflow on a set of 132 putative and structurally diverse aromatase inhibitors obtained from a typical industrial screening study. We extended the workflow with machine learning methods to automatically cluster training and test compounds in order to maximize the number of explained compounds in one or more predictive LIE models. The method uses protein–ligand interaction profiles obtained from Molecular Dynamics (MD) trajectories to help model search and define the applicability domain of the resolved models. Our method was successful in accounting for 86% of the data set in 3 robust models that show high correlation between calculated and observed values for ligand-binding free energies (RMSE < 2.5 kJ mol–1), with good cross-validation statistics. PMID:28776988

Quantitative analysis of weak interactions by Lattice energy calculation, Hirshfeld surface and DFT studies of sulfamonomethoxine

NASA Astrophysics Data System (ADS)

Patel, Kinjal D.; Patel, Urmila H.

2017-01-01

Sulfamonomethoxine, 4-Amino-N-(6-methoxy-4-pyrimidinyl) benzenesulfonamide (C11H12N4O3S), is investigated by single crystal X-ray diffraction technique. Pair of N-H⋯N and C-H⋯O intermolecular interactions along with π···π interaction are responsible for the stability of the molecular packing of the structure. In order to understand the nature of the interactions and their quantitative contributions towards the crystal packing, the 3D Hirshfeld surface and 2D fingerprint plot analysis are carried out. PIXEL calculations are performed to determine the lattice energies correspond to intermolecular interactions in the crystal structure. Ab initio quantum chemical calculations of sulfamonomethoxine (SMM) have been performed by B3LYP method, using 6-31G** basis set with the help of Schrodinger software. The computed geometrical parameters are in good agreement with the experimental data. The Mulliken charge distribution, calculated using B3LYP method to confirm the presence of electron acceptor and electron donor atoms, responsible for intermolecular hydrogen bond interactions hence the molecular stability.

Two-baryon systems from HAL QCD method and the mirage in the temporal correlation of the direct method

NASA Astrophysics Data System (ADS)

Iritani, Takumi

2018-03-01

Both direct and HAL QCD methods are currently used to study the hadron interactions in lattice QCD. In the direct method, the eigen-energy of two-particle is measured from the temporal correlation. Due to the contamination of excited states, however, the direct method suffers from the fake eigen-energy problem, which we call the "mirage problem," while the HAL QCD method can extract information from all elastic states by using the spatial correlation. In this work, we further investigate systematic uncertainties of the HAL QCD method such as the quark source operator dependence, the convergence of the derivative expansion of the non-local interaction kernel, and the single baryon saturation, which are found to be well controlled. We also confirm the consistency between the HAL QCD method and the Lüscher's finite volume formula. Based on the HAL QCD potential, we quantitatively confirm that the mirage plateau in the direct method is indeed caused by the contamination of excited states.

Bioluminescence Resonance Energy Transfer System for Measuring Dynamic Protein-Protein Interactions in Bacteria

PubMed Central

Cui, Boyu; Wang, Yao; Song, Yunhong; Wang, Tietao; Li, Changfu; Wei, Yahong

2014-01-01

ABSTRACT Protein-protein interactions are important for virtually every biological process, and a number of elegant approaches have been designed to detect and evaluate such interactions. However, few of these methods allow the detection of dynamic and real-time protein-protein interactions in bacteria. Here we describe a bioluminescence resonance energy transfer (BRET) system based on the bacterial luciferase LuxAB. We found that enhanced yellow fluorescent protein (eYFP) accepts the emission from LuxAB and emits yellow fluorescence. Importantly, BRET occurred when LuxAB and eYFP were fused, respectively, to the interacting protein pair FlgM and FliA. Furthermore, we observed sirolimus (i.e., rapamycin)-inducible interactions between FRB and FKBP12 and a dose-dependent abolishment of such interactions by FK506, the ligand of FKBP12. Using this system, we showed that osmotic stress or low pH efficiently induced multimerization of the regulatory protein OmpR and that the multimerization induced by low pH can be reversed by a neutralizing agent, further indicating the usefulness of this system in the measurement of dynamic interactions. This method can be adapted to analyze dynamic protein-protein interactions and the importance of such interactions in bacterial processes such as development and pathogenicity. PMID:24846380

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

PubMed Central

Gunner, MR; Baker, Nathan A.

2017-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. PMID:27497160

Electron correlation contribution to the physisorption of CO on MgF2(110).

PubMed

Hammerschmidt, Lukas; Müller, Carsten; Paulus, Beate

2012-03-28

We have performed CCSD(T), MP2, and DF-LMP2 calculations of the interaction energy of CO on the MgF(2)(110) surface by applying the method of increments and an embedded cluster model. In addition, we performed periodic HF, B3LYP, and DF-LMP2 calculations and compare them to the cluster results. The incremental CCSD(T) calculations predict an interaction energy of E(int) = -0.37 eV with a C-down orientation of CO above a Mg(2+) ion at the surface with a basis set of VTZ quality. We find that electron correlation constitutes about 50% of the binding energy and a detailed evaluation of the increments shows that the largest contribution to the correlation energy originates from the CO interaction with the closest F ions on the second layer.

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

PubMed

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

2006-05-18

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

Localized-overlap approach to calculations of intermolecular interactions

NASA Astrophysics Data System (ADS)

Rob, Fazle

Symmetry-adapted perturbation theory (SAPT) based on the density functional theory (DFT) description of the monomers [SAPT(DFT)] is one of the most robust tools for computing intermolecular interaction energies. Currently, one can use the SAPT(DFT) method to calculate interaction energies of dimers consisting of about a hundred atoms. To remove the methodological and technical limits and extend the size of the systems that can be calculated with the method, a novel approach has been proposed that redefines the electron densities and polarizabilities in a localized way. In the new method, accurate but computationally expensive quantum-chemical calculations are only applied for the regions where it is necessary and for other regions, where overlap effects of the wave functions are negligible, inexpensive asymptotic techniques are used. Unlike other hybrid methods, this new approach is mathematically rigorous. The main benefit of this method is that with the increasing size of the system the calculation scales linearly and, therefore, this approach will be denoted as local-overlap SAPT(DFT) or LSAPT(DFT). As a byproduct of developing LSAPT(DFT), some important problems concerning distributed molecular response, in particular, the unphysical charge-flow terms were eliminated. Additionally, to illustrate the capabilities of SAPT(DFT), a potential energy function has been developed for an energetic molecular crystal of 1,1-diamino-2,2-dinitroethylene (FOX-7), where an excellent agreement with the experimental data has been found.

Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors

NASA Astrophysics Data System (ADS)

Fales, B. Scott; Shu, Yinan; Levine, Benjamin G.; Hohenstein, Edward G.

2017-09-01

A new complete active space configuration interaction (CASCI) method was recently introduced that uses state-averaged natural orbitals from the configuration interaction singles method (configuration interaction singles natural orbital CASCI, CISNO-CASCI). This method has been shown to perform as well or better than state-averaged complete active space self-consistent field for a variety of systems. However, further development and testing of this method have been limited by the lack of available analytic first derivatives of the CISNO-CASCI energy as well as the derivative coupling between electronic states. In the present work, we present a Lagrangian-based formulation of these derivatives as well as a highly efficient implementation of the resulting equations accelerated with graphical processing units. We demonstrate that the CISNO-CASCI method is practical for dynamical simulations of photochemical processes in molecular systems containing hundreds of atoms.

Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors.

PubMed

Fales, B Scott; Shu, Yinan; Levine, Benjamin G; Hohenstein, Edward G

2017-09-07

A new complete active space configuration interaction (CASCI) method was recently introduced that uses state-averaged natural orbitals from the configuration interaction singles method (configuration interaction singles natural orbital CASCI, CISNO-CASCI). This method has been shown to perform as well or better than state-averaged complete active space self-consistent field for a variety of systems. However, further development and testing of this method have been limited by the lack of available analytic first derivatives of the CISNO-CASCI energy as well as the derivative coupling between electronic states. In the present work, we present a Lagrangian-based formulation of these derivatives as well as a highly efficient implementation of the resulting equations accelerated with graphical processing units. We demonstrate that the CISNO-CASCI method is practical for dynamical simulations of photochemical processes in molecular systems containing hundreds of atoms.

Deterministic alternatives to the full configuration interaction quantum Monte Carlo method for strongly correlated systems

NASA Astrophysics Data System (ADS)

Tubman, Norm; Whaley, Birgitta

The development of exponential scaling methods has seen great progress in tackling larger systems than previously thought possible. One such technique, full configuration interaction quantum Monte Carlo, allows exact diagonalization through stochastically sampling of determinants. The method derives its utility from the information in the matrix elements of the Hamiltonian, together with a stochastic projected wave function, which are used to explore the important parts of Hilbert space. However, a stochastic representation of the wave function is not required to search Hilbert space efficiently and new deterministic approaches have recently been shown to efficiently find the important parts of determinant space. We shall discuss the technique of Adaptive Sampling Configuration Interaction (ASCI) and the related heat-bath Configuration Interaction approach for ground state and excited state simulations. We will present several applications for strongly correlated Hamiltonians. This work was supported through the Scientific Discovery through Advanced Computing (SciDAC) program funded by the U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research and Basic Energy Sciences.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

PubMed

Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

NASA Astrophysics Data System (ADS)

Henke, Paul S.; Mak, Chi H.

2014-08-01

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-03-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.

PubMed

Henke, Paul S; Mak, Chi H

2014-08-14

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg(2+) that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

First Principles based methods and applications for realistic simulations on complex soft materials to develop new materials for energy, health, and environmental sustainability

NASA Astrophysics Data System (ADS)

Goddard, William

2013-03-01

For soft materials applications it is essential to obtain accurate descriptions of the weak (London dispersion, electrostatic) interactions between nonbond units, to include interactions with and stabilization by solvent, and to obtain accurate free energies and entropic changes during chemical, physical, and thermal processing. We will describe some of the advances being made in first principles based methods for treating soft materials with applications selected from new organic electrodes and electrolytes for batteries and fuel cells, forward osmosis for water cleanup, extended matter stable at ambient conditions, and drugs for modulating activation of GCPR membrane proteins,

Method Of Characterizing An Electrode Binder

DOEpatents

Cocciantelli, Jean-Michel; Coco, Isabelle; Villenave, Jean-Jacques

1999-05-11

In a method of characterizing a polymer binder for cell electrodes in contact with an electrolyte and including a current collector and a paste containing an electrochemically active material and said binder, a spreading coefficient of the binder on the active material is calculated from the measured angle of contact between standard liquids and the active material and the binder, respectively. An interaction energy of the binder with the electrolyte is calculated from the measured angle of contact between the electrolyte and the binder. The binder is selected such that the spreading coefficient is less than zero and the interaction energy is at least 60 mJ/m.sup.2.

Spin and Pseudospin Symmetries of Hellmann Potential with Three Tensor Interactions Using Nikiforov-Uvarov Method

NASA Astrophysics Data System (ADS)

Akpan, N. Ikot; Hassan, Hassanabadi; Tamunoimi, M. Abbey

2015-12-01

The Dirac equation with Hellmann potential is presented in the presence of Coulomb-like tensor (CLT), Yukawa-like tensor (YLT), and Hulthen-type tensor (HLT) interactions by using Nikiforov-Uvarov method. The bound state energy spectra and the radial wave functions are obtained approximately within the framework of spin and pseudospin symmetries limit. We have also reported some numerical results and figures to show the effects of the tensor interactions. Special cases of the potential are also discussed.

Insight on the formation of chitosan nanoparticles through ionotropic gelation with tripolyphosphate.

PubMed

Koukaras, Emmanuel N; Papadimitriou, Sofia A; Bikiaris, Dimitrios N; Froudakis, George E

2012-10-01

This work reports details pertaining to the formation of chitosan nanoparticles that we prepare by the ionic gelation method. The molecular interactions of the ionic cross-linking of chitosan with tripolyphosphate have been investigated and elucidated by means of all-electron density functional theory. Solvent effects have been taken into account using implicit models. We have identified primary-interaction ionic cross-linking configurations that we define as H-link, T-link, and M-link, and we have quantified the corresponding interaction energies. H-links, which display high interaction energies and are also spatially broadly accessible, are the most probable cross-linking configurations. At close range, proton transfer has been identified, with maximum interaction energies ranging from 12.3 up to 68.3 kcal/mol depending on the protonation of the tripolyphosphate polyanion and the relative coordination of chitosan with tripolyphosphate. On the basis of our results for the linking types (interaction energies and torsion bias), we propose a simple mechanism for their impact on the chitosan/TPP nanoparticle formation process. We introduce the β ratio, which is derived from the commonly used α ratio but is more fundamental since it additionally takes into account structural details of the oligomers.

Targeting the cell wall of Mycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem with L,D-transpeptidase 2.

PubMed

Silva, José Rogério A; Bishai, William R; Govender, Thavendran; Lamichhane, Gyanu; Maguire, Glenn E M; Kruger, Hendrik G; Lameira, Jeronimo; Alves, Cláudio N

2016-01-01

The single crystal X-ray structure of the extracellular portion of the L,D-transpeptidase (ex-LdtMt2 - residues 120-408) enzyme was recently reported. It was observed that imipenem and meropenem inhibit activity of this enzyme, responsible for generating L,D-transpeptide linkages in the peptidoglycan layer of Mycobacterium tuberculosis. Imipenem is more active and isothermal titration calorimetry experiments revealed that meropenem is subjected to an entropy penalty upon binding to the enzyme. Herein, we report a molecular modeling approach to obtain a molecular view of the inhibitor/enzyme interactions. The average binding free energies for nine commercially available inhibitors were calculated using MM/GBSA and Solvation Interaction Energy (SIE) approaches and the calculated energies corresponded well with the available experimentally observed results. The method reproduces the same order of binding energies as experimentally observed for imipenem and meropenem. We have also demonstrated that SIE is a reasonably accurate and cost-effective free energy method, which can be used to predict carbapenem affinities for this enzyme. A theoretical explanation was offered for the experimental entropy penalty observed for meropenem, creating optimism that this computational model can serve as a potential computational model for other researchers in the field.

About increase of the large transvere momentum processes fraction in hA interactions at energies 5.10(14) - 10(16) eV according to the data on E.A.S. hadrons

NASA Technical Reports Server (NTRS)

Danilova, T. V.; Dubovy, A. G.; Erlykin, A. D.; Nesterova, N. M.; Chubenko, A. P.

1985-01-01

The lateral distributions of extensive air showers (EAS) hadrons obtained at Tien-Shan array are compared with the simulations. The simulation data have been treated in the same way as experimental data, including the recording method. The comparison shows that the experimental hadron lateral distributions are wider than simulated ones. On the base of this result the conclusion is drawn that the fraction of processes with large p (perpendicular) increases in hadron-air interactions at energies 5 x 10 to the 14 to 10 to the 16 eV compared with accelerator data in p-p interactions at lower energies.

Many-body localization in a long range XXZ model with random-field

NASA Astrophysics Data System (ADS)

Li, Bo

2016-12-01

Many-body localization (MBL) in a long range interaction XXZ model with random field are investigated. Using the exact diagonal method, the MBL phase diagram with different tuning parameters and interaction range is obtained. It is found that the phase diagram of finite size results supplies strong evidence to confirm that the threshold interaction exponent α = 2. The tuning parameter Δ can efficiently change the MBL edge in high energy density stats, thus the system can be controlled to transfer from thermal phase to MBL phase by changing Δ. The energy level statistics data are consistent with result of the MBL phase diagram. However energy level statistics data cannot detect the thermal phase correctly in extreme long range case.

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Ham, Sihyun

2011-07-01

We report the development of an atomic decomposition method of the protein solvation free energy in water, which ascribes global change in the solvation free energy to local changes in protein conformation as well as in hydration structure. So far, empirical decomposition analyses based on simple continuum solvation models have prevailed in the study of protein-protein interactions, protein-ligand interactions, as well as in developing scoring functions for computer-aided drug design. However, the use of continuum solvation model suffers serious drawbacks since it yields the protein free energy landscape which is quite different from that of the explicit solvent model and since it does not properly account for the non-polar hydrophobic effects which play a crucial role in biological processes in water. Herein, we develop an exact and general decomposition method of the solvation free energy that overcomes these hindrances. We then apply this method to elucidate the molecular origin for the solvation free energy change upon the conformational transitions of 42-residue amyloid-beta protein (Aβ42) in water, whose aggregation has been implicated as a primary cause of Alzheimer's disease. We address why Aβ42 protein exhibits a great propensity to aggregate when transferred from organic phase to aqueous phase.

Simple and exact approach to the electronic polarization effect on the solvation free energy: formulation for quantum-mechanical/molecular-mechanical system and its applications to aqueous solutions.

PubMed

Takahashi, Hideaki; Omi, Atsushi; Morita, Akihiro; Matubayasi, Nobuyuki

2012-06-07

We present a simple and exact numerical approach to compute the free energy contribution δμ in solvation due to the electron density polarization and fluctuation of a quantum-mechanical solute in the quantum-mechanical/molecular-mechanical (QM/MM) simulation combined with the theory of the energy representation (QM/MM-ER). Since the electron density fluctuation is responsible for the many-body QM-MM interactions, the standard version of the energy representation method cannot be applied directly. Instead of decomposing the QM-MM polarization energy into the pairwise additive and non-additive contributions, we take sum of the polarization energies in the QM-MM interaction and adopt it as a new energy coordinate for the method of energy representation. Then, it is demonstrated that the free energy δμ can be exactly formulated in terms of the energy distribution functions for the solution and reference systems with respect to this energy coordinate. The benchmark tests were performed to examine the numerical efficiency of the method with respect to the changes in the individual properties of the solvent and the solute. Explicitly, we computed the solvation free energy of a QM water molecule in ambient and supercritical water, and also the free-energy change associated with the isomerization reaction of glycine from neutral to zwitterionic structure in aqueous solution. In all the systems examined, it was demonstrated that the computed free energy δμ agrees with the experimental value, irrespective of the choice of the reference electron density of the QM solute. The present method was also applied to a prototype reaction of adenosine 5'-triphosphate hydrolysis where the effect of the electron density fluctuation is substantial due to the excess charge. It was demonstrated that the experimental free energy of the reaction has been accurately reproduced with the present approach.

Theoretical investigation of gas-phase molecular complex formation between 2-hydroxy thiophenol and a water molecule.

PubMed

Kumar Deb, Debojit; Sarkar, Biplab

2017-01-18

The torsional potential of OH and SH rotations in 2-hydroxy thiophenol is systematically studied using the MP2 ab initio method. The outcome of state-of-the-art calculations is used in the investigation of the structures and conformational preferences of 2-hydroxy thiophenol and aims at further interaction studies with a gas phase water molecule. SCS-MP2 and CCSD(T) complete basis set (CBS) limit interaction energies for these complexes are presented. The SCS-MP2/CBS limit is achieved using various two-point extrapolation methods with aug-cc-pVDZ and aug-cc-pVTZ basis sets. The CCSD(T) correction term is determined as the difference between CCSD(T) and SCS-MP2 interaction energies calculated using a smaller basis set. The effect of counterpoise correction on the extrapolation to the CBS limit is discussed. The performance of DFT based wB97XD, M06-2X and B3LYP-D3 functionals is tested against the benchmark energy from ab initio calculations. Hydrogen bond interactions are characterized by carrying out QTAIM, NCIPLOT, NBO and SAPT analyses.

Periodic Anderson model with correlated conduction electrons: Variational and exact diagonalization study

NASA Astrophysics Data System (ADS)

Hagymási, I.; Itai, K.; Sólyom, J.

2012-06-01

We investigate an extended version of the periodic Anderson model (the so-called periodic Anderson-Hubbard model) with the aim to understand the role of interaction between conduction electrons in the formation of the heavy-fermion and mixed-valence states. Two methods are used: (i) variational calculation with the Gutzwiller wave function optimizing numerically the ground-state energy and (ii) exact diagonalization of the Hamiltonian for short chains. The f-level occupancy and the renormalization factor of the quasiparticles are calculated as a function of the energy of the f orbital for a wide range of the interaction parameters. The results obtained by the two methods are in reasonably good agreement for the periodic Anderson model. The agreement is maintained even when the interaction between band electrons, Ud, is taken into account, except for the half-filled case. This discrepancy can be explained by the difference between the physics of the one- and higher-dimensional models. We find that this interaction shifts and widens the energy range of the bare f level, where heavy-fermion behavior can be observed. For large-enough Ud this range may lie even above the bare conduction band. The Gutzwiller method indicates a robust transition from Kondo insulator to Mott insulator in the half-filled model, while Ud enhances the quasiparticle mass when the filling is close to half filling.

Ground-state energies of simple metals

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1974-01-01

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

Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors.

PubMed

Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

2017-06-01

The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy. In addition, we analyzed benzodiazepine derivatives that are high-affinity ligands for BRDs and examined differences in the CH/π interactions of the amino acid residues. We further surveyed changes in the charges of the amino acid residues among individual ligands, performed pair interaction energy decomposition analysis and estimated the water profile within the ligand binding site. Thus, useful insights for drug design were provided. Through these analyses and considerations, we show that the FMO method is a useful drug design tool to evaluate the process of FBDD and to explore PPI inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Interaction of dyes CD–1 and SD–1 with the surface of oligodimethysiloxane

NASA Astrophysics Data System (ADS)

Chausov, D. N.

2018-03-01

We carried out the modeling orientation of the dyes CD–1 and SD–1 relative to the surface of oligodimethysiloxane using the atom–atom potentials method. We have discovered the dependence of the interaction energy in dyes molecules on the angles which characterizes their orientation relative to the surface of the oligodimethysiloxane crystal. It was found out that the obtained energy value of interaction with the surface can explain weak adhesive qualities of the dyes and the orientation type relative to the surface. We identified the break– loose force for the dyes on the oligodimethysiloxane crystal surface.

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

Pederson, Mark R.; Baruah, Tunna; Basurto, Luis

We have applied a recently developed method to incorporate the self-interaction correction through Fermi orbitals to Mg-porphyrin, C{sub 60}, and pentacene molecules. The Fermi-Löwdin orbitals are localized and unitarily invariant to the Kohn-Sham orbitals from which they are constructed. The self-interaction-corrected energy is obtained variationally leading to an optimum set of Fermi-Löwdin orbitals (orthonormalized Fermi orbitals) that gives the minimum energy. A Fermi orbital, by definition, is dependent on a certain point which is referred to as the descriptor position. The degree to which the initial choice of descriptor positions influences the variational approach to the minimum and the complexitymore » of the energy landscape as a function of Fermi-orbital descriptors is examined in detail for Mg-porphyrin. The applications presented here also demonstrate that the method can be applied to larger molecular systems containing a few hundred electrons. The atomization energy of the C{sub 60} molecule within the Fermi-Löwdin-orbital self-interaction-correction approach is significantly improved compared to local density approximation in the Perdew-Wang 92 functional and generalized gradient approximation of Perdew-Burke-Ernzerhof functionals. The eigenvalues of the highest occupied molecular orbitals show qualitative improvement.« less

[Detection of protein-protein interactions by FRET and BRET methods].

PubMed

Matoulková, E; Vojtěšek, B

2014-01-01

Nowadays, in vivo protein-protein interaction studies have become preferable detecting meth-ods that enable to show or specify (already known) protein interactions and discover their inhibitors. They also facilitate detection of protein conformational changes and discovery or specification of signaling pathways in living cells. One group of in vivo methods enabling these findings is based on fluorescent resonance energy transfer (FRET) and its bio-luminescent modification (BRET). They are based on visualization of protein-protein interactions via light or enzymatic excitation of fluorescent or bio-luminescent proteins. These methods allow not only protein localization within the cell or its organelles (or small animals) but they also allow us to quantify fluorescent signals and to discover weak or strong interaction partners. In this review, we explain the principles of FRET and BRET, their applications in the characterization of protein-protein interactions and we describe several findings using these two methods that clarify molecular and cellular mechanisms and signals related to cancer biology.

Energy and contact of the one-dimensional Fermi polaron at zero and finite temperature.

PubMed

Doggen, E V H; Kinnunen, J J

2013-07-12

We use the T-matrix approach for studying highly polarized homogeneous Fermi gases in one dimension with repulsive or attractive contact interactions. Using this approach, we compute ground state energies and values for the contact parameter that show excellent agreement with exact and other numerical methods at zero temperature, even in the strongly interacting regime. Furthermore, we derive an exact expression for the value of the contact parameter in one dimension at zero temperature. The model is then extended and used for studying the temperature dependence of ground state energies and the contact parameter.

HZEFRG1: An energy-dependent semiempirical nuclear fragmentation model

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.; Wilson, John W.; Tripathi, Ram K.; Norbury, John W.; Badavi, Francis F.; Khan, Ferdous

1993-01-01

Methods for calculating cross sections for the breakup of high-energy heavy ions by the combined nuclear and coulomb fields of the interacting nuclei are presented. The nuclear breakup contributions are estimated with an abrasion-ablation model of heavy ion fragmentation that includes an energy-dependent, mean free path. The electromagnetic dissociation contributions arising from the interacting coulomb fields are estimated by using Weizsacker-Williams theory extended to include electric dipole and electric quadrupole contributions. The complete computer code that implements the model is included as an appendix. Extensive comparisons of cross section predictions with available experimental data are made.

Benchmark results for few-body hypernuclei

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

Ruffino, Fabrizio Ferrari; Lonardoni, Diego; Barnea, Nir

2017-03-16

Here, the Non-Symmetrized Hyperspherical Harmonics method (NSHH) is introduced in the hypernuclear sector and benchmarked with three different ab-initio methods, namely the Auxiliary Field Diffusion Monte Carlo method, the Faddeev–Yakubovsky approach and the Gaussian Expansion Method. Binding energies and hyperon separation energies of three- to five-body hypernuclei are calculated by employing the two-body ΛN component of the phenomenological Bodmer–Usmani potential, and a hyperon-nucleon interaction simulating the scattering phase shifts given by NSC97f. The range of applicability of the NSHH method is briefly discussed.

The visible touch: in planta visualization of protein-protein interactions by fluorophore-based methods

PubMed Central

Bhat, Riyaz A; Lahaye, Thomas; Panstruga, Ralph

2006-01-01

Non-invasive fluorophore-based protein interaction assays like fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC, also referred to as "split YFP") have been proven invaluable tools to study protein-protein interactions in living cells. Both methods are now frequently used in the plant sciences and are likely to develop into standard techniques for the identification, verification and in-depth analysis of polypeptide interactions. In this review, we address the individual strengths and weaknesses of both approaches and provide an outlook about new directions and possible future developments for both techniques. PMID:16800872

Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme

NASA Astrophysics Data System (ADS)

Yamamori, Yu; Matubayasi, Nobuyuki

2017-06-01

The effects of urea and its alkylated derivatives on the structure of T4-lysozyme were analyzed from the standpoint of energetics. Molecular dynamics simulations were conducted with explicit solvent, and the energy-representation method was employed to compute the free energy of transfer of the protein from pure-water solvent to the mixed solvents of water with urea, methylurea, 1,1-dimethylurea, and isopropylurea. Through the decomposition of the transfer free energy into the cosolvent and water contributions, it was observed that the former is partially cancelled by the latter and governs the total free energy of transfer. To determine the interaction component responsible for the transfer energetics, the correlations of the transfer free energy were also examined against the change in the solute-solvent interaction energy upon transfer and the corresponding changes in the electrostatic, van der Waals, and excluded-volume components. It was then found over the set of protein structures ranging from native to (partially) unfolded ones that the transfer free energy changes in parallel with the van der Waals component even when the cosolvent is alkylated. The electrostatic and excluded-volume components play minor roles in the structure modification of the protein, and the denaturing ability of alkylurea is brought by the van der Waals interaction.

Methodology to improve design of accelerated life tests in civil engineering projects.

PubMed

Lin, Jing; Yuan, Yongbo; Zhou, Jilai; Gao, Jie

2014-01-01

For reliability testing an Energy Expansion Tree (EET) and a companion Energy Function Model (EFM) are proposed and described in this paper. Different from conventional approaches, the EET provides a more comprehensive and objective way to systematically identify external energy factors affecting reliability. The EFM introduces energy loss into a traditional Function Model to identify internal energy sources affecting reliability. The combination creates a sound way to enumerate the energies to which a system may be exposed during its lifetime. We input these energies into planning an accelerated life test, a Multi Environment Over Stress Test. The test objective is to discover weak links and interactions among the system and the energies to which it is exposed, and design them out. As an example, the methods are applied to the pipe in subsea pipeline. However, they can be widely used in other civil engineering industries as well. The proposed method is compared with current methods.

Precise calculations in simulations of the interaction of low energy neutrons with nano-dispersed media

NASA Astrophysics Data System (ADS)

Artem'ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.

2016-01-01

We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2-5 nm and for neutron energies 3 × 10-7-10-3 eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.

Communication: Local energetic analysis of the interfacial and surface energies of graphene from the single layer to graphite

NASA Astrophysics Data System (ADS)

Kocherlakota, Lakshmi S.; Krajina, Brad A.; Overney, René M.

2015-12-01

Recent advances in scanning probe methods that provide direct access to the surface free energy of inorganic layered materials in terms of the Hamaker constant yield energetic values for monolayer graphene that differ substantially, by a factor of around 0.4, from bulk graphite. The onset of bulk deviating energy values was observed at a multilayer slab thickness of ˜3 nm, corresponding to a layer number of 10. The findings, complemented with extractions from water contact angle measurements and calculated interlayer binding energies, find short-range ordinary van der Waals interactions to be most prominently affected by dimensional constraints and many-body interactions.

Communication: Local energetic analysis of the interfacial and surface energies of graphene from the single layer to graphite.

PubMed

Kocherlakota, Lakshmi S; Krajina, Brad A; Overney, René M

2015-12-28

Recent advances in scanning probe methods that provide direct access to the surface free energy of inorganic layered materials in terms of the Hamaker constant yield energetic values for monolayer graphene that differ substantially, by a factor of around 0.4, from bulk graphite. The onset of bulk deviating energy values was observed at a multilayer slab thickness of ∼3 nm, corresponding to a layer number of 10. The findings, complemented with extractions from water contact angle measurements and calculated interlayer binding energies, find short-range ordinary van der Waals interactions to be most prominently affected by dimensional constraints and many-body interactions.

An improved quasi-diabatic representation of the 1, 2, 3{sup 1}A coupled adiabatic potential energy surfaces of phenol in the full 33 internal coordinates

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

Zhu, Xiaolei, E-mail: virtualzx@gmail.com; Malbon, Christopher L., E-mail: clmalbon@gmail.com; Yarkony, David R., E-mail: yarkony@jhu.edu

2016-03-28

In a recent work we constructed a quasi-diabatic representation, H{sup d}, of the 1, 2, 3{sup 1}A adiabatic states of phenol from high level multireference single and double excitation configuration interaction electronic structure data, energies, energy gradients, and derivative couplings. That H{sup d} accurately describes surface minima, saddle points, and also regions of strong nonadiabatic interactions, reproducing the locus of conical intersection seams and the coordinate dependence of the derivative couplings. The present work determines the accuracy of H{sup d} for describing phenol photodissociation. Additionally, we demonstrate that a modest energetic shift of two diabats yields a quantifiably more accuratemore » H{sup d} compared with experimental energetics. The analysis shows that in favorable circumstances it is possible to use single point energies obtained from the most reliable electronic structure methods available, including methods for which the energy gradients and derivative couplings are not available, to improve the quality of a global representation of several coupled potential energy surfaces. Our data suggest an alternative interpretation of kinetic energy release measurements near λ{sub phot} ∼ 248 nm.« less

Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1

NASA Astrophysics Data System (ADS)

Anisimov, Victor M.; Ziemys, Arturas; Kizhake, Smitha; Yuan, Ziyan; Natarajan, Amarnath; Cavasotto, Claudio N.

2011-11-01

The C-terminal domain of BRCA1(BRCT) is involved in the DNA repair pathway by recognizing the pSXXF motif in interacting proteins. It has been reported that short peptides containing this motif bind to BRCA1(BRCT) in the micromolar range with high specificity. In this work, the binding of pSXXF peptides has been studied computationally and experimentally in order to characterize their interaction with BRCA1(BRCT). Elucidation of the contacts that drive the protein-ligand interaction is critical for the development of high affinity small-molecule BRCA1 inhibitors. Molecular dynamics (MD) simulations revealed the key role of threonine at the peptide P+2 position in providing structural rigidity to the ligand in the bound state. The mutation at P+1 had minor effects. Peptide extension at the N-terminal position with the naphthyl amino acid exhibited a modest increase in binding affinity, what could be explained by the dispersion interaction of the naphthyl side-chain with a hydrophobic patch. Three in silico end-point methods were considered for the calculation of binding free energy. The Molecular Mechanics Poisson-Boltzmann Surface Area and the Solvated Interaction Energy methods gave reasonable agreement with experimental data, exhibiting a Pearlman predictive index of 0.71 and 0.78, respectively. The MM-quantum mechanics-surface area method yielded improved results, which was characterized by a Pearlman index of 0.78. The correlation coefficients were 0.59, 0.61 and 0.69, respectively. The ability to apply a QM level of theory within an end-point binding free energy protocol may provide a way for a consistent improvement of accuracy in computer-aided drug design.

Extended maximum likelihood halo-independent analysis of dark matter direct detection data

DOE PAGES

Gelmini, Graciela B.; Georgescu, Andreea; Gondolo, Paolo; ...

2015-11-24

We extend and correct a recently proposed maximum-likelihood halo-independent method to analyze unbinned direct dark matter detection data. Instead of the recoil energy as independent variable we use the minimum speed a dark matter particle must have to impart a given recoil energy to a nucleus. This has the advantage of allowing us to apply the method to any type of target composition and interaction, e.g. with general momentum and velocity dependence, and with elastic or inelastic scattering. We prove the method and provide a rigorous statistical interpretation of the results. As first applications, we find that for dark mattermore » particles with elastic spin-independent interactions and neutron to proton coupling ratio f n/f p=-0.7, the WIMP interpretation of the signal observed by CDMS-II-Si is compatible with the constraints imposed by all other experiments with null results. We also find a similar compatibility for exothermic inelastic spin-independent interactions with f n/f p=-0.8.« less

Dissipative time-dependent quantum transport theory.

