Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated.

PubMed

Ivanov, Sergei D; Grant, Ian M; Marx, Dominik

2015-09-28

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

PubMed

Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

2016-08-25

Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

Ab initio theory of the N2V defect in diamond for quantum memory implementation

NASA Astrophysics Data System (ADS)

Udvarhelyi, Péter; Thiering, Gergő; Londero, Elisa; Gali, Adam

2017-10-01

The N2V defect in diamond is characterized by means of ab initio methods relying on density functional theory calculated parameters of a Hubbard model Hamiltonian. It is shown that this approach appropriately describes the energy levels of correlated excited states induced by this defect. By determining its critical magneto-optical parameters, we propose to realize a long-living quantum memory by N2V defect, i.e., H 3 color center in diamond.

Spectroscopic fingerprints of toroidal nuclear quantum delocalization via ab initio path integral simulations.

PubMed

Schütt, Ole; Sebastiani, Daniel

2013-04-05

We investigate the quantum-mechanical delocalization of hydrogen in rotational symmetric molecular systems. To this purpose, we perform ab initio path integral molecular dynamics simulations of a methanol molecule to characterize the quantum properties of hydrogen atoms in a representative system by means of their real-space and momentum-space densities. In particular, we compute the spherically averaged momentum distribution n(k) and the pseudoangular momentum distribution n(kθ). We interpret our results by comparing them to path integral samplings of a bare proton in an ideal torus potential. We find that the hydroxyl hydrogen exhibits a toroidal delocalization, which leads to characteristic fingerprints in the line shapes of the momentum distributions. We can describe these specific spectroscopic patterns quantitatively and compute their onset as a function of temperature and potential energy landscape. The delocalization patterns in the projected momentum distribution provide a promising computational tool to address the intriguing phenomenon of quantum delocalization in condensed matter and its spectroscopic characterization. As the momentum distribution n(k) is also accessible through Nuclear Compton Scattering experiments, our results will help to interpret and understand future measurements more thoroughly. Copyright © 2012 Wiley Periodicals, Inc.

Embedding Fragment ab Initio Model Potentials in CASSCF/CASPT2 Calculations of Doped Solids: Implementation and Applications.

PubMed

Swerts, Ben; Chibotaru, Liviu F; Lindh, Roland; Seijo, Luis; Barandiaran, Zoila; Clima, Sergiu; Pierloot, Kristin; Hendrickx, Marc F A

2008-04-01

In this article, we present a fragment model potential approach for the description of the crystalline environment as an extension of the use of embedding ab initio model potentials (AIMPs). The biggest limitation of the embedding AIMP method is the spherical nature of its model potentials. This poses problems as soon as the method is applied to crystals containing strongly covalently bonded structures with highly nonspherical electron densities. The newly proposed method addresses this problem by keeping the full electron density as its model potential, thus allowing one to group sets of covalently bonded atoms into fragments. The implementation in the MOLCAS 7.0 quantum chemistry package of the new method, which we call the embedding fragment ab inito model potential method (embedding FAIMP), is reported here, together with results of CASSCF/CASPT2 calculations. The developed methodology is applied for two test problems: (i) the investigation of the lowest ligand field states (2)A1 and (2)B1 of the Cr(V) defect in the YVO4 crystal and (ii) the investigation of the lowest ligand field and ligand-metal charge transfer (LMCT) states at the Mn(II) substitutional impurity doped into CaCO3. Comparison with similar calculations involving AIMPs for all environmental atoms, including those from covalently bounded units, shows that the FAIMP treatment of the YVO4 units surrounding the CrO4(3-) cluster increases the excitation energy (2)B1 → (2)A1 by ca. 1000 cm(-1) at the CASSCF level of calculation. In the case of the Mn(CO3)6(10-) cluster, the FAIMP treatment of the CO3(2-) units of the environment give smaller corrections, of ca. 100 cm(-1), for the ligand-field excitation energies, which is explained by the larger ligands of this cluster. However, the correction for the energy of the lowest LMCT transition is found to be ca. 600 cm(-1) for the CASSCF and ca. 1300 cm(-1) for the CASPT2 calculation.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

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

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previousmore » spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.« less

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

NASA Astrophysics Data System (ADS)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment.

PubMed

Liu, Hanchao; Wang, Yimin; Bowman, Joel M

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Ab initio relaxation times and time-dependent Hamiltonians within the steepest-entropy-ascent quantum thermodynamic framework

NASA Astrophysics Data System (ADS)

Kim, Ilki; von Spakovsky, Michael R.

2017-08-01

Quantum systems driven by time-dependent Hamiltonians are considered here within the framework of steepest-entropy-ascent quantum thermodynamics (SEAQT) and used to study the thermodynamic characteristics of such systems. In doing so, a generalization of the SEAQT framework valid for all such systems is provided, leading to the development of an ab initio physically relevant expression for the intrarelaxation time, an important element of this framework and one that had as of yet not been uniquely determined as an integral part of the theory. The resulting expression for the relaxation time is valid as well for time-independent Hamiltonians as a special case and makes the description provided by the SEAQT framework more robust at the fundamental level. In addition, the SEAQT framework is used to help resolve a fundamental issue of thermodynamics in the quantum domain, namely, that concerning the unique definition of process-dependent work and heat functions. The developments presented lead to the conclusion that this framework is not just an alternative approach to thermodynamics in the quantum domain but instead one that uniquely sheds new light on various fundamental but as of yet not completely resolved questions of thermodynamics.

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

Thiessen, P. A.; Treder, H.-J.

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

2015-07-15

There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

NASA Astrophysics Data System (ADS)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

PubMed

Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-16

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

DOE PAGES

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.; ...

2018-04-19

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

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

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

Quantum Theory of Jaynes' Principle, Bayes' Theorem, and Information

NASA Astrophysics Data System (ADS)

Haken, Hermann

2014-12-01

After a reminder of Jaynes' maximum entropy principle and of my quantum theoretical extension, I consider two coupled quantum systems A,B and formulate a quantum version of Bayes' theorem. The application of Feynman's disentangling theorem allows me to calculate the conditional density matrix ρ (A|B) , if system A is an oscillator (or a set of them), linearly coupled to an arbitrary quantum system B. Expectation values can simply be calculated by means of the normalization factor of ρ (A|B) that is derived.

Increasing the efficiency and accuracy of time-resolved electronic spectra calculations with on-the-fly ab initio quantum dynamics methods

NASA Astrophysics Data System (ADS)

Vanicek, Jiri

2014-03-01

Rigorous quantum-mechanical calculations of coherent ultrafast electronic spectra remain difficult. I will present several approaches developed in our group that increase the efficiency and accuracy of such calculations: First, we justified the feasibility of evaluating time-resolved spectra of large systems by proving that the number of trajectories needed for convergence of the semiclassical dephasing representation/phase averaging is independent of dimensionality. Recently, we further accelerated this approximation with a cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. The accuracy of potential energy surfaces was increased by combining the dephasing representation with accurate on-the-fly ab initio electronic structure calculations, including nonadiabatic and spin-orbit couplings. Finally, the inherent semiclassical approximation was removed in the exact quantum Gaussian dephasing representation, in which semiclassical trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. Among other examples I will present an on-the-fly ab initio semiclassical dynamics calculation of the dispersed time-resolved stimulated emission spectrum of the 54-dimensional azulene. This research was supported by EPFL and by the Swiss National Science Foundation NCCR MUST (Molecular Ultrafast Science and Technology) and Grant No. 200021124936/1.

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

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

Xie, Binbin; Liu, Lihong; Cui, Ganglong

2015-11-21

In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as themore » final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.« less

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

PubMed

Hagiwara, Yohsuke; Tateno, Masaru

2010-10-20

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

Characterization of Asia 1 sdAb from Camels Bactrianus (C. bactrianus) and Conjugation with Quantum Dots for Imaging FMDV in BHK-21 Cells

PubMed Central

Shang, Youjun; Sun, Shiqi; Zhou, Guangqing; Jin, Ye; Tian, Hong; Wu, Jinyan; Liu, Xiangtao

2013-01-01

Foot-and-mouth disease (FMD), caused by FMD virus (FMDV), is a highly contagious viral disease affecting cloven-hoofed animals. Camelids have a unique immunoglobulin profile, with the smallest functional heavy-chain antibodies (sdAb or VHH) naturally devoid of light chains with antigen-binding capacity. We screened and characterized five sdAbs against FMDV by immunized library from C. bactrianus with Asia 1 virus-like particles (VLPs). Three of five recombinant sdAbs were stably expressed in E.coli, remained highly soluble, and were serotype-specific for VP1 protein of FMDV Asia 1 by ELISA. These failed to completely neutralize the Asia 1 virus. According to the KD value of binding affinity to three sdAbs, which ranged from 0.44 to 0.71 nm by SPR, sdAb-C6 was selected and conjugated with Zn/CdSe quantum dots (QDs) to form a QDs-C6 probe, which was used to trace and image the subcellular location of FMDV in BHK-21 cells. The results show that FMD virions were observed from 3 h.p.i., and most of virions were distributed on one side of the nucleus in the cytoplasm. We demonstrate the utility of sdAbs as functionalized QDs are powerful tools for FMDV research. PMID:23737944

Parallel Quantum Circuit in a Tunnel Junction

NASA Astrophysics Data System (ADS)

Faizy Namarvar, Omid; Dridi, Ghassen; Joachim, Christian

2016-07-01

Spectral analysis of 1 and 2-states per line quantum bus are normally sufficient to determine the effective Vab(N) electronic coupling between the emitter and receiver states through the bus as a function of the number N of parallel lines. When Vab(N) is difficult to determine, an Heisenberg-Rabi time dependent quantum exchange process must be triggered through the bus to capture the secular oscillation frequency Ωab(N) between those states. Two different linear and regimes are demonstrated for Ωab(N) as a function of N. When the initial preparation is replaced by coupling of the quantum bus to semi-infinite electrodes, the resulting quantum transduction process is not faithfully following the Ωab(N) variations. Because of the electronic transparency normalisation to unity and of the low pass filter character of this transduction, large Ωab(N) cannot be captured by the tunnel junction. The broadly used concept of electrical contact between a metallic nanopad and a molecular device must be better described as a quantum transduction process. At small coupling and when N is small enough not to compensate for this small coupling, an N2 power law is preserved for Ωab(N) and for Vab(N).