PubMed

Zhang, Yu; Yam, Chi Yung; Chen, GuanHua

2013-04-28

A dissipative time-dependent quantum transport theory is developed to treat the transient current through molecular or nanoscopic devices in presence of electron-phonon interaction. The dissipation via phonon is taken into account by introducing a self-energy for the electron-phonon coupling in addition to the self-energy caused by the electrodes. Based on this, a numerical method is proposed. For practical implementation, the lowest order expansion is employed for the weak electron-phonon coupling case and the wide-band limit approximation is adopted for device and electrodes coupling. The corresponding hierarchical equation of motion is derived, which leads to an efficient and accurate time-dependent treatment of inelastic effect on transport for the weak electron-phonon interaction. The resulting method is applied to a one-level model system and a gold wire described by tight-binding model to demonstrate its validity and the importance of electron-phonon interaction for the quantum transport. As it is based on the effective single-electron model, the method can be readily extended to time-dependent density functional theory.

Interactions of cephalexin with bovine serum albumin: displacement reaction and molecular docking.

PubMed

Hamishehkar, Hamed; Hosseini, Soheila; Naseri, Abdolhossein; Safarnejad, Azam; Rasoulzadeh, Farzaneh

2016-01-01

Introduction: The drug-plasma protein interaction is a fundamental issue in guessing and checking the serious drug side effects related with other drugs. The purpose of this research was to study the interaction of cephalexin with bovine serum albumin (BSA) and displacement reaction using site probes. Methods: The interaction mechanism concerning cephalexin (CPL) with BSA was investigated using various spectroscopic methods and molecular modeling method. The binding sites number, n, apparent binding constant, K, and thermodynamic parameters, ΔG 0 , ΔH 0 , and ΔS 0 were considered at different temperatures. To evaluate the experimental results, molecular docking modeling was calculated. Results: The distance, r=1.156 nm between BSA and CPL were found in accordance with the Forster theory of non-radiation energy transfer (FRET) indicating energy transfer occurs between BSA and CPL. According to the binding parameters and ΔG 0 = negative values and ΔS 0 = 28.275 j mol -1 K -1 , a static quenching process is effective in the CPL-BSA interaction spontaneously. ΔG 0 for the CPL-BSA complex obtained from the docking simulation is -28.99 kj mol -1 , which is close to experimental ΔG of binding, -21.349 kj mol -1 that indicates a good agreement between the results of docking methods and experimental data. Conclusion: The outcomes of spectroscopic methods revealed that the conformation of BSA changed during drug-BSA interaction. The results of FRET propose that CPL quenches the fluorescence of BSA by static quenching and FRET. The displacement study showed that phenylbutazon and ketoprofen displaced CPL, indicating that its binding site on albumin is site I and Gentamicin cannot be displaced from the binding site of CPL. All results of molecular docking method agreed with the results of experimental data.

A computational study of anion-modulated cation-π interactions.

PubMed

Carrazana-García, Jorge A; Rodríguez-Otero, Jesús; Cabaleiro-Lago, Enrique M

2012-05-24

The interaction of anions with cation-π complexes formed by the guanidinium cation and benzene was thoroughly studied by means of computational methods. Potential energy surface scans were performed in order to evaluate the effect of the anion coming closer to the cation-π pair. Several structures of guanidinium-benzene complexes and anion approaching directions were examined. Supermolecule calculations were performed on ternary complexes formed by guanidinium, benzene, and one anion and the interaction energy was decomposed into its different two- and three-body contributions. The interaction energies were further dissected into their electrostatic, exchange, repulsion, polarization and dispersion contributions by means of local molecular orbital energy decomposition analysis. The results confirm that, besides the electrostatic cation-anion attraction, the effect of the anion over the cation-π interaction is mainly due to polarization and can be rationalized following the changes in the anion-π and the nonadditive (three-body) terms of the interaction. When the cation and the anion are on the same side of the π system, the three-body interaction is anticooperative, but when the anion and the cation are on opposite sides of the π system, the three-body interaction is cooperative. As far as we know, this is the first study where this kind of analysis is carried out with a structured cation as guanidinium with a significant biological interest.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

PubMed

Gunner, M R; Baker, N A

2016-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. © 2016 Elsevier Inc. All rights reserved.

Outstanding performance of configuration interaction singles and doubles using exact exchange Kohn-Sham orbitals in real-space numerical grid method

NASA Astrophysics Data System (ADS)

Lim, Jaechang; Choi, Sunghwan; Kim, Jaewook; Kim, Woo Youn

2016-12-01

To assess the performance of multi-configuration methods using exact exchange Kohn-Sham (KS) orbitals, we implemented configuration interaction singles and doubles (CISD) in a real-space numerical grid code. We obtained KS orbitals with the exchange-only optimized effective potential under the Krieger-Li-Iafrate (KLI) approximation. Thanks to the distinctive features of KLI orbitals against Hartree-Fock (HF), such as bound virtual orbitals with compact shapes and orbital energy gaps similar to excitation energies; KLI-CISD for small molecules shows much faster convergence as a function of simulation box size and active space (i.e., the number of virtual orbitals) than HF-CISD. The former also gives more accurate excitation energies with a few dominant configurations than the latter, even with many more configurations. The systematic control of basis set errors is straightforward in grid bases. Therefore, grid-based multi-configuration methods using exact exchange KS orbitals provide a promising new way to make accurate electronic structure calculations.

Estimates of the Attenuation Rates of Baroclinic Tidal Energy Caused by Resonant Interactions Among Internal Waves based on the Weak Turbulence Theory

NASA Astrophysics Data System (ADS)

Onuki, Y.; Hibiya, T.

2016-02-01

The baroclinic tides are thought to be the dominant energy source for turbulent mixing in the ocean interior. In contrast to the geography of the energy conversion rates from the barotropic to baroclinic tides, which has been clarified in recent numerical studies, the global distribution of the energy sink for the resulting low-mode baroclinic tides remains obscure. A key to resolve this issue is the resonant wave-wave interactions, which transfer part of the baroclinic tidal energy to the background internal wave field enhancing the local energy dissipation rates. Recent field observations and numerical studies have pointed out that parametric subharmonic instability (PSI), one of the resonant interactions, causes significant energy sink of baroclinic tidal energy at mid-latitudes. The purpose of this study is to analyze the quantitative aspect of PSI to demonstrate the global distribution of the intensity of resonant wave interactions, namely, the attenuation rate of low-mode baroclinic tidal energy. Our approach is basically following the weak turbulence theory, which is the standard theory for resonant wave-wave interactions, where techniques of singular perturbation and statistical physics are employed. This study is, however, different from the classical theory in some points; we have reformulated the weak turbulence theory to be applicable to low-mode internal waves and also developed its numerical calculation method so that the effects of stratification profile and oceanic total depth can be taken into account. We have calculated the attenuation rate of low-mode baroclinic tidal waves interacting with the background Garrett-Munk internal wave field. The calculated results clearly show the rapid attenuation of baroclinic tidal energy at mid-latitudes, in agreement with the results from field observations and also show the zonal inhomogeneity of the attenuation rate caused by the density structures associated with the subtropical gyre. This study is expected to contribute to clarify the global distribution of the dissipation rates of baroclinic tidal energy.

Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions

NASA Astrophysics Data System (ADS)

Nguyen, Thuong T.; Székely, Eszter; Imbalzano, Giulio; Behler, Jörg; Csányi, Gábor; Ceriotti, Michele; Götz, Andreas W.; Paesani, Francesco

2018-06-01

The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enables routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body (MB) expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials (PIPs), neural networks, and Gaussian approximation potentials (GAPs) in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, Behler-Parrinello neural network-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms.

A critical analysis of computational protein design with sparse residue interaction graphs

PubMed Central

Georgiev, Ivelin S.

2017-01-01

Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation (GMEC). To efficiently find the GMEC, protein design algorithms must methodically reduce the conformational search space. By applying distance and energy cutoffs, the protein system to be designed can thus be represented using a sparse residue interaction graph, where the number of interacting residue pairs is less than all pairs of mutable residues, and the corresponding GMEC is called the sparse GMEC. However, ignoring some pairwise residue interactions can lead to a change in the energy, conformation, or sequence of the sparse GMEC vs. the original or the full GMEC. Despite the widespread use of sparse residue interaction graphs in protein design, the above mentioned effects of their use have not been previously analyzed. To analyze the costs and benefits of designing with sparse residue interaction graphs, we computed the GMECs for 136 different protein design problems both with and without distance and energy cutoffs, and compared their energies, conformations, and sequences. Our analysis shows that the differences between the GMECs depend critically on whether or not the design includes core, boundary, or surface residues. Moreover, neglecting long-range interactions can alter local interactions and introduce large sequence differences, both of which can result in significant structural and functional changes. Designs on proteins with experimentally measured thermostability show it is beneficial to compute both the full and the sparse GMEC accurately and efficiently. To this end, we show that a provable, ensemble-based algorithm can efficiently compute both GMECs by enumerating a small number of conformations, usually fewer than 1000. This provides a novel way to combine sparse residue interaction graphs with provable, ensemble-based algorithms to reap the benefits of sparse residue interaction graphs while avoiding their potential inaccuracies. PMID:28358804

Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion-corrected density functional theory study.

PubMed

Mukherjee, Sanchita; Kailasam, Senthilkumar; Bansal, Manju; Bhattacharyya, Dhananjay

2014-01-01

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3'-endo sugars and this demands C1'-C1' distance of about 5.4 Å along the chains. Consideration of an energy penalty term for deviation of C1'-C1' distance from the mean value, to the recent DFT-D functionals, specifically ωB97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014. Copyright © 2013 Wiley Periodicals, Inc.

Interaction of Benzimidazoles and Benzotriazole: Its Corrosion Protection Properties on Mild Steel in Hydrochloric Acid

NASA Astrophysics Data System (ADS)

Ramya, K.; Mohan, Revathi; Joseph, Abraham

2014-11-01

Synergistic hydrogen-bonded interaction of alkyl benzimidazoles and 1,2,3-benzotrizole and its corrosion protection properties on mild steel in hydrochloric acid at different temperatures have been studied using polarization, EIS, adsorption, surface studies, and computational methods. The extent of synergistic interaction increases with temperature. Quantum chemical approach is used to calculate some electronic properties of the molecules and to ascertain the synergistic interaction, inhibitive effect, and molecular structures. The corrosion inhibition efficiencies and the global chemical reactivity relate to some parameters, such as total energy, E HOMO, E LUMO, and gap energy (Δ E). 1,2,3-Benzotrizole interacts with benzimidazoles derivatives up to a bond length of approximately 1.99 Å. This interaction represents the formation of a hydrogen bond between the 1,2,3-benzotrizole and benzimidazoles. This synergistic interaction of 1,2,3-benzotrizole and benzimidazole derivatives offers extended inhibition efficiency toward mild steel in hydrochloric acid.

Composite Socio-Technical Systems: A Method for Social Energy Systems

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

Zhang, Yingchen; He, Fulin; Hao, Jun

In order to model and study the interactions between social on technical systems, a systemic method, namely the composite socio-technical systems (CSTS), is proposed to incorporate social systems, technical systems and the interaction mechanism between them. A case study on University of Denver (DU) campus grid is presented in paper to demonstrate the application of the proposed method. In the case study, the social system, technical system, and the interaction mechanism are defined and modelled within the framework of CSTS. Distributed and centralized control and management schemes are investigated, respectively, and numerical results verifies the feasibility and performance of themore » proposed composite system method.« less

Thermophysical properties of simple liquid metals: A brief review of theory

NASA Technical Reports Server (NTRS)

Stroud, David

1993-01-01

In this paper, we review the current theory of the thermophysical properties of simple liquid metals. The emphasis is on thermodynamic properties, but we also briefly discuss the nonequilibrium properties of liquid metals. We begin by defining a 'simple liquid metal' as one in which the valence electrons interact only weakly with the ionic cores, so that the interaction can be treated by perturbation theory. We then write down the equilibrium Hamiltonian of a liquid metal as a sum of five terms: the bare ion-ion interaction, the electron-electron interaction, the bare electron-ion interaction, and the kinetic energies of electrons and ions. Since the electron-ion interaction can be treated by perturbation, the electronic part contributes in two ways to the Helmholtz free energy: it gives a density-dependent term which is independent of the arrangement of ions, and it acts to screen the ion-ion interaction, giving rise to effective ion-ion pair potentials which are density-dependent, in general. After sketching the form of a typical pair potential, we briefly enumerate some methods for calculating the ionic distribution function and hence the Helmholtz free energy of the liquid: monte Carlo simulations, molecular dynamics simulations, and thermodynamic perturbation theory. The final result is a general expression for the Helmholtz free energy of the liquid metal. It can be used to calculate a wide range of thermodynamic properties of simple metal liquids, which we enumerate. They include not only a range of thermodynamic coefficients of both metals and alloys, but also many aspects of the phase diagram, including freezing curves of pure elements and phase diagrams of liquid alloys (including liquidus and solidus curves). We briefly mention some key discoveries resulting from previous applications of this method, and point out that the same methods work for other materials not normally considered to be liquid metals (such as colloidal suspensions, in which the suspended microspheres behave like ions screened by the salt solution in which they are suspended). We conclude with a brief discussion of some non-equilibrium (i.e., transport) properties which can be treated by an extension of these methods. These include electrical resistivity, thermal conductivity, viscosity, atomic self-diffusion coefficients, concentration diffusion coefficients in alloys, surface tension and thermal emissivity. Finally, we briefly mention two methods by which the theory might be extended to non-simple liquid metals: these are empirical techniques (i.e., empirical two- and three-body potentials), and numerical many-body approaches. Both may be potentially applicable to extremely complex systems, such as nonstoichiometric liquid semiconductor alloys.

Efficient conformational space exploration in ab initio protein folding simulation.

PubMed

Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

2015-08-01

Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.

Evaluation of drug-carrier interactions in quaternary powder mixtures containing perindopril tert-butylamine and indapamide.

PubMed

Voelkel, Adam; Milczewska, Kasylda; Teżyk, Michał; Milanowski, Bartłomiej; Lulek, Janina

2016-04-30

Interactions occurring between components in the quaternary powder mixtures consisting of perindopril tert-butylamine, indapamide (active pharmaceutical ingredients), carrier substance and hydrophobic colloidal silica were examined. Two grades of lactose monohydrate: Spherolac(®) 100 and Granulac(®) 200 and two types of microcrystalline cellulose: M101D+ and Vivapur(®) 102 were used as carriers. We determined the size distribution (laser diffraction method), morphology (scanning electron microscopy) and a specific surface area of the powder particles (by nitrogen adsorption-desorption). For the determination of the surface energy of powder mixtures the method of inverse gas chromatography was applied. Investigated mixtures were characterized by surface parameters (dispersive component of surface energy, specific interactions parameters, specific surface area), work of adhesion and cohesion as well as Flory-Huggins parameter χ23('). Results obtained for all quaternary powder mixtures indicate existence of interactions between components. The strongest interactions occur for both blends with different types of microcrystalline cellulose (PM-1 and PM-4) while much weaker ones for powder mixtures with various types of lactose (PM-2 and PM-3). Published by Elsevier B.V.

The Water-Energy-Food Nexus: Advancing Innovative, Policy-Relevant Methods

NASA Astrophysics Data System (ADS)

Crootof, A.; Albrecht, T.; Scott, C. A.

2017-12-01

The water-energy-food (WEF) nexus is rapidly expanding in scholarly literature and policy settings as a novel way to address complex Anthropocene challenges. The nexus approach aims to identify tradeoffs and synergies of water, energy, and food systems, internalize social and environmental impacts, and guide development of cross-sectoral policies. However, a primary limitation of the nexus approach is the absence - or gaps and inconsistent use - of adequate methods to advance an innovative and policy-relevant nexus approach. This paper presents an analytical framework to identify robust nexus methods that align with nexus thinking and highlights innovative nexus methods at the frontier. The current state of nexus methods was assessed with a systematic review of 245 journal articles and book chapters. This review revealed (a) use of specific and reproducible methods for nexus assessment is uncommon - less than one-third of the reviewed studies present explicit methods; (b) nexus methods frequently fall short of capturing interactions among water, energy, and food - the very concept they purport to address; (c) assessments strongly favor quantitative approaches - 70% use primarily quantitative tools; (d) use of social science methods is limited (26%); and (e) many nexus methods are confined to disciplinary silos - only about one-quarter combine methods from diverse disciplines and less than one-fifth utilize both quantitative and qualitative approaches. Despite some pitfalls of current nexus methods, there are a host of studies that offer innovative approaches to help quantify nexus linkages and interactions among sectors, conceptualize dynamic feedbacks, and support mixed method approaches to better understand WEF systems. Applying our analytical framework to all 245 studies, we identify, and analyze herein, seventeen studies that implement innovative multi-method and cross-scalar tools to demonstrate promising advances toward improved nexus assessment. This paper finds that, to make the WEF nexus effective as a policy-relevant analytical tool, methods are needed that incorporate social and political dimensions of water, energy, and food; utilize multiple and interdisciplinary approaches; and engage stakeholders and policy-makers.

Regime of validity of the pairing Hamiltonian in the study of Fermi gases

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

Chang, S. Y.; Pandharipande, V. R.

2006-06-01

The ground state energy and pairing gap of the interacting Fermi gases calculated by the ab initio stochastic method are compared with those estimated from the Bardeen-Cooper-Schrieffer pairing Hamiltonian. We discuss the ingredients of this Hamiltonian in various regimes of interaction strength. In the weakly interacting (1/ak{sub F}<<0) regime the BCS Hamiltonian should describe Landau quasiparticle energies and interactions, on the other hand, in the strongly pairing regime, that is, 1/ak{sub F} > or approx. 0, it becomes part of the bare Hamiltonian. However, the bare BCS Hamiltonian is not adequate for describing atomic gases in the regime of weakmore » to moderate interaction strength -{infinity}<1/ak{sub F}<0 such as ak{sub F}{approx}-1.« less

Interaction of slow highly charged ions with a metal surface covered with a thin dielectric film. The role of the neutralization energy in the nanostructures formation

NASA Astrophysics Data System (ADS)

Majkić, M. D.; Nedeljković, N. N.; Dojčilović, R. J.

2017-09-01

We consider the slow highly charged ions impinging upon a metal surface covered with a thin dielectric film, and formation of the surface nanostructures (craters) from the standpoint of the required energy. For the moderate ionic velocities, the size of the surface features depends on the deposited kinetic energy of the projectile and the ionic neutralization energy. The neutralization energy is calculated by employing the recently developed quasi-resonant two-state vector model for the intermediate Rydberg state population and the micro-staircase model for the cascade neutralization. The electron interactions with the ionic core, polarized dielectric and charge induced on the metal surface are modelled by the appropriate asymptotic expressions and the method for calculation of the effective ionic charges in the dielectric is proposed. The results are presented for the interaction of \\text{X}{{\\text{e}}Z+} ions (velocity v=0.25 a.u.; 25) with the metal surface (Co) covered with a thin dielectric film, for model values of dielectric constant inside the interaction region. In the absence of dielectric film, the neutralization energy is lower than the potential (ionization) energy due to the incomplete neutralization. The presence of dielectric film additionally decreases the neutralization energy. We calculate the projectile neutralization energy in the perturbed dielectric (perturbation is caused by the ionic motion and the surface structure formation). We correlate the neutralization energy added to the deposited kinetic energy with the experimentally obtained energy necessary for the formation of the nano-crater of a given depth.

Interaction of Repetitively Pulsed High Energy Laser Radiation With Matter

NASA Astrophysics Data System (ADS)

Hugenschmidt, Manfred

1986-10-01

The paper is concerned with laser target interaction processes involving new methods of improving the overall energy balance. As expected theoretically, this can be achieved with high repetition rate pulsed lasers even for initially highly reflecting materials, such as metals. Experiments were performed by using a pulsed CO2 laser at mean powers up to 2 kW and repetition rates up to 100 Hz. The rates of temperature rise of aluminium for example were thereby increased by lore than a factor of 3 as compared to cw-radiation of comparable power density. Similar improvements were found for the overall absorptivities that were increased by this method by more than an order of magnitude.

Accurate double many-body expansion potential energy surface for the 2(1)A' state of N2O.

PubMed

Li, Jing; Varandas, António J C

2014-08-28

An accurate double many-body expansion potential energy surface is reported for the 2(1)A' state of N2O. The new double many-body expansion (DMBE) form has been fitted to a wealth of ab initio points that have been calculated at the multi-reference configuration interaction level using the full-valence-complete-active-space wave function as reference and the cc-pVQZ basis set, and subsequently corrected semiempirically via double many-body expansion-scaled external correlation method to extrapolate the calculated energies to the limit of a complete basis set and, most importantly, the limit of an infinite configuration interaction expansion. The topographical features of the novel potential energy surface are then examined in detail and compared with corresponding attributes of other potential functions available in the literature. Exploratory trajectories have also been run on this DMBE form with the quasiclassical trajectory method, with the thermal rate constant so determined at room temperature significantly enhancing agreement with experimental data.

Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging.

PubMed

Hughes, Timothy J; Kandathil, Shaun M; Popelier, Paul L A

2015-02-05

As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1). Copyright © 2013 Elsevier B.V. All rights reserved.

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction.

PubMed

Yang, Yang; Yu, Haibo; York, Darrin; Cui, Qiang; Elstner, Marcus

2007-10-25

The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge-charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and a modification of the Coulomb scaling to improve the electrostatic treatment within the second-order terms. These modifications lead to a significant improvement in the description of hydrogen-bonding interactions and proton affinities of biologically relevant molecules.

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

PubMed

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Tetraquark candidate Zc(3900) from coupled-channel scattering - how to extract hadronic interactions? -

NASA Astrophysics Data System (ADS)

Ikeda, Yoichi

2018-03-01

We present recent progress of lattice QCD studies on hadronic interactions which play a crucial role to understand the properties of atomic nuclei and hadron resonances. There are two methods, the plateau method (or the direct method) and the HAL QCD method, to study the hadronic interactions. In the plateau method, the determination of a ground state energy from the temporal correlation functions of multi-hadron systems is a key to reliably extract the physical observables. It turns out that, due to the contamination of excited elastic scattering states nearby, one can easily be misled by a fake plateau into extracting the ground state energy. We introduce a consistency check (sanity check) which can rule out obviously false results obtained from a fake plateau, and find that none of the results obtained at the moment for two-baryon systems in the plateau method pass the test. On the other hand, the HAL QCD method is free from the fake-plateau problem. We investigate the systematic uncertainties of the HAL QCD method, which are found to be well controlled. On the basis of the HAL QCD method, the structure of the tetraquark candidate Zc(3900), which was experimentally reported in e+e- collisions, is studied by the s-wave two-meson coupled-channel scattering. The results show that the Zc(3900) is not a conventional resonance but a threshold cusp. A semi-phenomenological analysis with the coupled-channel interaction to the experimentally observed decay mode is also presented to confirm the conclusion.

Correlation, Breit and Quantum Electrodynamics effects on energy level and transition properties of W54+ ion

NASA Astrophysics Data System (ADS)

Ding, Xiaobin; Sun, Rui; Koike, Fumihiro; Kato, Daiji; Murakami, Izumi; Sakaue, Hiroyuki A.; Dong, Chenzhong

2017-03-01

The electron correlation effects and Breit interaction as well as Quantum Electro-Dynamics (QED) effects were expected to have important contribution to the energy level and transition properties of heavy highly charged ions. The ground states [Ne]3s23p63d2 and first excited states [Ne]3s23p53d3 of W54+ ion have been studied by using Multi-Configuration Dirac-Fock method with the implementation of Grasp2K package. A restricted active space method was employed to investigate the correlation contribution from different models. The Breit interaction and QED effects were taken into account in the relativistic configuration interaction calculation with the converged wavefunction. It is found that the correlation contribution from 3s and 3p orbital have important contribution to the energy level, transition wavelength and probability of the ground and the first excited state of W54+ ion. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, Grzegorz Karwasz.

Wetting transitions on patterned surfaces with diffuse interaction potentials embedded in a Young-Laplace formulation

NASA Astrophysics Data System (ADS)

Pashos, G.; Kokkoris, G.; Papathanasiou, A. G.; Boudouvis, A. G.

2016-01-01

The Minimum Energy Paths (MEPs) of wetting transitions on pillared surfaces are computed with the Young-Laplace equation, augmented with a pressure term that accounts for liquid-solid interactions. The interactions are smoothed over a short range from the solid phase, therefore facilitating the numerical solution of problems concerning wetting on complex surface patterns. The patterns may include abrupt geometric features, e.g., arrays of rectangular pillars, where the application of the unmodified Young-Laplace is not practical. The MEPs are obtained by coupling the augmented Young-Laplace with the modified string method from which the energy barriers of wetting transitions are eventually extracted. We demonstrate the method on a wetting transition that is associated with the breakdown of superhydrophobic behavior, i.e., the transition from the Cassie-Baxter state to the Wenzel state, taking place on a superhydrophobic pillared surface. The computed energy barriers quantify the resistance of the system to these transitions and therefore, they can be used to evaluate superhydrophobic performance or provide guidelines for optimal pattern design.

Interface-facilitated energy transport in coupled Frenkel-Kontorova chains

NASA Astrophysics Data System (ADS)

Su, Rui-Xia; Yuan, Zong-Qiang; Wang, Jun; Zheng, Zhi-Gang

2016-04-01

The role of interface couplings on the energy transport of two coupled Frenkel-Kontorova (FK) chains is explored through numerical simulations. In general, it is expected that the interface couplings result in the suppression of heat conduction through the coupled system due to the additional interface phonon-phonon scattering. In the present paper, it is found that the thermal conductivity increases with increasing intensity of interface interactions for weak inter-chain couplings, whereas the heat conduction is suppressed by the interface interaction in the case of strong inter-chain couplings. Based on the phonon spectral energy density method, we demonstrate that the enhancement of energy transport results from the excited phonon modes (in addition to the intrinsic phonon modes), while the strong interface phonon-phonon scattering results in the suppressed energy transport.

The Importance of Electron Correlation on Stacking Interaction of Adenine-Thymine Base-Pair Step in B-DNA: A Quantum Monte Carlo Study.

PubMed

Hongo, Kenta; Cuong, Nguyen Thanh; Maezono, Ryo

2013-02-12

We report fixed-node diffusion Monte Carlo (DMC) calculations of stacking interaction energy between two adenine(A)-thymine(T) base pairs in B-DNA (AA:TT), for which reference data are available, obtained from a complete basis set estimate of CCSD(T) (coupled-cluster with singles, doubles, and perturbative triples). We consider four sets of nodal surfaces obtained from self-consistent field calculations and examine how the different nodal surfaces affect the DMC potential energy curves of the AA:TT molecule and the resulting stacking energies. We find that the DMC potential energy curves using the different nodes look similar to each other as a whole. We also benchmark the performance of various quantum chemistry methods, including Hartree-Fock (HF) theory, second-order Møller-Plesset perturbation theory (MP2), and density functional theory (DFT). The DMC and recently developed DFT results of the stacking energy reasonably agree with the reference, while the HF, MP2, and conventional DFT methods give unsatisfactory results.

Self-consistent field for fragmented quantum mechanical model of large molecular systems.

PubMed

Jin, Yingdi; Su, Neil Qiang; Xu, Xin; Hu, Hao

2016-01-30

Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods. © 2015 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

Mu, Yan; Gao, Yi Qin

2007-09-01

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

A study of effective atomic numbers and electron densities of some vitamins for electron, H, He and C ion interactions

NASA Astrophysics Data System (ADS)

Büyükyıldız, M.

2017-09-01

The radiological properties of some vitamins such as Retinol, Beta-carotene, Riboflavin, Niacin, Niacinamide, Pantothenic acid, Pyridoxine, Pyridoxamine, Pyridoxal, Biotin, Folic acid, Ascorbic acid, Cholecalciferol, Alpha-tocopherol, Gamma-tocopherol, Phylloquinone have been investigated with respect to total electron interaction and some heavy charged particle interaction as means of effective atomic numbers (Z_{eff}) and electron densities (N_{eff}) for the first time. Calculations were performed for total electron interaction and heavy ions such as H, He and C ion interactions in the energy region 10keV-10MeV by using a logarithmic interpolation method. Variations in Z_{eff}'s and N_{eff}'s of given vitamins have been studied according to the energy of electron or heavy charged particles, and significant variations have been observed for all types of interaction in the given energy region. The maximum values of Z_{eff} have been found in the different energy regions for different interactions remarkably and variations in N_{eff} seem approximately to be the same with variation in Z_{eff} for the given vitamins as expected. Z_{eff} values of some vitamins were plotted together and compared with each other for electron, H, He and C interactions and the ratios of Z_{eff}/ < A > have been changed in the range of 0.25-0.36, 0.20-0.36, 0.22-0.35 and 0.20-0.35 for electron, H, He and C interactions, respectively.

Interactions Between Energy Drink Consumption and Sleep Problems: Associations with Alcohol Use Among Young Adolescents.

PubMed

Marmorstein, Naomi R

2017-09-01

Background: Energy drink consumption and sleep problems are both associated with alcohol use among adolescents. In addition, caffeine consumption (including energy drinks) is associated with sleep problems. However, information about how these three constructs may interact is limited. The goal of this study was to examine potential interactions between energy drink consumption and sleep problems in the concurrent prediction of alcohol use among young adolescents. Coffee and soda consumption were also examined for comparison. Methods: Participants from the Camden Youth Development Study were included ( n  = 127; mean age = 13.1; 68% Hispanic, 29% African American) and questionnaire measures of frequency of caffeinated beverage consumption (energy drinks, coffee, and soda), sleep (initial insomnia, sleep disturbances, daytime fatigue, and sleep duration), and alcohol consumption were used. Regression analyses were conducted to examine interactions between caffeinated beverage consumption and sleep in the concurrent prediction of alcohol use. Results: Energy drink consumption interacted with initial insomnia and daytime fatigue to concurrently predict particularly frequent alcohol use among those with either of these sleep-related problems and energy drink consumption. The pattern of results for coffee consumption was similar for insomnia but reached only a trend level of significance. Results of analyses examining soda consumption were nonsignificant. Conclusions: Young adolescents who both consume energy drinks and experience initial insomnia and/or daytime fatigue are at particularly high risk for alcohol use. Coffee consumption appears to be associated with similar patterns. Longitudinal research is needed to explain the developmental pathways by which these associations emerge, as well as mediators and moderators of these associations.

Cosmic ray radiography of the damaged cores of the Fukushima reactors

DOE PAGES

Borozdin, Konstantin; Greene, Steven; Lukić, Zarija; ...

2012-10-11

The passage of muons through matter is dominated by the Coulomb interaction with electrons and nuclei. The interaction with the electrons leads to continuous energy loss and stopping of the muons. The interaction with nuclei leads to angle “diffusion.” Two muon-imaging methods that use flux attenuation and multiple Coulomb scattering of cosmic-ray muons are being studied as tools for diagnosing the damaged cores of the Fukushima reactors. Here, we compare these two methods. We conclude that the scattering method can provide detailed information about the core. Lastly, attenuation has low contrast and little sensitivity to the core.

Systematic size study of an insect antifreeze protein and its interaction with ice.

PubMed

Liu, Kai; Jia, Zongchao; Chen, Guangju; Tung, Chenho; Liu, Ruozhuang

2005-02-01

Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations.

Systematic Size Study of an Insect Antifreeze Protein and Its Interaction with Ice

PubMed Central

Liu, Kai; Jia, Zongchao; Chen, Guangju; Tung, Chenho; Liu, Ruozhuang

2005-01-01

Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The β-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations. PMID:15713600

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Rifai, Eko Aditya; van Dijk, Marc; Vermeulen, Nico P. E.; Geerke, Daan P.

2018-01-01

Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.

Renormalization of effective interactions in a negative charge transfer insulator

NASA Astrophysics Data System (ADS)

Seth, Priyanka; Peil, Oleg E.; Pourovskii, Leonid; Betzinger, Markus; Friedrich, Christoph; Parcollet, Olivier; Biermann, Silke; Aryasetiawan, Ferdi; Georges, Antoine

2017-11-01

We compute from first principles the effective interaction parameters appropriate for a low-energy description of the rare-earth nickelate LuNiO3 involving the partially occupied eg states only. The calculation uses the constrained random-phase approximation and reveals that the effective on-site Coulomb repulsion is strongly reduced by screening effects involving the oxygen-p and nickel-t2 g states. The long-range component of the effective low-energy interaction is also found to be sizable. As a result, the effective on-site interaction between parallel-spin electrons is reduced down to a small negative value. This validates effective low-energy theories of these materials that were proposed earlier. Electronic structure methods combined with dynamical mean-field theory are used to construct and solve an appropriate low-energy model and explore its phase diagram as a function of the on-site repulsion and Hund's coupling. For the calculated values of these effective interactions, we find that in agreement with experiments, LuNiO3 is a metal without disproportionation of the eg occupancy when considered in its orthorhombic structure, while the monoclinic phase is a disproportionated insulator.

Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions.

PubMed

Tauer, Tony P; Sherrill, C David

2005-11-24

The benzene dimer is the simplest prototype of pi-pi interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of pi-pi interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three- and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10% of what would be estimated from benzene dimer energies at the same geometries.

Alternative method for evaluating the pair energy of nucleons in nuclei

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

Nurmukhamedov, A. M., E-mail: fattah52@mail.ru

2015-12-15

An alternative method for determining the odd–even effect parameter related to special features of the Casimir operator in Wigner’s mass formula for nuclei is proposed. A procedure for calculating this parameter is presented. The proposed method relies on a geometric interpretation of the Casimir operator, experimental data concerning the contribution of spin–orbit interaction to the nuclear mass for even–even and odd–odd nuclei, and systematics of energy gaps in the spectra of excited states of even–even nuclei.