Parallel Quantum Circuit in a Tunnel Junction

PubMed Central

Faizy Namarvar, Omid; Dridi, Ghassen; Joachim, Christian

2016-01-01

Spectral analysis of 1 and 2-states per line quantum bus are normally sufficient to determine the effective Vab(N) electronic coupling between the emitter and receiver states through the bus as a function of the number N of parallel lines. When Vab(N) is difficult to determine, an Heisenberg-Rabi time dependent quantum exchange process must be triggered through the bus to capture the secular oscillation frequency Ωab(N) between those states. Two different linear and regimes are demonstrated for Ωab(N) as a function of N. When the initial preparation is replaced by coupling of the quantum bus to semi-infinite electrodes, the resulting quantum transduction process is not faithfully following the Ωab(N) variations. Because of the electronic transparency normalisation to unity and of the low pass filter character of this transduction, large Ωab(N) cannot be captured by the tunnel junction. The broadly used concept of electrical contact between a metallic nanopad and a molecular device must be better described as a quantum transduction process. At small coupling and when N is small enough not to compensate for this small coupling, an N2 power law is preserved for Ωab(N) and for Vab(N). PMID:27453262

Parallel Quantum Circuit in a Tunnel Junction.

PubMed

Faizy Namarvar, Omid; Dridi, Ghassen; Joachim, Christian

2016-07-25

Spectral analysis of 1 and 2-states per line quantum bus are normally sufficient to determine the effective Vab(N) electronic coupling between the emitter and receiver states through the bus as a function of the number N of parallel lines. When Vab(N) is difficult to determine, an Heisenberg-Rabi time dependent quantum exchange process must be triggered through the bus to capture the secular oscillation frequency Ωab(N) between those states. Two different linear and regimes are demonstrated for Ωab(N) as a function of N. When the initial preparation is replaced by coupling of the quantum bus to semi-infinite electrodes, the resulting quantum transduction process is not faithfully following the Ωab(N) variations. Because of the electronic transparency normalisation to unity and of the low pass filter character of this transduction, large Ωab(N) cannot be captured by the tunnel junction. The broadly used concept of electrical contact between a metallic nanopad and a molecular device must be better described as a quantum transduction process. At small coupling and when N is small enough not to compensate for this small coupling, an N(2) power law is preserved for Ωab(N) and for Vab(N).

Superconducting quantum circuits theory and application

NASA Astrophysics Data System (ADS)

Deng, Xiuhao

Superconducting quantum circuit models are widely used to understand superconducting devices. This thesis consists of four studies wherein the superconducting quantum circuit is used to illustrate challenges related to quantum information encoding and processing, quantum simulation, quantum signal detection and amplification. The existence of scalar Aharanov-Bohm phase has been a controversial topic for decades. Scalar AB phase, defined as time integral of electric potential, gives rises to an extra phase factor in wavefunction. We proposed a superconducting quantum Faraday cage to detect temporal interference effect as a consequence of scalar AB phase. Using the superconducting quantum circuit model, the physical system is solved and resulting AB effect is predicted. Further discussion in this chapter shows that treating the experimental apparatus quantum mechanically, spatial scalar AB effect, proposed by Aharanov-Bohm, can't be observed. Either a decoherent interference apparatus is used to observe spatial scalar AB effect, or a quantum Faraday cage is used to observe temporal scalar AB effect. The second study involves protecting a quantum system from losing coherence, which is crucial to any practical quantum computation scheme. We present a theory to encode any qubit, especially superconducting qubits, into a universal quantum degeneracy point (UQDP) where low frequency noise is suppressed significantly. Numerical simulations for superconducting charge qubit using experimental parameters show that its coherence time is prolong by two orders of magnitude using our universal degeneracy point approach. With this improvement, a set of universal quantum gates can be performed at high fidelity without losing too much quantum coherence. Starting in 2004, the use of circuit QED has enabled the manipulation of superconducting qubits with photons. We applied quantum optical approach to model coupled resonators and obtained a four-wave mixing toolbox to operate photons

Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

NASA Astrophysics Data System (ADS)

Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

1997-07-01

Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

Ab initio study of novel carbon nanofoam structure as an anode material for Li secondary battery

NASA Astrophysics Data System (ADS)

Park, Hanjin; Park, Sora; Kang, Seoung-Hun; Kwon, Young-Kyun

2014-03-01

Using ab inito density functional theory, we investigate the adsorption and diffusion properties of Li atoms on a new carbon nanostructure, which may be used as an anode of Li secondary battery. We focus on a special carbon nanofoam structure consisting of Schwarzite structures with negative Gaussian curvature as core parts, which are interconnected through (4,4) CNT segments. Considering the symmetry of the nanofoam structure, we find various Li adsorption sites exhibiting relatively large binding energies (>= 2 . 00 eV). Based on these adsorption sites, we identify several diffusion paths on the outside or inside surface of the nanofoam structure and examine the diffusion barriers along the paths. Our results show that Li atom can diffuse almost freely due to its low energy barriers on both outside and inside surfaces. Finally, we also evaluate the energy gain tendency and the volume expansion as well as the average binding energy while adding Li atoms to estimate the Li-capacity and recyclability of the system, which are important characterisitics for anode materials. We conclude that the carbon nanofoam structure would be better as an anode material than graphite in Li capacity and volume expansion.

New ab initio potential surfaces and three-dimensional quantum dynamics for transition state spectroscopy in ozone photodissociation

NASA Astrophysics Data System (ADS)

Yamashita, Koichi; Morokuma, Keiji; Le Quéré, Frederic; Leforestier, Claude

1992-04-01

New ab initio potential energy surfaces (PESs) of the ground and B ( 1B 2) states of ozone have been calculated with the CASSCF-SECI/DZP method to describe the three-dimensional photodissociation process. The dissociation energy of the ground state and the vertical barrier height of the B PES are obtained to be 0.88 and 1.34 eV, respectively, in better agreement with the experimental values than the previous calculation. The photodissociation autocorrelation function, calculated on the new B PES, based on exact three-dimensional quantum dynamics, reproduces well the main recurrence feature extracted from the experimental spectra.

Ab initio theory of spin-orbit coupling for quantum bits in diamond exhibiting dynamic Jahn-Teller effect

NASA Astrophysics Data System (ADS)

Gali, Adam; Thiering, Gergő

Dopants in solids are promising candidates for implementations of quantum bits for quantum computing. In particular, the high-spin negatively charged nitrogen-vacancy defect (NV) in diamond has become a leading contender in solid-state quantum information processing. The initialization and readout of the spin is based on the spin-selective decay of the photo-excited electron to the ground state which is mediated by spin-orbit coupling between excited states states and phonons. Generally, the spin-orbit coupling plays a crucial role in the optical spinpolarization and readout of NV quantum bit (qubit) and alike. Strong electron-phonon coupling in dynamic Jahn-Teller (DJT) systems can substantially influence the effective strength of spin-orbit coupling. Here we show by ab initio supercell density functional theory (DFT) calculations that the intrinsic spin-orbit coupling is strongly damped by DJT effect in the triplet excited state that has a consequence on the rate of non-radiative decay. This theory is applied to the ground state of silicon-vacancy (SiV) and germanium-vacancy (GeV) centers in their negatively charged state that can also act like qubits. We show that the intrinsic spin-orbit coupling in SiV and GeV centers is in the 100 GHz region, in contrast to the NV center of 10 GHz region. Our results provide deep insight in the nature of SiV and GeV qubits in diamond. EU FP7 DIADEMS project (Contract No. 611143).

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations

NASA Astrophysics Data System (ADS)

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-01

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and/or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S1) as well as the second excited singlet (S2) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S1 state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S2 state. Ab initio calculations using the density functional theory at B3LYP/6-31G** level corroborate well with the experimental observations.

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations.

PubMed

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-28

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and∕or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S(1)) as well as the second excited singlet (S(2)) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S(1) state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S(2) state. Ab initio calculations using the density functional theory at B3LYP∕6-31G∗∗ level corroborate well with the experimental observations.

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.

UTChem - A Program for Ab Initio Quantum Chemistry

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

Yanai, Takeshi; Nakano, Haruyuki; Nakajima, Takahito

2003-06-18

UTChem is a quantum chemistry software developed by Hirao's group at the University of Tokyo. UTChem is a research product of our work to develop new and better theoretical methods in quantum chemistry.