Illustrating chaos: a schematic discretization of the general three-body problem in Newtonian gravity

NASA Astrophysics Data System (ADS)

Leigh, Nathan W. C.; Wegsman, Shalma

2018-05-01

We present a formalism for constructing schematic diagrams to depict chaotic three-body interactions in Newtonian gravity. This is done by decomposing each interaction into a series of discrete transformations in energy- and angular momentum-space. Each time a transformation is applied, the system changes state as the particles re-distribute their energy and angular momenta. These diagrams have the virtue of containing all of the quantitative information needed to fully characterize most bound or unbound interactions through time and space, including the total duration of the interaction, the initial and final stable states in addition to every intervening temporary meta-stable state. As shown via an illustrative example for the bound case, prolonged excursions of one of the particles, which by far dominates the computational cost of the simulations, are reduced to a single discrete transformation in energy- and angular momentum-space, thereby potentially mitigating any computational expense. We further generalize our formalism to sequences of (unbound) three-body interactions, as occur in dense stellar environments during binary hardening. Finally, we provide a method for dynamically evolving entire populations of binaries via three-body scattering interactions, using a purely analytic formalism. In principle, the techniques presented here are adaptable to other three-body problems that conserve energy and angular momentum.

Modeling of the phase equilibria of polystyrene in methylcyclohexane with semi-empirical quantum mechanical methods I.

PubMed

Wilczura-Wachnik, Hanna; Jónsdóttir, Svava Osk

2003-04-01

A method for calculating interaction parameters traditionally used in phase-equilibrium computations in low-molecular systems has been extended for the prediction of solvent activities of aromatic polymer solutions (polystyrene+methylcyclohexane). Using ethylbenzene as a model compound for the repeating unit of the polymer, the intermolecular interaction energies between the solvent molecule and the polymer were simulated. The semiempirical quantum chemical method AM1, and a method for sampling relevant internal orientations for a pair of molecules developed previously were used. Interaction energies are determined for three molecular pairs, the solvent and the model molecule, two solvent molecules and two model molecules, and used to calculated UNIQUAC interaction parameters, a(ij) and a(ji). Using these parameters, the solvent activities of the polystyrene 90,000 amu+methylcyclohexane system, and the total vapor pressures of the methylcyclohexane+ethylbenzene system were calculated. The latter system was compared to experimental data, giving qualitative agreement. Figure Solvent activities for the methylcylcohexane(1)+polystyrene(2) system at 316 K. Parameters aij (blue line) obtained with the AM1 method; parameters aij (pink line) from VLE data for the ethylbenzene+methylcyclohexane system. The abscissa is the polymer weight fraction defined as y2(x1)=(1mx1)M2/[x1M1+(1mx1)M2], where x1 is the solvent mole fraction and Mi are the molecular weights of the components.

The interaction between a HSP-70 gene variant with dietary calories in determining serum markers of inflammation and cardiovascular risk.

PubMed

Mehramiz, Mehrane; Hassanian, Seyed Mahdi; Mardan-Nik, Maryam; Pasdar, Alireza; Jamialahmadi, Khadijeh; Fiuji, Hamid; Moetamani-Ahmadi, Mehrdad; Parizadeh, Seyed Mohammad Reza; Moohebati, Mohsen; Heidari-Bakavoli, Alireza; Ebrahimi, Mahmoud; Ferns, Gordon A; Ghayour-Mobarhan, Majid; Avan, Amir

2017-10-24

The high prevalence of cardiovascular disease (CVD) globally is attributable to an interaction between environmental and genetic factors. Gene × diet interaction studies aim to explore how a modifiable factor interacts with genetic predispositions. Here we have explored the interaction of a heat shock protein (HSP70) gene polymorphism (+1267A > G) with dietary intake and their possible association with serum C-reactive protein (CRP), an inflammatory marker, that is a major component of CVD risk. HSP70 genotype was determined using a TaqMan real time PCR based method.Dietary intake was assessed using a dietary questionnaire. Serum high sensitivity (Hs) CRP and other cardiovascular risk factors were assessed by routine methods. This included coronary angioplasty to determine the presence of coronary artery stenosis. There were significant differences between serum lipid profile and Hs-CRP across the genotypes for Hsp70. The carriers of G allele had higher serum hs-CRP concentrations, compared with the AA homozygotes, with the wild genotype. Interaction analysis showed the association was modulated by total energy intake; the interaction of high energy intake with GG genotype: RERI = 0.77, AP = 0.26, S = 1.6. We have found a significant association between the +1267A > G variant of the HSP70 gene with cardiovascular risk factors and serum hs-CRP concentrations. It is possible that a low energy diet could ameliorate the unfavorable effects of G allele of HSP70. Copyright © 2017 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

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

PubMed

Panigrahi, Swati; Pal, Rahul; Bhattacharyya, Dhananjay

2011-12-01

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

Combining symmetry breaking and restoration with configuration interaction: A highly accurate many-body scheme applied to the pairing Hamiltonian

NASA Astrophysics Data System (ADS)

Ripoche, J.; Lacroix, D.; Gambacurta, D.; Ebran, J.-P.; Duguet, T.

2017-01-01

Background: Ab initio many-body methods have been developed over the past ten years to address mid-mass nuclei. In their best current level of implementation, their accuracy is of the order of a few percent error on the ground-state correlation energy. Recently implemented variants of these methods are operating a breakthrough in the description of medium-mass open-shell nuclei at a polynomial computational cost while putting state-of-the-art models of internucleon interactions to the test. Purpose: As progress in the design of internucleon interactions is made, and as questions one wishes to answer are refined in connection with increasingly available experimental data, further efforts must be made to tailor many-body methods that can reach an even higher precision for an even larger number of observable quantum states or nuclei. The objective of the present work is to contribute to such a quest by designing and testing a new many-body scheme. Methods: We formulate a truncated configuration-interaction method that consists of diagonalizing the Hamiltonian in a highly truncated subspace of the total N -body Hilbert space. The reduced Hilbert space is generated via the particle-number projected BCS state along with projected seniority-zero two- and four-quasiparticle excitations. Furthermore, the extent by which the underlying BCS state breaks U(1 ) symmetry is optimized in the presence of the projected two- and four-quasiparticle excitations. This constitutes an extension of the so-called restricted variation after projection method in use within the frame of multireference energy density functional calculations. The quality of the newly designed method is tested against exact solutions of the so-called attractive pairing Hamiltonian problem. Results: By construction, the method reproduces exact results for N =2 and N =4 . For N =(8 ,16 ,20 ) , the error in the ground-state correlation energy is less than (0.006%, 0.1%, 0.15%) across the entire range of internucleon coupling defining the pairing Hamiltonian and driving the normal-to-superfluid quantum phase transition. The presently proposed method offers the advantage of automatic access to the low-lying spectroscopy, which it does with high accuracy. Conclusions: The numerical cost of the newly designed variational method is polynomial (N6) in system size. This method achieves unprecedented accuracy for the ground-state correlation energy, effective pairing gap, and one-body entropy as well as for the excitation energy of low-lying states of the attractive pairing Hamiltonian. This constitutes a sufficiently strong motivation to envision its application to realistic nuclear Hamiltonians in view of providing a complementary, accurate, and versatile ab initio description of mid-mass open-shell nuclei in the future.

Relativistic calculation of correlational energy for a helium-like atom

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

Palchikov, V.G.

This paper presents an analytical method for calculating the firstorder correlational energy from the electron interaction, taking account of lag effects. Explicit analytical expressions are obtained for radial matrix elements. The nonrelativistic limit is investigated. The given method may be used to calculate correlation effects in higher orders of perturbation theory (second and higher orders with respect to 1/z) using the Strum expansion for the Coulomb Green's functions.

Comparison of the quadratic configuration interaction and coupled cluster approaches to electron correlation including the effect of triple excitations

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Lee, Timothy J.; Rendell, Alistair P.

1990-01-01

The recently proposed quadratic configuration interaction (QCI) method is compared with the more rigorous coupled cluster (CC) approach for a variety of chemical systems. Some of these systems are well represented by a single-determinant reference function and others are not. The finite order singles and doubles correlation energy, the perturbational triples correlation energy, and a recently devised diagnostic for estimating the importance of multireference effects are considered. The spectroscopic constants of CuH, the equilibrium structure of cis-(NO)2 and the binding energies of Be3, Be4, Mg3, and Mg4 were calculated using both approaches. The diagnostic for estimating multireference character clearly demonstrates that the QCI method becomes less satisfactory than the CC approach as non-dynamical correlation becomes more important, in agreement with a perturbational analysis of the two methods and the numerical estimates of the triple excitation energies they yield. The results for CuH show that the differences between the two methods become more apparent as the chemical systems under investigation becomes more multireference in nature and the QCI results consequently become less reliable. Nonetheless, when the system of interest is dominated by a single reference determinant both QCI and CC give very similar results.

Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors

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

Kamiya, Muneaki; Hirata, So; Valiev, Marat

2008-02-19

Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of themore » cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.« less

The suppression of radiation reaction and laser field depletion in laser-electron beam interaction

NASA Astrophysics Data System (ADS)

Ong, J. F.; Moritaka, T.; Takabe, H.

2018-03-01

The effects of radiation reaction (RR) have been studied extensively by using the interaction of ultraintense lasers with a counter-propagating relativistic electron. At the laser intensity at the order of 1023 W/cm2, the effects of RR are significant in a few laser periods for a relativistic electron. However, a laser at such intensity is tightly focused and the laser energy is usually assumed to be fixed. Then, the signal of RR and energy conservation cannot be guaranteed. To assess the effects of RR in a tightly focused laser pulse and the evolution of the laser energy, we simulated this interaction with a beam of 109 electrons by means of a Particle-In-Cell method. We observe that the effects of RR are suppressed due to the ponderomotive force and accompanied by a non-negligible amount of laser field energy reduction. This is because the ponderomotive force prevents the electrons from approaching the center of the laser pulse and leads to an interaction at the weaker field region. At the same time, the laser energy is absorbed through ponderomotive acceleration. Thus, the kinetic energy of the electron beam has to be carefully selected such that the effects of RR become obvious.

Ab-initio adsorption study of chitosan on functionalized graphene: critical role of van der Waals interactions.

PubMed

Rahman, R; Mazumdar, D

2012-03-01

We investigate the adsorption process of an organic biomolecule (chitosan) on epoxy-functionalized graphene using ab-initio density functional methods incorporating van-der-waals (vdW) interactions. The role of London dispersion force on the cohesive energy and conformal preference of the molecule is quantitatively elucidated. Functionalizing graphene with epoxy leads to weak hydrogen-bond interactions with chitosan. Binding energy values increase by over an order of magnitude after including vdW corrections, implying that dispersive interactions dominate the physisorption process. Conformal study show binding upto 30 kcal/mol when the molecule is oriented with the hydroxyl group approaching the functionalized graphene. Our study advances the promise of functionalized graphene for a variety of applications.

Micro-Environmental Signature of The Interactions between Druggable Target Protein, Dipeptidyl Peptidase-IV, and Anti-Diabetic Drugs.

PubMed

Chakraborty, Chiranjib; Mallick, Bidyut; Sharma, Ashish Ranjan; Sharma, Garima; Jagga, Supriya; Doss, C George Priya; Nam, Ju-Suk; Lee, Sang-Soo

2017-01-01

Druggability of a target protein depends on the interacting micro-environment between the target protein and drugs. Therefore, a precise knowledge of the interacting micro-environment between the target protein and drugs is requisite for drug discovery process. To understand such micro-environment, we performed in silico interaction analysis between a human target protein, Dipeptidyl Peptidase-IV (DPP-4), and three anti-diabetic drugs (saxagliptin, linagliptin and vildagliptin). During the theoretical and bioinformatics analysis of micro-environmental properties, we performed drug-likeness study, protein active site predictions, docking analysis and residual interactions with the protein-drug interface. Micro-environmental landscape properties were evaluated through various parameters such as binding energy, intermolecular energy, electrostatic energy, van der Waals'+H-bond+desolvo energy (E VHD ) and ligand efficiency (LE) using different in silico methods. For this study, we have used several servers and software, such as Molsoft prediction server, CASTp server, AutoDock software and LIGPLOT server. Through micro-environmental study, highest log P value was observed for linagliptin (1.07). Lowest binding energy was also observed for linagliptin with DPP-4 in the binding plot. We also identified the number of H-bonds and residues involved in the hydrophobic interactions between the DPP-4 and the anti-diabetic drugs. During interaction, two H-bonds and nine residues, two H-bonds and eleven residues as well as four H-bonds and nine residues were found between the saxagliptin, linagliptin as well as vildagliptin cases and DPP-4, respectively. Our in silico data obtained for drug-target interactions and micro-environmental signature demonstrates linagliptin as the most stable interacting drug among the tested anti-diabetic medicines.

Thermal Stability and Kinetic Study of Fluvoxamine Stability in Binary Samples with Lactose.

PubMed

Ghaderi, Faranak; Nemati, Mahboob; Siahi-Shadbad, Mohammad Reza; Valizadeh, Hadi; Monajjemzadeh, Farnaz

2017-04-01

Purpose: In the present study the incompatibility of FLM (fluvoxamine) with lactose in solid state mixtures was investigated. The compatibility was evaluated using different physicochemical methods such as differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy and mass spectrometry. Methods: Non-Isothermally stressed physical mixtures were used to calculate the solid-state kinetic parameters. Different thermal models such as Friedman, Flynn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS) were used for the characterization of the drug-excipient interaction. Results: Overall, the incompatibility of FLM with lactose as a reducing carbohydrate was successfully evaluated and the activation energy of this interaction was calculated. Conclusion: In this research the lactose and FLM Maillard interaction was proved using physicochemical techniques including DSC and FTIR. It was shown that DSC- based kinetic analysis provides fast and versatile kinetic comparison of Arrhenius activation energies for different pharmaceutical samples.

Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

PubMed

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2012-07-15

The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Thermal Stability and Kinetic Study of Fluvoxamine Stability in Binary Samples with Lactose

PubMed Central

Ghaderi, Faranak; Nemati, Mahboob; Siahi-Shadbad, Mohammad Reza; Valizadeh, Hadi; Monajjemzadeh, Farnaz

2017-01-01

Purpose: In the present study the incompatibility of FLM (fluvoxamine) with lactose in solid state mixtures was investigated. The compatibility was evaluated using different physicochemical methods such as differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy and mass spectrometry. Methods: Non-Isothermally stressed physical mixtures were used to calculate the solid–state kinetic parameters. Different thermal models such as Friedman, Flynn–Wall–Ozawa (FWO) and Kissinger–Akahira–Sunose (KAS) were used for the characterization of the drug-excipient interaction. Results: Overall, the incompatibility of FLM with lactose as a reducing carbohydrate was successfully evaluated and the activation energy of this interaction was calculated. Conclusion: In this research the lactose and FLM Maillard interaction was proved using physicochemical techniques including DSC and FTIR. It was shown that DSC- based kinetic analysis provides fast and versatile kinetic comparison of Arrhenius activation energies for different pharmaceutical samples. PMID:28507936

Computed secondary-particle energy spectra following nonelastic neutron interactions with C-12 for E(n) between 15 and 60 MeV: Comparisons of results from two calculational methods

NASA Astrophysics Data System (ADS)

Dickens, J. K.

1991-04-01

The organic scintillation detector response code SCINFUL has been used to compute secondary-particle energy spectra, d(sigma)/dE, following nonelastic neutron interactions with C-12 for incident neutron energies between 15 and 60 MeV. The resulting spectra are compared with published similar spectra computed by Brenner and Prael who used an intranuclear cascade code, including alpha clustering, a particle pickup mechanism, and a theoretical approach to sequential decay via intermediate particle-unstable states. The similarities of and the differences between the results of the two approaches are discussed.

Spectroscopic signatures of localization with interacting photons in superconducting qubits

NASA Astrophysics Data System (ADS)

Roushan, P.; Neill, C.; Tangpanitanon, J.; Bastidas, V. M.; Megrant, A.; Barends, R.; Chen, Y.; Chen, Z.; Chiaro, B.; Dunsworth, A.; Fowler, A.; Foxen, B.; Giustina, M.; Jeffrey, E.; Kelly, J.; Lucero, E.; Mutus, J.; Neeley, M.; Quintana, C.; Sank, D.; Vainsencher, A.; Wenner, J.; White, T.; Neven, H.; Angelakis, D. G.; Martinis, J.

2017-12-01

Quantized eigenenergies and their associated wave functions provide extensive information for predicting the physics of quantum many-body systems. Using a chain of nine superconducting qubits, we implement a technique for resolving the energy levels of interacting photons. We benchmark this method by capturing the main features of the intricate energy spectrum predicted for two-dimensional electrons in a magnetic field—the Hofstadter butterfly. We introduce disorder to study the statistics of the energy levels of the system as it undergoes the transition from a thermalized to a localized phase. Our work introduces a many-body spectroscopy technique to study quantum phases of matter.

Conductance of two-dimensional waveguide in presence of the Rashba spin-orbit interaction

NASA Astrophysics Data System (ADS)

Liu, Duan-Yang; Xia, Jian-Bai

2018-04-01

By using the transfer matrix method, we investigated spin transport in some straight structures in presence of the Rashba spin-orbit interaction. It is proved that the interference of two spin states is the same as that in one-dimensional Datta-Das spin field-effect transistor. The conductance of these structures has been calculated. Conductance quantization is common in these waveguides when we change the Fermi energy and the width of the waveguide. Using a periodic system of quadrate stubs and changing the Fermi energy, a nearly square-wave conductance can be obtained in some regions of the Fermi energy.

Electron trajectory evaluation in laser-plasma interaction for effective output beam

NASA Astrophysics Data System (ADS)

Zobdeh, P.; Sadighi-Bonabi, R.; Afarideh, H.

2010-06-01

Using the ellipsoidal cavity model, the quasi-monoenergetic electron output beam in laser-plasma interaction is described. By the cavity regime the quality of electron beam is improved in comparison with those generated from other methods such as periodic plasma wave field, spheroidal cavity regime and plasma channel guided acceleration. Trajectory of electron motion is described as hyperbolic, parabolic or elliptic paths. We find that the self-generated electron bunch has a smaller energy width and more effective gain in energy spectrum. Initial condition for the ellipsoidal cavity is determined by laser-plasma parameters. The electron trajectory is influenced by its position, energy and cavity electrostatic potential.

Verification of fluid-structure-interaction algorithms through the method of manufactured solutions for actuator-line applications

NASA Astrophysics Data System (ADS)

Vijayakumar, Ganesh; Sprague, Michael

2017-11-01

Demonstrating expected convergence rates with spatial- and temporal-grid refinement is the ``gold standard'' of code and algorithm verification. However, the lack of analytical solutions and generating manufactured solutions presents challenges for verifying codes for complex systems. The application of the method of manufactured solutions (MMS) for verification for coupled multi-physics phenomena like fluid-structure interaction (FSI) has only seen recent investigation. While many FSI algorithms for aeroelastic phenomena have focused on boundary-resolved CFD simulations, the actuator-line representation of the structure is widely used for FSI simulations in wind-energy research. In this work, we demonstrate the verification of an FSI algorithm using MMS for actuator-line CFD simulations with a simplified structural model. We use a manufactured solution for the fluid velocity field and the displacement of the SMD system. We demonstrate the convergence of both the fluid and structural solver to second-order accuracy with grid and time-step refinement. This work was funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Wind Energy Technologies Office, under Contract No. DE-AC36-08-GO28308 with the National Renewable Energy Laboratory.

Chlorinated paraffins wrapping of carbon nanotubes: A theoretical investigation

NASA Astrophysics Data System (ADS)

Ding, Qiuyue; Ding, Ning; Chen, Xiangfeng; Wu, Chi-Man Lawrence

2018-04-01

How nanomaterials interact with pollutants is the central for understanding their environmental behavior and practical application. In this work, molecular dynamics (MD) and density functional theoretical (DFT) methods were used to investigated the influence of carbon chain length, degree of chlorination, chain configuration, and chirality of chlorinated paraffin (CP) and diameter of single-walled carbon nanotubes (SWNTs) on the interaction between CPs and SWNTs. The simulation results demonstrated that CP chain length and chlorination degree played considerably important roles in determining interaction strength between SWNTs and CPs. The interaction energies increased with increasing chain length and chlorination degree. The chirality of SWNT exerted negligible influence on the interaction energy between SWNTs and CPs. On the contrary, interaction energy increased with increasing radius of SWNTs due to the surface curvatures. This result was rationalized by considering the decrease in SWNT curvature with increasing radius, which resulted in plane-like CNT wall. The negligible influence of CP chain configurations was attributed to relative flexibility of CP carbon chains, which can wrap on tubes through conformational changes with low-energy barriers. MD results indicated that CPs could adsorb on SWNT surface rapidly in aqueous environment. Charge transfer and electronic density results indicated that the interaction between CPs and SWNTs was physisorption in nature. This work provides fundamental information regarding SWNTs as sorbents for CPs extraction and adsorptive removal from environmental water system.

Apparatuses for large area radiation detection and related method

DOEpatents

Akers, Douglas W; Drigert, Mark W

2015-04-28

Apparatuses and a related method relating to radiation detection are disclosed. In one embodiment, an apparatus includes a first scintillator and a second scintillator adjacent to the first scintillator, with each of the first scintillator and second scintillator being structured to generate a light pulse responsive to interacting with incident radiation. The first scintillator is further structured to experience full energy deposition of a first low-energy radiation, and permit a second higher-energy radiation to pass therethrough and interact with the second scintillator. The apparatus further includes a plurality of light-to-electrical converters operably coupled to the second scintillator and configured to convert light pulses generated by the first scintillator and the second scintillator into electrical signals. The first scintillator and the second scintillator exhibit at least one mutually different characteristic for an electronic system to determine whether a given light pulse is generated by the first scintillator or the second scintillator.

Theoretical study of the initial non-radiative 1 Bu → 2 Ag transition in the fluorescence quenching of s-trans-butadiene: Electronic structure methods and quantum dynamics

NASA Astrophysics Data System (ADS)

Komainda, A.; Lefrancois, D.; Dreuw, A.; Köppel, H.

2017-01-01

The photodynamics of s-trans-butadiene in the 6 eV excitation energy range is investigated by ab initio quantum dynamical methods, paying particular attention to the nonadiabatic coupling between the 1Bu and 2Ag singlet excited states. The existence of a conical intersection between their potential energy surfaces is confirmed. Key parameters of the system, like the energy gap between the interacting states and their coupling strength, are critically assessed. Up to eight nuclear degrees of freedom are considered in the dynamical treatment and are shown to lead to a more realistic description of the interactions. The gas phase (jet) UV absorption spectrum is well reproduced. The related ultrafast nonradiative population transfer from 1Bu to 2Ag is the initial processes leading to fluorescence quenching of trans-butadiene.

Impact induced damage assessment by means of Lamb wave image processing

NASA Astrophysics Data System (ADS)

Kudela, Pawel; Radzienski, Maciej; Ostachowicz, Wieslaw

2018-03-01

The aim of this research is an analysis of full wavefield Lamb wave interaction with impact-induced damage at various impact energies in order to find out the limitation of the wavenumber adaptive image filtering method. In other words, the relation between impact energy and damage detectability will be shown. A numerical model based on the time domain spectral element method is used for modeling of Lamb wave propagation and interaction with barely visible impact damage in a carbon-epoxy laminate. Numerical studies are followed by experimental research on the same material with an impact damage induced by various energy and also a Teflon insert simulating delamination. Wavenumber adaptive image filtering and signal processing are used for damage visualization and assessment for both numerical and experimental full wavefield data. It is shown that it is possible to visualize and assess the impact damage location, size and to some extent severity by using the proposed technique.

Strong correlation in incremental full configuration interaction

NASA Astrophysics Data System (ADS)

Zimmerman, Paul M.

2017-06-01

Incremental Full Configuration Interaction (iFCI) reaches high accuracy electronic energies via a many-body expansion of the correlation energy. In this work, the Perfect Pairing (PP) ansatz replaces the Hartree-Fock reference of the original iFCI method. This substitution captures a large amount of correlation at zero-order, which allows iFCI to recover the remaining correlation energy with low-order increments. The resulting approach, PP-iFCI, is size consistent, size extensive, and systematically improvable with increasing order of incremental expansion. Tests on multiple single bond, multiple double bond, and triple bond dissociations of main group polyatomics using double and triple zeta basis sets demonstrate the power of the method for handling strong correlation. The smooth dissociation profiles that result from PP-iFCI show that FCI-quality ground state computations are now within reach for systems with up to about 10 heavy atoms.

Surface patterning of soft polymer film-coated cylinders via an electric field.

PubMed

Li, Bo; Li, Yue; Xu, Guang-Kui; Feng, Xi-Qiao

2009-11-04

Using the linear stability analysis method, we investigate the surface wrinkling of a thin polymer coating on a cylinder in an externally applied electric field. It is demonstrated that energy competition between surface energy, van der Waals interactive potential energy and electrostatic interaction energy may lead to ordered patterns on the film surface. The analytical solutions are derived for the critical conditions of both longitudinal and circumferential instabilities. The wavelengths of the generated surface patterns can be mediated by changing the magnitude of the electric field. Our analysis shows that the surface morphology is sensitive to the curvature radius of the fiber, especially in the micrometer and nanometer length scales. Furthermore, we suggest a potential approach for fabricating hierarchical patterns on curved surfaces.

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c

NASA Astrophysics Data System (ADS)

Karino, Yasuhito; Matubayasi, Nobuyuki

2011-01-01

The relationship between the protein conformation and the hydration effect is investigated for the equilibrium fluctuation of cytochrome c. To elucidate the hydration effect with explicit solvent, the solvation free energy of the protein immersed in water was calculated using the molecular dynamics simulation coupled with the method of energy representation. The variations of the protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation. The roles of the attractive and repulsive components in the protein-water interaction are further examined for the solvation free energy. The attractive component represented as the average sum of protein-water interaction energy is dominated by the electrostatic effect and is correlated to the solvation free energy through the linear-response-type relationship. No correlation with the (total) solvation free energy is seen, on the other hand, for the repulsive component expressed as the excluded-volume effect.

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

Deconstructing Free Energies in the Law of Matching Water Affinities.

PubMed

Shi, Yu; Beck, Thomas

2017-03-09

The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

PubMed

Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

2017-05-04

Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C 1 mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast, the interaction energy between the cellulose and water is too weak to dissolve cellulose in water.

Inferring the microscopic surface energy of protein-protein interfaces from mutation data.

PubMed

Moal, Iain H; Dapkūnas, Justas; Fernández-Recio, Juan

2015-04-01

Mutations at protein-protein recognition sites alter binding strength by altering the chemical nature of the interacting surfaces. We present a simple surface energy model, parameterized with empirical ΔΔG values, yielding mean energies of -48 cal mol(-1) Å(-2) for interactions between hydrophobic surfaces, -51 to -80 cal mol(-1) Å(-2) for surfaces of complementary charge, and 66-83 cal mol(-1) Å(-2) for electrostatically repelling surfaces, relative to the aqueous phase. This places the mean energy of hydrophobic surface burial at -24 cal mol(-1) Å(-2) . Despite neglecting configurational entropy and intramolecular changes, the model correlates with empirical binding free energies of a functionally diverse set of rigid-body interactions (r = 0.66). When used to rerank docking poses, it can place near-native solutions in the top 10 for 37% of the complexes evaluated, and 82% in the top 100. The method shows that hydrophobic burial is the driving force for protein association, accounting for 50-95% of the cohesive energy. The model is available open-source from http://life.bsc.es/pid/web/surface_energy/ and via the CCharpPPI web server http://life.bsc.es/pid/ccharppi/. © 2015 Wiley Periodicals, Inc.

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

PubMed

Surles, M C; Richardson, J S; Richardson, D C; Brooks, F P

1994-02-01

We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions. Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrange-multiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded beta-ribbon into an approximate beta-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and (2) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed.

Theoretical study of the dependence of single impurity Anderson model on various parameters within distributional exact diagonalization method

NASA Astrophysics Data System (ADS)

Syaina, L. P.; Majidi, M. A.

2018-04-01

Single impurity Anderson model describes a system consisting of non-interacting conduction electrons coupled with a localized orbital having strongly interacting electrons at a particular site. This model has been proven successful to explain the phenomenon of metal-insulator transition through Anderson localization. Despite the well-understood behaviors of the model, little has been explored theoretically on how the model properties gradually evolve as functions of hybridization parameter, interaction energy, impurity concentration, and temperature. Here, we propose to do a theoretical study on those aspects of a single impurity Anderson model using the distributional exact diagonalization method. We solve the model Hamiltonian by randomly generating sampling distribution of some conducting electron energy levels with various number of occupying electrons. The resulting eigenvalues and eigenstates are then used to define the local single-particle Green function for each sampled electron energy distribution using Lehmann representation. Later, we extract the corresponding self-energy of each distribution, then average over all the distributions and construct the local Green function of the system to calculate the density of states. We repeat this procedure for various values of those controllable parameters, and discuss our results in connection with the criteria of the occurrence of metal-insulator transition in this system.

Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation

NASA Astrophysics Data System (ADS)

Zhao, Yanxiang; Kwan, Yuen-Yick; Che, Jianwei; Li, Bo; McCammon, J. Andrew

2013-07-01

A phase-field variational implicit-solvent approach is developed for the solvation of charged molecules. The starting point of such an approach is the representation of a solute-solvent interface by a phase field that takes one value in the solute region and another in the solvent region, with a smooth transition from one to the other on a small transition layer. The minimization of an effective free-energy functional of all possible phase fields determines the equilibrium conformations and free energies of an underlying molecular system. All the surface energy, the solute-solvent van der Waals interaction, and the electrostatic interaction are coupled together self-consistently through a phase field. The surface energy results from the minimization of a double-well potential and the gradient of a field. The electrostatic interaction is described by the Coulomb-field approximation. Accurate and efficient methods are designed and implemented to numerically relax an underlying charged molecular system. Applications to single ions, a two-plate system, and a two-domain protein reveal that the new theory and methods can capture capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics simulations. Comparisons of the phase-field and the original sharp-interface variational approaches are discussed.

Study of Wave-Particle Interactions for Whistler Mode Waves at Oblique Angles by Utilizing the Gyroaveraging Method

NASA Astrophysics Data System (ADS)

Hsieh, Yi-Kai; Omura, Yoshiharu

2017-10-01

We investigate the properties of whistler mode wave-particle interactions at oblique wave normal angles to the background magnetic field. We find that electromagnetic energy of waves at frequencies below half the electron cyclotron frequency can flow nearly parallel to the ambient magnetic field. We thereby confirm that the gyroaveraging method, which averages the cyclotron motion to the gyrocenter and reduces the simulation from two-dimensional to one-dimensional, is valid for oblique wave-particle interaction. Multiple resonances appear for oblique propagation but not for parallel propagation. We calculate the possible range of resonances with the first-order resonance condition as a function of electron kinetic energy and equatorial pitch angle. To reveal the physical process and the efficiency of electron acceleration by multiple resonances, we assume a simple uniform wave model with constant amplitude and frequency in space and time. We perform test particle simulations with electrons starting at specific equatorial pitch angles and kinetic energies. The simulation results show that multiple resonances contribute to acceleration and pitch angle scattering of energetic electrons. Especially, we find that electrons with energies of a few hundred keV can be accelerated efficiently to a few MeV through the n = 0 Landau resonance.

Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data.

PubMed

Saberi, Saeed; Farré, Pau; Cuvier, Olivier; Emberly, Eldon

2015-05-23

A variety of DNA binding proteins are involved in regulating and shaping the packing of chromatin. They aid the formation of loops in the DNA that function to isolate different structural domains. A recent experimental technique, Hi-C, provides a method for determining the frequency of such looping between all distant parts of the genome. Given that the binding locations of many chromatin associated proteins have also been measured, it has been possible to make estimates for their influence on the long-range interactions as measured by Hi-C. However, a challenge in this analysis is the predominance of non-specific contacts that mask out the specific interactions of interest. We show that transforming the Hi-C contact frequencies into free energies gives a natural method for separating out the distance dependent non-specific interactions. In particular we apply Principal Component Analysis (PCA) to the transformed free energy matrix to identify the dominant modes of interaction. PCA identifies systematic effects as well as high frequency spatial noise in the Hi-C data which can be filtered out. Thus it can be used as a data driven approach for normalizing Hi-C data. We assess this PCA based normalization approach, along with several other normalization schemes, by fitting the transformed Hi-C data using a pairwise interaction model that takes as input the known locations of bound chromatin factors. The result of fitting is a set of predictions for the coupling energies between the various chromatin factors and their effect on the energetics of looping. We show that the quality of the fit can be used as a means to determine how much PCA filtering should be applied to the Hi-C data. We find that the different normalizations of the Hi-C data vary in the quality of fit to the pairwise interaction model. PCA filtering can improve the fit, and the predicted coupling energies lead to biologically meaningful insights for how various chromatin bound factors influence the stability of DNA loops in chromatin.

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods.

PubMed

Antony, Jens; Grimme, Stefan; Liakos, Dimitrios G; Neese, Frank

2011-10-20

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.

Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods

NASA Astrophysics Data System (ADS)

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F.; Ingrosso, Francesca

2014-07-01

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.

Low-lying excited states of model proteins: Performances of the CC2 method versus multireference methods

NASA Astrophysics Data System (ADS)

Ben Amor, Nadia; Hoyau, Sophie; Maynau, Daniel; Brenner, Valérie

2018-05-01

A benchmark set of relevant geometries of a model protein, the N-acetylphenylalanylamide, is presented to assess the validity of the approximate second-order coupled cluster (CC2) method in studying low-lying excited states of such bio-relevant systems. The studies comprise investigations of basis-set dependence as well as comparison with two multireference methods, the multistate complete active space 2nd order perturbation theory (MS-CASPT2) and the multireference difference dedicated configuration interaction (DDCI) methods. First of all, the applicability and the accuracy of the quasi-linear multireference difference dedicated configuration interaction method have been demonstrated on bio-relevant systems by comparison with the results obtained by the standard MS-CASPT2. Second, both the nature and excitation energy of the first low-lying excited state obtained at the CC2 level are very close to the Davidson corrected CAS+DDCI ones, the mean absolute deviation on the excitation energy being equal to 0.1 eV with a maximum of less than 0.2 eV. Finally, for the following low-lying excited states, if the nature is always well reproduced at the CC2 level, the differences on excitation energies become more important and can depend on the geometry.

Low-lying excited states of model proteins: Performances of the CC2 method versus multireference methods.