Quantum Dynamics Scattering Study of AB+CDE Reactions: A Seven Dimensional Treatment for the H2+C2H Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou

2003-01-01

A time-dependent wave-packet approach is presented for the quantum dynamics study of the AB+CDE reaction system for zero total angular momentum. A seven-degree-of-freedom calculation is employed to study the chemical reaction of H2+C2H yields H + C2H2 by treating C2H as a linear molecule. Initial state selected reaction probabilities are presented for various initial ro-vibrational states. This study shows that vibrational excitation of H2 enhances the reaction probability, whereas the excitation of C2H has only a small effect on the reactivity. An integral cross section is also reported for the initial ground states of H2 and C2H. The theoretical and experimental results agree with each other very well when the calculated seven dimensional results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculations.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

NASA Astrophysics Data System (ADS)

Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

2016-05-01

The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

Thomson backscattering diagnostics of nanosecond electron bunches in high space charge regime

NASA Astrophysics Data System (ADS)

Plachinda, Pavel

The trend over the last 50 years of down-scaling the silicon transistor to achieve faster computations has led to doubling of the number of transistors and computation speed over about every two years. However, this trend cannot be maintained due to the fundamental limitations of silicon as the main material for the semiconducting industry. Therefore, there is an active search for exploration of alternate materials. Among the possible candidates that can may be able to replace silicon is graphene which has recently gained the most attention. Unique properties of graphene include exceedingly high carrier mobility, tunable band gap, huge optical density of a monolayer, anomalous quantum Hall effect, and many others. To be suitable for microelectronic applications the material should be semiconductive, i.e. have a non-zero band gap. Pristine graphene is a semimetal, but by the virtue of doping the graphene surface with different molecules and radicals a band gap can be opened. Because the electronic properties of all materials are intimately related to their atomic structure, characterization of molecular and electronic structure of functionalizing groups is of high interest. The ab-inito (from the first principles) calculations provide a unique opportunity to study the influence of the dopants and thus allow exploration of the physical phenomena in functionalized graphene structures. This ability paves the road to probe the properties based on the intuitive structural information only. A great advantage of this approach lies in the opportunity for quick screening of various atomic structures. We conducted a series of ab-inito investigations of graphene functionalized with covalently and hapticly bound groups, and demonstrated possible practical usage of functionalized graphene for microelectronic and optical applications. This investigation showed that it is possible produce band gaps in graphene (i.e., produce semiconducting graphene) of about 1 eV, without

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Towards ab initio Calculations with the Dynamical Vertex Approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

2018-04-01

While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

Ab Initio Simulation of Charge Transfer at the Semiconductor Quantum Dot/TiO 2 Interface in Quantum Dot-Sensitized Solar Cells

DOE PAGES

Xin, Xukai; Li, Bo; Jung, Jaehan; ...

2014-07-24

Quantum dot-sensitized solar cells (QDSSCs) have emerged as a promising solar architecture for next-generation solar cells. The QDSSCs exhibit a remarkably fast electron transfer from the quantum dot (QD) donor to the TiO 2 acceptor with size quantization properties of QDs that allows for the modulation of band energies to control photoresponse and photoconversion efficiency of solar cells. In order to understand the mechanisms that underpin this rapid charge transfer, the electronic properties of CdSe and PbSe QDs with different sizes on the TiO 2 substrate are simulated using a rigorous ab initio density functional method. Our method capitalizes onmore » localized orbital basis set, which is computationally less intensive. Quite intriguingly, a remarkable set of electron bridging states between QDs and TiO 2 occurring via the strong bonding between the conduction bands of QDs and TiO 2 is revealed. Such bridging states account for the fast adiabatic charge transfer from the QD donor to the TiO 2 acceptor, and may be a general feature for strongly coupled donor/acceptor systems. All the QDs/TiO 2 systems exhibit type II band alignments, with conduction band offsets that increase with the decrease in QD size. This facilitates the charge transfer from QDs donors to TiO 2 acceptors and explains the dependence of the increased charge transfer rate with the decreased QD size.« less

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

Full-Dimensional Quantum Calculations of Vibrational Levels of NH4(+) and Isotopomers on An Accurate Ab Initio Potential Energy Surface.

PubMed

Yu, Hua-Gen; Han, Huixian; Guo, Hua

2016-04-14

Vibrational energy levels of the ammonium cation (NH4(+)) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4(+) and ND4(+) exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. The low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm(-1).

Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.

PubMed

Tavernelli, Ivano

2015-03-17

Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics

Ab-initio calculations of the proton location in topaz-OH, Al2SiO4(OH)2

NASA Astrophysics Data System (ADS)

Churakov, S. V.; Wunder, B.

The position of hydrogen in the structure of topaz-OH was determined by means of ab-initio quantum-mechanic calculations. Static lattice energy calculations predict the existence of four non-equivalent positions of protons, which are characterized by O4-H1... O1, O4-H2... O2, O4-H3... O3 and O4-H4... O4 hydrogen bonds. The distribution of the protons between positions of local equilibrium is controlled by the proton-proton avoidance rule and the strength of the hydrogen bonds. The most favourable configuration of hydrogen atoms is achieved for adjacent protons, which form O4-H3... O3 and O4-H4... O4 hydrogen bonds, respectively. The thermal excitation of atoms at a temperature of 55 K is large enough for the hydrogen atoms occasionally to change their positions to form O4-H1... O1 and O4-H2... O2 bonds. At ambient pressures and higher temperatures the protons are in a dynamic exchange between the allowed positions of local minima. As a consequence, for nearly room-temperature conditions, the dynamic change between different structural configurations leads to the violation of all possible symmetry elements and with that to space group #E5/E5#1. The flipping of the protons between different sites is achieved by simple rotation of the OH-dipole and does not produce any significant distortion of the framework of topaz, whose symmetry remains that of the space group Pbnm. Therefore, no reduction of symmetry has been observed in former X-ray studies on topaz-OH. Calculated IR absorption spectra of topaz-OH were found to be in good agreement with measured spectra. According to the calculations, the two favourable configurations of protons might correspond to the measured peak splitting within the OH-stretching range. An experimentally observed low-frequency band at 3520 cm-1 was assigned to the OH-stretching of the O4-H3... O3 bond, while the band at 3600 cm-1 was attributed to OH-stretching of the O4-H4... O4 hydrogen bond. The broad peak in FAR-IR frequency range at 100

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

Full-dimensional quantum calculations of vibrational levels of NH 4 + and isotopomers on an accurate ab initio potential energy surface

DOE PAGES

Hua -Gen Yu; Han, Huixian; Guo, Hua

2016-03-29

Vibrational energy levels of the ammonium cation (NH 4 +) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH 4 + and ND 4 + exhibit a polyad structure, characterized by a collective quantum number P = 2(v 1 + v 3) + v 2 + v 4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data ismore » better than 1 cm –1.« less

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Time-dependent wave packet simulations of transport through Aharanov-Bohm rings with an embedded quantum dot.

PubMed

Kreisbeck, C; Kramer, T; Molina, R A

2017-04-20

We have performed time-dependent wave packet simulations of realistic Aharonov-Bohm (AB) devices with a quantum dot embedded in one of the arms of the interferometer. The AB ring can function as a measurement device for the intrinsic transmission phase through the quantum dot, however, care has to be taken in analyzing the influence of scattering processes in the junctions of the interferometer arms. We consider a harmonic quantum dot and show how the Darwin-Fock spectrum emerges as a unique pattern in the interference fringes of the AB oscillations.

Ab initio calculation of the G peak intensity of graphene: Laser-energy and Fermi-energy dependence and importance of quantum interference effects

NASA Astrophysics Data System (ADS)

Reichardt, Sven; Wirtz, Ludger

2017-05-01

We present the results of a diagrammatic, fully ab initio calculation of the G peak intensity of graphene. The flexibility and generality of our approach enables us to go beyond the previous analytical calculations in the low-energy regime. We study the laser and Fermi energy dependence of the G peak intensity and analyze the contributions from resonant and nonresonant electronic transitions. In particular, we explicitly demonstrate the importance of quantum interference and nonresonant states for the G peak process. Our method of analysis and computational concept is completely general and can easily be applied to study other materials as well.

The coherent interlayer resistance of a single, rotated interface between two stacks of AB graphite

NASA Astrophysics Data System (ADS)

Habib, K. M. Masum; Sylvia, Somaia S.; Ge, Supeng; Neupane, Mahesh; Lake, Roger K.

2013-12-01

The coherent, interlayer resistance of a misoriented, rotated interface between two stacks of AB graphite is determined for a variety of misorientation angles. The quantum-resistance of the ideal AB stack is on the order of 1 to 10 mΩ μm2. For small rotation angles, the coherent interlayer resistance exponentially approaches the ideal quantum resistance at energies away from the charge neutrality point. Over a range of intermediate angles, the resistance increases exponentially with cell size for minimum size unit cells. Larger cell sizes, of similar angles, may not follow this trend. The energy dependence of the interlayer transmission is described.

SAXS-WAXS studies of the low-resolution structure in solution of xylose/glucose isomerase from Streptomyces rubiginosus

NASA Astrophysics Data System (ADS)

Kozak, Maciej; Taube, Michał

2009-10-01

The structure and conformation of molecule of xylose/glucose isomerase from Streptomyces rubiginosus in solution (at pH 6 and 7.6; with and without the substrate) has been studied by small- and wide-angle scattering of synchrotron radiation (SAXS-WAXS). On the basis of the SAXS-WAXS data, the low-resolution structure in solution has been reconstructed using ab inito methods. A comparison of the models of glucose isomerase shows only small differences between the model in solution and the crystal structure.

Ab Initio Quantum Monte Carlo Simulation of the Warm Dense Electron Gas in the Thermodynamic Limit

DOE PAGES

Dornheim, Tobias; Groth, Simon; Sjostrom, Travis; ...

2016-10-07

Here we perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N = 1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy F xc of the macroscopic electron gas withmore » an unprecedented accuracy of | Δ V | / | V | , | Δ F xc | / | F | xc ~ 10 $-$3. Finally, a comparison of our new data to the recent parametrization of F xc by Karasiev et al. [Phys. Rev. Lett. 112, 076403 (2014)] reveals significant deviations to the latter.« less

Quantum-ring spin interference device tuned by quantum point contacts

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

Diago-Cisneros, Leo; Mireles, Francisco

2013-11-21

We introduce a spin-interference device that comprises a quantum ring (QR) with three embedded quantum point contacts (QPCs) and study theoretically its spin transport properties in the presence of Rashba spin-orbit interaction. Two of the QPCs conform the lead-to-ring junctions while a third one is placed symmetrically in the upper arm of the QR. Using an appropriate scattering model for the QPCs and the S-matrix scattering approach, we analyze the role of the QPCs on the Aharonov-Bohm (AB) and Aharonov-Casher (AC) conductance oscillations of the QR-device. Exact formulas are obtained for the spin-resolved conductances of the QR-device as a functionmore » of the confinement of the QPCs and the AB/AC phases. Conditions for the appearance of resonances and anti-resonances in the spin-conductance are derived and discussed. We predict very distinctive variations of the QR-conductance oscillations not seen in previous QR proposals. In particular, we find that the interference pattern in the QR can be manipulated to a large extend by varying electrically the lead-to-ring topological parameters. The latter can be used to modulate the AB and AC phases by applying gate voltage only. We have shown also that the conductance oscillations exhibits a crossover to well-defined resonances as the lateral QPC confinement strength is increased, mapping the eigenenergies of the QR. In addition, unique features of the conductance arise by varying the aperture of the upper-arm QPC and the Rashba spin-orbit coupling. Our results may be of relevance for promising spin-orbitronics devices based on quantum interference mechanisms.« less

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good

Andreev bound states probed in three-terminal quantum dots

NASA Astrophysics Data System (ADS)

Gramich, J.; Baumgartner, A.; Schönenberger, C.

2017-11-01

Andreev bound states (ABSs) are well-defined many-body quantum states that emerge from the hybridization of individual quantum dot (QD) states with a superconductor and exhibit very rich and fundamental phenomena. We demonstrate several electron transport phenomena mediated by ABSs that form on three-terminal carbon nanotube (CNT) QDs, with one superconducting (S) contact in the center and two adjacent normal-metal (N) contacts. Three-terminal spectroscopy allows us to identify the coupling to the N contacts as the origin of the Andreev resonance (AR) linewidths and to determine the critical coupling strengths to S, for which a ground state (or quantum phase) transition in such S-QD systems can occur. In addition, we ascribe replicas of the lowest-energy ABS resonance to transitions between the ABS and odd-parity excited QD states, a process we call excited state ABS resonances. In the conductance between the two N contacts we find a characteristic pattern of positive and negative differential subgap conductance, which we explain by considering two nonlocal processes, the creation of Cooper pairs in S by electrons from both N terminals, and a transport mechanism we call resonant ABS tunneling, possible only in multiterminal QD devices. In the latter process, electrons are transferred via the ABS without effectively creating Cooper pairs in S. The three-terminal geometry also allows spectroscopy experiments with different boundary conditions, for example by leaving S floating. Surprisingly, we find that, depending on the boundary conditions and the device parameters, the experiments either show single-particle Coulomb blockade resonances, ABS characteristics, or both in the same measurements, seemingly contradicting the notion of ABSs replacing the single-particle states as eigenstates of the QD. We qualitatively explain these results as originating from the finite time scale required for the coherent oscillations between the superposition states after a single

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

NASA Astrophysics Data System (ADS)

Kubas, Adam; Hoffmann, Felix; Heck, Alexander; Oberhofer, Harald; Elstner, Marcus; Blumberger, Jochen

2014-03-01

We introduce a database (HAB11) of electronic coupling matrix elements (Hab) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute Hab values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

Quantum state preparation of homonuclear molecular ions enabled via a cold buffer gas: An ab initio study for the H2+ and the D2+ case

NASA Astrophysics Data System (ADS)

Schiller, S.; Kortunov, I.; Hernández Vera, M.; Gianturco, F.; da Silva, H.

2017-04-01

Precision vibrational spectroscopy of the molecular hydrogen ions is of significant interest for determining fundamental constants, for searching for new forces, and for testing quantum electrodynamics calculations. Future experiments can profit from the ability of preparing molecular hydrogen ions at ultralow kinetic energy and in preselected internal states, with respect to vibration, rotation, and spin degrees of freedom. For the homonuclear ions (H2+ , D2+ ), direct laser cooling of the rotational degree of freedom is not feasible. We show by quantum calculations that rotational cooling by cold He buffer gas is an effective approach. For this purpose we have computed the energy-dependent cross sections for rotationally elastic and inelastic collisions, h2+ (v =0 ,N ) +He → h2+ (v =0 ,N') +He (where h =H ,D ) , using ab initio coupled-channel calculations. We find that rotational cooling to the lowest rotational state is possible within tens of seconds under experimentally realistic conditions. We furthermore describe possible protocols for the preparation of a single quantum state, where also the spin state is well defined.

Ab initio theories for light nuclei and neutron stars

NASA Astrophysics Data System (ADS)

Gezerlis, Alexandros

2016-09-01

In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).

Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

NASA Astrophysics Data System (ADS)

Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

Polarization effects on quantum levels in InN/GaN quantum wells.

PubMed

Lin, Wei; Li, Shuping; Kang, Junyong

2009-12-02

Polarization effects on quantum states in InN/GaN quantum wells have been investigated by means of ab initio calculation and spectroscopic ellipsometry. Through the position-dependent partial densities of states, our results show that the polarization modified by the strain with different well thickness leads to an asymmetry band bending of the quantum well. The quantum levels are identified via the band structures and their square wave function distributions are analyzed by the partial charge densities. Further theoretical and experimental comparison of the imaginary part of the dielectric function show that the overall transition probability increases under larger polarization fields, which can be attributable to the fact that the excited quantum states of 2h have a greater overlap with 1e states and enhance other hole quantum states in the well by a hybridization. These results would provide a new approach to improve the transition probability and light emission by enhancing the polarization fields in a proper way.

Molecular Line and Continuum Opacities for Modeling of Extrasolar Giant Planet and Cool Stellar Atmospheres

NASA Technical Reports Server (NTRS)

Weck, P. F.; Schweitzer, A.; Stancil, P. C.; Hauschildt, P. H.; Kirby, K.; Yamaguchi, Y.; Allen, W. D.

2002-01-01

The molecular line and continuum opacities are investigated in the atmospheres of cool stars and Extrasolar Giant Planets (EGPs). Using a combination of ab inito and experimentally derived potential curves and dipole transition moments, accurate data have been calculated for rovibrationally-resolved oscillator strengths and photodissociation cross sections in the B' (sup 2)Sigma+ (left arrow) X (sup 2)Sigma+ and A (sup 2)Pi (left arrow) X (sup 2)Sigma+ band systems in MgH. We also report our progress on the study of the electronic structure of LiCl and FeH.

Hydrogen atom abstraction from aldehydes - OH + H2CO and O + H2CO

NASA Technical Reports Server (NTRS)

Dupuis, M.; Lester, W. A., Jr.

1984-01-01

The essential features of the potential energy surfaces governing hydrogen abstraction from formaldehyde by oxygen atom and hydroxyl radical have been characterized with ab inito multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) wave functions. The results are consistent with a very small activation energy for the OH + H2CO reaction, and an activation energy of a few kcal/mol for the O + H2CO reaction. In the transition state structure of both systems, the attacking oxygen atom is nearly collinear with the attacked CH bond.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Ab Initio Analysis of Auger-Assisted Electron Transfer.

PubMed

Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

2015-01-15

Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

Free Quantum Field Theory from Quantum Cellular Automata

NASA Astrophysics Data System (ADS)

Bisio, Alessandro; D'Ariano, Giacomo Mauro; Perinotti, Paolo; Tosini, Alessandro

2015-10-01

After leading to a new axiomatic derivation of quantum theory (see D'Ariano et al. in Found Phys, 2015), the new informational paradigm is entering the domain of quantum field theory, suggesting a quantum automata framework that can be regarded as an extension of quantum field theory to including an hypothetical Planck scale, and with the usual quantum field theory recovered in the relativistic limit of small wave-vectors. Being derived from simple principles (linearity, unitarity, locality, homogeneity, isotropy, and minimality of dimension), the automata theory is quantum ab-initio, and does not assume Lorentz covariance and mechanical notions. Being discrete it can describe localized states and measurements (unmanageable by quantum field theory), solving all the issues plaguing field theory originated from the continuum. These features make the theory an ideal framework for quantum gravity, with relativistic covariance and space-time emergent solely from the interactions, and not assumed a priori. The paper presents a synthetic derivation of the automata theory, showing how the principles lead to a description in terms of a quantum automaton over a Cayley graph of a group. Restricting to Abelian groups we show how the automata recover the Weyl, Dirac and Maxwell dynamics in the relativistic limit. We conclude with some new routes about the more general scenario of non-Abelian Cayley graphs. The phenomenology arising from the automata theory in the ultra-relativistic domain and the analysis of corresponding distorted Lorentz covariance is reviewed in Bisio et al. (Found Phys 2015, in this same issue).

Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

2002-01-01

The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

Ab initio rate constants from hyperspherical quantum scattering: Application to H+C2H6 and H+CH3OH

NASA Astrophysics Data System (ADS)

Kerkeni, Boutheïna; Clary, David C.

2004-10-01

The dynamics and kinetics of the abstraction reactions of H atoms with ethane and methanol have been studied using a quantum mechanical procedure. Bonds being broken and formed are treated with explicit hyperspherical quantum dynamics. The ab initio potential energy surfaces for these reactions have been developed from a minimal number of grid points (average of 48 points) and are given by analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimized using the second order perturbation theory method with a correlation consistent polarized valence triple zeta basis set. Single point energies are calculated on the optimized geometries with the coupled cluster theory and the same basis set. The reaction of H with C2H6 is endothermic by 1.5 kcal/mol and has a vibrationally adiabatic barrier of 12 kcal/mol. The reaction of H with CH3OH presents two reactive channels: the methoxy and the hydroxymethyl channels. The former is endothermic by 0.24 kcal/mol and has a vibrationally adiabatic barrier of 13.29 kcal/mol, the latter reaction is exothermic by 7.87 kcal/mol and has a vibrationally adiabatic barrier of 8.56 kcal/mol. We report state-to-state and state-selected cross sections together with state-to-state rate constants for the title reactions. Thermal rate constants for these reactions exhibit large quantum tunneling effects when compared to conventional transition state theory results. For H+CH3OH, it is found that the CH2OH product is the dominant channel, and that the CH3O channel contributes just 2% at 500 K. For both reactions, rate constants are in good agreement with some measurements.

Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

ERIC Educational Resources Information Center

Halpern, Arthur M.

2011-01-01

A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

Ab initio simulation of particle momentum distributions in high-pressure water

NASA Astrophysics Data System (ADS)

Ceriotti, M.

2014-12-01

Applying pressure to water reduces the average oxygen-oxygen distance, and facilitates the delocalisation of protons along the hydrogen bond. This pressure-induced delocalisation is further enhanced by the quantum nature of hydrogen nuclei, which is very significant even well above room temperature. Here we will evaluate the quantum kinetic energy and the particle momentum distribution of hydrogen and oxygen nuclei in water at extreme pressure, using ab initio path integral molecular dynamics. We will show that (transient) dissociation of water molecules induce measurable changes in the kinetic energy hydrogen atoms, although current deep inelastic scattering experiments are probably unable to capture the heterogeneity of the sample.

Oriented conjugation of single-domain antibodies and quantum dots.

PubMed

Brazhnik, Kristina; Nabiev, Igor; Sukhanova, Alyona

2014-01-01

Nanoparticle-based biodetection routinely employs monoclonal antibodies (mAbs) for targeting. However, the large size of mAbs limits the number of ligands per nanoparticle and severely restricts the bioavailability and distribution of these probes in a sample. Furthermore, conventional conjugation techniques provide nanoprobes with irregular orientation of mAbs on the nanoparticle surface and often provoke mAb unfolding. Here, we describe a protocol for engineering a new generation of ultrasmall diagnostic nanoprobes through oriented conjugation of semiconductor quantum dots (QDs) with 13 kDa single-domain antibodies (sdAbs) derived from llama immunoglobulin G (IgG). The sdAbs are conjugated with QDs in a highly oriented manner via an additional cysteine residue specifically integrated into the sdAb C-terminus. The resultant nanoprobes are <12 nm in diameter, ten times smaller in volume compared to the known alternatives. They have been proved highly efficient in flow cytometry and immunuhistochemical diagnostics. This approach can be easily extended to other semiconductor and plasmonic nanoparticles.

Energy barriers and rates of tautomeric transitions in DNA bases: ab initio quantum chemical study.

PubMed

Basu, Soumalee; Majumdar, Rabi; Das, Gourab K; Bhattacharyya, Dhananjay

2005-12-01

Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual DNA bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants.

On the Origin of Quantum Diffusion Coefficient and Quantum Potential

NASA Astrophysics Data System (ADS)

Gupta, Aseem

2016-03-01

Synchronizability of space and time experiences between different inhabitants of a spacetime is abstracted as a fundamental premise of Classical physics. Absence thereof i.e. desynchronization between space and time experiences of a system under study and the observer is then studied for a single dimension single particle system. Desynchronization fundamentally makes probability concepts enter physics ab-initio and not as secondary tools to deal with situations wherein incomplete information in situation following perfectly deterministic dynamics demands its introduction. Desynchronization model based on Poisson distribution of events vis-à-vis an observer, leads to expectation of particle's motion as a Brownian motion deriving Nelson's quantum diffusion coefficient naturally, without needing to postulate it. This model also incorporates physical effects akin to those of Bohm's Quantum Potential, again without needing any sub-quantum medium. Schrodinger's equation is shown to be derivable incorporating desynchronization only of space while Quantum Field Theory is shown to model desynchronization of time as well. Fundamental suggestion of the study is that it is desynchronization that is at the root of quantum phenomena rather than sub-micro scales of spacetime. Absence of possibility of synchronization between system's space and time and those of observer is studied. Mathematical modeling of desynchronized evolution explains some intriguing aspects of Quantum Mechanical theory.

Ab initio quantum mechanical calculation of the reaction probability for the Cl-+PH2Cl→ClPH2+Cl- reaction

NASA Astrophysics Data System (ADS)

Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.

2013-11-01

The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

The ab-initio density matrix renormalization group in practice.

PubMed

Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

2015-01-21

The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

Quantum Monte Carlo Methods for First Principles Simulation of Liquid Water

ERIC Educational Resources Information Center

Gergely, John Robert

2009-01-01

Obtaining an accurate microscopic description of water structure and dynamics is of great interest to molecular biology researchers and in the physics and quantum chemistry simulation communities. This dissertation describes efforts to apply quantum Monte Carlo methods to this problem with the goal of making progress toward a fully "ab initio"…

Lead selenide quantum dot polymer nanocomposites

NASA Astrophysics Data System (ADS)

Waldron, Dennis L.; Preske, Amanda; Zawodny, Joseph M.; Krauss, Todd D.; Gupta, Mool C.

2015-02-01

Optical absorption and fluorescence properties of PbSe quantum dots (QDs) in an Angstrom Bond AB9093 epoxy polymer matrix to form a nanocomposite were investigated. To the authors’ knowledge, this is the first reported use of AB9093 as a QD matrix material and it was shown to out-perform the more common poly(methyl methacrylate) matrix in terms of preserving the optical properties of the QD, resulting in the first reported quantum yield (QY) for PbSe QDs in a polymer matrix, 26%. The 1-s first excitonic absorption peak of the QDs in a polymer matrix red shifted 65 nm in wavelength compared to QDs in a hexane solution, while the emission peak in the polymer matrix red shifted by 38 nm. The fluorescence QY dropped from 55% in hexane to 26% in the polymer matrix. A time resolved fluorescence study of the QDs showed single exponential lifetimes of 2.34 and 1.34 μs in toluene solution and the polymer matrix respectively.

Prospect of quantum anomalous Hall and quantum spin Hall effect in doped kagome lattice Mott insulators.

PubMed

Guterding, Daniel; Jeschke, Harald O; Valentí, Roser

2016-05-17

Electronic states with non-trivial topology host a number of novel phenomena with potential for revolutionizing information technology. The quantum anomalous Hall effect provides spin-polarized dissipation-free transport of electrons, while the quantum spin Hall effect in combination with superconductivity has been proposed as the basis for realizing decoherence-free quantum computing. We introduce a new strategy for realizing these effects, namely by hole and electron doping kagome lattice Mott insulators through, for instance, chemical substitution. As an example, we apply this new approach to the natural mineral herbertsmithite. We prove the feasibility of the proposed modifications by performing ab-initio density functional theory calculations and demonstrate the occurrence of the predicted effects using realistic models. Our results herald a new family of quantum anomalous Hall and quantum spin Hall insulators at affordable energy/temperature scales based on kagome lattices of transition metal ions.

Quantum calculations of the rate constant for the O(3P)+HCl reaction on new ab initio 3A″ and 3A' surfaces

NASA Astrophysics Data System (ADS)

Xie, Tiao; Bowman, Joel M.; Peterson, K. A.; Ramachandran, B.

2003-11-01

We report the thermal rate constant of the O(3P)+HCl→OH+Cl reaction calculated from 200 to 3200 K, using new fits to extensive ab initio calculations [B. Ramachandran and K. A. Peterson, J. Chem. Phys. 119, 9590 (2003), preceding paper]. The rate constants are obtained for both the 3A″ and 3A' surfaces using exact quantum reactive scattering calculations for selected values of the total angular momentum and the J-shifting approximation for both the 3A″ and 3A' surfaces. The results are compared with the ICVT/μOMT rate constants calculated by the POLYRATE program and all available experimental data. Other related high-energy reaction channels are also studied qualitatively for their contribution to the total thermal rate constant at high temperature.

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Memories of AB

NASA Astrophysics Data System (ADS)

Vaks, V. G.