PubMed

Ben Amor, Nadia; Hoyau, Sophie; Maynau, Daniel; Brenner, Valérie

2018-05-14

A benchmark set of relevant geometries of a model protein, the N-acetylphenylalanylamide, is presented to assess the validity of the approximate second-order coupled cluster (CC2) method in studying low-lying excited states of such bio-relevant systems. The studies comprise investigations of basis-set dependence as well as comparison with two multireference methods, the multistate complete active space 2nd order perturbation theory (MS-CASPT2) and the multireference difference dedicated configuration interaction (DDCI) methods. First of all, the applicability and the accuracy of the quasi-linear multireference difference dedicated configuration interaction method have been demonstrated on bio-relevant systems by comparison with the results obtained by the standard MS-CASPT2. Second, both the nature and excitation energy of the first low-lying excited state obtained at the CC2 level are very close to the Davidson corrected CAS+DDCI ones, the mean absolute deviation on the excitation energy being equal to 0.1 eV with a maximum of less than 0.2 eV. Finally, for the following low-lying excited states, if the nature is always well reproduced at the CC2 level, the differences on excitation energies become more important and can depend on the geometry.

Understanding the physical dynamics and ecological interactions in tidal stream energy environments

NASA Astrophysics Data System (ADS)

Fraser, Shaun; Williamson, Benjamin J.; Nikora, Vladimir; Scott, Beth E.

2017-04-01

Tidal stream energy devices are intended to operate in energetic physical environments characterised by high flows and extreme turbulence. These environments are often of ecological importance to a range of marine species. Understanding the physical dynamics and ecological interactions at fine scales in such sites is essential for device/array design and to understand environmental impacts. However, investigating fine scale characteristics requires high resolution field measurements which are difficult to attain and interpret, with data often confounded by interference related to turbulence. Consequently, field observations in tidal stream energy environments are limited and require the development of specialised analysis methods and so significant knowledge gaps are still present. The seabed mounted FLOWBEC platform is addressing these knowledge gaps using upward facing instruments to collect information from around marine energy infrastructure. Multifrequency and multibeam echosounder data provide detailed information on the distribution and interactions of biological targets, such as fish and diving seabirds, while simultaneously recording the scales and intensity of turbulence. Novel processing methodologies and instrument integration techniques have been developed which combine different data types and successfully separates signal from noise to reveal new evidence about the behaviour of mobile species and the structure of turbulence at all speeds of the tide and throughout the water column. Multiple platform deployments in the presence and absence of marine energy infrastructure reveal the natural characteristics of high energy sites, and enable the interpretation of the physical and biological impacts of tidal stream devices. These methods and results are relevant to the design and consenting of marine renewable energy technologies, and provide novel information on the use of turbulence for foraging opportunities in high energy sites by mobile species.

A comparative study of gamma-ray interaction and absorption in some building materials using Zeff-toolkit

NASA Astrophysics Data System (ADS)

Mann, Kulwinder Singh; Heer, Manmohan Singh; Rani, Asha

2016-07-01

The gamma-ray shielding behaviour of a material can be investigated by determining its various interaction and energy-absorption parameters (such as mass attenuation coefficients, mass energy absorption coefficients, and corresponding effective atomic numbers and electron densities). Literature review indicates that the effective atomic number (Zeff) has been used as extensive parameters for evaluating the effects and defect in the chosen materials caused by ionising radiations (X-rays and gamma-rays). A computer program (Zeff-toolkit) has been designed for obtaining the mean value of effective atomic number calculated by three different methods. A good agreement between the results obtained with Zeff-toolkit, Auto_Zeff software and experimentally measured values of Zeff has been observed. Although the Zeff-toolkit is capable of computing effective atomic numbers for both photon interaction (Zeff,PI) and energy absorption (Zeff,En) using three methods in each. No similar computer program is available in the literature which simultaneously computes these parameters simultaneously. The computed parameters have been compared and correlated in the wide energy range (0.001-20 MeV) for 10 commonly used building materials. The prominent variations in these parameters with gamma-ray photon energy have been observed due to the dominance of various absorption and scattering phenomena. The mean values of two effective atomic numbers (Zeff,PI and Zeff,En) are equivalent at energies below 0.002 MeV and above 0.3 MeV, indicating the dominance of gamma-ray absorption (photoelectric and pair production) over scattering (Compton) at these energies. Conversely in the energy range 0.002-0.3 MeV, the Compton scattering of gamma-rays dominates the absorption. From the 10 chosen samples of building materials, 2 soils showed better shielding behaviour than did other 8 materials.

Ab initio calculations, structure, NBO and NCI analyses of Xsbnd H⋯π interactions

NASA Astrophysics Data System (ADS)

Wu, Qiyang; Su, He; Wang, Hongyan; Wang, Hui

2018-02-01

The performance of ab initio methods (MP2, DFT/B3LYP, random-phase approximation (RPA), CCSD(T) and QCISD(T)) in predicting interaction energy of Xsbnd H⋯π (Xsbnd H = HCCH, HCl, HF; π = C2H2, C2H4, C6H6) hydrogen complexes are assessed systematically. The CCSD(T)/CBS benchmarks of interaction energy are reported. It is found that RPA agrees well with CCSD(T)/CBS benchmarks and experimental results. CCSD(T) and QCISD(T) perform the best only when compared with CCSD(T)/CBS benchmarks, MP2 performs well only for experimental data. B3LYP provides the worst accuracy. Additionally, the equilibrium structure, interaction type of Xsbnd H⋯π hydrogen complexes are investigated by the natural bond orbital (NBO) and the non-covalent interaction index (NCI).

Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Castells, Victoria; Van Tassel, Paul R.

2005-02-01

Proteins often undergo changes in internal conformation upon interacting with a surface. We investigate the thermodynamics of surface induced conformational change in a lattice model protein using a multicanonical Monte Carlo method. The protein is a linear heteropolymer of 27 segments (of types A and B) confined to a cubic lattice. The segmental order and nearest neighbor contact energies are chosen to yield, in the absence of an adsorbing surface, a unique 3×3×3 folded structure. The surface is a plane of sites interacting either equally with A and B segments (equal affinity surface) or more strongly with the A segments (A affinity surface). We use a multicanonical Monte Carlo algorithm, with configuration bias and jump walking moves, featuring an iteratively updated sampling function that converges to the reciprocal of the density of states 1/Ω(E), E being the potential energy. We find inflection points in the configurational entropy, S(E)=klnΩ(E), for all but a strongly adsorbing equal affinity surface, indicating the presence of free energy barriers to transition. When protein-surface interactions are weak, the free energy profiles F(E)=E-TS(E) qualitatively resemble those of a protein in the absence of a surface: a free energy barrier separates a folded, lowest energy state from globular, higher energy states. The surface acts in this case to stabilize the globular states relative to the folded state. When the protein surface interactions are stronger, the situation differs markedly: the folded state no longer occurs at the lowest energy and free energy barriers may be absent altogether.

Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case

NASA Astrophysics Data System (ADS)

Ucisik, Melek N.; Dashti, Danial S.; Faver, John C.; Merz, Kenneth M.

2011-08-01

An energy expansion (binding energy decomposition into n-body interaction terms for n ≥ 2) to express the receptor-ligand binding energy for the fragmented HIV II protease-Indinavir system is described to address the role of cooperativity in ligand binding. The outcome of this energy expansion is compared to the total receptor-ligand binding energy at the Hartree-Fock, density functional theory, and semiempirical levels of theory. We find that the sum of the pairwise interaction energies approximates the total binding energy to ˜82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. The contribution of the three-body interactions amounts to 18.7%, 3.8%, and 1.4% for HF, M06-L, and PM6-DH2, respectively. We find that the expansion can be safely truncated after n = 3. That is, the contribution of the interactions involving more than three parties to the total binding energy of Indinavir to the HIV II protease receptor is negligible. Overall, we find that the two-body terms represent a good approximation to the total binding energy of the system, which points to pairwise additivity in the present case. This basic principle of pairwise additivity is utilized in fragment-based drug design approaches and our results support its continued use. The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions.

Method for Predicting the Energy Characteristics of Li-Ion Cells Designed for High Specific Energy

NASA Technical Reports Server (NTRS)

Bennett, William, R.

2012-01-01

Novel electrode materials with increased specific capacity and voltage performance are critical to the NASA goals for developing Li-ion batteries with increased specific energy and energy density. Although performance metrics of the individual electrodes are critically important, a fundamental understanding of the interactions of electrodes in a full cell is essential to achieving the desired performance, and for establishing meaningful goals for electrode performance in the first place. This paper presents design considerations for matching positive and negative electrodes in a viable design. Methods for predicting cell-level performance, based on laboratory data for individual electrodes, are presented and discussed.

Scientific Computation Application Partnerships in Materials and Chemical Sciences, Charge Transfer and Charge Transport in Photoactivated Systems, Developing Electron-Correlated Methods for Excited State Structure and Dynamics in the NWChem Software Suite

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

Cramer, Christopher J.

Charge transfer and charge transport in photoactivated systems are fundamental processes that underlie solar energy capture, solar energy conversion, and photoactivated catalysis, both organometallic and enzymatic. We developed methods, algorithms, and software tools needed for reliable treatment of the underlying physics for charge transfer and charge transport, an undertaking with broad applicability to the goals of the fundamental-interaction component of the Department of Energy Office of Basic Energy Sciences and the exascale initiative of the Office of Advanced Scientific Computing Research.

Quantum Tunneling Contribution for the Activation Energy in Microwave-Induced Reactions.

PubMed

Kuhnen, Carlos A; Dall'Oglio, Evandro L; de Sousa, Paulo T

2017-08-03

In this study, a quantum approach is presented to explain microwave-enhanced reaction rates by considering the tunneling effects in chemical reactions. In the Arrhenius equation, the part of the Hamiltonian relative to the interaction energy during tunneling, between the particle that tunnels and the electrical field defined in the medium, whose spatial component is specified by its rms value, is taken into account. An approximate evaluation of the interaction energy leads to a linear dependence of the effective activation energy on the applied field. The evaluation of the rms value of the field for pure liquids and reaction mixtures, through their known dielectric properties, leads to an appreciable reduction in the activation energies for the proton transfer process in these liquids. The results indicate the need to move toward the use of more refined methods of modern quantum chemistry to calculate more accurately field-induced reaction rates and effective activation energies.

The Effects of Domestic Energy Consumption on Urban Development Using System Dynamics

NASA Astrophysics Data System (ADS)

Saryazdi, M. D.; Homaei, N.; Arjmand, A.

2018-05-01

In developed countries, people have learned to follow efficient consumption patterns, while in developing countries, such as Iran, these patterns are not well executed. A large amount of energy is almost consumed in buildings and houses and though the consumption patterns varies in different societies, various energy policies are required to meet the consumption challenges. So far, several papers and more than ten case studies have worked on the relationship between domestic energy consumption and urban development, however these researches did not analyzed the impact of energy consumption on urban development. Therefore, this paper attempts to examine the interactions between the energy consumption and urban development by using system dynamics as the most widely used methods for complex problems. The proposed approach demonstrates the interactions using causal loop and flow diagrams and finally, suitable strategies will be proposed for urban development through simulations of different scenarios.

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures

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

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003)] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here in this paper, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013)] tomore » obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S = 1/2, we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.« less

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures

DOE PAGES

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; ...

2018-04-20

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003)] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here in this paper, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013)] tomore » obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S = 1/2, we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.« less

Use of the PIXEL method to investigate gas adsorption in metal–organic frameworks† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ce00555a Click here for additional data file. Click here for additional data file. Click here for additional data file.

PubMed Central

Maloney, Andrew G. P.; Wood, Peter A.

2016-01-01

PIXEL has been used to perform calculations of adsorbate-adsorbent interaction energies between a range of metal–organic frameworks (MOFs) and simple guest molecules. Interactions have been calculated for adsorption between MOF-5 and Ar, H2, and N2; Zn2(BDC)2(TED) (BDC = 1,4-benzenedicarboxylic acid, TED = triethylenediamine) and H2; and HKUST-1 and CO2. The locations of the adsorption sites and the calculated energies, which show differences in the Coulombic or dispersion characteristic of the interaction, compare favourably to experimental data and literature energy values calculated using density functional theory. PMID:28496380

Complex-energy approach to sum rules within nuclear density functional theory

DOE PAGES

Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; ...

2015-04-27

The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish anmore » efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.« less

Methodology to Improve Design of Accelerated Life Tests in Civil Engineering Projects

PubMed Central

Lin, Jing; Yuan, Yongbo; Zhou, Jilai; Gao, Jie

2014-01-01

For reliability testing an Energy Expansion Tree (EET) and a companion Energy Function Model (EFM) are proposed and described in this paper. Different from conventional approaches, the EET provides a more comprehensive and objective way to systematically identify external energy factors affecting reliability. The EFM introduces energy loss into a traditional Function Model to identify internal energy sources affecting reliability. The combination creates a sound way to enumerate the energies to which a system may be exposed during its lifetime. We input these energies into planning an accelerated life test, a Multi Environment Over Stress Test. The test objective is to discover weak links and interactions among the system and the energies to which it is exposed, and design them out. As an example, the methods are applied to the pipe in subsea pipeline. However, they can be widely used in other civil engineering industries as well. The proposed method is compared with current methods. PMID:25111800

Estimation of the Invisible Energy in Extensive Air Showers with the Data Collected by the Pierre Auger Observatory

NASA Astrophysics Data System (ADS)

Mariazzi, Analisa

The determination of the energy of primary cosmic rays from their extensive air showers using the fluorescence technique requires an estimation of the energy carried away by particles reaching the ground that do not deposit all their energy in the atmosphere. This estimation is typically made using Monte Carlo simulations and depends on the assumed primary particle mass and on model predictions for hadron-air collisions at high energies. In this work we review the method that the Pierre Auger Collaboration uses to obtain the invisible energy directly from hybrid events measured simultaneously with the fluorescence and the surface detectors of the Pierre Auger Observatory. As a corroboration of these results, a new method for the determination of the invisible energy using an independent data set is also presented. Both methods agree within systematic uncertainties, reducing significantly the biases related to differences between the high energy hadronic interaction models and data.

System and method for single-phase, single-stage grid-interactive inverter

DOEpatents

Liu, Liming; Li, Hui

2015-09-01

The present invention provides for the integration of distributed renewable energy sources/storages utilizing a cascaded DC-AC inverter, thereby eliminating the need for a DC-DC converter. The ability to segment the energy sources and energy storages improves the maintenance capability and system reliability of the distributed generation system, as well as achieve wide range reactive power compensation. In the absence of a DC-DC converter, single stage energy conversion can be achieved to enhance energy conversion efficiency.

In silico prediction of drug solubility: 2. Free energy of solvation in pure melts.

PubMed

Lüder, Kai; Lindfors, Lennart; Westergren, Jan; Nordholm, Sture; Kjellander, Roland

2007-02-22

The solubility of drugs in water is investigated in a series of papers and in the current work. The free energy of solvation, DeltaG*(vl), of a drug molecule in its pure drug melt at 673.15 K (400 degrees C) has been obtained for 46 drug molecules using the free energy perturbation method. The simulations were performed in two steps where first the Coulomb and then the Lennard-Jones interactions were scaled down from full to no interaction. The results have been interpreted using a theory assuming that DeltaG*(vl) = DeltaG(cav) + E(LJ) + E(C)/2 where the free energy of cavity formation, DeltaG(cav), in these pure drug systems was obtained using hard body theories, and E(LJ) and E(C) are the Lennard-Jones and Coulomb interaction energies, respectively, of one molecule with the other ones. Since the main parameter in hard body theories is the volume fraction, an equation of state approach was used to estimate the molecular volume. Promising results were obtained using a theory for hard oblates, in which the oblate axial ratio was calculated from the molecular surface area and volume obtained from simulations. The Coulomb term, E(C)/2, is half of the Coulomb energy in accord with linear response, which showed good agreement with our simulation results. In comparison with our previous results on free energy of hydration, the Coulomb interactions in pure drug systems are weaker, and the van der Waals interactions play a more important role.

Maximum-Likelihood Methods for Processing Signals From Gamma-Ray Detectors

PubMed Central

Barrett, Harrison H.; Hunter, William C. J.; Miller, Brian William; Moore, Stephen K.; Chen, Yichun; Furenlid, Lars R.

2009-01-01

In any gamma-ray detector, each event produces electrical signals on one or more circuit elements. From these signals, we may wish to determine the presence of an interaction; whether multiple interactions occurred; the spatial coordinates in two or three dimensions of at least the primary interaction; or the total energy deposited in that interaction. We may also want to compute listmode probabilities for tomographic reconstruction. Maximum-likelihood methods provide a rigorous and in some senses optimal approach to extracting this information, and the associated Fisher information matrix provides a way of quantifying and optimizing the information conveyed by the detector. This paper will review the principles of likelihood methods as applied to gamma-ray detectors and illustrate their power with recent results from the Center for Gamma-ray Imaging. PMID:20107527

Adaptive Monte Carlo methods

NASA Astrophysics Data System (ADS)

Fasnacht, Marc

We develop adaptive Monte Carlo methods for the calculation of the free energy as a function of a parameter of interest. The methods presented are particularly well-suited for systems with complex energy landscapes, where standard sampling techniques have difficulties. The Adaptive Histogram Method uses a biasing potential derived from histograms recorded during the simulation to achieve uniform sampling in the parameter of interest. The Adaptive Integration method directly calculates an estimate of the free energy from the average derivative of the Hamiltonian with respect to the parameter of interest and uses it as a biasing potential. We compare both methods to a state of the art method, and demonstrate that they compare favorably for the calculation of potentials of mean force of dense Lennard-Jones fluids. We use the Adaptive Integration Method to calculate accurate potentials of mean force for different types of simple particles in a Lennard-Jones fluid. Our approach allows us to separate the contributions of the solvent to the potential of mean force from the effect of the direct interaction between the particles. With contributions of the solvent determined, we can find the potential of mean force directly for any other direct interaction without additional simulations. We also test the accuracy of the Adaptive Integration Method on a thermodynamic cycle, which allows us to perform a consistency check between potentials of mean force and chemical potentials calculated using the Adaptive Integration Method. The results demonstrate a high degree of consistency of the method.

Binary colloidal structures assembled through Ising interactions

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

NASA Astrophysics Data System (ADS)

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

2012-10-01

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error.

PubMed

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T; Dannenberg, J J

2012-10-07

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

PubMed Central

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

2012-01-01

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states. PMID:23039587

Recent Developments in Non-Fermi Liquid Theory

NASA Astrophysics Data System (ADS)

Lee, Sung-Sik

2018-03-01

Non-Fermi liquids are unconventional metals whose physical properties deviate qualitatively from those of noninteracting fermions due to strong quantum fluctuations near Fermi surfaces. They arise when metals are subject to singular interactions mediated by soft collective modes. In the absence of well-defined quasiparticles, universal physics of non-Fermi liquids is captured by interacting field theories which replace Landau Fermi liquid theory. However, it has been difficult to understand their universal low-energy physics due to a lack of theoretical methods that take into account strong quantum fluctuations in the presence of abundant low-energy degrees of freedom. In this review, we discuss two approaches that have been recently developed for non-Fermi liquid theory with emphasis on two space dimensions. The first is a perturbative scheme based on a dimensional regularization, which achieves a controlled access to the low-energy physics by tuning the codimension of Fermi surface. The second is a nonperturbative approach which treats the interaction ahead of the kinetic term through a non-Gaussian scaling called interaction-driven scaling. Examples of strongly coupled non-Fermi liquids amenable to exact treatments through the interaction-driven scaling are discussed.

Excited state free energy calculations of Cy3 in different environments

NASA Astrophysics Data System (ADS)

Sawangsang, Pilailuk; Buranachai, Chittanon; Punwong, Chutintorn

2015-05-01

Cy3, a cyanine dye, is one of the most widely used dyes in investigating the structure and dynamics of biomolecules by means of fluorescence methods. However, Cy3 fluorescence emission is strongly competed by trans-cis isomerization, whose efficiency is dictated by the isomerization energy barrier and the environment of Cy3. The fluorescence quantum yield of Cy3 is very low when the dye is free in homogeneous solution but it is considerably enhanced in an environment that rigidifies the structure, e.g. when it is attached to a DNA strand. In this work, the barriers for isomerization on the excited state of free Cy3, and Cy3 attached to single- and double-stranded DNA in methanol, are presented. The free energy and subsequently the isomerization barrier calculations are performed using the umbrella sampling technique with the weighted histogram analysis method. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is employed to provide the potential energy surfaces for the excited state dynamics simulations in umbrella sampling. The semiempirical floating occupation molecular orbital configuration interaction method is used for electronic excited state calculations of the QM region (Cy3). From the free energy calculations, the barrier of Cy3 attached to the single-stranded DNA is highest, in agreement with previously reported experimental results. This is likely due to the stacking interaction between Cy3 and DNA. Such a stacking interaction is likely associated with steric hindrance that prevents the rotation around the conjugated bonds of Cy3. If Cy3 experiences high steric hindrance, it has a higher isomerization barrier and thus the efficiency of fluorescence emission increases.

Preferred orientation of albumin adsorption on a hydrophilic surface from molecular simulation.

PubMed

Hsu, Hao-Jen; Sheu, Sheh-Yi; Tsay, Ruey-Yug

2008-12-01

In general, non-specific protein adsorption follows a two-step procedure, i.e. first adsorption onto a surface in native form, and a subsequent conformational change on the surface. In order to predict the subsequent conformational change, it is important to determine the preferred orientation of an adsorbed protein in the first step of the adsorption. In this work, a method based on finding the global minimum of the interaction potential energy of an adsorbed protein has been developed to delineate the preferred orientations for the adsorption of human serum albumin (HSA) on a model surface with a hydrophilic self-assembled monolayer (SAM). For computational efficiency, solvation effects were greatly simplified by only including the dampening of electrostatic effects while neglecting contributions due to the competition of water molecules for the functional groups on the surface. A contour map obtained by systematic rotation of a molecule in conjunction with perpendicular motion to the surface gives the minimum interaction energy of the adsorbed molecule at various adsorption orientations. Simulation results show that for an -OH terminated SAM surface, a "back-on" orientation of HSA is the preferred orientation. The projection area of this adsorption orientation corresponds with the "triangular-side-on" adsorption of a heart shaped HSA molecule. The method proposed herein is able to provide results which are consistent with those predicted by Monte Carlo (MC) simulations with a substantially less computing cost. The high computing efficiency of the current method makes it possible to be implemented as a design tool for the control of protein adsorption on surfaces; however, before this can be fully realized, these methods must be further developed to enable interaction free energy to be calculated in place of potential energy, along with a more realistic representation of solvation effects.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Observation of anisotropic interactions between metastable atoms and target molecules by two-dimensional collisional ionization electron spectroscopy

NASA Astrophysics Data System (ADS)

Kishimoto, Naoki; Ohno, Koichi

Excited metastable atoms colliding with target molecules can sensitively probe outer properties of molecules by chemi-ionization (Penning ionization) from molecular orbitals in the outer region, since metastable atoms cannot penetrate into the repulsive interaction wall around the molecules. By means of two-dimensional measurements using kinetic energy analysis of electrons combined with a velocity-resolved metastable beam, one can obtain information on the anisotropic interaction between the colliding particles without any control of orientation or alignment of target molecules. We have developed a classical trajectory method to calculate the collision energy dependence of partial ionization cross-sections (CEDPICS) on the anisotropic interaction potential energy surface, which has enabled us to study stereodynamics between metastable atoms and target molecules as well as the spatial distribution of molecular orbitals and electron ejection functions which have a relation with entrance and exit channels of the reaction. Based on the individual CEDPICS, the electronic structure of molecules can also be elucidated.

Semi-automated segmentation of neuroblastoma nuclei using the gradient energy tensor: a user driven approach

NASA Astrophysics Data System (ADS)

Kromp, Florian; Taschner-Mandl, Sabine; Schwarz, Magdalena; Blaha, Johanna; Weiss, Tamara; Ambros, Peter F.; Reiter, Michael

2015-02-01

We propose a user-driven method for the segmentation of neuroblastoma nuclei in microscopic fluorescence images involving the gradient energy tensor. Multispectral fluorescence images contain intensity and spatial information about antigene expression, fluorescence in situ hybridization (FISH) signals and nucleus morphology. The latter serves as basis for the detection of single cells and the calculation of shape features, which are used to validate the segmentation and to reject false detections. Accurate segmentation is difficult due to varying staining intensities and aggregated cells. It requires several (meta-) parameters, which have a strong influence on the segmentation results and have to be selected carefully for each sample (or group of similar samples) by user interactions. Because our method is designed for clinicians and biologists, who may have only limited image processing background, an interactive parameter selection step allows the implicit tuning of parameter values. With this simple but intuitive method, segmentation results with high precision for a large number of cells can be achieved by minimal user interaction. The strategy was validated on handsegmented datasets of three neuroblastoma cell lines.

Coupling Visualization, Simulation, and Deep Learning for Ensemble Steering of Complex Energy Models: Preprint

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

Potter, Kristin C; Brunhart-Lupo, Nicholas J; Bush, Brian W

We have developed a framework for the exploration, design, and planning of energy systems that combines interactive visualization with machine-learning based approximations of simulations through a general purpose dataflow API. Our system provides a visual inter- face allowing users to explore an ensemble of energy simulations representing a subset of the complex input parameter space, and spawn new simulations to 'fill in' input regions corresponding to new enegery system scenarios. Unfortunately, many energy simula- tions are far too slow to provide interactive responses. To support interactive feedback, we are developing reduced-form models via machine learning techniques, which provide statistically soundmore » esti- mates of the full simulations at a fraction of the computational cost and which are used as proxies for the full-form models. Fast com- putation and an agile dataflow enhance the engagement with energy simulations, and allow researchers to better allocate computational resources to capture informative relationships within the system and provide a low-cost method for validating and quality-checking large-scale modeling efforts.« less

Gamma-rays attenuation of zircons from Cambodia and South Africa at different energies: A new technique for identifying the origin of gemstone

NASA Astrophysics Data System (ADS)

Limkitjaroenporn, P.; Kaewkhao, J.

2014-10-01

In this work, the gamma-rays interaction properties of zircons from Cambodia and South Africa have been studied. The densities of Cambodian and South African's zircons are 4.6716±0.0040 g/cm3 and 4.5505±0.0018 g/cm3, respectively. The mass attenuation coefficient and the effective atomic number of gemstones were measured with the gamma-ray in energies range 223-662 keV using the Compton scattering technique. The mass attenuation coefficients of both zircons decreased with the increasing of gamma-rays energies. The different mass attenuation coefficients between the two zircons observed at gamma-ray energies below 400 keV are attributed to the differences in the photoelectric interaction. The effective atomic number of zircons was decreased with the increasing of gamma-ray energies and showed totally different values between the Cambodia and South Africa sources. The origins of the two zircons could be successfully identified by the method based on gamma-rays interaction with matter with advantage of being a non-destructive testing.

Quasiparticle energy bands and Fermi surfaces of monolayer NbSe2

NASA Astrophysics Data System (ADS)

Kim, Sejoong; Son, Young-Woo

2017-10-01

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

Light-Nuclei Spectra from Chiral Dynamics

NASA Astrophysics Data System (ADS)

Piarulli, M.; Baroni, A.; Girlanda, L.; Kievsky, A.; Lovato, A.; Lusk, Ewing; Marcucci, L. E.; Pieper, Steven C.; Schiavilla, R.; Viviani, M.; Wiringa, R. B.

2018-02-01

In recent years local chiral interactions have been derived and implemented in quantum Monte Carlo methods in order to test to what extent the chiral effective field theory framework impacts our knowledge of few- and many-body systems. In this Letter, we present Green's function Monte Carlo calculations of light nuclei based on the family of local two-body interactions presented by our group in a previous paper in conjunction with chiral three-body interactions fitted to bound- and scattering-state observables in the three-nucleon sector. These interactions include Δ intermediate states in their two-pion-exchange components. We obtain predictions for the energy levels and level ordering of nuclei in the mass range A =4 - 12 , accurate to ≤2 % of the binding energy, in very satisfactory agreement with experimental data.

Non-equilibrium magnetic interactions in strongly correlated systems

NASA Astrophysics Data System (ADS)

Secchi, A.; Brener, S.; Lichtenstein, A. I.; Katsnelson, M. I.

2013-06-01

We formulate a low-energy theory for the magnetic interactions between electrons in the multi-band Hubbard model under non-equilibrium conditions determined by an external time-dependent electric field which simulates laser-induced spin dynamics. We derive expressions for dynamical exchange parameters in terms of non-equilibrium electronic Green functions and self-energies, which can be computed, e.g., with the methods of time-dependent dynamical mean-field theory. Moreover, we find that a correct description of the system requires, in addition to exchange, a new kind of magnetic interaction, that we name twist exchange, which formally resembles Dzyaloshinskii-Moriya coupling, but is not due to spin-orbit, and is actually due to an effective three-spin interaction. Our theory allows the evaluation of the related time-dependent parameters as well.

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

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

Mardirossian, Narbe; Head-Gordon, Martin

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2016-11-09

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

A high level computational study of the CH4/CF4 dimer: how does it compare with the CH4/CH4 and CF4/CF4 dimers?

NASA Astrophysics Data System (ADS)

Biller, Matthew J.; Mecozzi, Sandro

2012-04-01

The interaction within the methane-methane (CH4/CH4), perfluoromethane-perfluoromethane (CF4/CF4) methane-perfluoromethane dimers (CH4/CF4) was calculated using the Hartree-Fock (HF) method, multiple orders of Møller-Plesset perturbation theory [MP2, MP3, MP4(DQ), MP4(SDQ), MP4(SDTQ)], and coupled cluster theory [CCSD, CCSD(T)], as well as the PW91, B97D, and M06-2X density functional theory (DFT) functionals. The basis sets of Dunning and coworkers (aug-cc-pVxZ, x = D, T, Q), Krishnan and coworkers [6-311++G(d,p), 6-311++G(2d,2p)], and Tsuzuki and coworkers [aug(df, pd)-6-311G(d,p)] were used. Basis set superposition error (BSSE) was corrected via the counterpoise method in all cases. Interaction energies obtained with the MP2 method do not fit with the experimental finding that the methane-perfluoromethane system phase separates at 94.5 K. It was not until the CCSD(T) method was considered that the interaction energy of the methane-perfluoromethane dimer (-0.69 kcal mol-1) was found to be intermediate between the methane (-0.51 kcal mol-1) and perfluoromethane (-0.78 kcal mol-1) dimers. This suggests that a perfluoromethane molecule interacts preferentially with another perfluoromethane (by about 0.09 kcal mol-1) than with a methane molecule. At temperatures much lower than the CH4/CF4 critical solution temperature of 94.5 K, this energy difference becomes significant and leads perfluoromethane molecules to associate with themselves, forming a phase separation. The DFT functionals yielded erratic results for the three dimers. Further development of DFT is needed in order to model dispersion interactions in hydrocarbon/perfluorocarbon systems.

A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N-H···O=C and C-H···O=C hydrogen-bonded complexes.

PubMed

Li, Shu-Shi; Huang, Cui-Ying; Hao, Jiao-Jiao; Wang, Chang-Sheng

2014-03-05

In this article, a polarizable dipole-dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen-bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N-H, C=O, and C-H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole-dipole interaction model to a series of hydrogen-bonded complexes containing the N-H···O=C and C-H···O=C hydrogen bonds, such as simple amide-amide dimers, base-base dimers, peptide-base dimers, and β-sheet models. We find that a simple two-term function, only containing the permanent dipole-dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6-31G(d) method, whereas the high-quality counterpoise-corrected (CP-corrected) MP2/aug-cc-pVTZ interaction energies for the hydrogen-bonded complexes can be well-reproduced by a four-term function which involves the permanent dipole-dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole-dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen-bonded complexes are further discussed. Copyright © 2013 Wiley Periodicals, Inc.

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

PubMed

Sponer, Jiří; Sponer, Judit E; Mládek, Arnošt; Jurečka, Petr; Banáš, Pavel; Otyepka, Michal

2013-12-01

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. Copyright © 2013 Wiley Periodicals, Inc.

A study on the interactions of amino acids with nitrogen doped graphene; docking, MD simulation, and QM/MM studies.

PubMed

Ghadari, Rahim

2016-02-14

The binding properties of twenty amino acids with nitrogen-doped graphene structures were studied using docking, MD simulation, and QM/MM methods. TDDFT studies were carried out to investigate the change in the electronic properties of the amino acids because of the presence of the solvent and nitrogen-doped graphene. The results revealed that π-π interactions between the amino acids with a benzene moiety and the surface of the graphene are the most important interactions. The observed red shifts in the TDDFT results which were related to the lower LUMO energies and higher HOMO energies are consistent with this statement.

Potential Energy Curves and Collisions Integrals of Air Components. 2; Interactions Involving Ionized Atoms

NASA Technical Reports Server (NTRS)

Stallcop, James R.; Partridge, Harry; Levin, Eugene; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Collision integrals are fundamental quantities required to determine the transport properties of the environment surrounding aerospace vehicles in the upper atmosphere. These collision integrals can be determined as a function of temperature from the potential energy curves describing the atomic and molecular collisions. Ab initio calculations provide a practical method of computing the required interaction potentials. In this work we will discuss recent advances in scattering calculations with an emphasis on the accuracy that is obtainable. Results for interactions of the atoms and ionized atoms of nitrogen and oxygen will be reviewed and their application to the determination of transport properties, such as diffusion and viscosity coefficients, will be examined.

The origins of the directionality of noncovalent intermolecular interactions.

PubMed

Wang, Changwei; Guan, Liangyu; Danovich, David; Shaik, Sason; Mo, Yirong

2016-01-05

The recent σ-hole concept emphasizes the contribution of electrostatic attraction to noncovalent bonds, and implies that the electrostatic force has an angular dependency. Here a set of clusters, which includes hydrogen bonding, halogen bonding, chalcogen bonding, and pnicogen bonding systems, is investigated to probe the magnitude of covalency and its contribution to the directionality in noncovalent bonding. The study is based on the block-localized wavefunction (BLW) method that decomposes the binding energy into the steric and the charge transfer (CT) (hyperconjugation) contributions. One unique feature of the BLW method is its capability to derive optimal geometries with only steric effect taken into account, while excluding the CT interaction. The results reveal that the overall steric energy exhibits angular dependency notably in halogen bonding, chalcogen bonding, and pnicogen bonding systems. Turning on the CT interactions further shortens the intermolecular distances. This bond shortening enhances the Pauli repulsion, which in turn offsets the electrostatic attraction, such that in the final sum, the contribution of the steric effect to bonding is diminished, leaving the CT to dominate the binding energy. In several other systems particularly hydrogen bonding systems, the steric effect nevertheless still plays the major role whereas the CT interaction is minor. However, in all cases, the CT exhibits strong directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the covalency in noncovalent bonds. © 2015 Wiley Periodicals, Inc.