2013-06-01

I had the good fortune to be a student of A. B. Migdal - AB, as we called him in person or in his absence - and to work in the sector he headed at the Kurchatov Institute, along with his other students and my friends, including Vitya Galitsky, Spartak Belyayev and Tolya Larkin. I was especially close with AB in the second half of the 1950s, the years most important for my formation, and AB's contribution to this formation was very great. To this day, I've often quoted AB on various occasions, as it's hard to put things better or more precisely than he did; I tell friends stories heard from AB, because these stories enhance life as AB himself enhanced it; my daughter is named Tanya after AB's wife Tatyana Lvovna, and so on. In what follows, I'll recount a few episodes in my life in which AB played an important or decisive role, and then will share some other memories of AB...

Ab initio optimization principle for the ground states of translationally invariant strongly correlated quantum lattice models.

PubMed

Ran, Shi-Ju

2016-05-01

In this work, a simple and fundamental numeric scheme dubbed as ab initio optimization principle (AOP) is proposed for the ground states of translational invariant strongly correlated quantum lattice models. The idea is to transform a nondeterministic-polynomial-hard ground-state simulation with infinite degrees of freedom into a single optimization problem of a local function with finite number of physical and ancillary degrees of freedom. This work contributes mainly in the following aspects: (1) AOP provides a simple and efficient scheme to simulate the ground state by solving a local optimization problem. Its solution contains two kinds of boundary states, one of which play the role of the entanglement bath that mimics the interactions between a supercell and the infinite environment, and the other gives the ground state in a tensor network (TN) form. (2) In the sense of TN, a novel decomposition named as tensor ring decomposition (TRD) is proposed to implement AOP. Instead of following the contraction-truncation scheme used by many existing TN-based algorithms, TRD solves the contraction of a uniform TN in an opposite way by encoding the contraction in a set of self-consistent equations that automatically reconstruct the whole TN, making the simulation simple and unified; (3) AOP inherits and develops the ideas of different well-established methods, including the density matrix renormalization group (DMRG), infinite time-evolving block decimation (iTEBD), network contractor dynamics, density matrix embedding theory, etc., providing a unified perspective that is previously missing in this fields. (4) AOP as well as TRD give novel implications to existing TN-based algorithms: A modified iTEBD is suggested and the two-dimensional (2D) AOP is argued to be an intrinsic 2D extension of DMRG that is based on infinite projected entangled pair state. This paper is focused on one-dimensional quantum models to present AOP. The benchmark is given on a transverse Ising

Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Wang, Yimin; Braams, Bastiaan J.; Bowman, Joel M.; Carter, Stuart; Tew, David P.

2008-06-01

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and ``exact'' full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased ``fixed-node'' diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm-1 in Cartesian coordinates and 22.6 cm-1 in normal coordinates, with an uncertainty of 2-3 cm-1. This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm-1. The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm-1. These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm-1, and agree well with the experimental values of 21.6 and 2.9 cm-1 for the H and D transfer, respectively.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

PubMed

Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

2008-06-14

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

Attaching quantum dots to HER2 specific phage antibodies

NASA Astrophysics Data System (ADS)

Chu, Viet Ha; Nghiem, Thi Ha Lien; Huyen La, Thi; Dieu Thuy Ung, Thi; Huan Le, Quang; Thuan Tong, Kim; Liem Nguyen, Quang; Nhung Tran, Hong

2010-06-01

This work presents the results of the attachment of Qdot 655 ITKTM amino (PEG) quantum dots (QDs) (Invitrogen) and CdTe QDs (provided by Institute of Materials Science, VAST) to HER2 (Human Epidermal growth factor Receptor 2) specific phage antibodies (Abs) (provided by Institute of Biotechnology, VAST) in solution. The QDs were attached to the phage display specific HER2 Abs to form a complex QD-Ab. The QDs and complex QD-Ab were characterized by UV-VIS spectroscopy, transmission electron microscopy (TEM) and fluorescence microscopy. The fluorescence images show the QDs conjugated to the phage. Due to the QDs attaching to the surface, the phage dimensions were amplified, so its shape could be observed by optical microscopy. The complex QD-Ab was stable and lasted for a month. The results illustrate the value of the HER2 phage-QD complex as a cancer detection platform.

Magnetic edge states in Aharonov-Bohm graphene quantum rings

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

Farghadan, R., E-mail: rfarghadan@kashanu.ac.ir; Heidari Semiromi, E.; Saffarzadeh, A.

2013-12-07

The effect of electron-electron interaction on the electronic structure of Aharonov-Bohm (AB) graphene quantum rings (GQRs) is explored theoretically using the single-band tight-binding Hamiltonian and the mean-field Hubbard model. The electronic states and magnetic properties of hexagonal, triangular, and circular GQRs with different sizes and zigzag edge terminations are studied. The results show that, although the AB oscillations in the all types of nanoring are affected by the interaction, the spin splitting in the AB oscillations strongly depends on the geometry and the size of graphene nanorings. We found that the total spin of hexagonal and circular rings is zeromore » and therefore, no spin splitting can be observed in the AB oscillations. However, the non-zero magnetization of the triangular rings breaks the degeneracy between spin-up and spin-down electrons, which produces spin-polarized AB oscillations.« less

A new ab initio potential energy surface of LiClH (1A') system and quantum dynamics calculation for Li + HCl (v = 0, j = 0-2) → LiCl + H reaction

NASA Astrophysics Data System (ADS)

Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying

2017-04-01

A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.

Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

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

Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.

2015-09-14

We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t tomore » be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.« less

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

Ab Initio Modeling of Molecular Radiation

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Schwenke, David

2014-01-01

Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

mAbs

PubMed Central

2009-01-01

The twenty two monoclonal antibodies (mAbs) currently marketed in the U.S. have captured almost half of the top-20 U.S. therapeutic biotechnology sales for 2007. Eight of these products have annual sales each of more than $1 B, were developed in the relatively short average period of six years, qualified for FDA programs designed to accelerate drug approval, and their cost has been reimbursed liberally by payers. With growth of the product class driven primarily by advancements in protein engineering and the low probability of generic threats, mAbs are now the largest class of biological therapies under development. The high cost of these drugs and the lack of generic competition conflict with a financially stressed health system, setting reimbursement by payers as the major limiting factor to growth. Advances in mAb engineering are likely to result in more effective mAb drugs and an expansion of the therapeutic indications covered by the class. The parallel development of biomarkers for identifying the patient subpopulations most likely to respond to treatment may lead to a more cost-effective use of these drugs. To achieve the success of the current top-tier mAbs, companies developing new mAb products must adapt to a significantly more challenging commercial environment. PMID:20061824

Perturbational treatment of spin-orbit coupling for generally applicable high-level multi-reference methods

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

Mai, Sebastian; Marquetand, Philipp; González, Leticia

2014-08-21

An efficient perturbational treatment of spin-orbit coupling within the framework of high-level multi-reference techniques has been implemented in the most recent version of the COLUMBUS quantum chemistry package, extending the existing fully variational two-component (2c) multi-reference configuration interaction singles and doubles (MRCISD) method. The proposed scheme follows related implementations of quasi-degenerate perturbation theory (QDPT) model space techniques. Our model space is built either from uncontracted, large-scale scalar relativistic MRCISD wavefunctions or based on the scalar-relativistic solutions of the linear-response-theory-based multi-configurational averaged quadratic coupled cluster method (LRT-MRAQCC). The latter approach allows for a consistent, approximatively size-consistent and size-extensive treatment of spin-orbitmore » coupling. The approach is described in detail and compared to a number of related techniques. The inherent accuracy of the QDPT approach is validated by comparing cuts of the potential energy surfaces of acrolein and its S, Se, and Te analoga with the corresponding data obtained from matching fully variational spin-orbit MRCISD calculations. The conceptual availability of approximate analytic gradients with respect to geometrical displacements is an attractive feature of the 2c-QDPT-MRCISD and 2c-QDPT-LRT-MRAQCC methods for structure optimization and ab inito molecular dynamics simulations.« less

Ab initio quantum chemical study of electron transfer in carboranes

NASA Astrophysics Data System (ADS)

Pati, Ranjit; Pineda, Andrew C.; Pandey, Ravindra; Karna, Shashi P.

2005-05-01

The electron transfer (ET) properties of 10- and 12-vertex carboranes are investigated by the ab initio Hartree-Fock method within the Marcus-Hush (MH) two-state model and the Koopman theorem (KT) approach. The calculated value of the ET coupling matrix element, VAB, is consistently higher in the KT approach than in the MH two-state model. For the carborane molecules functionalized by -CH 2 groups at C-vertices, VAB strongly depends on the relative orientation of the planes containing the terminal -CH 2 groups. The predicted conformation dependence of VAB offers a molecular mechanism to control ET between two active centers in molecular systems.

Network-Forming Nanoclusters in Binary As-S/Se Glasses: From Ab Initio Quantum Chemical Modeling to Experimental Evidences.

PubMed

Hyla, M

2017-12-01

Network-forming As 2 (S/Se) m nanoclusters are employed to recognize expected variations in a vicinity of some remarkable compositions in binary As-Se/S glassy systems accepted as signatures of optimally constrained intermediate topological phases in earlier temperature-modulated differential scanning calorimetry experiments. The ab initio quantum chemical calculations performed using the cation-interlinking network cluster approach show similar oscillating character in tendency to local chemical decomposition but obvious step-like behavior in preference to global phase separation on boundary chemical compounds (pure chalcogen and stoichiometric arsenic chalcogenides). The onsets of stability are defined for chalcogen-rich glasses, these being connected with As 2 Se 5 (Z = 2.29) and As 2 S 6 (Z = 2.25) nanoclusters for As-Se and As-S glasses, respectively. The physical aging effects result preferentially from global phase separation in As-S glass system due to high localization of covalent bonding and local demixing on neighboring As 2 Se m+1 and As 2 Se m-1 nanoclusters in As-Se system. These nanoclusters well explain the lower limits of reversibility windows in temperature-modulated differential scanning calorimetry, but they cannot be accepted as signatures of topological phase transitions in respect to the rigidity theory.

Scanning Gate Microscopy on a Quantum Hall Interferometer

NASA Astrophysics Data System (ADS)

Martins, Frederico; Hackens, Benoit; Dutu, Augustin; Bayot, Vincent; Sellier, Hermann; Huant, Serge; Desplanque, Ludovic; Wallart, Xavier; Pala, Marco

2010-03-01

We perform scanning gate microscopy (SGM) experiments [1] at very low temperature (down to 100 mK) in the Quantum Hall regime on a mesoscopic quantum ring (QR) patterned in an InGaAs/InAlAs heterostructure. Close to integer filling factors ν=6, 8 and 10,the magnetoresistance of the QR is decorated with fast periodic oscillations, with a magnetic field period close to AB/ν, where AB is the Aharonov-Bohm period. We analyze the data in terms of electron tunneling between edge states trapped inside the QR and those transmitted through the QR openings [2]. SGM images reveal that the tip-induced perturbation of the electron confining potential gives rise to a rich pattern of narrow and wide concentric conductance fringes in the vicinity of the QR. [1] F. Martins et al. Phys. Rev. Lett. 99 136807 (2007); B. Hackens et al. Nat. Phys. 2 826 (2006). [2] B. Rosenow and B. I. Halperin, Phys. Rev. Lett. 98, 106801 (2007).

New insights into mechanistic photoisomerization of ethylene-bridged azobenzene from ab initio multiple spawning simulation.

PubMed

Liu, Lihong; Wang, Yating; Fang, Qiu

2017-02-14

Ethylene-bridged azobenzene (br-AB) has aroused broad interests due to its unique photoswitching properties. Numerous dynamical simulations have been performed for the br-AB photoisomerization, which focused mainly on the conformational effect and the funnel role of minimum-energy conical intersection (MECI) on the mechanism. In the present work, we use the "full quantum" ab initio multiple spawning method to simulate the br-AB photoisomerization, which provides new insights into the mechanism. Upon irradiation of br-AB to the first excited singlet state (S 1 ), most of the excess energies are trapped in the azo-moiety. Since the intramolecular vibrational energy redistribution is slower than the S 1 relaxation processes, the nonadiabatic transition from S 1 to the ground state (S 0 ) occurs in the vicinity of high-energy crossing seam and even the largest probabilities of the S 1 → S 0 transition are not distributed in the MECI regions. Once decaying to the S 0 state through the high-energy region, the subsequent isomerization and re-formation of the initial isomer are ultrafast processes in the S 0 state. It is the nonergodic behavior of the S 1 and S 0 dynamics that is mainly responsible for the unique photoswitching properties of the ethylene-bridged azobenzene, which will be discussed in detail.

Hybrid classical/quantum simulation for infrared spectroscopy of water

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

Atomic-scale investigation of nuclear quantum effects of surface water: Experiments and theory

NASA Astrophysics Data System (ADS)

Guo, Jing; Li, Xin-Zheng; Peng, Jinbo; Wang, En-Ge; Jiang, Ying

2017-12-01

Quantum behaviors of protons in terms of tunneling and zero-point motion have significant effects on the macroscopic properties, structure, and dynamics of water even at room temperature or higher. In spite of tremendous theoretical and experimental efforts, accurate and quantitative description of the nuclear quantum effects (NQEs) is still challenging. The main difficulty lies in that the NQEs are extremely susceptible to the structural inhomogeneity and local environments, especially when interfacial systems are concerned. In this review article, we will highlight the recent advances of scanning tunneling microscopy and spectroscopy (STM/S), which allows the access to the quantum degree of freedom of protons both in real and energy space. In addition, we will also introduce recent development of ab initio path-integral molecular dynamics (PIMD) simulations at surfaces/interfaces, in which both the electrons and nuclei are treated as quantum particles in contrast to traditional ab initio molecular dynamics (MD). Then we will discuss how the combination of STM/S and PIMD are used to directly visualize the concerted quantum tunneling of protons within the water clusters and quantify the impact of zero-point motion on the strength of a single hydrogen bond (H bond) at a water/solid interface. Those results may open up the new possibility of exploring the exotic quantum states of light nuclei at surfaces, as well as the quantum coupling between the electrons and nuclei.

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

Predicted phototoxicities of carbon nano-material by quantum mechanical calculations

EPA Science Inventory

The purpose of this research is to develop a predictive model for the phototoxicity potential of carbon nanomaterials (fullerenols and single-walled carbon nanotubes). This model is based on the quantum mechanical (ab initio) calculations on these carbon-based materials and compa...

Topological Quantum Phase Transitions in Two-Dimensional Hexagonal Lattice Bilayers

NASA Astrophysics Data System (ADS)

Zhai, Xuechao; Jin, Guojun

2013-09-01

Since the successful fabrication of graphene, two-dimensional hexagonal lattice structures have become a research hotspot in condensed matter physics. In this short review, we theoretically focus on discussing the possible realization of a topological insulator (TI) phase in systems of graphene bilayer (GBL) and boron nitride bilayer (BNBL), whose band structures can be experimentally modulated by an interlayer bias voltage. Under the bias, a band gap can be opened in AB-stacked GBL but is still closed in AA-stacked GBL and significantly reduced in AA- or AB-stacked BNBL. In the presence of spin-orbit couplings (SOCs), further demonstrations indicate whether the topological quantum phase transition can be realized strongly depends on the stacking orders and symmetries of structures. It is observed that a bulk band gap can be first closed and then reopened when the Rashba SOC increases for gated AB-stacked GBL or when the intrinsic SOC increases for gated AA-stacked BNBL. This gives a distinct signal for a topological quantum phase transition, which is further characterized by a jump of the ℤ2 topological invariant. At fixed SOCs, the TI phase can be well switched by the interlayer bias and the phase boundaries are precisely determined. For AA-stacked GBL and AB-stacked BNBL, no strong TI phase exists, regardless of the strength of the intrinsic or Rashba SOCs. At last, a brief overview is given on other two-dimensional hexagonal materials including silicene and molybdenum disulfide bilayers.

On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

PubMed

Noel, Yves; D'arco, Philippe; Demichelis, Raffaella; Zicovich-Wilson, Claudio M; Dovesi, Roberto

2010-03-01

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented. (c) 2009 Wiley Periodicals, Inc.

Sensitivity-Enhancement of FRET Immunoassays by Multiple-Antibody Conjugation on Quantum Dots.

PubMed

Annio, Giacomo; Jennings, Travis; Tagit, Oya; Hildebrandt, Niko

2018-05-23

Quantum dots (QDs) are not only advantageous for color-tuning, improved brightness, and high stability, but their nanoparticle surfaces also allow for the attachment of many biomolecules. Because IgG antibodies (ABs) are in the same size range of biocompatible QDs and the AB orientation after conjugation to the QD is often random, it is difficult to predict if few or many ABs per QD will lead to an efficient AB-QD conjugate. This is particularly true for homogeneous Förster resonance energy transfer (FRET) sandwich immunoassays, for which the ABs on the QD must bind a biomarker that needs to bind a second AB-FRET-conjugate. Here, we investigate the performance of Tb-to-QD FRET immunoassays against total prostate specific antigen (TPSA) by changing the number of ABs per QD while leaving all the other assay components unchanged. We first characterize the AB-QD conjugation by various spectroscopic, microscopic, and chromatographic techniques and then quantify the TPSA immunoassay performance regarding sensitivity, limit of detection, and dynamic range. Our results show that an increasing conjugation ratio leads to significantly enhanced FRET immunoassays. These findings will be highly important for developing QD-based immunoassays in which the concentrations of both ABs and QDs can significantly influence the assay performance.

Quantum probability and conceptual combination in conjunctions.

PubMed

Hampton, James A

2013-06-01

I consider the general problem of category conjunctions in the light of Pothos & Busemeyer (P&B)'s quantum probability (QP) account of the conjunction fallacy. I argue that their account as presented cannot capture the "guppy effect" - the case in which a class is a better member of a conjunction A^B than it is of either A or B alone.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

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

Genderen, E. van; Clabbers, M. T. B.; Center for Cellular Imaging and NanoAnalytics

A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at roommore » temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)« less

Ab initio non-adiabatic study of the 4pσ B'' 1Σ+u state of H2

NASA Astrophysics Data System (ADS)

Glass-Maujean, M.; Schmoranzer, H.

2018-05-01

Fully ab initio non-adiabatic multichannel quantum defect calculations of the 4pσ B'' 1∑u+ energy levels, line intensities and widths, based on the latest quantum-chemical clamped-nuclei calculations of Wolniewicz and collaborators are presented for H2. The B″ state corresponds to the inner well of the ? state. The B'' v ≥ 1 levels are rapidly predissociated through vibrational coupling with the 3pσ B' 1Σ+u continuum so that coupled-equation calculations become unstable. Multichannel quantum defect theory, on the other hand, is demonstrated to be particularly suited to this situation. Experimental data as level energies, line intensities and dissociation widths were revisited and corrected. Reinvestigating previously published spectra, several new lines were assigned.