Density functional theory study on the influence of pyrrolidine substituent of C60 bisadduct on its supramolecular interaction with porphine

NASA Astrophysics Data System (ADS)

Zhao, Li-Hong; Weng, Jun-Ying; Zhao, Wei; Ruan, Wen-Juan; Xin, Fei; Zhang, Ying-Hui

2013-09-01

Calculation using three kinds of density functional theory (DFT) methods revealed that the nonbonded interaction of pyrrolidine-functionalized C60 bisadducts with porphine derivatives (MP: M = Zn, 2H) was significantly affected by pyrrolidine substituents. Several types of the stable interaction configurations of trans-3 C60 bisadduct/ZnP complex (abbreviated as tran-3/ZnP) were compared. The association energy predicted by the wB97XD method was larger than that predicted by CAM-B3LYP and BHandH functionals. The results showed that the closer approach of porphine ring to the two pyrrolidine substituents, the larger the association energy of the complex. This trend was ascribed to the additional C-H⋯π interaction between the pyrrolidine and porphine rings. The natural bond orbital analysis proved the existence of an additional charge transfer process between the porphine and pyrrolidine rings for the t-I type of trans-3/porphine complexes. The red shift of absorption peaks of porphine were predicted in consistent with general experimental results.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure.

PubMed

Chang, Wendi; Akselrod, Gleb M; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole-dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopant molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole-dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole-dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure

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

Chang, Wendi; Akselrod, Gleb M.; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole–dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopantmore » molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole–dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole–dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.« less

Interaction of the NO 3pπ (C {sup 2}Π) Rydberg state with RG (RG = Ne, Kr, and Xe): Potential energy surfaces and spectroscopy

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

Ershova, Olga V.; Besley, Nicholas A., E-mail: Nick.Besley@nottingham.ac.uk; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk

2015-01-21

We present new potential energy surfaces for the interaction of NO(C {sup 2}Π) with each of Ne, Kr, and Xe. The potential energy surfaces have been calculated using second order Møller-Plesset perturbation theory, exploiting a procedure to converge the reference Hartree-Fock wavefunction for the excited states: the maximum overlap method. The bound rovibrational states obtained from the surfaces are used to simulate the electronic spectra and their appearance is in good agreement with available (2+1) REMPI spectra. We discuss the assignment and appearance of these spectra, comparing to that of NO-Ar.

Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field

NASA Astrophysics Data System (ADS)

Jing, Zhifeng; Qi, Rui; Liu, Chengwen; Ren, Pengyu

2017-10-01

The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.

Energy harvesting from the interaction of a Lamb dipole with a flexible cantilever

NASA Astrophysics Data System (ADS)

Tang, Hui; Wang, Chenglei

2017-11-01

Energy harvesting from interactions of coherent flow structures with flexible solid structures can be used for powering miniature electronic devices. Although effective, the fundamental mechanism of such an energy extraction process has not been fully understood. Therefore, this study aims to provide more physical insights into this problem. The coherent flow structure is represented by a Lamb dipole, and the solid structure is assumed as a two-dimensional flexible cantilever. The cantilever is placed along the propagation direction of the dipole, with its fixed end initially towards or away from the dipole and its lateral distance from the dipole center varied. As the dipole passes through the cantilever, the latter can extract energy from the former through effective interactions. Such a two-dimensional fluid-structure interaction problem is numerically studied at a low Reynolds number of 200 using a lattice Boltzmann method (LBM) based numerical framework. The simulation results reveal that the flexible cantilever with a moderate stiffness is more beneficial to the energy harvesting, and it can scavenge more energy from the ambient vortices when its fixed end is initially away from the dipole with a relatively small lateral distance. The authors gratefully acknowledge the financial support for this study from the Research Grants Council of Hong Kong under General Research Fund (Project No. PolyU 152493/16E).

Structural expansions for the ground state energy of a simple metal

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1973-01-01

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

Investigation of radiological properties of some shielding materials on charged and uncharged radiation interaction for neutron generator

NASA Astrophysics Data System (ADS)

Büyükyıldız, Mehmet

2017-04-01

Radiation interaction parameters such as total stopping power, projected range (longitudinal and lateral) straggling, mass attenuation coefficient, effective atomic number (Zeff) and electron density (Neff) of some shielding materials were investigated for photon and heavy charged particle interactions. The ranges, stragglings and mass attenuation coefficients were calculated for the high-density polyethylene(HDPE), borated polyethylene (BPE), brick (common silica), concrete (regular), wood, water, stainless steel (304), aluminum (alloy 6061-O), lead and bismuth using SRIM Monte Carlo software and WinXCom program. In addition, effective atomic numbers (Zeff) and electron densities (Neff) of HDPE, BPE, brick (common silica), concrete (regular), wood, water, stainless steel (304) and aluminum (alloy 6061-O) were calculated in the energy region 10 keV-100 MeV using mass stopping powers and mass attenuation coefficients. Two different methods namely direct and interpolation procedures were used to calculate Zeff for comparison and significant differences were determined between the methods. Variations of the ranges, longitudinal and lateral stragglings of water, concrete and stainless steel (304) were compared with each other in the continuous kinetic energy region and discussed with respect to their Zeffs. Moreover, energy absorption buildup factors (EABF) and exposure buildup factors (EBF) of the materials were determined for gamma rays as well and were compared with each other for different photon energies and different mfps in the photon energy region 0.015-15 MeV.

Extension of the ratio method to low energy

DOE PAGES

Colomer, Frederic; Capel, Pierre; Nunes, F. M.; ...

2016-05-25

The ratio method has been proposed as a means to remove the reaction model dependence in the study of halo nuclei. Originally, it was developed for higher energies but given the potential interest in applying the method at lower energy, in this work we explore its validity at 20 MeV/nucleon. The ratio method takes the ratio of the breakup angular distribution and the summed angular distribution (which includes elastic, inelastic and breakup) and uses this observable to constrain the features of the original halo wave function. In this work we use the Continuum Discretized Coupled Channel method and the Coulomb-correctedmore » Dynamical Eikonal Approximation for the study. We study the reactions of 11Be on 12C, 40Ca and 208Pb at 20 MeV/nucleon. We compare the various theoretical descriptions and explore the dependence of our result on the core-target interaction. Lastly, our study demonstrates that the ratio method is valid at these lower beam energies.« less

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

PubMed

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

2012-02-05

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

Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method.

PubMed

Ngo, Son Tung; Mai, Binh Khanh; Hiep, Dinh Minh; Li, Mai Suan

2015-10-01

The binding mechanism of AC1NX476 to HIV-1 protease wild type and mutations was studied by the docking and molecular dynamics simulations. The binding free energy was calculated using the double-annihilation binding free energy method. It is shown that the binding affinity of AC1NX476 to wild type is higher than not only ritonavir but also darunavir, making AC1NX476 become attractive candidate for HIV treatment. Our theoretical results are in excellent agreement with the experimental data as the correlation coefficient between calculated and experimentally measured binding free energies R = 0.993. Residues Asp25-A, Asp29-A, Asp30-A, Ile47-A, Gly48-A, and Val50-A from chain A, and Asp25-B from chain B play a crucial role in the ligand binding. The mutations were found to reduce the receptor-ligand interaction by widening the binding cavity, and the binding propensity is mainly driven by the van der Waals interaction. Our finding may be useful for designing potential drugs to combat with HIV. © 2015 John Wiley & Sons A/S.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

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

Zheng, Xiaogang; Biesiada, Marek; Cao, Shuo

A new compilation of 012 angular-size/redshift data for compact radio quasars from very-long-baseline interferometry (VLBI) surveys motivates us to revisit the interaction between dark energy and dark matter with these probes reaching high redshifts z ∼ 3.0. In this paper, we investigate observational constraints on different phenomenological interacting dark energy (IDE) models with the intermediate-luminosity radio quasars acting as individual standard rulers, combined with the newest BAO and CMB observation from Planck results acting as statistical rulers. The results obtained from the MCMC method and other statistical methods including figure of Merit and Information Criteria show that: (1) Compared withmore » the current standard candle data and standard clock data, the intermediate-luminosity radio quasar standard rulers , probing much higher redshifts, could provide comparable constraints on different IDE scenarios. (2) The strong degeneracies between the interaction term and Hubble constant may contribute to alleviate the tension of H {sub 0} between the recent Planck and HST measurements. (3) Concerning the ranking of competing dark energy models, IDE with more free parameters are substantially penalized by the BIC criterion, which agrees very well with the previous results derived from other cosmological probes.« less

Isotropic C6, C8 and C10 interaction coefficients for CH 4, C 2H 6, C 3H 8, n-C 4H 10 and cyclo- C3H 6

NASA Astrophysics Data System (ADS)

Thomas, Gerald F.; Mulder, Fred; Meath, William J.

1980-12-01

The non-empirical generalized Kirkwood, Unsöld, and the single-Δ Unsöld methods (with double-zeta quality SCF wave-functions) are used to calculate isotropic dispersion (and induction) energy coefficients C2n, with n ⩽ 5, for interactions involving ground state CH 4, C 2H 6, C 3H 8, n-C 4H 10 and cyclo-C 3H 6. Results are also given for the related multipole polarizabilities α l, multipole sums S1/(0) and S1(-1) which are evaluated using sum rules, and the permanent multipole moments. for l = 1 (dipole) to l = 3 (octupole). Estimates of the reliability of the non-empirical methods, for the type of molecules considered, are obtained by a comparison with accurate literature values of α 1S1(-1) and C6. This, and the asymptotic properties of the multipolar expansion of the dispersion energy, the use to discuss recommended representation for the isotropic long range interaction energies through R-10 where R is the intermolecular separation.

NREL Supports Innovative Offshore Wind Energy Projects | News | NREL

Science.gov Websites

installation, operation, and maintenance methods for wind turbines located far from shore. Fishermen's Energy will also use the twisted-jacket foundation for the five 5-MW turbines it plans to install 3 miles off about offshore wind and investigate interactions between turbines. Principle Power will install five 6

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

Nesterov, V. A., E-mail: archerix@ukpost.ua

On the basis of the energy-density method, the effect of simultaneously taking into account the Pauli exclusion principle and the monopole and quadrupole polarizations of interacting nuclei on their interaction potential is considered for the example of the {sup 16}O + {sup 16}O system by using the wave function for the two-center shell model. The calculations performed in the adiabatic approximation reveal that the inclusion of the Pauli exclusion principle and the polarization of interacting nuclei, especially their quadrupole polarization, has a substantial effect on the potential of the nucleus-nucleus interaction.

Decomposition of Intermolecular Interactions in the Crystal Structure of Some Diacetyl Platinum(II) Complexes: Combined Hirshfeld, AIM, and NBO Analyses.

PubMed

Soliman, Saied M; Barakat, Assem

2016-12-06

Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM) analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II) complexes. Using AIM and natural bond orbital (NBO) analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance. The electron densities (ρ(r)) at the bond critical points (0.0031-0.0156 e/a₀³) fall within the typical range for H-bonding interactions. Also, the positive values of the Laplacian of the electron density (∇²ρ(r)) revealed the depletion of electronic charge on the interatomic path, another characteristic feature of closed-shell interactions. The ratios of the absolute potential energy density to the kinetic energy density (| V (r)|/ G (r)) and ρ(r) are highest for the O2⋯H15-N3 interaction in [Pt(COMe)₂(2-pyCMe=NNH₂)] (1); hence, this interaction has the highest covalent character of all the O⋯H intermolecular interactions. Interestingly, in [Pt(COMe)₂(H₂NN=CMe-CMe=NNH₂)] (3), there are significant N-H⋯Pt interactions. Using the NBO method, the second-order interaction energies, E (2) , of these interactions range from 3.894 to 4.061 kJ/mol. Furthermore, the hybrid Pt orbitals involved in these interactions are comprised of d xy , d xz , and s atomic orbitals.

GEOPHYSICS, ASTRONOMY AND ASTROPHYSICS: Numerical method of studying nonlinear interactions between long waves and multiple short waves

NASA Astrophysics Data System (ADS)

Xie, Tao; Kuang, Hai-Lan; William, Perrie; Zou, Guang-Hui; Nan, Cheng-Feng; He, Chao; Shen, Tao; Chen, Wei

2009-07-01

Although the nonlinear interactions between a single short gravity wave and a long wave can be solved analytically, the solution is less tractable in more general cases involving multiple short waves. In this work we present a numerical method of studying nonlinear interactions between a long wave and multiple short harmonic waves in infinitely deep water. Specifically, this method is applied to the calculation of the temporal and spatial evolutions of the surface elevations in which a given long wave interacts with several short harmonic waves. Another important application of our method is to quantitatively analyse the nonlinear interactions between an arbitrary short wave train and another short wave train. From simulation results, we obtain that the mechanism for the nonlinear interactions between one short wave train and another short wave train (expressed as wave train 2) leads to the energy focusing of the other short wave train (expressed as wave train 3). This mechanism occurs on wave components with a narrow frequency bandwidth, whose frequencies are near that of wave train 3.

The energy separation between the classical and nonclassical isomers of protonated acetylene - An extensive study in one- and n-particle space saturation

NASA Technical Reports Server (NTRS)

Lindh, Roland; Rice, Julia E.; Lee, Timothy J.

1991-01-01

The energy separation between the classical and nonclassical forms of protonated acetylene has been reinvestigated in light of the recent experimentally deduced lower bound to this value of 6.0 kcal/mol. The objective of the present study is to use state-of-the-art ab initio quantum mechanical methods to establish this energy difference to within chemical accuracy (i.e., about 1 kcal/mol). The one-particle basis sets include up to g-type functions and the electron correlation methods include single and double excitation coupled-cluster (CCSD), the CCSD(T) extension, multireference configuration interaction, and the averaged coupled-pair functional methods. A correction for zero-point vibrational energies has also been included, yielding a best estimate for the energy difference between the classical and nonclassical forms of 3.7 + or - 1.3 kcal/mol.

Exploring the possibility to store the mixed oxygen-hydrogen cluster in clathrate hydrate in molar ratio 1:2 (O2+2H2).

PubMed

Qin, Yan; Du, Qi-Shi; Xie, Neng-Zhong; Li, Jian-Xiu; Huang, Ri-Bo

2017-05-01

An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules. (3) The dimension of O 2 -2H 2 interaction structure is smaller than the dimension of CO 2 -2H 2 interaction structure. (4) The escaping energy of oxygen molecules from the hydrate cell is larger than that of the hydrogen molecules. (5) The high affinity of the oxygen molecules with both the water molecules and the hydrogen molecules may promote the stability of oxygen-hydrogen mixture in the clathrate hydrate. Therefore it is possible to store the mixed (O 2 +2H 2 ) cluster in clathrate hydrate. Copyright © 2017 Elsevier Inc. All rights reserved.

Scanning Synchronization of Colliding Bunches for MEIC Project

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

Derbenev, Yaroslav S.; Popov, V. P.; Chernousov, Yu D.

2015-09-01

Synchronization of colliding beams is one of the major issues of an electron-ion collider (EIC) design because of sensitivity of ion revolution frequency to beam energy. A conventional solution for this trouble is insertion of bent chicanes in the arcs space. In our report we consider a method to provide space coincidence of encountering bunches in the crab-crossing orbits Interaction Region (IR) while repetition rates of two beams do not coincide. The method utilizes pair of fast kickers realizing a bypass for the electron bunches as the way to equalize positions of the colliding bunches at the Interaction Point (IP).more » A dipole-mode warm or SRF cavities fed by the magnetron transmitters are used as fast kickers, allowing a broad-band phase and amplitude control. The proposed scanning synchronization method implies stabilization of luminosity at a maximum via a feedback loop. This synchronization method is evaluated as perspective for the Medium Energy Electron-Ion collider (MEIC) project of JLab with its very high bunch repetition rate.« less

Accurate, precise, and efficient theoretical methods to calculate anion-π interaction energies in model structures.

PubMed

Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Sun, Jianwei

2015-01-13

A correct description of the anion-π interaction is essential for the design of selective anion receptors and channels and important for advances in the field of supramolecular chemistry. However, it is challenging to do accurate, precise, and efficient calculations of this interaction, which are lacking in the literature. In this article, by testing sets of 20 binary anion-π complexes of fluoride, chloride, bromide, nitrate, or carbonate ions with hexafluorobenzene, 1,3,5-trifluorobenzene, 2,4,6-trifluoro-1,3,5-triazine, or 1,3,5-triazine and 30 ternary π-anion-π' sandwich complexes composed from the same monomers, we suggest domain-based local-pair natural orbital coupled cluster energies extrapolated to the complete basis-set limit as reference values. We give a detailed explanation of the origin of anion-π interactions, using the permanent quadrupole moments, static dipole polarizabilities, and electrostatic potential maps. We use symmetry-adapted perturbation theory (SAPT) to calculate the components of the anion-π interaction energies. We examine the performance of the direct random phase approximation (dRPA), the second-order screened exchange (SOSEX), local-pair natural-orbital (LPNO) coupled electron pair approximation (CEPA), and several dispersion-corrected density functionals (including generalized gradient approximation (GGA), meta-GGA, and double hybrid density functional). The LPNO-CEPA/1 results show the best agreement with the reference results. The dRPA method is only slightly less accurate and precise than the LPNO-CEPA/1, but it is considerably more efficient (6-17 times faster) for the binary complexes studied in this paper. For 30 ternary π-anion-π' sandwich complexes, we give dRPA interaction energies as reference values. The double hybrid functionals are much more efficient but less accurate and precise than dRPA. The dispersion-corrected double hybrid PWPB95-D3(BJ) and B2PLYP-D3(BJ) functionals perform better than the GGA and meta-GGA functionals for the present test set.

Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory.

PubMed

Thomas, Andrew S; Elcock, Adrian H

2006-06-21

Proteins and other biomolecules function in cellular environments that contain significant concentrations of dissolved salts and even simple salts such as NaCl can significantly affect both the kinetics and thermodynamics of macromolecular interactions. As one approach to directly observing the effects of salt on molecular associations, explicit-solvent molecular dynamics (MD) simulations have been used here to model the association of pairs of the amino acid analogues acetate and methylammonium in aqueous NaCl solutions of concentrations 0, 0.1, 0.3, 0.5, 1, and 2 M. By performing simulations of 500 ns duration for each salt concentration properly converged estimates of the free energy of interaction of the two molecules have been obtained for all intermolecular separation distances and geometries. The resulting free energy surfaces are shown to give significant new insights into the way salt modulates interactions between molecules containing both charged and hydrophobic groups and are shown to provide valuable new benchmarks for testing the description of salt effects provided by the simpler but faster Poisson-Boltzmann method. In addition, the complex many-dimensional free energy surfaces are shown to be decomposable into a number of one-dimensional effective energy functions. This decomposition (a) allows an unambiguous view of the qualitative differences between the salt dependence of electrostatic and hydrophobic interactions, (b) gives a clear rationalization for why salt exerts different effects on protein-protein association and dissociation rates, and (c) produces simplified energy functions that can be readily used in much faster Brownian dynamics simulations.

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes.

PubMed

Lee, Hochan; Lee, Gayeon; Jeon, Jonggu; Cho, Minhaeng

2012-01-12

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.

An accurate empirical method to predict the adsorption strength for π-orbital contained molecules on two dimensional materials.

PubMed

Li, Hongping; Wang, Changwei; Xun, Suhang; He, Jing; Jiang, Wei; Zhang, Ming; Zhu, Wenshuai; Li, Huaming

2018-06-01

To obtain the adsorption strength is the key point for materials design and parameters optimization in chemical engineering. Here we report a simple but accuracy method to estimate the adsorptive energies by counting the number of π-orbital involved atoms based on theoretical computations for hexagonal boron nitride (h-BN) and graphene. Computational results by density function theory (DFT) as well as spin-component scaled second-order Møller-Plesset perturbation theory (SCS-MP2) both confirm that the adsorptive energies correlate well with the number of π-orbital involved atoms for π-orbital contained molecules. The selected molecules (adsorbates) are commonly used in chemical industry, which contains C, N, S, O atoms. The predicted results for the proposed formulas agree well with the current and previous DFT calculated values both on h-BN and graphene surfaces. Further, it can be also used to predict the adsorptive energies for small π-orbital contained molecules on BN and carbon nanotubes. The interaction type for these adsorptions is typical π-π interaction. Further investigations show that the physical origin of these interactions source from the polar interactions between the adsorbents and adsorbates. Hence, for separation or removal of aromatic molecules, how to modify the aromaticity and polarity of both adsorbents and adsorbates will be the key points for experiments. Copyright © 2018 Elsevier Inc. All rights reserved.

Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation.

PubMed

Irwin, Benedict W J; Huggins, David J

2018-06-12

We present a general method called atom-wise free energy perturbation (AFEP), which extends a conventional molecular dynamics free energy perturbation (FEP) simulation to give the contribution to a free energy change from each atom. AFEP is derived from an expansion of the Zwanzig equation used in the exponential averaging method by defining that the system total energy can be partitioned into contributions from each atom. A partitioning method is assumed and used to group terms in the expansion to correspond to individual atoms. AFEP is applied to six example free energy changes to demonstrate the method. Firstly, the hydration free energies of methane, methanol, methylamine, methanethiol, and caffeine in water. AFEP highlights the atoms in the molecules that interact favorably or unfavorably with water. Finally AFEP is applied to the binding free energy of human immunodeficiency virus type 1 protease to lopinavir, and AFEP reveals the contribution of each atom to the binding free energy, indicating candidate areas of the molecule to improve to produce a more strongly binding inhibitor. FEP gives a single value for the free energy change and is already a very useful method. AFEP gives a free energy change for each "part" of the system being simulated, where part can mean individual atoms, chemical groups, amino acids, or larger partitions depending on what the user is trying to measure. This method should have various applications in molecular dynamics studies of physical, chemical, or biochemical phenomena, specifically in the field of computational drug discovery.

K-edge energy-based calibration method for photon counting detectors

NASA Astrophysics Data System (ADS)

Ge, Yongshuai; Ji, Xu; Zhang, Ran; Li, Ke; Chen, Guang-Hong

2018-01-01

In recent years, potential applications of energy-resolved photon counting detectors (PCDs) in the x-ray medical imaging field have been actively investigated. Unlike conventional x-ray energy integration detectors, PCDs count the number of incident x-ray photons within certain energy windows. For PCDs, the interactions between x-ray photons and photoconductor generate electronic voltage pulse signals. The pulse height of each signal is proportional to the energy of the incident photons. By comparing the pulse height with the preset energy threshold values, x-ray photons with specific energies are recorded and sorted into different energy bins. To quantitatively understand the meaning of the energy threshold values, and thus to assign an absolute energy value to each energy bin, energy calibration is needed to establish the quantitative relationship between the threshold values and the corresponding effective photon energies. In practice, the energy calibration is not always easy, due to the lack of well-calibrated energy references for the working energy range of the PCDs. In this paper, a new method was developed to use the precise knowledge of the characteristic K-edge energy of materials to perform energy calibration. The proposed method was demonstrated using experimental data acquired from three K-edge materials (viz., iodine, gadolinium, and gold) on two different PCDs (Hydra and Flite, XCounter, Sweden). Finally, the proposed energy calibration method was further validated using a radioactive isotope (Am-241) with a known decay energy spectrum.

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns.

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Cieplak, Marek; Maritan, Amos; Fedoroff, Nina V

2006-12-12

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems.

Are Anion/π Interactions Actually a Case of Simple Charge–Dipole Interactions?†

PubMed Central

Wheeler, Steven E.; Houk, K. N.

2011-01-01

Substituent effects in Cl− ••• C6H6−nXn complexes, models for anion/π interactions, have been examined using density functional theory and robust ab initio methods paired with large basis sets. Predicted interaction energies for 83 model Cl− ••• C6H6−nXn complexes span almost 40 kcal mol−1 and show an excellent correlation (r = 0.99) with computed electrostatic potentials. In contrast to prevailing models of anion/π interactions, which rely on substituent-induced changes in the aryl π-system, it is shown that substituent effects in these systems are due mostly to direct interactions between the anion and the substituents. Specifically, interaction energies for Cl− ••• C6H6−nXn complexes are recovered using a model system in which the substituents are isolated from the aromatic ring and π-resonance effects are impossible. Additionally, accurate potential energy curves for Cl− interacting with prototypical anion-binding arenes can be qualitatively reproduced by adding a classical charge–dipole interaction to the Cl− ••• C6H6 interaction potential. In substituted benzenes, binding of anions arises primarily from interactions of the anion with the local dipoles induced by the substituents, not changes in the interaction with the aromatic ring itself. When designing anion-binding motifs, phenyl rings should be viewed as a scaffold upon which appropriate substituents can be placed, because there are no attractive interactions between anions and the aryl π-system of substituted benzenes. PMID:20433187

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

The technology necessary to build net zero energy buildings (NZEBs) is ready and available today, however, building to net zero energy performance levels can be challenging. Energy efficiency measures, onsite energy generation resources, load matching and grid interaction, climatic factors, and local policies vary from location to location and require unique methods of constructing NZEBs. It is recommended that Components start looking into how to construct and operate NZEBs now as there is a learning curve to net zero construction and FY 2020 is just around the corner.

Rapid calculation method for Frenkel-type two-exciton states in one to three dimensions

NASA Astrophysics Data System (ADS)

Ajiki, Hiroshi

2014-07-01

Biexciton and two-exciton dissociated states of Frenkel-type excitons are well described by a tight-binding model with a nearest-neighbor approximation. Such two-exciton states in a finite-size lattice are usually calculated by numerical diagonalization of the Hamiltonian, which requires an increasing amount of computational time and memory as the lattice size increases. I develop here a rapid, memory-saving method to calculate the energies and wave functions of two-exciton states by employing a bisection method. In addition, an attractive interaction between two excitons in the tight-binding model can be obtained directly so that the biexciton energy agrees with the observed energy, without the need for the trial-and-error procedure implemented in the numerical diagonalization method.

A conservation and biophysics guided stochastic approach to refining docked multimeric proteins.

PubMed

Akbal-Delibas, Bahar; Haspel, Nurit

2013-01-01

We introduce a protein docking refinement method that accepts complexes consisting of any number of monomeric units. The method uses a scoring function based on a tight coupling between evolutionary conservation, geometry and physico-chemical interactions. Understanding the role of protein complexes in the basic biology of organisms heavily relies on the detection of protein complexes and their structures. Different computational docking methods are developed for this purpose, however, these methods are often not accurate and their results need to be further refined to improve the geometry and the energy of the resulting complexes. Also, despite the fact that complexes in nature often have more than two monomers, most docking methods focus on dimers since the computational complexity increases exponentially due to the addition of monomeric units. Our results show that the refinement scheme can efficiently handle complexes with more than two monomers by biasing the results towards complexes with native interactions, filtering out false positive results. Our refined complexes have better IRMSDs with respect to the known complexes and lower energies than those initial docked structures. Evolutionary conservation information allows us to bias our results towards possible functional interfaces, and the probabilistic selection scheme helps us to escape local energy minima. We aim to incorporate our refinement method in a larger framework which also enables docking of multimeric complexes given only monomeric structures.

Potential energy surface fitting by a statistically localized, permutationally invariant, local interpolating moving least squares method for the many-body potential: Method and application to N{sub 4}

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

Bender, Jason D.; Doraiswamy, Sriram; Candler, Graham V., E-mail: truhlar@umn.edu, E-mail: candler@aem.umn.edu

2014-02-07

Fitting potential energy surfaces to analytic forms is an important first step for efficient molecular dynamics simulations. Here, we present an improved version of the local interpolating moving least squares method (L-IMLS) for such fitting. Our method has three key improvements. First, pairwise interactions are modeled separately from many-body interactions. Second, permutational invariance is incorporated in the basis functions, using permutationally invariant polynomials in Morse variables, and in the weight functions. Third, computational cost is reduced by statistical localization, in which we statistically correlate the cutoff radius with data point density. We motivate our discussion in this paper with amore » review of global and local least-squares-based fitting methods in one dimension. Then, we develop our method in six dimensions, and we note that it allows the analytic evaluation of gradients, a feature that is important for molecular dynamics. The approach, which we call statistically localized, permutationally invariant, local interpolating moving least squares fitting of the many-body potential (SL-PI-L-IMLS-MP, or, more simply, L-IMLS-G2), is used to fit a potential energy surface to an electronic structure dataset for N{sub 4}. We discuss its performance on the dataset and give directions for further research, including applications to trajectory calculations.« less

Specific energy contributions from competing hydrogen-bonded structures in six polymorphs of phenobarbital.

PubMed

Gelbrich, Thomas; Braun, Doris E; Griesser, Ulrich J

2016-01-01

In solid state structures of organic molecules, identical sets of H-bond donor and acceptor functions can result in a range of distinct H-bond connectivity modes. Specifically, competing H-bond structures (HBSs) may differ in the quantitative proportion between one-point and multiple-point H-bond connections. For an assessment of such HBSs, the effects of their internal as well as external (packing) interactions need to be taken into consideration. The semi-classical density sums (SCDS-PIXEL) method, which enables the calculation of interaction energies for molecule-molecule pairs, was used to investigate six polymorphs of phenobarbital (Pbtl) with different quantitative proportions of one-point and two-point H-bond connections. The structures of polymorphs V and VI of Pbtl were determined from single crystal data. Two-point H-bond connections are inherently inflexible in their geometry and lie within a small PIXEL energy range (-45.7 to -49.7 kJ mol(-1)). One-point H-bond connections are geometrically less restricted and subsequently show large variations in their dispersion terms and total energies (-23.1 to -40.5 kJ mol(-1)). The comparison of sums of interaction energies in small clusters containing only the strongest intermolecular interactions showed an advantage for compact HBSs with multiple-point connections, whereas alternative HBSs based on one-point connections may enable more favourable overall packing interactions (i.e. V vs. III). Energy penalties associated with experimental intramolecular geometries relative to the global conformational energy minimum were calculated and used to correct total PIXEL energies. The estimated order of stabilities (based on PIXEL energies) is III > I > II > VI > X > V, with a difference of just 1.7 kJ mol(-1) between the three most stable forms. For an analysis of competing HBSs, one has to consider the contributions from internal H-bond and non-H-bond interactions, from the packing of multiple HBS instances and intramolecular energy penalties. A compact HBS based on multiple-point H-bond connections should typically lead to more packing alternatives and ultimately to a larger number of viable low-energy structures than a competing one-point HBS (i.e. dimer vs. catemer). Coulombic interaction energies associated with typical short intermolecular C-H···O contact geometries are small in comparison with dispersion effects associated with the packing complementary molecular shapes.Graphical abstractCompeting H-bond motifs can differ markedly in their energy contributions.

Baryon interactions in lattice QCD: the direct method vs. the HAL QCD potential method

NASA Astrophysics Data System (ADS)

Iritani, T.; HAL QCD Collaboration

We make a detailed comparison between the direct method and the HAL QCD potential method for the baryon-baryon interactions, taking the $\\Xi\\Xi$ system at $m_\\pi= 0.51$ GeV in 2+1 flavor QCD and using both smeared and wall quark sources. The energy shift $\\Delta E_\\mathrm{eff}(t)$ in the direct method shows the strong dependence on the choice of quark source operators, which means that the results with either (or both) source are false. The time-dependent HAL QCD method, on the other hand, gives the quark source independent $\\Xi\\Xi$ potential, thanks to the derivative expansion of the potential, which absorbs the source dependence to the next leading order correction. The HAL QCD potential predicts the absence of the bound state in the $\\Xi\\Xi$($^1$S$_0$) channel at $m_\\pi= 0.51$ GeV, which is also confirmed by the volume dependence of finite volume energy from the potential. We also demonstrate that the origin of the fake plateau in the effective energy shift $\\Delta E_\\mathrm{eff}(t)$ at $t \\sim 1$ fm can be clarified by a few low-lying eigenfunctions and eigenvalues on the finite volume derived from the HAL QCD potential, which implies that the ground state saturation of $\\Xi\\Xi$($^1$S$_0$) requires $t \\sim 10$ fm in the direct method for the smeared source on $(4.3 \\ \\mathrm{fm})^3$ lattice, while the HAL QCD method does not suffer from such a problem.

Understanding AuNP interaction with low-generation PAMAM dendrimers: a CIELab and deconvolution study

NASA Astrophysics Data System (ADS)

Jimenez-Ruiz, A.; Carnerero, J. M.; Castillo, P. M.; Prado-Gotor, R.

2017-01-01

Low-generation polyamidoamine (PAMAM) dendrimers are known to adsorb on the surface of gold nanoparticles (AuNPs) causing aggregation and color changes. In this paper, a thorough study of this affinity using absorption spectroscopy, colorimetric, and emission methods has been carried out. Results show that, for citrate-capped gold nanoparticles, interaction with the dendrimer is not only of an electrostatic character but instead occurs, at least in part, through the dendrimer's uncharged internal amino groups. The possibilities of the CIELab chromaticity system parameters' evolution have also been explored in order to quantify dendrimer interaction with the red-colored nanoparticles. By measuring and quantifying 17 nm citrate-capped AuNP color changes, which are strongly dependant on their aggregation state, binding free energies are obtained for the first time for these systems. Results are confirmed via an alternate fitting method which makes use of deconvolution parameters from absorbance spectra. Binding free energies obtained through the use of both means are in good agreement with each other.

Electric-field-induced modification in Curie temperature of Co monolayer on Pt(111)

NASA Astrophysics Data System (ADS)

Nakamura, Kohji; Oba, Mikito; Akiyama, Toru; Ito, Tomonori; Weinert, Michael

2015-03-01

Magnetism induced by an external electric field (E-field) has received much attention as a potential approach for controlling magnetism at the nano-scale with the promise of ultra-low energy power consumption. Here, the E-field-induced modification of the Curie temperature for a prototypical transition-metal thin layer of a Co monolayer on Pt(111) is investigated by first-principles calculations by using the full-potential linearized augmented plane wave method that treats spin-spiral structures in an E-field. An applied E-field modifies the magnon (spin-spiral formation) energies by a few meV, which leads to a modification of the exchange pair interaction parameters within the classical Heisenberg model. With inclusion of the spin-orbit coupling (SOC), the magnetocrystalline anisotropy and the Dzyaloshinskii-Morita interaction are obtained by the second variation SOC method. An E-field-induced modification of the Curie temperature is demonstrated by Monte Carlo simulations, in which a change in the exchange interaction is found to play a key role.

A density functional theory study on the interactions between dibenzothiophene and tetrafluoroborate-based ionic liquids.

PubMed

Lin, Jin; Lü, Renqing; Wu, Chongchong; Xiao, Ye; Liang, Fei; Famakinwa, Temilola

2017-04-01

The interactions between dibenzothiophene (DBT) and N-butyl-N-methylimidazolium tetrafluoroborate ([BMIM][BF 4 ]), N-butyl-N-methylmorpholinium tetrafluoroborate ([Bmmorpholinium][BF 4 ]), N-butyl-N-methylpiperdinium tetrafluoroborate ([BMPiper][BF 4 ]), N-butyl-N-methylpyrrolidinium tetrafluoroborate ([BMPyrro][BF 4 ]), and N-butylpyridinium tetrafluoroborate ([BPY][BF 4 ]) were investigated using density functional theory approach. Geometric, electron, and topological properties were analyzed using natural bond orbital, atoms in molecules theory, and noncovalent interaction methods in order to understand intermolecular interactions between DBT and ionic liquids. The result shows that hydrogen bond and van der Waals interactions are widespread in all the ionic liquids-DBT systems. Ion-π interactions between DBT and cation or anion are also observed, while π + -π interactions are only found in the [BMIM][BF 4 ]-DBT and [BPY][BF 4 ]-DBT systems. The order of interaction energy is [BPY][BF4]-DBT > [BMIM][BF 4 ]-DBT > [BMPiper][BF 4 ]-DBT > [BMPyrro][BF 4 ]-DBT > [BMmorpholinum][BF 4 ]-DBT. The energies between DBT and the two ionic liquids containing aromatic cations are significantly higher.

Light-Nuclei Spectra from Chiral Dynamics

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

Piarulli, M.; Baroni, A.; Girlanda, L.

In recent years local chiral interactions have been derived and implemented in quantum Monte Carlo methods in order to test to what extent the chiral effective field theory framework impacts our knowledge of few- and many-body systems. Here in this Letter, we present Green’s function Monte Carlo calculations of light nuclei based on the family of local two-body interactions presented by our group in a previous paper in conjunction with chiral three-body interactions fitted to bound- and scattering-state observables in the three-nucleon sector. These interactions include Δ intermediate states in their two-pion-exchange components. We obtain predictions for the energy levelsmore » and level ordering of nuclei in the mass range A=4–12, accurate to ≤2% of the binding energy, in very satisfactory agreement with experimental data.« less

Light-Nuclei Spectra from Chiral Dynamics

DOE PAGES

Piarulli, M.; Baroni, A.; Girlanda, L.; ...

2018-02-01

In recent years local chiral interactions have been derived and implemented in quantum Monte Carlo methods in order to test to what extent the chiral effective field theory framework impacts our knowledge of few- and many-body systems. Here in this Letter, we present Green’s function Monte Carlo calculations of light nuclei based on the family of local two-body interactions presented by our group in a previous paper in conjunction with chiral three-body interactions fitted to bound- and scattering-state observables in the three-nucleon sector. These interactions include Δ intermediate states in their two-pion-exchange components. We obtain predictions for the energy levelsmore » and level ordering of nuclei in the mass range A=4–12, accurate to ≤2% of the binding energy, in very satisfactory agreement with experimental data.« less

A low-dispersion, exactly energy-charge-conserving semi-implicit relativistic particle-in-cell algorithm

NASA Astrophysics Data System (ADS)

Chen, Guangye; Luis, Chacon; Bird, Robert; Stark, David; Yin, Lin; Albright, Brian

2017-10-01

Leap-frog based explicit algorithms, either ``energy-conserving'' or ``momentum-conserving'', do not conserve energy discretely. Time-centered fully implicit algorithms can conserve discrete energy exactly, but introduce large dispersion errors in the light-wave modes, regardless of timestep sizes. This can lead to intolerable simulation errors where highly accurate light propagation is needed (e.g. laser-plasma interactions, LPI). In this study, we selectively combine the leap-frog and Crank-Nicolson methods to produce a low-dispersion, exactly energy-and-charge-conserving PIC algorithm. Specifically, we employ the leap-frog method for Maxwell equations, and the Crank-Nicolson method for particle equations. Such an algorithm admits exact global energy conservation, exact local charge conservation, and preserves the dispersion properties of the leap-frog method for the light wave. The algorithm has been implemented in a code named iVPIC, based on the VPIC code developed at LANL. We will present numerical results that demonstrate the properties of the scheme with sample test problems (e.g. Weibel instability run for 107 timesteps, and LPI applications.

Discrete Variational Approach for Modeling Laser-Plasma Interactions

NASA Astrophysics Data System (ADS)

Reyes, J. Paxon; Shadwick, B. A.

2014-10-01

The traditional approach for fluid models of laser-plasma interactions begins by approximating fields and derivatives on a grid in space and time, leading to difference equations that are manipulated to create a time-advance algorithm. In contrast, by introducing the spatial discretization at the level of the action, the resulting Euler-Lagrange equations have particular differencing approximations that will exactly satisfy discrete versions of the relevant conservation laws. For example, applying a spatial discretization in the Lagrangian density leads to continuous-time, discrete-space equations and exact energy conservation regardless of the spatial grid resolution. We compare the results of two discrete variational methods using the variational principles from Chen and Sudan and Brizard. Since the fluid system conserves energy and momentum, the relative errors in these conserved quantities are well-motivated physically as figures of merit for a particular method. This work was supported by the U. S. Department of Energy under Contract No. DE-SC0008382 and by the National Science Foundation under Contract No. PHY-1104683.

Picking a Fight with Water, and Water Lost ... an Electron

NASA Astrophysics Data System (ADS)

Herr, Jonathan D.

The global need for energy is increasing, as is the importance of producing energy by green and renewable methodologies. This document outlines a research program dedicated to investigating a possible source for this form of energy generation and storage: solar fuels. The photon-induced splitting of water into molecular hydrogen and oxygen is currently hindered by large overpotentials from the oxidation half-reaction of water-splitting. This study concentrated on fundamental models of water-spitting chemistry, using a physical and computational chemistry analysis. The oxidation was first explored via ab initio electronic structure calculations of bare cationic water clusters, comprised of 2 to 21 molecules, in order to determine key electronic interactions that facilitate oxidation. Deeper understanding of these interactions could serve as guides for the development of viable water oxidation catalysts (WOC) designed to reduce overpotentials. The cationic water cluster study was followed by an investigation into hydrated copper (I) clusters, which acted as precursor models for real WOCs. Analyzing how the copper ion perturbed the properties of water clusters led to important electronic considerations for the development of WOCs, such as copper-water interactions that go beyond simple electrostatics. The importance of diagnostic thermodynamic properties, as well as anharmonic characteristics being persistent throughout oxidized water clusters, necessitated the use of quantum and classical molecular dynamics (MD) routines. Therefore, two new methods for accelerating computationally demanding classical and quantum MD methods were developed to increase their accessibility. The first method utilized a new form of electronic extrapolation - a linear prediction routine incorporating a Burg minimization - to decrease the iterations required for solving the electronic equations throughout the dynamics. The second method utilized a multiple-timestepping description of the potential energy term in the path integral molecular dynamics (PIMD) formalism. This method led to reductions of computational time by allowing the use of less computationally laborious methods for portions of the simulation and resulted in negligible increase of error. The determination of the fundamental driving forces within water oxidation and the development of acceleration techniques for important electronic structure methods will help drive progress into fully solar-initiated water oxidation.

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures.

PubMed

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; Tohyama, Takami

2018-04-01

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003)PRBMDO0163-182910.1103/PhysRevB.68.235106] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013)PRLTAO0031-900710.1103/PhysRevLett.111.010401] to obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S=1/2, we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures

NASA Astrophysics Data System (ADS)

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; Tohyama, Takami

2018-04-01

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003), 10.1103/PhysRevB.68.235106] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013), 10.1103/PhysRevLett.111.010401] to obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S =1 /2 , we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.

Nonparametric Determination of Redshift Evolution Index of Dark Energy

NASA Astrophysics Data System (ADS)

Ziaeepour, Houri

We propose a nonparametric method to determine the sign of γ — the redshift evolution index of dark energy. This is important for distinguishing between positive energy models, a cosmological constant, and what is generally called ghost models. Our method is based on geometrical properties and is more tolerant to uncertainties of other cosmological parameters than fitting methods in what concerns the sign of γ. The same parametrization can also be used for determining γ and its redshift dependence by fitting. We apply this method to SNLS supernovae and to gold sample of re-analyzed supernovae data from Riess et al. Both datasets show strong indication of a negative γ. If this result is confirmed by more extended and precise data, many of the dark energy models, including simple cosmological constant, standard quintessence models without interaction between quintessence scalar field(s) and matter, and scaling models are ruled out. We have also applied this method to Gurzadyan-Xue models with varying fundamental constants to demonstrate the possibility of using it to test other cosmologies.

Halo independent comparison of direct dark matter detection data

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

Gondolo, Paolo; Gelmini, Graciela B., E-mail: paolo@physics.utah.edu, E-mail: gelmini@physics.ucla.edu

We extend the halo-independent method of Fox, Liu, and Weiner to include energy resolution and efficiency with arbitrary energy dependence, making it more suitable for experiments to use in presenting their results. Then we compare measurements and upper limits on the direct detection of low mass ( ∼ 10 GeV) weakly interacting massive particles with spin-independent interactions, including the upper limit on the annual modulation amplitude from the CDMS collaboration. We find that isospin-symmetric couplings are severely constrained both by XENON100 and CDMS bounds, and that isospin-violating couplings are still possible at the lowest energies, while the tension of themore » higher energy CoGeNT bins with the CDMS modulation constraint remains. We find the CRESST-II signal is not compatible with the modulation signals of DAMA and CoGeNT.« less

Interactions in hydrogen of relativistic neon to nickel projectiles: Total charge-changing cross sections

NASA Astrophysics Data System (ADS)

Chen, C.-X.; Albergo, S.; Caccia, Z.; Costa, S.; Crawford, H. J.; Cronqvist, M.; Engelage, J.; Ferrando, P.; Fonte, R.; Greiner, L.; Guzik, T. G.; Insolia, A.; Jones, F. C.; Knott, C. N.; Lindstrom, P. J.; Mitchell, J. W.; Potenza, R.; Romanski, J.; Russo, G. V.; Soutoul, A.; Testard, O.; Tull, C. E.; Tuvé, C.; Waddington, C. J.; Webber, W. R.; Wefel, J. P.; Zhang, X.

1994-06-01

A liquid hydrogen target was used to study the nuclear fragmentation of beams of relativistic heavy ions, 22Ne to 58Ni, over an energy range 400 to 900 MeV/nucleon. The experiments were carried out at the Lawrence Berkeley Laboratory Bevalac HISS facility, using the charge-velocity-rigidity method to identify the charged fragments. Here we describe the general concept of the experiment and present total charge-changing cross sections obtained from 17 separate runs. These new measured cross sections display an energy dependence which follows semiempirical model predictions. The mass dependence of the cross sections behaves as predicted by optical models, but within the experimental energy range, the optical model parameters display a clear energy dependence. The isospin of the projectile nuclei also appears to be an important factor in the interaction process.

Dynamics of the diffusive DM-DE interaction – Dynamical system approach

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

Haba, Zbigniew; Stachowski, Aleksander; Szydłowski, Marek, E-mail: zhab@ift.uni.wroc.pl, E-mail: aleksander.stachowski@uj.edu.pl, E-mail: marek.szydlowski@uj.edu.pl

We discuss dynamics of a model of an energy transfer between dark energy (DE) and dark matter (DM) . The energy transfer is determined by a non-conservation law resulting from a diffusion of dark matter in an environment of dark energy. The relativistic invariance defines the diffusion in a unique way. The system can contain baryonic matter and radiation which do not interact with the dark sector. We treat the Friedman equation and the conservation laws as a closed dynamical system. The dynamics of the model is examined using the dynamical systems methods for demonstration how solutions depend on initialmore » conditions. We also fit the model parameters using astronomical observation: SNIa, H ( z ), BAO and Alcock-Paczynski test. We show that the model with diffuse DM-DE is consistent with the data.« less

Charge separation at nanoscale interfaces: energy-level alignment including two-quasiparticle interactions.

PubMed

Li, Huashan; Lin, Zhibin; Lusk, Mark T; Wu, Zhigang

2014-10-21

The universal and fundamental criteria for charge separation at interfaces involving nanoscale materials are investigated. In addition to the single-quasiparticle excitation, all the two-quasiparticle effects including exciton binding, Coulomb stabilization, and exciton transfer are considered, which play critical roles on nanoscale interfaces for optoelectronic applications. We propose a scheme allowing adding these two-quasiparticle interactions on top of the single-quasiparticle energy level alignment for determining and illuminating charge separation at nanoscale interfaces. Employing the many-body perturbation theory based on Green's functions, we quantitatively demonstrate that neglecting or simplifying these crucial two-quasiparticle interactions using less accurate methods is likely to predict qualitatively incorrect charge separation behaviors at nanoscale interfaces where quantum confinement dominates.

Simulations of Coulomb systems confined by polarizable surfaces using periodic Green functions.

PubMed

Dos Santos, Alexandre P; Girotto, Matheus; Levin, Yan

2017-11-14

We present an efficient approach for simulating Coulomb systems confined by planar polarizable surfaces. The method is based on the solution of the Poisson equation using periodic Green functions. It is shown that the electrostatic energy arising from the surface polarization can be decoupled from the energy due to the direct Coulomb interaction between the ions. This allows us to combine an efficient Ewald summation method, or any other fast method for summing over the replicas, with the polarization contribution calculated using Green function techniques. We apply the method to calculate density profiles of ions confined between the charged dielectric and metal surfaces.

Effects of particle size and adaptation duration on the digestible and metabolizable energy contents and digestibility of various chemical constituents in wheat for finishing pigs determined by the direct or indirect method.

PubMed

Fan, Yuanfang; Guo, Panpan; Yang, Yuyuan; Xia, Tian; Liu, Ling; Ma, Yongxi

2017-04-01

This experiment was conducted as a 3×2×2 factorial design to examine the effects of particle size (mean particle size of 331, 640, or 862 μm), evaluation method (direct vs indirect method) and adaptation duration (7 or 26 days) on the energy content and the apparent total tract digestibility (ATTD) of various chemical components in wheat when fed to finishing pigs. Forty-two barrows (Duroc×Landrace×Yorkshire) with an initial body weight of 63.0±0.8 kg were individually placed in metabolic cages and randomly allotted to 1 of 7 diets with 6 pigs fed each diet. For the indirect method, the pigs were fed either a corn-soybean meal based basal diet or diets in which 38.94% of the basal diet was substituted by wheat of the different particle sizes. In the direct method, the diets contained 97.34% wheat with the different particle sizes. For both the direct and indirect methods, the pigs were adapted to their diets for either 7 or 26 days. A reduction in particle size linearly increased the digestible energy (DE) and metabolizable energy (ME) contents as well as the ATTD of gross energy, crude protein, organic matter, ether extract (EE) and acid detergent fiber (ADF) (p<0.05), and had a trend to increase the ATTD of dry matter of wheat (p = 0.084). The DE, ME contents, and ATTD of gross energy, crude protein, dry matter and organic matter were higher (p<0.05) when determined by the direct method, but the ATTD of ADF, EE, and neutral detergent fiber were higher when determined by the indirect method (p<0.05). Prolongation of the adaption duration decreased the ATTD of neutral detergent fiber (p<0.05) and had a trend to increase the ATTD of EE (p = 0.061). There were no interactions between particle size and the duration of the adaptation duration. The ATTD of EE in wheat was influenced by a trend of interaction between method and adaptation duration (p = 0.074). The ATTD of ADF and EE in wheat was influenced by an interaction between evaluation method and wheat particle size such that there were linear equations (p<0.01) about ATTD of ADF and EE when determined by the direct method but quadratic equations (p = 0.073 and p = 0.088, respectively) about ATTD of ADF and EE when determined by the indirect method. Decreasing particle size can improve the DE and ME contents of wheat; both of the direct and indirect methods of evaluation are suitable for evaluating the DE and ME contents of wheat with different particle sizes; and an adaptation duration of 7 d is sufficient to evaluate DE and ME contents of wheat in finishing pigs.

Density functional theory calculations of the water interactions with ZrO2 nanoparticles Y2O3 doped

NASA Astrophysics Data System (ADS)

Subhoni, Mekhrdod; Kholmurodov, Kholmirzo; Doroshkevich, Aleksandr; Asgerov, Elmar; Yamamoto, Tomoyuki; Lyubchyk, Andrei; Almasan, Valer; Madadzada, Afag

2018-03-01

Development of a new electricity generation techniques is one of the most relevant tasks, especially nowadays under conditions of extreme growth in energy consumption. The exothermic heterogeneous electrochemical energy conversion to the electric energy through interaction of the ZrO2 based nanopowder system with atmospheric moisture is one of the ways of electric energy obtaining. The questions of conversion into the electric form of the energy of water molecules adsorption in 3 mol% Y2O3 doped ZrO2 nanopowder systems were investigated using the density functional theory calculations. The density functional theory calculations has been realized as in the Kohn-Sham formulation, where the exchange-correlation potential is approximated by a functional of the electronic density. The electronic density, total energy and band structure calculations are carried out using the all-electron, full potential, linear augmented plane wave method of the electronic density and related approximations, i.e. the local density, the generalized gradient and their hybrid approximations.

Imaging energy landscapes with concentrated diffusing colloidal probes

NASA Astrophysics Data System (ADS)

Bahukudumbi, Pradipkumar; Bevan, Michael A.

2007-06-01

The ability to locally interrogate interactions between particles and energetically patterned surfaces provides essential information to design, control, and optimize template directed self-assembly processes. Although numerous techniques are capable of characterizing local physicochemical surface properties, no current method resolves interactions between colloids and patterned surfaces on the order of the thermal energy kT, which is the inherent energy scale of equilibrium self-assembly processes. Here, the authors describe video microscopy measurements and an inverse Monte Carlo analysis of diffusing colloidal probes as a means to image three dimensional free energy and potential energy landscapes due to physically patterned surfaces. In addition, they also develop a consistent analysis of self-diffusion in inhomogeneous fluids of concentrated diffusing probes on energy landscapes, which is important to the temporal imaging process and to self-assembly kinetics. Extension of the concepts developed in this work suggests a general strategy to image multidimensional and multiscale physical, chemical, and biological surfaces using a variety of diffusing probes (i.e., molecules, macromolecules, nanoparticles, and colloids).

Tunneling of coupled methyl quantum rotors in 4-methylpyridine: Single rotor potential versus coupling interaction

NASA Astrophysics Data System (ADS)

Khazaei, Somayeh; Sebastiani, Daniel

2017-11-01

We study the influence of rotational coupling between a pair of methyl rotators on the tunneling spectrum in condensed phase. Two interacting adjacent methyl groups are simulated within a coupled-pair model composed of static rotational potential created by the chemical environment and the interaction potential between two methyl groups. We solve the two-dimensional time-independent Schrödinger equation analytically by expanding the wave functions on the basis set of two independent free-rotor functions. We investigate three scenarios which differ with respect to the relative strength of single-rotor and coupling potential. For each scenario, we illustrate the dependence of the energy level scheme on the coupling strength. It is found that the main determinant of splitting energy levels tends to be a function of the ratio of strengths of coupling and single-rotor potential. The tunnel splitting caused by coupling is maximized for the coupled rotors in which their total hindering potential is relatively shallow. Such a weakly hindered methyl rotational potential is predicted for 4-methylpyridine at low temperature. The experimental observation of multiple tunneling peaks arising from a single type of methyl group in 4-methylpyridine in the inelastic neutron scattering spectrum is widely attributed to the rotor-rotor coupling. In this regard, using a set of first-principles calculations combined with the nudged elastic band method, we investigate the rotational potential energy surface (PES) of the coaxial pairs of rotors in 4-methylpyridine. A Numerov-type method is used to numerically solve the two-dimensional time-independent Schrödinger equation for the calculated 2D-density functional theory profile. Our computed energy levels reproduce the observed tunneling transitions well. Moreover, the calculated density distribution of the three methyl protons resembles the experimental nuclear densities obtained from the Fourier difference method. By mapping the calculated first-principles PES on the model, it is confirmed that the hindering potential in 4-methylpyridine consists of proportionally shallow single-rotor potential to coupling interaction.

Tunneling of coupled methyl quantum rotors in 4-methylpyridine: Single rotor potential versus coupling interaction.

PubMed

Khazaei, Somayeh; Sebastiani, Daniel

2017-11-21

We study the influence of rotational coupling between a pair of methyl rotators on the tunneling spectrum in condensed phase. Two interacting adjacent methyl groups are simulated within a coupled-pair model composed of static rotational potential created by the chemical environment and the interaction potential between two methyl groups. We solve the two-dimensional time-independent Schrödinger equation analytically by expanding the wave functions on the basis set of two independent free-rotor functions. We investigate three scenarios which differ with respect to the relative strength of single-rotor and coupling potential. For each scenario, we illustrate the dependence of the energy level scheme on the coupling strength. It is found that the main determinant of splitting energy levels tends to be a function of the ratio of strengths of coupling and single-rotor potential. The tunnel splitting caused by coupling is maximized for the coupled rotors in which their total hindering potential is relatively shallow. Such a weakly hindered methyl rotational potential is predicted for 4-methylpyridine at low temperature. The experimental observation of multiple tunneling peaks arising from a single type of methyl group in 4-methylpyridine in the inelastic neutron scattering spectrum is widely attributed to the rotor-rotor coupling. In this regard, using a set of first-principles calculations combined with the nudged elastic band method, we investigate the rotational potential energy surface (PES) of the coaxial pairs of rotors in 4-methylpyridine. A Numerov-type method is used to numerically solve the two-dimensional time-independent Schrödinger equation for the calculated 2D-density functional theory profile. Our computed energy levels reproduce the observed tunneling transitions well. Moreover, the calculated density distribution of the three methyl protons resembles the experimental nuclear densities obtained from the Fourier difference method. By mapping the calculated first-principles PES on the model, it is confirmed that the hindering potential in 4-methylpyridine consists of proportionally shallow single-rotor potential to coupling interaction.

Obtaining source current density related to irregularly structured electromagnetic target field inside human body using hybrid inverse/FDTD method.

PubMed

Han, Jijun; Yang, Deqiang; Sun, Houjun; Xin, Sherman Xuegang

2017-01-01

Inverse method is inherently suitable for calculating the distribution of source current density related with an irregularly structured electromagnetic target field. However, the present form of inverse method cannot calculate complex field-tissue interactions. A novel hybrid inverse/finite-difference time domain (FDTD) method that can calculate the complex field-tissue interactions for the inverse design of source current density related with an irregularly structured electromagnetic target field is proposed. A Huygens' equivalent surface is established as a bridge to combine the inverse and FDTD method. Distribution of the radiofrequency (RF) magnetic field on the Huygens' equivalent surface is obtained using the FDTD method by considering the complex field-tissue interactions within the human body model. The obtained magnetic field distributed on the Huygens' equivalent surface is regarded as the next target. The current density on the designated source surface is derived using the inverse method. The homogeneity of target magnetic field and specific energy absorption rate are calculated to verify the proposed method.

Efficient and Robust Optimization for Building Energy Simulation

PubMed Central

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-01-01

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell’s Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell’s method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell’s Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell’s Hybrid method presently used in HVACSIM+. PMID:27325907

Efficient and Robust Optimization for Building Energy Simulation.

PubMed

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-06-15

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell's Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell's method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell's Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell's Hybrid method presently used in HVACSIM+.

Forster resonance energy transfer in the system of human serum albumin-xanthene dyes

NASA Astrophysics Data System (ADS)

Kochubey, V. I.; Pravdin, A. B.; Melnikov, A. G.; Konstantinova, I.; Alonova, I. V.

2016-04-01

The processes of interaction of fluorescent probes: eosin and erythrosine with human serum albumin (HSA) were studied by the methods of absorption and fluorescence spectroscopy. Extinction coefficients of probes were determined. Critical transfer radius and the energy transfer efficiency were defined by fluorescence quenching of HSA. Analysis of the excitation spectra of HSA revealed that the energy transfer process is carried out mainly between tryptophanyl and probes.

Potential energy distribution (PED) analysis of DFT calculated IR spectra of the most stable Li, Na, and Cu(I) diformate molecules

NASA Astrophysics Data System (ADS)

Jamróz, M. H.; Dobrowolski, J. Cz.

2001-05-01

For the most stable Li, Na, and Cu(I) diformates we present the vibrational spectra, supported by potential energy distribution (PED) analysis, and the interaction energies between formic acid and metal formate by the DFT (B3PW91) method. PED analysis of the theoretical spectra forms the basis for the elucidation of the future matrix isolation IR spectra.

Interaction of repetitively pulsed high energy laser radiation with matter

NASA Astrophysics Data System (ADS)

Hugenschmidt, M.

1986-05-01

Laser target interaction processes and methods of improving the overall energy balance are discussed. This can be achieved with high repetition rate pulsed lasers even for initially highly reflecting materials, such as metals. Experiments were performed using a pulsed CO2 laser at mean powers up to 2 KW and repetition rates up to 100 Hz. The rates of temperature rise of aluminum for example are increased by more than a factor of 3 as compared to cw-radiation of comparable power density. Similar improvements are found for the overall absorptivities, that are increased by more than an order of magnitude.

Neutron range spectrometer

DOEpatents

Manglos, S.H.

1988-03-10

A neutron range spectrometer and method for determining the neutron energy spectrum of a neutron emitting source are disclosed. Neutrons from the source are colliminated along a collimation axis and a position sensitive neutron counter is disposed in the path of the collimated neutron beam. The counter determines positions along the collimation axis of interactions between the neutrons in the neutron beam and a neutron-absorbing material in the counter. From the interaction positions, a computer analyzes the data and determines the neutron energy spectrum of the neutron beam. The counter is preferably shielded and a suitable neutron-absorbing material is He-3. 1 fig.

Approximation method for a spherical bound system in the quantum plasma

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

Mehramiz, A.; Sobhanian, S.; Mahmoodi, J.

2010-08-15

A system of quantum hydrodynamic equations has been used for investigating the dielectric tensor and dispersion equation of a semiconductor as a quantum magnetized plasma. Dispersion relations and their modifications due to quantum effects are derived for both longitudinal and transverse waves. The number of states and energy levels are analytically estimated for a spherical bound system embedded in a semiconductor quantum plasma. The results show that longitudinal waves decay rapidly and do not interact with the spherical bound system. The energy shifts caused by the spin-orbit interaction and the Zeeman effect are calculated.

Thomas-Fermi simulations of dense plasmas without pseudopotentials

NASA Astrophysics Data System (ADS)

Starrett, C. E.

2017-07-01

The Thomas-Fermi model for warm and hot dense matter is widely used to predict material properties such as the equation of state. However, for practical reasons current implementations use pseudopotentials for the electron-nucleus interaction instead of the bare Coulomb potential. This complicates the calculation and quantities such as free energy cannot be converged with respect to the pseudopotential parameters. We present a method that retains the bare Coulomb potential for the electron-nucleus interaction and does not use pseudopotentials. We demonstrate that accurate free energies are obtained by checking variational consistency. Examples for aluminum and iron plasmas are presented.

Computed secondary-particle energy spectra following nonelastic neutron interactions with sup 12 C for E sub n between 15 and 60 MeV: Comparisons of results from two calculational methods

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

Dickens, J.K.

1991-04-01

The organic scintillation detector response code SCINFUL has been used to compute secondary-particle energy spectra, d{sigma}/dE, following nonelastic neutron interactions with {sup 12}C for incident neutron energies between 15 and 60 MeV. The resulting spectra are compared with published similar spectra computed by Brenner and Prael who used an intranuclear cascade code, including alpha clustering, a particle pickup mechanism, and a theoretical approach to sequential decay via intermediate particle-unstable states. The similarities of and the differences between the results of the two approaches are discussed. 16 refs., 44 figs., 2 tabs.

Constraining the surface properties of effective Skyrme interactions

NASA Astrophysics Data System (ADS)

Jodon, R.; Bender, M.; Bennaceur, K.; Meyer, J.

2016-08-01

Background: Deformation energy surfaces map how the total binding energy of a nuclear system depends on the geometrical properties of intrinsic configurations, thereby providing a powerful tool to interpret nuclear spectroscopy and large-amplitude collective-motion phenomena such as fission. The global behavior of the deformation energy is known to be directly connected to the surface properties of the effective interaction used for its calculation. Purpose: The precise control of surface properties during the parameter adjustment of an effective interaction is key to obtain a reliable and predictive description of nuclear properties. The most relevant indicator is the surface-energy coefficient asurf. There are several possibilities for its definition and estimation, which are not fully equivalent and require a computational effort that can differ by orders of magnitude. The purpose of this study is threefold: first, to identify a scheme for the determination of asurf that offers the best compromise between robustness, precision, and numerical efficiency; second, to analyze the correlation between values for asurf and the characteristic energies of the fission barrier of 240Pu; and third, to lay out an efficient and robust procedure for how the deformation properties of the Skyrme energy density functional (EDF) can be constrained during the parameter fit. Methods: There are several frequently used possibilities to define and calculate the surface energy coefficient asurf of effective interactions built for the purpose of self-consistent mean-field calculations. The most direct access is provided by the model system of semi-infinite nuclear matter, but asurf can also be extracted from the systematics of binding energies of finite nuclei. Calculations can be carried out either self-consistently [Hartree-Fock (HF)], which incorporates quantal shell effects, or in one of the semiclassical extended Thomas-Fermi (ETF) or modified Thomas-Fermi (MTF) approximations. The latter is of particular interest because it provides asurf as a numerical integral without the need to solve self-consistent equations. Results for semi-infinite nuclear matter obtained with the HF, ETF, and MTF methods will be compared with one another and with asurf, as deduced from ETF calculations of very heavy fictitious nuclei. Results: The surface energy coefficient of 76 parametrizations of the Skyrme EDF have been calculated. Values obtained with the HF, ETF, and MTF methods are not identical, but differ by fairly constant systematic offsets. By contrast, extracting asurf from the binding energy of semi-infinite matter or of very large nuclei within the same method gives the same result within the numerical uncertainties. Conclusions: Despite having some drawbacks compared to the other methods studied here, the MTF approach provides sufficiently precise values for asurf such that it can be used as a very robust constraint on surface properties during a parameter fit at negligible additional cost. While the excitation energy of superdeformed states and the height of fission barriers is obviously strongly correlated to asurf, the presence of shell effects prevents a one-to-one correspondence between them. As in addition the value of asurf providing realistic fission barriers depends on the choices made for corrections for spurious motion, its "best value" (within a given scheme to calculate it) depends on the fit protocol. Through the construction of a series of eight parametrizations SLy5s1-SLy5s8 of the standard Skyrme EDF with systematically varied asurf value, it is shown how to arrive at a fit with realistic deformation properties.

Predicting helix orientation for coiled-coil dimers

PubMed Central

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

2008-01-01

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

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

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F., E-mail: Manuel.Ruiz@univ-lorraine.fr

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering themore » potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.« less

An Interactive Image Segmentation Method in Hand Gesture Recognition

PubMed Central

Chen, Disi; Li, Gongfa; Sun, Ying; Kong, Jianyi; Jiang, Guozhang; Tang, Heng; Ju, Zhaojie; Yu, Hui; Liu, Honghai

2017-01-01

In order to improve the recognition rate of hand gestures a new interactive image segmentation method for hand gesture recognition is presented, and popular methods, e.g., Graph cut, Random walker, Interactive image segmentation using geodesic star convexity, are studied in this article. The Gaussian Mixture Model was employed for image modelling and the iteration of Expectation Maximum algorithm learns the parameters of Gaussian Mixture Model. We apply a Gibbs random field to the image segmentation and minimize the Gibbs Energy using Min-cut theorem to find the optimal segmentation. The segmentation result of our method is tested on an image dataset and compared with other methods by estimating the region accuracy and boundary accuracy. Finally five kinds of hand gestures in different backgrounds are tested on our experimental platform, and the sparse representation algorithm is used, proving that the segmentation of hand gesture images helps to improve the recognition accuracy. PMID:28134818

Understanding the interactions of human follicle stimulating hormone with single-walled carbon nanotubes by molecular dynamics simulation and free energy analysis.

PubMed

Mahmoodi, Yasaman; Mehrnejad, Faramarz; Khalifeh, Khosrow

2018-01-01

Interactions of carbon nanotubes (CNTs) and blood proteins are of interest for nanotoxicology and nanomedicine. It is believed that the interactions of blood proteins and glycoproteins with CNTs may have important biological effects. In spite of many experimental studies of single-walled carbon nanotubes (SWCNT) and glycoproteins with different methods, little is known about the atomistic details of their association process or of structural alterations occurring in adsorbed glycoproteins. In this study, we have applied molecular dynamics simulation to investigate the interaction of follicle stimulating hormone (hFSH) with SWCNT. The aim of this work is to investigate possible mechanisms of nanotoxicity at a molecular level. We present details of the molecular dynamics, structure, and free energy of binding of hFSH on the surface of SWCNT. We find that hFSH in aqueous solution strongly adsorbs onto SWCNT via their concave surface as evidenced by high binding free energies for residues in both protein subunits. It was found that hydrophobic, π-cation, and π-π stacking interactions are the main driving forces for the adsorption of the protein at the nanotube surface.

Entanglement witnesses in spin models

NASA Astrophysics Data System (ADS)

Tóth, Géza

2005-01-01

We construct entanglement witnesses using fundamental quantum operators of spin models which contain two-particle interactions and have a certain symmetry. By choosing the Hamiltonian as such an operator, our method can be used for detecting entanglement by energy measurement. We apply this method to the Heisenberg model in a cubic lattice with a magnetic field, the XY model, and other familiar spin systems. Our method provides a temperature bound for separable states for systems in thermal equilibrium. We also study the Bose-Hubbard model and relate its energy minimum for separable states to the minimum obtained from the Gutzwiller ansatz.

Determining dark matter properties with a XENONnT/LZ signal and LHC Run 3 monojet searches

NASA Astrophysics Data System (ADS)

Baum, Sebastian; Catena, Riccardo; Conrad, Jan; Freese, Katherine; Krauss, Martin B.

2018-04-01

We develop a method to forecast the outcome of the LHC Run 3 based on the hypothetical detection of O (100 ) signal events at XENONnT. Our method relies on a systematic classification of renormalizable single-mediator models for dark matter-quark interactions and is valid for dark matter candidates of spin less than or equal to one. Applying our method to simulated data, we find that at the end of the LHC Run 3 only two mutually exclusive scenarios would be compatible with the detection of O (100 ) signal events at XENONnT. In the first scenario, the energy distribution of the signal events is featureless, as for canonical spin-independent interactions. In this case, if a monojet signal is detected at the LHC, dark matter must have spin 1 /2 and interact with nucleons through a unique velocity-dependent operator. If a monojet signal is not detected, dark matter interacts with nucleons through canonical spin-independent interactions. In a second scenario, the spectral distribution of the signal events exhibits a bump at nonzero recoil energies. In this second case, a monojet signal can be detected at the LHC Run 3; dark matter must have spin 1 /2 and interact with nucleons through a unique momentum-dependent operator. We therefore conclude that the observation of O (100 ) signal events at XENONnT combined with the detection, or the lack of detection, of a monojet signal at the LHC Run 3 would significantly narrow the range of possible dark matter-nucleon interactions. As we argued above, it can also provide key information on the dark matter particle spin.

Fiber lubrication: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Liu, Hongyi

Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence of water increases the attractive interaction energy of the diblock copolymer on the cellulose surface, compared with that on the PP surface. Water decreases the interaction energy of the triblock copolymer on the cellulose surface, compared with that on the PP surface. MesoDyn was adopted to investigate the self-assembled morphology of the triblock copolymer, in aqueous solution, confined and sheared at solid-liquid interfaces. In a bulk aqueous solution, when the polymer concentration reached 10% v/v, micelles were observed with PPO blocks in the core and PEO blocks in the shell of the micelles. At the concentrations of 25% and 50%, worm-like micelles and irregular cylinders were observed in solutions, respectively. The micelles were formed faster in aqueous solutions confined by cellulose surfaces than that in the bulk. The formed micelles were broken under shearing, which led to a depletion of polymers at the interfaces. During the shearing on the PP surfaces, the polymers were adsorbed on the surfaces protecting the PP surfaces. This simulation study in the fiber lubrication was in good agreement with the experimental results and so provided an approach to visualize the polymer configuration at the liquid-solid interface, predict the lubricant-surface systems, and theoretically guide the experiments of designing new/efficient lubricants for fibers.

On the physical origins of interaction-induced vibrational (hyper)polarizabilities.

PubMed

Zaleśny, Robert; Garcia-Borràs, Marc; Góra, Robert W; Medved', Miroslav; Luis, Josep M

2016-08-10

This paper presents the results of a pioneering exploration of the physical origins of vibrational contributions to the interaction-induced electric properties of molecular complexes. In order to analyze the excess nuclear relaxation (hyper)polarizabilities, a new scheme was proposed which relies on the computationally efficient Bishop-Hasan-Kirtman method for determining the nuclear relaxation contributions to electric properties. The extension presented herein is general and can be used with any interaction-energy partitioning method. As an example, in this study we employed the variational-perturbational interaction-energy decomposition scheme (at the MP2/aug-cc-pVQZ level) and the extended transition state method by employing three exchange-correlation functionals (BLYP, LC-BLYP, and LC-BLYP-dDsC) to study the excess properties of the HCN dimer. It was observed that the first-order electrostatic contribution to the excess nuclear relaxation polarizability cancels with the negative exchange repulsion term out to a large extent, resulting in a positive value of Δα(nr) due to the contributions from the delocalization and the dispersion terms. In the case of the excess nuclear relaxation first hyperpolarizability, the pattern of interaction contributions is very similar to that for Δα(nr), both in terms of their sign as well as relative magnitude. Finally, our results show that the LC-BLYP and LC-BLYP-dDsC functionals, which yield smaller values of the orbital relaxation term than BLYP, are more successful in predicting excess properties.

Resonant electronic excitation energy transfer by exchange mechanism in the quantum dot system

NASA Astrophysics Data System (ADS)

Chikalova-Luzina, O. P.; Samosvat, D. M.; Vyatkin, V. M.; Zegrya, G. G.

2017-11-01

A microscopic theory of nonradiative resonance energy transfer between spherical A3B5 semiconductor quantum dots by the exchange mechanism is suggested. The interdot Coulomb interaction is taken into consideration. It is assumed that the quantum dot-donor and the quantum dot-acceptor are made from the same A3B5 compound and are embedded in the matrix of another material that produces potential barriers for electrons and holes. The dependences of the energy transfer rate on the quantum-dot system parameters are found in the frame of the Kane model that provides the most adequate description of the real spectra of A3B5 semiconductors. The analytical treatment is carried out with using the density matrix method, which enabled us to perform an energy transfer analysis both in the weak-interaction approximation and in the strong-interaction approximation. The numerical calculations showed the saturation of the energy transfer rate at the distances between the donor and the acceptor approaching the contact one. The contributions of the exchange and direct Coulomb intractions can be of the same order at the small distances and can have the same value in the saturation range.

Positrons in surface physics

NASA Astrophysics Data System (ADS)

Hugenschmidt, Christoph

2016-12-01

Within the last decade powerful methods have been developed to study surfaces using bright low-energy positron beams. These novel analysis tools exploit the unique properties of positron interaction with surfaces, which comprise the absence of exchange interaction, repulsive crystal potential and positron trapping in delocalized surface states at low energies. By applying reflection high-energy positron diffraction (RHEPD) one can benefit from the phenomenon of total reflection below a critical angle that is not present in electron surface diffraction. Therefore, RHEPD allows the determination of the atom positions of (reconstructed) surfaces with outstanding accuracy. The main advantages of positron annihilation induced Auger-electron spectroscopy (PAES) are the missing secondary electron background in the energy region of Auger-transitions and its topmost layer sensitivity for elemental analysis. In order to enable the investigation of the electron polarization at surfaces low-energy spin-polarized positrons are used to probe the outermost electrons of the surface. Furthermore, in fundamental research the preparation of well defined surfaces tailored for the production of bound leptonic systems plays an outstanding role. In this report, it is envisaged to cover both the fundamental aspects of positron surface interaction and the present status of surface studies using modern positron beam techniques.

A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

PubMed

Wang, Changwei; Danovich, David; Shaik, Sason; Mo, Yirong

2017-04-11

Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off". Turning off the charge transfer mixing can be achieved by employing the block-localized wave function (BLW) method, which is an ab initio valence bond (VB) method. Further, with the BLW method, the overall stability gained in the formation of a complex can be analyzed in terms of a few physically meaningful terms. Thus, the BLW method provides a unified and physically lucid way to explore the nature of red- and blue-shifting phenomena in both hydrogen and halogen bonding complexes. In this study, a direct correlation between the total stability and the variation of the Y-A bond length is established based on our BLW computations, and the consistent roles of all energy components are clarified. The n(D) → σ*(Y-A) electron transfer stretches the Y-A bond, while the polarization due to the approach of interacting moieties reduces the HOMO-LUMO gap and results in a stronger orbital mixing within the YA monomer. As a consequence, both the charge transfer and polarization stabilize bonding systems with the Y-A bond stretched and red-shift the vibrational frequency of the Y-A bond. Notably, the energy of the frozen wave function is the only energy component which prefers the shrinking of the Y-A bond and thus is responsible for the associated blue-shifting. The total variations of the Y-A bond length and the corresponding stretching vibrational frequency are thus determined by the competition between the frozen-energy term and the sum of polarization and charge transfer energy terms. Because the frozen energy is composed of electrostatic and Pauli exchange interactions and frequency shifting is a long-range phenomenon, we conclude that long-range electrostatic interaction is the driving force behind the frozen energy term.

Electronic conductance of a poly(p-phenylene)-like nanowire in the presence of thermal atomic vibrations

NASA Astrophysics Data System (ADS)

Shariati, Ashrafalsadat; Rabani, Hassan; Mardaani, Mohammad

2017-10-01

We present a theoretical method based on Green’s function technique and tight-binding approach as well as harmonic approximation in order to calculate the coherent electronic conductance of an extended poly(p-phenylene) oligomer in the presence of thermal atomic vibrations. We study two proposed mass-spring models for atomic vibrations: one, including rigid benzene rings connected to each other by vibrating bonds; and in another, the bonds along the oligomer vibrate even in the benzene rings. The electron-phonon (e-ph) interaction influences the electron hopping energies linearly with respect to atomic displacements. The model shows that the conductance spectra exhibit some new energy gaps in the presence of e-ph interaction even at zero temperature. The conductance is more affected by e-ph interaction when the atomic vibrations are supposed to be present in the benzene rings. At the edges of the band energy and central gap, the phonon-assisted phenomena can be observed. Generally, the increasing e-ph interaction strength as well as temperature destroys the electronic conductance especially in the resonance region.

Congested Aggregation via Newtonian Interaction

NASA Astrophysics Data System (ADS)

Craig, Katy; Kim, Inwon; Yao, Yao

2018-01-01

We consider a congested aggregation model that describes the evolution of a density through the competing effects of nonlocal Newtonian attraction and a hard height constraint. This provides a counterpoint to existing literature on repulsive-attractive nonlocal interaction models, where the repulsive effects instead arise from an interaction kernel or the addition of diffusion. We formulate our model as the Wasserstein gradient flow of an interaction energy, with a penalization to enforce the constraint on the height of the density. From this perspective, the problem can be seen as a singular limit of the Keller-Segel equation with degenerate diffusion. Two key properties distinguish our problem from previous work on height constrained equations: nonconvexity of the interaction kernel (which places the model outside the scope of classical gradient flow theory) and nonlocal dependence of the velocity field on the density (which causes the problem to lack a comparison principle). To overcome these obstacles, we combine recent results on gradient flows of nonconvex energies with viscosity solution theory. We characterize the dynamics of patch solutions in terms of a Hele-Shaw type free boundary problem and, using this characterization, show that in two dimensions patch solutions converge to a characteristic function of a disk in the long-time limit, with an explicit rate on the decay of the energy. We believe that a key contribution of the present work is our blended approach, combining energy methods with viscosity solution theory.

Calculating binding free energies for protein-carbohydrate complexes.

PubMed

Hadden, Jodi A; Tessier, Matthew B; Fadda, Elisa; Woods, Robert J

2015-01-01

A variety of computational techniques may be applied to compute theoretical binding free energies for protein-carbohydrate complexes. Elucidation of the intermolecular interactions, as well as the thermodynamic effects, that contribute to the relative strength of receptor binding can shed light on biomolecular recognition, and the resulting initiation or inhibition of a biological process. Three types of free energy methods are discussed here, including MM-PB/GBSA, thermodynamic integration, and a non-equilibrium alternative utilizing SMD. Throughout this chapter, the well-known concanavalin A lectin is employed as a model system to demonstrate the application of these methods to the special case of carbohydrate binding.

Computation of free energy profiles with parallel adaptive dynamics

NASA Astrophysics Data System (ADS)

Lelièvre, Tony; Rousset, Mathias; Stoltz, Gabriel

2007-04-01

We propose a formulation of an adaptive computation of free energy differences, in the adaptive biasing force or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows us to present a truly unifying framework for these methods, and to prove convergence results for certain classes of algorithms. From a numerical viewpoint, a parallel implementation of these methods is very natural, the replicas interacting through the reconstructed free energy. We demonstrate how to improve this parallel implementation by resorting to some selection mechanism on the replicas. This is illustrated by computations on a model system of conformational changes.

Predicting catalyst-support interactions between metal nanoparticles and amorphous silica supports

NASA Astrophysics Data System (ADS)

Ewing, Christopher S.; Veser, Götz; McCarthy, Joseph J.; Lambrecht, Daniel S.; Johnson, J. Karl

2016-10-01

Metal-support interactions significantly affect the stability and activity of supported catalytic nanoparticles (NPs), yet there is no simple and reliable method for estimating NP-support interactions, especially for amorphous supports. We present an approach for rapid prediction of catalyst-support interactions between Pt NPs and amorphous silica supports for NPs of various sizes and shapes. We use density functional theory calculations of 13 atom Pt clusters on model amorphous silica supports to determine linear correlations relating catalyst properties to NP-support interactions. We show that these correlations can be combined with fast discrete element method simulations to predict adhesion energy and NP net charge for NPs of larger sizes and different shapes. Furthermore, we demonstrate that this approach can be successfully transferred to Pd, Au, Ni, and Fe NPs. This approach can be used to quickly screen stability and net charge transfer and leads to a better fundamental understanding of catalyst-support interactions.

Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design.

PubMed

Xie, Neng-Zhong; Du, Qi-Shi; Li, Jian-Xiu; Huang, Ri-Bo

2015-01-01

Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.

Surface properties of calcium and magnesium oxide nanopowders grafted with unsaturated carboxylic acids studied with inverse gas chromatography.

PubMed

Maciejewska, Magdalena; Krzywania-Kaliszewska, Alicja; Zaborski, Marian

2012-09-28

Inverse gas chromatography (IGC) was applied at infinite dilution to evaluate the surface properties of calcium and magnesium oxide nanoparticles and the effect of surface grafted unsaturated carboxylic acid on the nanopowder donor-acceptor characteristics. The dispersive components (γ(s)(D)) of the free energy of the nanopowders were determined by Gray's method, whereas their tendency to undergo specific interactions was estimated based on the electron donor-acceptor approach presented by Papirer. The calcium and magnesium oxide nanoparticles exhibited high surface energies (79 mJ/m² and 74 mJ/m², respectively). Modification of nanopowders with unsaturated carboxylic acids decreased their specific adsorption energy. The lowest value of γ(s)(D) was determined for nanopowders grafted with undecylenic acid, approximately 55 mJ/m². The specific interactions were characterised by the molar free energy (ΔG(A)(SP)) and molar enthalpy (ΔH(A)(SP)) of adsorption as well as the donor and acceptor interaction parameters (K(A), K(D)). Copyright © 2012 Elsevier B.V. All rights reserved.

Excitonic energy transfer in light-harvesting complexes in purple bacteria

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

Ye Jun; Sun Kewei; Zhao Yang

Two distinct approaches, the Frenkel-Dirac time-dependent variation and the Haken-Strobl model, are adopted to study energy transfer dynamics in single-ring and double-ring light-harvesting (LH) systems in purple bacteria. It is found that the inclusion of long-range dipolar interactions in the two methods results in significant increase in intra- or inter-ring exciton transfer efficiency. The dependence of exciton transfer efficiency on trapping positions on single rings of LH2 (B850) and LH1 is similar to that in toy models with nearest-neighbor coupling only. However, owing to the symmetry breaking caused by the dimerization of BChls and dipolar couplings, such dependence has beenmore » largely suppressed. In the studies of coupled-ring systems, both methods reveal an interesting role of dipolar interactions in increasing energy transfer efficiency by introducing multiple intra/inter-ring transfer paths. Importantly, the time scale (4 ps) of inter-ring exciton transfer obtained from polaron dynamics is in good agreement with previous studies. In a double-ring LH2 system, non-nearest neighbor interactions can induce symmetry breaking, which leads to global and local minima of the average trapping time in the presence of a non-zero dephasing rate, suggesting that environment dephasing helps preserve quantum coherent energy transfer when the perfect circular symmetry in the hypothetic system is broken. This study reveals that dipolar coupling between chromophores may play an important role in the high energy transfer efficiency in the LH systems of purple bacteria and many other natural photosynthetic systems.« less

Search for neutrino oscillations in the MINOS experiment by using quasi-elastic interactions

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

Piteira, Rodolphe

2005-09-29

The enthusiasm of the scientific community for studying oscillations of neutrinos is equaled only by the mass of their detectors. The MINOS experiment determines and compares the near spectrum of muonic neutrinos from the NUMI beam to the far one, in order to measure two oscillation parameters: Δmmore » $$2\\atop{23}$$ and sin 2 (2θ 23). The spectra are obtained by analyzing the charged current interactions which difficulty lies in identifying the interactions products (e.g. muons). An alternative method identifying the traces of muons, bent by the magnetic field of the detectors, and determining their energies is presented in this manuscript. The sensitivity of the detectors is optimal for the quasi-elastic interactions, for which a selection method is proposed, to study their oscillation. Even though it reduces the statistics, such a study introduces fewer systematic errors, constituting the ideal method on the long range.« less

Modeling Adsorption and Reactions of Organic Molecules at Metal Surfaces

PubMed Central

2014-01-01

Conspectus The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdWsurf method that accurately accounts for the collective electronic response effects enables reliable modeling of structure and stability for a broad class of organic molecules adsorbed on metal surfaces. This method was demonstrated to achieve quantitative accuracy for aromatic hydrocarbons (benzene, naphthalene, anthracene, and diindenoperylene), C60, and sulfur/oxygen-containing molecules (thiophene, NTCDA, and PTCDA) on close-packed and stepped metal surfaces, leading to an overall accuracy of 0.1 Å in adsorption heights and 0.1 eV in binding energies with respect to state-of-the-art experiments. An unexpected finding is that vdW interactions contribute more to the binding of strongly bound molecules on transition-metal surfaces than for molecules physisorbed on coinage metals. The accurate inclusion of vdW interactions also significantly improves tilting angles and adsorption heights for all the studied molecules, and can qualitatively change the potential-energy surface for adsorbed molecules with flexible functional groups. Activation barriers for molecular switches and reaction precursors are modified as well. PMID:24915492

New Method for Measuring the Anchoring Energy of Strongly-Bound Membrane-Associated Proteins [Method for measuring the anchoring energy of strongly-bound membrane-associated proteins].

DOE PAGES

Kent, Michael S.; La Bauve, Elisa; Vernon, Briana C.; ...

2016-02-01

Here, we describe a new method to measure the activation energy required to remove a strongly-bound membrane-associated protein from a lipid membrane (anchoring energy). It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method was used to determine anchoring energy for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. We also measured the binding energy of sE at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipidmore » bilayer. The anchoring energy (37 +/- 1.7 kcal/mol, 20% PG) was found to be much larger than the binding energy (7.8 +/- 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. But, trimerization alone is insufficient to account for the observed difference in energies, and we conclude that some energy dissipation occurs during the release process. This new method to determine anchoring energy should be useful to understand the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.« less

New Method for Measuring the Anchoring Energy of Strongly-Bound Membrane-Associated Proteins [Method for measuring the anchoring energy of strongly-bound membrane-associated proteins].

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

Kent, Michael S.; La Bauve, Elisa; Vernon, Briana C.

Here, we describe a new method to measure the activation energy required to remove a strongly-bound membrane-associated protein from a lipid membrane (anchoring energy). It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method was used to determine anchoring energy for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. We also measured the binding energy of sE at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipidmore » bilayer. The anchoring energy (37 +/- 1.7 kcal/mol, 20% PG) was found to be much larger than the binding energy (7.8 +/- 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. But, trimerization alone is insufficient to account for the observed difference in energies, and we conclude that some energy dissipation occurs during the release process. This new method to determine anchoring energy should be useful to understand the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.« less

Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits

NASA Astrophysics Data System (ADS)

Spiriti, Justin; Zuckerman, Daniel M.

2015-12-01

Traditional coarse-graining based on a reduced number of interaction sites often entails a significant sacrifice of chemical accuracy. As an alternative, we present a method for simulating large systems composed of interacting macromolecules using an energy tabulation strategy previously devised for small rigid molecules or molecular fragments [S. Lettieri and D. M. Zuckerman, J. Comput. Chem. 33, 268-275 (2012); J. Spiriti and D. M. Zuckerman, J. Chem. Theory Comput. 10, 5161-5177 (2014)]. We treat proteins as rigid and construct distance and orientation-dependent tables of the interaction energy between them. Arbitrarily detailed interactions may be incorporated into the tables, but as a proof-of-principle, we tabulate a simple α-carbon Gō-like model for interactions between dimeric subunits of the hepatitis B viral capsid. This model is significantly more structurally realistic than previous models used in capsid assembly studies. We are able to increase the speed of Monte Carlo simulations by a factor of up to 6700 compared to simulations without tables, with only minimal further loss in accuracy. To obtain further enhancement of sampling, we combine tabulation with the weighted ensemble (WE) method, in which multiple parallel simulations are occasionally replicated or pruned in order to sample targeted regions of a reaction coordinate space. In the initial study reported here, WE is able to yield pathways of the final ˜25% of the assembly process.

Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

PubMed

Makarewicz, Jan; Shirkov, Leonid

2016-05-28

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

Development of an energy storage tank model

NASA Astrophysics Data System (ADS)

Buckley, Robert Christopher

A linearized, one-dimensional finite difference model employing an implicit finite difference method for energy storage tanks is developed, programmed with MATLAB, and demonstrated for different applications. A set of nodal energy equations is developed by considering the energy interactions on a small control volume. The general method of solving these equations is described as are other features of the simulation program. Two modeling applications are presented: the first using a hot water storage tank with a solar collector and an absorption chiller to cool a building in the summer, the second using a molten salt storage system with a solar collector and steam power plant to generate electricity. Recommendations for further study as well as all of the source code generated in the project are also provided.

A convenient method for synthesis of glyconanoparticles for colorimetric measuring carbohydrate-protein interactions

PubMed Central

Chuang, Yen-Jun; Zhou, Xichun; Pan, Zhengwei; Turchi, Craig

2009-01-01

Carbohydrate functionalized nanoparticles, i.e., the glyconanoparticles, have wide application ranging from studies of carbohydrate-protein interactions, in vivo cell imaging, biolabeling, etc. Currently reported methods for preparation of glyconanoaprticles require multi-step modifications of carbohydrates moieties to conjugate to nanoparticle surface. However, the required synthetic manipulations are difficult and time consuming. We report herewith a simple and versatile method for preparing glyconanoparticles. This method is based on the utilization of clean and convenient microwave irradiation energy for one-step, site-specific conjugation of unmodified carbohydrates onto hydrazide-functionalized Au nanoparticles. A colorimetric assay that utilizes the ensemble of gold glyconanoparticles and Concanavalin A (ConA) was also presented. This feasible assay system was developed to analyze multivalent interactions and to determine the dissociation constant (Kd) for five kind of Au glyconanoparticles with lectin. Surface plasmon changes of the Au glyconanparticles as a function of lectin-carbohydrate interactions were measured and the dissociation constants were determined based on non-linear curve fitting. The strength of the interaction of carbohydrates with ConA was found to be as follows: Maltose > Mannose > Glucose > Lactose > MAN5. PMID:19698698

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

PubMed Central

Lezon, Timothy R.; Banavar, Jayanth R.; Cieplak, Marek; Maritan, Amos; Fedoroff, Nina V.

2006-01-01

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems. PMID:17138668

Quantum Monte Carlo calculations of light nuclei with local chiral two- and three-nucleon interactions

DOE PAGES

Lynn, J. E.; Tews, I.; Carlson, J.; ...

2017-11-30

Local chiral effective field theory interactions have recently been developed and used in the context of quantum Monte Carlo few- and many-body methods for nuclear physics. In this paper, we go over detailed features of local chiral nucleon-nucleon interactions and examine their effect on properties of the deuteron, paying special attention to the perturbativeness of the expansion. We then turn to three-nucleon interactions, focusing on operator ambiguities and their interplay with regulator effects. We then discuss the nuclear Green's function Monte Carlo method, going over both wave-function correlations and approximations for the two- and three-body propagators. Finally, following this, wemore » present a range of results on light nuclei: Binding energies and distribution functions are contrasted and compared, starting from several different microscopic interactions.« less

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

NASA Astrophysics Data System (ADS)

Yoshida, Norio

2018-05-01

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

Performance of local correlation methods for halogen bonding: The case of Br{sub 2}–(H{sub 2}O){sub n},n = 4,5 clusters and Br{sub 2}@5{sup 12}6{sup 2} clathrate cage

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

Batista-Romero, Fidel A.; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón, E-mail: ramon@uaem.mx

The performance of local correlation methods is examined for the interactions present in clusters of bromine with water where the combined effect of hydrogen bonding (HB), halogen bonding (XB), and hydrogen-halogen (HX) interactions lead to many interesting properties. Local methods reproduce all the subtleties involved such as many-body effects and dispersion contributions provided that specific methodological steps are followed. Additionally, they predict optimized geometries that are nearly free of basis set superposition error that lead to improved estimates of spectroscopic properties. Taking advantage of the local correlation energy partitioning scheme, we compare the different interaction environments present in small clustersmore » and those inside the 5{sup 12}6{sup 2} clathrate cage. This analysis allows a clear identification of the reasons supporting the use of local methods for large systems where non-covalent interactions play a key role.« less

Probing the Interaction between Cyclic ADTC1 Ac-CADTPPVC-NH2) Peptide with EC1-EC2 domain of E-cadherin using Molecular Docking Approach

NASA Astrophysics Data System (ADS)

Siahaan, P.; Wuning, S.; Manna, A.; Prasasty, V. D.; Hudiyanti, D.

2018-04-01

Deeply understanding that intermolecular interaction between molecules on the paracellular pathway has given insight to its microscopic and macroscopic properties. In the paracellular pathway, synthetic cyclic ADTC1 (Ac-CADTPPVC-NH2) peptide has been studied to modulate EC1-EC2 domain, computationally using molecular docking method. The aim of this research is to probe the effect of amino acid alanine (A) of ADTC1 on its interaction properties. The study carried out in two steps: 1. the optimization using GROMACS v4.6.5 program and; 2. Determination of the interaction properties using AutoDock 4.2 program. The interaction was done for A-J box, and the best position of the binding site and binding energy on the OC and CC ADTC1 peptides against the EC1-EC2 domain of E-cadherin was selected. The result showed that the CC of the F box ADTC1 has the best interaction with binding energy of - 26.36 kJ/mol and its energy was lower than ADTC5 without alanine amino acid. ADTC1 interacted with EC1 of EC1-EC2 on Asp1, Trp2, Val3, Ile4, Ile24, Lys25, Ser26, Asn27, and Met92 residues.

Probing vibrational activities, electronic properties, molecular docking and Hirshfeld surfaces analysis of 4-chlorophenyl ({[(1E)-3-(1H-imidazol-1-yl)-1-phenylpropylidene]amino}oxy)methanone: A promising anti-Candida agent

NASA Astrophysics Data System (ADS)

Jayasheela, K.; Al-Wahaibi, Lamya H.; Periandy, S.; Hassan, Hanan M.; Sebastian, S.; Xavier, S.; Daniel, Joseph C.; El-Emam, Ali A.; Attia, Mohamed I.

2018-05-01

The promising anti-Candida agent, 4-chlorophenyl ({[1E-3(1H-imidazole-1-yl)-1-phenylpropylidene}oxy)methanone (4-CPIPM) was comprehensively characterized by FT-IR, FT-Raman, UV, as well as 1H and 13C spectroscopic techniques. The theoretical calculations in the current study utilized Gaussian 09 W software with DFT approach of the B3LYP/6-311++G(d,p) method. The experimental X-ray diffraction data of the 4-CPIPM molecule were compared with the optimized structure and showed well agreement. Intermolecular electronic interactions and their stabilization energies have been analyzed by natural bond orbital method. Potential energy distribution confirmed the normal fundamental mode of vibration with the aid of MOLVIB software. The chemical shift values of the 1H and 13C spectra of the title compound were computed using gauge independent atomic orbital and the results were compared with the experimental values. The time-dependent density function theory method was used to predict the electronic, absorption wavelength and frontier molecular orbital energies. The HOMO-LUMO plots proved the charge transfer in the molecular system of the title compound through conjugated paths. The molecular electrostatic potential analysis provided the electrophilic and nucleophilic reactive sites in the title molecule which have been analyzed using Hirshfeld surface and two dimensions fingerprint plots. Non covalent interactions were also studied using reduced density gradient analysis and color filled electron density diagram. Molecular docking studies of the ligand-protein interactions along with their binding energies were carried out aiming to explain the potent anti-Candida activity of the title molecule.

Communication: Exact analytical derivatives for the domain-based local pair natural orbital MP2 method (DLPNO-MP2)

NASA Astrophysics Data System (ADS)

Pinski, Peter; Neese, Frank

2018-01-01

Electron correlation methods based on pair natural orbitals (PNOs) have gained an increasing degree of interest in recent years, as they permit energy calculations to be performed on systems containing up to many hundred atoms, while maintaining chemical accuracy for reaction energies. We present an approach for taking exact analytical first derivatives of the energy contributions in the simplest method of the family of Domain-based Local Pair Natural Orbital (DLPNO) methods, closed-shell DLPNO-MP2. The Lagrangian function contains constraints to account for the relaxation of PNOs. RI-MP2 reference geometries are reproduced accurately, as exemplified for four systems with a substantial degree of nonbonding interactions. By the example of electric field gradients, we demonstrate that omitting PNO-specific constraints can lead to dramatic errors for orbital-relaxed properties.

Method for detection of nuclear-plasma interactions in a 134Xe-doped exploding pusher at the National Ignition Facility

DOE PAGES

Bleuel, Daniel L.; Bernstein, Lee A.; Brand, Christopher A.; ...

2016-06-10

Angular momentum changes due to nuclear-plasma interactions on highly-excited nuclei in high energy density plasmas created at the National Ignition Facility can be measured through a change in isomer feeding following gamma emission. Here, we propose an experiment to detect these effects in 133Xe* in exploding pusher capsules.

Unusual interactions above 100 TeV: A review of cosmic ray experiments with emulsion chambers

NASA Technical Reports Server (NTRS)

Yodh, D. B.

1977-01-01

A method is given for analyzing the space correlated collection of jets (gamma ray families) with energies greater than 100 TeV in Pb or Fe absorber sampled by photosensitive layers in an emulsion chamber. Events analyzed indicate large multiplicities of particles in the primary hadron-air interaction, and a marked absence of neutral pions.

Method for detection of nuclear-plasma interactions in a 134Xe-doped exploding pusher at the National Ignition Facility

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

Bleuel, Daniel L.; Bernstein, Lee A.; Brand, Christopher A.

Angular momentum changes due to nuclear-plasma interactions on highly-excited nuclei in high energy density plasmas created at the National Ignition Facility can be measured through a change in isomer feeding following gamma emission. Here, we propose an experiment to detect these effects in 133Xe* in exploding pusher capsules.

A Safe and Interactive Method of Illuminating Discharge Tubes for Studying Emission Spectra

ERIC Educational Resources Information Center

Lu, Zhe

2012-01-01

Discharge tubes are useful tools for teaching emission spectra and the discrete energy levels of the Bohr model. A new setup uses a plasma globe to illuminate the discharge tube and allows a higher degree of interactivity owing to the omission of a traditional, high-voltage power source. The decreased power consumption also reduces the heating of…

Development and Application of Explicitly Correlated Wave Function Based Methods for the Investigation of Optical Properties of Semiconductor Nanomaterials

NASA Astrophysics Data System (ADS)

Elward, Jennifer Mary

Semiconductor nanoparticles, or quantum dots (QDs), are well known to have very unique optical and electronic properties. These properties can be controlled and tailored as a function of several influential factors, including but not limited to the particle size and shape, effect of composition and heterojunction as well as the effect of ligand on the particle surface. This customizable nature leads to extensive experimental and theoretical research on the capabilities of these quantum dots for many application purposes. However, in order to be able to understand and thus further the development of these materials, one must first understand the fundamental interaction within these nanoparticles. In this thesis, I have developed a theoretical method which is called electron-hole explicitly correlated Hartee-Fock (eh-XCHF). It is a variational method for solving the electron-hole Schrodinger equation and has been used in this work to study electron-hole interaction in semiconductor quantum dots. The method was benchmarked with respect to a parabolic quantum dot system, and ground state energy and electron-hole recombination probability were computed. Both of these properties were found to be in good agreement with expected results. Upon successful benchmarking, I have applied the eh-XCHF method to study optical properties of several quantum dot systems including the effect of dot size on exciton binding energy and recombination probability in a CdSe quantum dot, the effect of shape on a CdSe quantum dot, the effect of heterojunction on a CdSe/ZnS quantum dot and the effect of quantum dot-biomolecule interaction within a CdSe-firefly Luciferase protein conjugate system. As metrics for assessing the effect of these influencers on the electron-hole interaction, the exciton binding energy, electron-hole recombination probability and the average electron-hole separation distance have been computed. These excitonic properties have been found to be strongly infuenced by the changing composition of the particle. It has also been found through this work that the explicitly correlated method performs very well when computing these properties as it provides a feasible computational route to compare to both experimental and other theoretical results.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

2009-03-14

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai

2009-03-01

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Regularization method for large eddy simulations of shock-turbulence interactions

NASA Astrophysics Data System (ADS)

Braun, N. O.; Pullin, D. I.; Meiron, D. I.

2018-05-01

The rapid change in scales over a shock has the potential to introduce unique difficulties in Large Eddy Simulations (LES) of compressible shock-turbulence flows if the governing model does not sufficiently capture the spectral distribution of energy in the upstream turbulence. A method for the regularization of LES of shock-turbulence interactions is presented which is constructed to enforce that the energy content in the highest resolved wavenumbers decays as k - 5 / 3, and is computed locally in physical-space at low computational cost. The application of the regularization to an existing subgrid scale model is shown to remove high wavenumber errors while maintaining agreement with Direct Numerical Simulations (DNS) of forced and decaying isotropic turbulence. Linear interaction analysis is implemented to model the interaction of a shock with isotropic turbulence from LES. Comparisons to analytical models suggest that the regularization significantly improves the ability of the LES to predict amplifications in subgrid terms over the modeled shockwave. LES and DNS of decaying, modeled post shock turbulence are also considered, and inclusion of the regularization in shock-turbulence LES is shown to improve agreement with lower Reynolds number DNS.

An adhesive contact mechanics formulation based on atomistically induced surface traction

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

Fan, Houfu; Ren, Bo; Li, Shaofan, E-mail: shaofan@berkeley.edu

2015-12-01

In this work, we have developed a novel multiscale computational contact formulation based on the generalized Derjuguin approximation for continua that are characterized by atomistically enriched constitutive relations in order to study macroscopic interaction between arbitrarily shaped deformable continua. The proposed adhesive contact formulation makes use of the microscopic interaction forces between individual particles in the interacting bodies. In particular, the double-layer volume integral describing the contact interaction (energy, force vector, matrix) is converted into a double-layer surface integral through a mathematically consistent approach that employs the divergence theorem and a special partitioning technique. The proposed contact model is formulatedmore » in the nonlinear continuum mechanics framework and implemented using the standard finite element method. With no large penalty constant, the stiffness matrix of the system will in general be well-conditioned, which is of great significance for quasi-static analysis. Three numerical examples are presented to illustrate the capability of the proposed method. Results indicate that with the same mesh configuration, the finite element computation based on the surface integral approach is faster and more accurate than the volume integral based approach. In addition, the proposed approach is energy preserving even in a very long dynamic simulation.« less

A Vision for Co-optimized T&D System Interaction with Renewables and Demand Response

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

Anderson, Lindsay; Zéphyr, Luckny; Cardell, Judith B.

The evolution of the power system to the reliable, efficient and sustainable system of the future will involve development of both demand- and supply-side technology and operations. The use of demand response to counterbalance the intermittency of renewable generation brings the consumer into the spotlight. Though individual consumers are interconnected at the low-voltage distribution system, these resources are typically modeled as variables at the transmission network level. In this paper, a vision for cooptimized interaction of distribution systems, or microgrids, with the high-voltage transmission system is described. In this framework, microgrids encompass consumers, distributed renewables and storage. The energy managementmore » system of the microgrid can also sell (buy) excess (necessary) energy from the transmission system. Preliminary work explores price mechanisms to manage the microgrid and its interactions with the transmission system. Wholesale market operations are addressed through the development of scalable stochastic optimization methods that provide the ability to co-optimize interactions between the transmission and distribution systems. Modeling challenges of the co-optimization are addressed via solution methods for large-scale stochastic optimization, including decomposition and stochastic dual dynamic programming.« less

A Vision for Co-optimized T&D System Interaction with Renewables and Demand Response

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

Anderson, C. Lindsay; Zéphyr, Luckny; Liu, Jialin

The evolution of the power system to the reliable, effi- cient and sustainable system of the future will involve development of both demand- and supply-side technology and operations. The use of demand response to counterbalance the intermittency of re- newable generation brings the consumer into the spotlight. Though individual consumers are interconnected at the low-voltage distri- bution system, these resources are typically modeled as variables at the transmission network level. In this paper, a vision for co- optimized interaction of distribution systems, or microgrids, with the high-voltage transmission system is described. In this frame- work, microgrids encompass consumers, distributed renewablesmore » and storage. The energy management system of the microgrid can also sell (buy) excess (necessary) energy from the transmission system. Preliminary work explores price mechanisms to manage the microgrid and its interactions with the transmission system. Wholesale market operations are addressed through the devel- opment of scalable stochastic optimization methods that provide the ability to co-optimize interactions between the transmission and distribution systems. Modeling challenges of the co-optimization are addressed via solution methods for large-scale stochastic op- timization, including decomposition and stochastic dual dynamic programming.« less

Third-Order Incremental Dual-Basis Set Zero-Buffer Approach: An Accurate and Efficient Way To Obtain CCSD and CCSD(T) Energies.

PubMed

Zhang, Jun; Dolg, Michael

2013-07-09

An efficient way to obtain accurate CCSD and CCSD(T) energies for large systems, i.e., the third-order incremental dual-basis set zero-buffer approach (inc3-db-B0), has been developed and tested. This approach combines the powerful incremental scheme with the dual-basis set method, and along with the new proposed K-means clustering (KM) method and zero-buffer (B0) approximation, can obtain very accurate absolute and relative energies efficiently. We tested the approach for 10 systems of different chemical nature, i.e., intermolecular interactions including hydrogen bonding, dispersion interaction, and halogen bonding; an intramolecular rearrangement reaction; aliphatic and conjugated hydrocarbon chains; three compact covalent molecules; and a water cluster. The results show that the errors for relative energies are <1.94 kJ/mol (or 0.46 kcal/mol), for absolute energies of <0.0026 hartree. By parallelization, our approach can be applied to molecules of more than 30 atoms and more than 100 correlated electrons with high-quality basis set such as cc-pVDZ or cc-pVTZ, saving computational cost by a factor of more than 10-20, compared to traditional implementation. The physical reasons of the success of the inc3-db-B0 approach are also analyzed.

A theoretical study of the dissociative recombination of SH+ with electrons through the 2Π states of SH.

PubMed

Kashinski, D O; Talbi, D; Hickman, A P; Di Nallo, O E; Colboc, F; Chakrabarti, K; Schneider, I F; Mezei, J Zs

2017-05-28

A quantitative theoretical study of the dissociative recombination of SH + with electrons has been carried out. Multireference, configuration interaction calculations were used to determine accurate potential energy curves for SH + and SH. The block diagonalization method was used to disentangle strongly interacting SH valence and Rydberg states and to construct a diabatic Hamiltonian whose diagonal matrix elements provide the diabatic potential energy curves. The off-diagonal elements are related to the electronic valence-Rydberg couplings. Cross sections and rate coefficients for the dissociative recombination reaction were calculated with a stepwise version of the multichannel quantum defect theory, using the molecular data provided by the block diagonalization method. The calculated rates are compared with the most recent measurements performed on the ion Test Storage Ring (TSR) in Heidelberg, Germany.

Ion hole formation and nonlinear generation of electromagnetic ion cyclotron waves: THEMIS observations

NASA Astrophysics Data System (ADS)

Shoji, Masafumi; Miyoshi, Yoshizumi; Katoh, Yuto; Keika, Kunihiro; Angelopoulos, Vassilis; Kasahara, Satoshi; Asamura, Kazushi; Nakamura, Satoko; Omura, Yoshiharu

2017-09-01

Electromagnetic plasma waves are thought to be responsible for energy exchange between charged particles in space plasmas. Such an energy exchange process is evidenced by phase space holes identified in the ion distribution function and measurements of the dot product of the plasma wave electric field and the ion velocity. We develop a method to identify ion hole formation, taking into consideration the phase differences between the gyromotion of ions and the electromagnetic ion cyclotron (EMIC) waves. Using this method, we identify ion holes in the distribution function and the resulting nonlinear EMIC wave evolution from Time History of Events and Macroscale Interactions during Substorms (THEMIS) observations. These ion holes are key to wave growth and frequency drift by the ion currents through nonlinear wave-particle interactions, which are identified by a computer simulation in this study.

Hyperspherical lowest-order constrained-variational approximation to resonant Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Sze, M. W. C.; Sykes, A. G.; Blume, D.; Bohn, J. L.

2018-03-01

We study the ground-state properties of a system of N harmonically trapped bosons of mass m interacting with two-body contact interactions, from small to large scattering lengths. This is accomplished in a hyperspherical coordinate system that is flexible enough to describe both the overall scale of the gas and two-body correlations. By adapting the lowest-order constrained-variational method, we are able to semiquantitatively attain Bose-Einstein condensate ground-state energies even for gases with infinite scattering length. In the large-particle-number limit, our method provides analytical estimates for the energy per particle E0/N ≈2.5 N1 /3ℏ ω and two-body contact C2/N ≈16 N1 /6√{m ω /ℏ } for a Bose gas on resonance, where ω is the trap frequency.

Calculated temperature dependence of elastic constants and phonon dispersion of hcp and bcc beryllium

NASA Astrophysics Data System (ADS)

Hahn, Steven; Arapan, Sergiu; Harmon, Bruce; Eriksson, Olle

2011-03-01

Conventional first principle methods for calculating lattice dynamics are unable to calculate high temperature thermophysical properties of materials containing modes that are entropically stabilized. In this presentation we use a relatively new approach called self-consistent ab initio lattice dynamics (SCAILD) to study the hcp to bcc transition (1530 K) in beryllium. The SCAILD method goes beyond the harmonic approximation to include phonon-phonon interactions and produces a temperature-dependent phonon dispersion. In the high temperature bcc structure, phonon-phonon interactions dynamically stabilize the N-point phonon. Fits to the calculated phonon dispersion were used to determine the temperature dependence of the elastic constants in the hcp and bcc phases. Work at the Ames Laboratory was supported by the Department of Energy-Basic Energy Sciences under Contract No. DE-AC02-07CH11358.

Visualizing the orientational dependence of an intermolecular potential

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

2016-02-01

Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

Accuracy of Dual-Energy Virtual Monochromatic CT Numbers: Comparison between the Single-Source Projection-Based and Dual-Source Image-Based Methods.

PubMed

Ueguchi, Takashi; Ogihara, Ryota; Yamada, Sachiko

2018-03-21

To investigate the accuracy of dual-energy virtual monochromatic computed tomography (CT) numbers obtained by two typical hardware and software implementations: the single-source projection-based method and the dual-source image-based method. A phantom with different tissue equivalent inserts was scanned with both single-source and dual-source scanners. A fast kVp-switching feature was used on the single-source scanner, whereas a tin filter was used on the dual-source scanner. Virtual monochromatic CT images of the phantom at energy levels of 60, 100, and 140 keV were obtained by both projection-based (on the single-source scanner) and image-based (on the dual-source scanner) methods. The accuracy of virtual monochromatic CT numbers for all inserts was assessed by comparing measured values to their corresponding true values. Linear regression analysis was performed to evaluate the dependency of measured CT numbers on tissue attenuation, method, and their interaction. Root mean square values of systematic error over all inserts at 60, 100, and 140 keV were approximately 53, 21, and 29 Hounsfield unit (HU) with the single-source projection-based method, and 46, 7, and 6 HU with the dual-source image-based method, respectively. Linear regression analysis revealed that the interaction between the attenuation and the method had a statistically significant effect on the measured CT numbers at 100 and 140 keV. There were attenuation-, method-, and energy level-dependent systematic errors in the measured virtual monochromatic CT numbers. CT number reproducibility was comparable between the two scanners, and CT numbers had better accuracy with the dual-source image-based method at 100 and 140 keV. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Study of photonuclear muon interactions at Baksan underground scintillation telescope

NASA Technical Reports Server (NTRS)

Bakatanov, V. N.; Chudakov, A. E.; Dadykin, V. L.; Novoseltsev, Y. F.; Achkasov, V. M.; Semenov, A. M.; Stenkin, Y. V.

1985-01-01

The method of pion-muon-electron decays recording was used to distinguish between purely electron-photon and hadronic cascades, induced by high energy muons underground. At energy approx. 1 Tev a ratio of the number of hadronic to electromagnetic cascades was found equal 0.11 + or - .03 in agreement with expectation. But, at an energy approx. 4 Tev a sharp increase of this ratio was indicated though not statistically sound (0.52 + or - .13).

Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes.

PubMed

Risthaus, Tobias; Grimme, Stefan

2013-03-12

A new test set (S12L) containing 12 supramolecular noncovalently bound complexes is presented and used to evaluate seven different methods to account for dispersion in DFT (DFT-D3, DFT-D2, DFT-NL, XDM, dDsC, TS-vdW, M06-L) at different basis set levels against experimental, back-corrected reference energies. This allows conclusions about the performance of each method in an explorative research setting on "real-life" problems. Most DFT methods show satisfactory performance but, due to the largeness of the complexes, almost always require an explicit correction for the nonadditive Axilrod-Teller-Muto three-body dispersion interaction to get accurate results. The necessity of using a method capable of accounting for dispersion is clearly demonstrated in that the two-body dispersion contributions are on the order of 20-150% of the total interaction energy. MP2 and some variants thereof are shown to be insufficient for this while a few tested D3-corrected semiempirical MO methods perform reasonably well. Overall, we suggest the use of this benchmark set as a "sanity check" against overfitting to too small molecular cases.

Free energy calculations of glycosaminoglycan-protein interactions.

PubMed

Gandhi, Neha S; Mancera, Ricardo L

2009-10-01

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Interaction of D2 with H2O amorphous ice studied by temperature-programmed desorption experiments.

PubMed

Amiaud, L; Fillion, J H; Baouche, S; Dulieu, F; Momeni, A; Lemaire, J L

2006-03-07

The gas-surface interaction of molecular hydrogen D2 with a thin film of porous amorphous solid water (ASW) grown at 10 K by slow vapor deposition has been studied by temperature-programmed-desorption (TPD) experiments. Molecular hydrogen diffuses rapidly into the porous network of the ice. The D2 desorption occurring between 10 and 30 K is considered here as a good probe of the effective surface of ASW interacting with the gas. The desorption kinetics have been systematically measured at various coverages. A careful analysis based on the Arrhenius plot method has provided the D2 binding energies as a function of the coverage. Asymmetric and broad distributions of binding energies were found, with a maximum population peaking at low energy. We propose a model for the desorption kinetics that assumes a complete thermal equilibrium of the molecules with the ice film. The sample is characterized by a distribution of adsorption sites that are filled according to a Fermi-Dirac statistic law. The TPD curves can be simulated and fitted to provide the parameters describing the distribution of the molecules as a function of their binding energy. This approach contributes to a correct description of the interaction of molecular hydrogen with the surface of possibly porous grain mantles in the interstellar medium.

Microscopic time-dependent analysis of neutrons transfers at low-energy nuclear reactions with spherical and deformed nuclei

NASA Astrophysics Data System (ADS)

Samarin, Viacheslav

2014-03-01

Time-dependent Schrödinger equation is numerically solved by difference method for external neutrons of nuclei 6He, 18O, 48Са, 238U at their grazing collisions with energies in the vicinity of a Coulomb barrier. The spin-orbital interaction and Pauli's exclusion principle were taken into consideration during the solution.

Nearshore Current Model Workshop Summary.

DTIC Science & Technology

1983-09-01

dissipation , and wave-current interaction. b. Incorporation into models of wave-breaking. c. Parameterization of turbulence in models. d. Incorporation...into models of surf zone energy dissipation . e. Methods to specify waves and currents on the boundaries of the grid. f. Incorporation into models of...also recommended. Improvements should include nonlinear and irregular wave effects and improved models of wave-breaking and wave energy dissipation in

A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Qian, Ping

2006-08-14

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.

Molecular insight into γ-γ tubulin lateral interactions within the γ-tubulin ring complex (γ-TuRC)

NASA Astrophysics Data System (ADS)

Suri, Charu; Hendrickson, Triscia W.; Joshi, Harish C.; Naik, Pradeep Kumar

2014-09-01

γ-tubulin is essential for the nucleation and organization of mitotic microtubules in dividing cells. It is localized at the microtubule organizing centers and mitotic spindle fibres. The most well accepted hypothesis for the initiation of microtubule polymerization is that α/β-tubulin dimers add onto a γ-tubulin ring complex (γTuRC), in which adjacent γ-tubulin subunits bind to the underlying non-tubulin components of the γTuRC. This template thus determines the resulting microtubule lattice. In this study we use molecular modelling and molecular dynamics simulations, combined with computational MM-PBSA/MM-GBSA methods, to determine the extent of the lateral atomic interaction between two adjacent γ-tubulins within the γTuRC. To do this we simulated a γ-γ homodimer for 10 ns and calculated the ensemble average of binding free energies of -107.76 kcal/mol by the MM-PBSA method and of -87.12 kcal/mol by the MM-GBSA method. These highly favourable binding free energy values imply robust lateral interactions between adjacent γ-tubulin subunits in addition to their end-interactions longitudinally with other proteins of γTuRC. Although the functional reconstitution of γ-TuRC subunits and their stepwise in vitro assembly from purified components is not yet feasible, we nevertheless wanted to recognize hotspot amino acids responsible for key γ-γ interactions. Our free energy decomposition data from converting a compendium of amino acid residues identified an array of hotspot amino acids. A subset of such mutants can be expressed in vivo in living yeast. Because γTuRC is important for the growth of yeast, we could test whether this subset of the hotspot mutations support growth of yeast. Consistent with our model, γ-tubulin mutants that fall into our identified hotspot do not support yeast growth.

Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

DOE PAGES

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

2015-06-04

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

PubMed Central

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

Tetrahedral silsesquioxane-C2H2Ti complex for hydrogen storage

NASA Astrophysics Data System (ADS)

Konda, Ravinder; Tavhare, Priyanka; Ingale, Nilesh; Chaudhari, Ajay

2018-04-01

The interaction of molecular hydrogen with tetrahedral silsesquioxane (T4)-C2H2Ti complex has been studied using Density Functional Theory with M06-2X functional and MP2 method with 6-311++G** basis set. T4-C2H2Ti complex can absorb maximum five hydrogen molecules with the gravimetric hydrogen storage capacity of 3.4 wt %. Adsorption energy calculations show that H2 adsorption on T4-C2H2Ti complex is favorable at room temperature by both the methods. We have studied the effect of temperature and pressure on Gibbs free energy corrected adsorption energies. Molecular dynamics simulations for H2 adsorbed T4-C2H2Ti complex have also been performed at 300K and show that loosely bonded H2 molecule flies away within 1fs. Various interaction energies within the complex are studied. Stability of a complex is predicted by means of a gap between Highest Occupied Molecular Orbital (HUMO) and Lowest Unoccupied Molecular Orbital (LUMO). The H2 desorption temperature for T4-C2H2Ti complex is calculated with Van't Hoff equation and it is found to be 229K.

Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations.

PubMed

Chen, Jianzhong; Yang, Maoyou; Hu, Guodong; Shi, Shuhua; Yi, Changhong; Zhang, Qinggang

2009-10-01

The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with molecular dynamics (MD) simulations were used to investigate the functional role of protonation in human immunodeficiency virus type 1 (HIV-1) protease complexed with the inhibitor BEA369. Our results demonstrate that protonation of two aspartic acids (Asp25/Asp25') has a strong influence on the dynamics behavior of the complex, the binding free energy of BEA369, and inhibitor-residue interactions. Relative binding free energies calculated using the MM-PBSA method show that protonation of Asp25 results in the strongest binding of BEA369 to HIV-1 protease. Inhibitor-residue interactions computed by the theory of free energy decomposition also indicate that protonation of Asp25 has the most favorable effect on binding of BEA369. In addition, hydrogen-bond analysis based on the trajectories of the MD simulations shows that protonation of Asp25 strongly influences the water-mediated link of a conserved water molecule, Wat301. We expect that the results of this study will contribute significantly to binding calculations for BEA369, and to the design of high affinity inhibitors.

Re-examining the tetraphenyl-arsonium/tetraphenyl-borate (TATB) hypothesis for single-ion solvation free energies

NASA Astrophysics Data System (ADS)

Pollard, Travis P.; Beck, Thomas L.

2018-06-01

Attempts to establish an absolute single-ion hydration free energy scale have followed multiple strategies. Two central themes consist of (1) employing bulk pair thermodynamic data and an underlying interfacial-potential-free model to partition the hydration free energy into individual contributions [Marcus, Latimer, and tetraphenyl-arsonium/tetraphenyl-borate (TATB) methods] or (2) utilizing bulk thermodynamic and cluster data to estimate the free energy to insert a proton into water, including in principle an interfacial potential contribution [the cluster pair approximation (CPA)]. While the results for the hydration free energy of the proton agree remarkably well between the three approaches in the first category, the value differs from the CPA result by roughly +10 kcal/mol, implying a value for the effective electrochemical surface potential of water of -0.4 V. This paper provides a computational re-analysis of the TATB method for single-ion free energies using quasichemical theory. A previous study indicated a significant discrepancy between the free energies of hydration for the TA cation and the TB anion. We show that the main contribution to this large computed difference is an electrostatic artifact arising from modeling interactions in periodic boundaries. No attempt is made here to develop more accurate models for the local ion/solvent interactions that may lead to further small free energy differences between the TA and TB ions, but the results clarify the primary importance of interfacial potential effects for analysis of the various free energy scales. Results are also presented, related to the TATB assumption in the organic solvents dimethyl sulfoxide and 1,2-dichloroethane.

[Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

PubMed

Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

2013-01-01

To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

Direct Observation of Domain-Wall Surface Tension by Deflating or Inflating a Magnetic Bubble

NASA Astrophysics Data System (ADS)

Zhang, Xueying; Vernier, Nicolas; Zhao, Weisheng; Yu, Haiming; Vila, Laurent; Zhang, Yue; Ravelosona, Dafiné

2018-02-01

The surface energy of a magnetic domain wall (DW) strongly affects its static and dynamic behaviors. However, this effect is seldom directly observed, and some of the related phenomena are not well understood. Moreover, a reliable method to quantify the DW surface energy is still absent. Here, we report a series of experiments in which the DW surface energy becomes a dominant parameter. We observe that a semicircular magnetic domain bubble can spontaneously collapse under the Laplace pressure induced by DW surface energy. We further demonstrate that the surface energy can lead to a geometrically induced pinning when the DW propagates in a Hall cross or from a nanowire into a nucleation pad. Based on these observations, we develop two methods to quantify the DW surface energy, which can be very helpful in the estimation of intrinsic parameters such as Dzyaloshinskii-Moriya interactions or exchange stiffness in magnetic ultrathin films.

An Improved Neutron Transport Algorithm for HZETRN

NASA Technical Reports Server (NTRS)

Slaba, Tony C.; Blattnig, Steve R.; Clowdsley, Martha S.; Walker, Steven A.; Badavi, Francis F.

2010-01-01

Long term human presence in space requires the inclusion of radiation constraints in mission planning and the design of shielding materials, structures, and vehicles. In this paper, the numerical error associated with energy discretization in HZETRN is addressed. An inadequate numerical integration scheme in the transport algorithm is shown to produce large errors in the low energy portion of the neutron and light ion fluence spectra. It is further shown that the errors result from the narrow energy domain of the neutron elastic cross section spectral distributions, and that an extremely fine energy grid is required to resolve the problem under the current formulation. Two numerical methods are developed to provide adequate resolution in the energy domain and more accurately resolve the neutron elastic interactions. Convergence testing is completed by running the code for various environments and shielding materials with various energy grids to ensure stability of the newly implemented method.

Modern problems of thermodynamics

NASA Astrophysics Data System (ADS)

Novikov, I. I.

2012-12-01

The role of energy and methods of its saving for the development of human society and life are analyzed. The importance of future use of space energy flows and energy of water and air oceans is emphasized. The authors consider the idea of the unit for production of electric energy and pure substances using sodium chloride which reserves are limitless on the planet. Looking retrospectively at the development of power engineering from the elementary fire to modern electric power station, we see that the used method of heat production, namely by direct interaction of fuel and oxidizer, is the simplest. However, it may be possible to combust coal, i.e., carbon in salt melt, for instance, sodium chloride that would be more rational and efficient. If the stated problems are solved positively, we would master all energy properties of the substance; and this is the main problem of thermodynamics being one of the sciences on energy.

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

PubMed Central

Fiorucci, Sébastien; Zacharias, Martin

2010-01-01

Abstract Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. PMID:20441756

Polarizable atomistic calculation of site energy disorder in amorphous Alq3.

PubMed

Nagata, Yuki

2010-02-01

A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8-hydroxyquinolinato)aluminum (Alq(3)) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight-binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq(3) and the effect of the polarization on the site energy disorder is discussed.

Collisional quenching at ultralow energies: controlling efficiency with internal state selection.

PubMed

Bovino, S; Bodo, E; Gianturco, F A

2007-12-14

Calculations have been carried out for the vibrational quenching of excited H(2) molecules which collide with Li(+) ions at ultralow energies. The dynamics has been treated exactly using the well-known quantum coupled-channel expansions over different initial vibrational levels. The overall interaction potential has been obtained from the calculations carried out earlier by our group using highly correlated ab initio methods. The results indicate that specific features of the scattering observables, e.g., the appearance of Ramsauer-Townsend minima in elastic channel cross sections and the marked increase of the cooling rates from specific initial states, can be linked to potential properties at vanishing energies (sign and size of scattering lengths) and to the presence of either virtual states or bound states. The suggestion is made such that by selecting the initial state preparation of the molecular partners, the ionic interactions would be amenable to controlling quenching efficiency at ultralow energies.

Mesoscale Thermodynamic Analysis of Atomic-Scale Dislocation-Obstacle Interactions Simulated by Molecular Dynamics

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

Monet, Giath; Bacon, David J; Osetskiy, Yury N

2010-01-01

Given the time and length scales in molecular dynamics (MD) simulations of dislocation-defect interactions, quantitative MD results cannot be used directly in larger scale simulations or compared directly with experiment. A method to extract fundamental quantities from MD simulations is proposed here. The first quantity is a critical stress defined to characterise the obstacle resistance. This mesoscopic parameter, rather than the obstacle 'strength' designed for a point obstacle, is to be used for an obstacle of finite size. At finite temperature, our analyses of MD simulations allow the activation energy to be determined as a function of temperature. The resultsmore » confirm the proportionality between activation energy and temperature that is frequently observed by experiment. By coupling the data for the activation energy and the critical stress as functions of temperature, we show how the activation energy can be deduced at a given value of the critical stress.« less

A budget of energy transfer in a sustained vocal folds vibration in glottis

NASA Astrophysics Data System (ADS)

Zhang, Lucy; Yang, Jubiao; Krane, Michael

2016-11-01

A set of force and energy balance equations using the control volume approach is derived based on the first principles of physics for a sustained vocal folds vibration in glottis. The control volume analysis is done for compressible airflow in a moving and deforming control volume in the vicinity of the vocal folds. The interaction between laryngeal airflow and vocal folds are successfully simulated using the modified Immersed Finite Element Method (mIFEM), a fully coupled approach to simulate fluid-structure interactions. Detailed mathematical terms are separated out for deeper physical understanding and utilization of mechanical energy is quantified with the derived equation. The results show that majority of energy input is consumed for driving laryngeal airflow, while a smaller portion is for compensating viscous losses in and sustaining the vibration of the vocal folds. We acknowledge the funding support of NIH 2R01DC005642-10A1.

Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes.

PubMed

Lee, Mi Kyung; Coker, David F

2016-08-18

An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation.

Probing neutrino mass hierarchy by comparing the charged-current and neutral-current interaction rates of supernova neutrinos

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

Lai, Kwang-Chang; Leung Center for Cosmology and Particle Astrophysics; Lee, Fei-Fan

2016-07-22

The neutrino mass hierarchy is one of the neutrino fundamental properties yet to be determined. We introduce a method to determine neutrino mass hierarchy by comparing the interaction rate of neutral current (NC) interactions, ν(ν-bar)+p→ν(ν-bar)+p, and inverse beta decays (IBD), ν-bar{sub e}+p→n+e{sup +}, of supernova neutrinos in scintillation detectors. Neutrino flavor conversions inside the supernova are sensitive to neutrino mass hierarchy. Due to Mikheyev-Smirnov-Wolfenstein effects, the full swapping of ν-bar{sub e} flux with the ν-bar{sub x} (x=μ, τ) one occurs in the inverted hierarchy, while such a swapping does not occur in the normal hierarchy. As a result, more highmore » energy IBD events occur in the detector for the inverted hierarchy than the high energy IBD events in the normal hierarchy. By comparing IBD interaction rate with the mass hierarchy independent NC interaction rate, one can determine the neutrino mass hierarchy.« less

Probing neutrino mass hierarchy by comparing the charged-current and neutral-current interaction rates of supernova neutrinos

NASA Astrophysics Data System (ADS)

Lai, Kwang-Chang; Lee, Fei-Fan; Lee, Feng-Shiuh; Lin, Guey-Lin; Liu, Tsung-Che; Yang, Yi

2016-07-01

The neutrino mass hierarchy is one of the neutrino fundamental properties yet to be determined. We introduce a method to determine neutrino mass hierarchy by comparing the interaction rate of neutral current (NC) interactions, ν(bar nu) + p → ν(bar nu) + p, and inverse beta decays (IBD), bar nue + p → n + e+, of supernova neutrinos in scintillation detectors. Neutrino flavor conversions inside the supernova are sensitive to neutrino mass hierarchy. Due to Mikheyev-Smirnov-Wolfenstein effects, the full swapping of bar nue flux with the bar nux (x = μ, τ) one occurs in the inverted hierarchy, while such a swapping does not occur in the normal hierarchy. As a result, more high energy IBD events occur in the detector for the inverted hierarchy than the high energy IBD events in the normal hierarchy. By comparing IBD interaction rate with the mass hierarchy independent NC interaction rate, one can determine the neutrino mass hierarchy.

Ab initio study of the RbSr electronic structure: potential energy curves, transition dipole moments, and permanent electric dipole moments.

PubMed

Pototschnig, Johann V; Krois, Günter; Lackner, Florian; Ernst, Wolfgang E

2014-12-21

Excited states and the ground state of the diatomic molecule RbSr were calculated by post Hartree-Fock molecular orbital theory up to 22 000 cm(-1). We applied a multireference configuration interaction calculation based on multiconfigurational self-consistent field wave functions. Both methods made use of effective core potentials and core polarization potentials. Potential energy curves, transition dipole moments, and permanent electric dipole moments were determined for RbSr and could be compared with other recent calculations. We found a good agreement with experimental spectra, which have been obtained recently by helium nanodroplet isolation spectroscopy. For the lowest two asymptotes (Rb (5s (2)S) + Sr (5s4d (3)P°) and Rb (5p (2)P°) + Sr (5s(2) (1)S)), which exhibit a significant spin-orbit coupling, we included relativistic effects by two approaches, one applying the Breit-Pauli Hamiltonian to the multireference configuration interaction wave functions, the other combining a spin-orbit Hamiltonian and multireference configuration interaction potential energy curves. Using the results for the relativistic potential energy curves that correspond to the Rb (5s (2)S) + Sr (5s4d (3)P°) asymptote, we have simulated dispersed fluorescence spectra as they were recently measured in our lab. The comparison with experimental data allows to benchmark both methods and demonstrate that spin-orbit coupling has to be included for the lowest states of RbSr.

A periodic energy decomposition analysis method for the investigation of chemical bonding in extended systems

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

Raupach, Marc; Tonner, Ralf, E-mail: tonner@chemie.uni-marburg.de

The development and first applications of a new periodic energy decomposition analysis (pEDA) scheme for extended systems based on the Kohn-Sham approach to density functional theory are described. The pEDA decomposes the bonding energy between two fragments (e.g., the adsorption energy of a molecule on a surface) into several well-defined terms: preparation, electrostatic, Pauli repulsion, and orbital relaxation energies. This is complemented by consideration of dispersion interactions via a pairwise scheme. One major extension toward a previous implementation [Philipsen and Baerends, J. Phys. Chem. B 110, 12470 (2006)] lies in the separate discussion of electrostatic and Pauli and the additionmore » of a dispersion term. The pEDA presented here for an implementation based on atomic orbitals can handle restricted and unrestricted fragments for 0D to 3D systems considering periodic boundary conditions with and without the determination of fragment occupations. For the latter case, reciprocal space sampling is enabled. The new method gives comparable results to established schemes for molecular systems and shows good convergence with respect to the basis set (TZ2P), the integration accuracy, and k-space sampling. Four typical bonding scenarios for surface-adsorbate complexes were chosen to highlight the performance of the method representing insulating (CO on MgO(001)), metallic (H{sub 2} on M(001), M = Pd, Cu), and semiconducting (CO and C{sub 2}H{sub 2} on Si(001)) substrates. These examples cover diverse substrates as well as bonding scenarios ranging from weakly interacting to covalent (shared electron and donor acceptor) bonding. The results presented lend confidence that the pEDA will be a powerful tool for the analysis of surface-adsorbate bonding in the future, enabling the transfer of concepts like ionic and covalent bonding, donor-acceptor interaction, steric repulsion, and others to extended systems.« less

Calculation of protein-ligand binding affinities.

PubMed

Gilson, Michael K; Zhou, Huan-Xiang

2007-01-01

Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.

Carbon dioxide capture using covalent organic frameworks (COFs) type material-a theoretical investigation.

PubMed

Dash, Bibek

2018-04-26

The present work deals with a density functional theory (DFT) study of porous organic framework materials containing - groups for CO 2 capture. In this study, first principle calculations were performed for CO 2 adsorption using N-containing covalent organic framework (COFs) models. Ab initio and DFT-based methods were used to characterize the N-containing porous model system based on their interaction energies upon complexing with CO 2 and nitrogen gas. Binding energies (BEs) of CO 2 and N 2 molecules with the polymer framework were calculated with DFT methods. Hybrid B3LYP and second order MP2 methods combined with of Pople 6-31G(d,p) and correlation consistent basis sets cc-pVDZ, cc-pVTZ and aug-ccVDZ were used to calculate BEs. The effect of linker groups in the designed covalent organic framework model system on the CO 2 and N 2 interactions was studied using quantum calculations.

Fast, metadynamics-based method for prediction of the stereochemistry-dependent relative free energies of ligand-receptor interactions.

PubMed

Plazinska, Anita; Plazinski, Wojciech; Jozwiak, Krzysztof

2014-04-30

The computational approach applicable for the molecular dynamics (MD)-based techniques is proposed to predict the ligand-protein binding affinities dependent on the ligand stereochemistry. All possible stereoconfigurations are expressed in terms of one set of force-field parameters [stereoconfiguration-independent potential (SIP)], which allows for calculating all relative free energies by only single simulation. SIP can be used for studying diverse, stereoconfiguration-dependent phenomena by means of various computational techniques of enhanced sampling. The method has been successfully tested on the β2-adrenergic receptor (β2-AR) binding the four fenoterol stereoisomers by both metadynamics simulations and replica-exchange MD. Both the methods gave very similar results, fully confirming the presence of stereoselective effects in the fenoterol-β2-AR interactions. However, the metadynamics-based approach offered much better efficiency of sampling which allows for significant reduction of the unphysical region in SIP. Copyright © 2014 Wiley Periodicals, Inc.

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

Azadi, Sam, E-mail: s.azadi@ucl.ac.uk; Cohen, R. E.

We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimalmore » VMC and DMC binding energies of −2.3(4) and −2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is −2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.« less

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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