Anharmonic and Quantum Fluctuations in Molecular Crystals from Ab Initio Simulations

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

Molecular crystals often exist in multiple competing polymorphs which are challenging to be predicted computationally, but show significantly different physicochemical properties. This challenge is not due only to the combinatorial search space, but also to the complex interplay of subtle effects determine the relative stability of different structures. Here we estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects, by using a series of different flavors of thermodynamic integration. As an example, for the two most stable forms of paracetamol we find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our studies indicate that anharmonic free energies could play an important role for molecular crystals composed by large molecules and opens the way for a systematic inclusion of these effects in order to obtain a predictive screening of structures.

Ab Initio Optimized Effective Potentials for Real Molecules in Optical Cavities: Photon Contributions to the Molecular Ground State

PubMed Central

2018-01-01

We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density-functional theory (QEDFT).1−5 Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical cavities and described in full real space. While the first example is a two-dimensional system and allows to benchmark the employed approximations, the latter two examples demonstrate that the correlated electron-photon interaction appreciably distorts the ground-state electronic structure of a real molecule. By using this scheme, we not only construct typical electronic observables, such as the electronic ground-state density, but also illustrate how photon observables, such as the photon number, and mixed electron-photon observables, for example, electron–photon correlation functions, become accessible in a density-functional theory (DFT) framework. This work constitutes the first three-dimensional ab initio calculation within the new QEDFT formalism and thus opens up a new computational route for the ab initio study of correlated electron–photon systems in quantum cavities. PMID:29594185

Physical reasons of emission transformation in infrared CdSeTe/ZnS quantum dots at bioconjugation

NASA Astrophysics Data System (ADS)

Torchynska, T. V.

2015-04-01

The core/shell CdSeTe/ZnS quantum dots (QDs) with emission at 780-800 nm (1.55-1.60 eV) have been studied by means of photoluminescence (PL) and Raman scattering methods in the nonconjugated state and after conjugation to different antibodies (Ab): (i) mouse monoclonal [8C9] human papilloma virus Ab, anti-HPV 16-E7 Ab, (ii) mouse monoclonal [C1P5] human papilloma virus HPV16 E6+HPV18 E6 Ab, and (iii) pseudo rabies virus (PRV) Ab. The transformations of PL and Raman scattering spectra of QDs, stimulated by conjugated antibodies, have been revealed and discussed. The energy band diagram of core/shell CdSeTe/ZnS QDs has been designed that helps to analyze the PL spectra and their transformations at the bioconjugation. It is shown that the core in CdSeTe/ZnS QDs is complex and including the type II quantum well. The last fact permits to explain the nature of infrared (IR) optical transitions (1.55-1.60 eV) and the high energy PL band (1.88-1.94 eV) in the nonconjugated and bioconjugated QDs. A set of physical reasons has been analyzed with the aim to explain the transformation of PL spectra in bioconjugated QDs. Finally it is shown that two factors are responsible for the PL spectrum transformation at bioconjugation to charged antibodies: (i) the change of energy band profile in QDs and (ii) the shift of QD energy levels in the strong quantum confinement case. The effect of PL spectrum transformation is useful for the study of QD bioconjugation to specific antibodies and can be a powerful technique for early medical diagnostics.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

PubMed

Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

2016-05-12

An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

NASA Technical Reports Server (NTRS)

Kahn, L. R.

1982-01-01

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

PubMed

Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

2018-06-12

We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

The AB Doradus system revisited: The dynamical mass of AB Dor A/C

NASA Astrophysics Data System (ADS)

Azulay, R.; Guirado, J. C.; Marcaide, J. M.; Martí-Vidal, I.; Ros, E.; Tognelli, E.; Jauncey, D. L.; Lestrade, J.-F.; Reynolds, J. E.

2017-10-01

Context. The study of pre-main-sequence (PMS) stars with model-independent measurements of their masses is essential to check the validity of theoretical models of stellar evolution. The well-known PMS binary AB Dor A/C is an important benchmark for this task, since it displays intense and compact radio emission, which makes possible the application of high-precision astrometric techniques to this system. Aims: We aim to revisit the dynamical masses of the components of AB Dor A/C to refine earlier comparisons between the measurements of stellar parameters and the predictions of stellar models. Methods: We observed in phase-reference mode the binary AB Dor A/C, 0.2'' separation, with the Australian Long Baseline Array at 8.4 GHz. The astrometric information resulting from our observations was analyzed along with previously reported VLBI, optical (Hipparcos), and infrared measurements. Results: The main star AB Dor A is clearly detected in all the VLBI observations, which allowed us to analyze the orbital motion of the system and to obtain model-independent dynamical masses of 0.90 ± 0.08 M⊙ and 0.090 ± 0.008 M⊙, for AB Dor A and AB Dor C, respectively. Comparisons with PMS stellar evolution models favor and age of 40-50 Myr for AB Dor A and of 25-120 Myr for AB Dor C. Conclusions: We show that the orbital motion of the AB Dor A/C system is remarkably well determined, leading to precise estimates of the dynamical masses. Comparison of our results with the prediction of evolutionary models support the observational evidence that theoretical models tend to slightly underestimate the mass of the low-mass stars.

Comparison of In Vitro Activity of Liposomal Nystatin against Aspergillus Species with Those of Nystatin, Amphotericin B (AB) Deoxycholate, AB Colloidal Dispersion, Liposomal AB, AB Lipid Complex, and Itraconazole

PubMed Central

Oakley, Karen L.; Moore, Caroline B.; Denning, David W.

1999-01-01

We compared the in vitro activity of liposomal nystatin (Nyotran) with those of other antifungal agents against 60 Aspergillus isolates. Twelve isolates were itraconazole resistant. For all isolates, geometric mean (GM) MICs (micrograms per milliliter) were 2.30 for liposomal nystatin, 0.58 for itraconazole, 0.86 for amphotericin B (AB) deoxycholate, 9.51 for nystatin, 2.07 for liposomal AB, 2.57 for AB lipid complex, and 0.86 for AB colloidal dispersion. Aspergillus terreus (GM, 8.72 μg/ml; range, 8 to 16 μg/ml) was significantly less susceptible to all of the polyene drugs than all other species (P = 0.0001). PMID:10223948

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Hydrogen atom in a quantum plasma environment under the influence of Aharonov-Bohm flux and electric and magnetic fields.

PubMed

Falaye, Babatunde James; Sun, Guo-Hua; Silva-Ortigoza, Ramón; Dong, Shi-Hai

2016-05-01

This study presents the confinement influences of Aharonov-Bohm (AB) flux and electric and magnetic fields directed along the z axis and encircled by quantum plasmas on the hydrogen atom. The all-inclusive effects result in a strongly attractive system while the localizations of quantum levels change and the eigenvalues decrease. We find that the combined effect of the fields is stronger than a solitary effect and consequently there is a substantial shift in the bound state energy of the system. We also find that to perpetuate a low-energy medium for the hydrogen atom in quantum plasmas, a strong electric field and weak magnetic field are required, whereas the AB flux field can be used as a regulator. The application of the perturbation technique utilized in this paper is not restricted to plasma physics; it can also be applied in molecular physics.

A permutationally invariant full-dimensional ab initio potential energy surface for the abstraction and exchange channels of the H + CH{sub 4} system

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

Li, Jun, E-mail: jli15@cqu.edu.cn, E-mail: zhangdh@dicp.ac.cn; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131; Chen, Jun

2015-05-28

We report a permutationally invariant global potential energy surface (PES) for the H + CH{sub 4} system based on ∼63 000 data points calculated at a high ab initio level (UCCSD(T)-F12a/AVTZ) using the recently proposed permutation invariant polynomial-neural network method. The small fitting error (5.1 meV) indicates a faithful representation of the ab initio points over a large configuration space. The rate coefficients calculated on the PES using tunneling corrected transition-state theory and quasi-classical trajectory are found to agree well with the available experimental and previous quantum dynamical results. The calculated total reaction probabilities (J{sub tot} = 0) including themore » abstraction and exchange channels using the new potential by a reduced dimensional quantum dynamic method are essentially the same as those on the Xu-Chen-Zhang PES [Chin. J. Chem. Phys. 27, 373 (2014)].« less

Analysis of finite-strain equations of state for solids under high pressures

NASA Astrophysics Data System (ADS)

Sushil, K.; Arunesh, K.; Singh, P. K.; Sharma, B. S.

2004-10-01

We have reformulated equations of state (EOS) for solids based on Lagrangian and Eulerian strains following the method developed by Stacey [Phys. Earth Planet. Inter. 128 (2001) 179]. The expressions thus obtained are used conveniently to assess the validity of various EOS for different types of solids. The logarithmic EOS based on the Hencky measure of finite-strain is also modified by including the higher terms arising from the fourth-order contribution in the Taylor series expansion of the free energy. The results are obtained for pressure (P), isothermal bulk modulus (KT) and its pressure derivative (dKT/dP) for Ne, Ar, Al, Cu, LiH and MgO solids for a wide range of compressions (V/V0) down to 0.5. The results determined from the finite-strain equations are compared with those obtained from the Vinet-Rydberg equation and the Shanker equation, which are based on the interatomic potential energy functions. The results are also compared with the ab inito values reported by Hama and Suito [J. Phys.: Condens. Matter 8 (1996) 67] determined from first-principles calculations using the augmented plane wave method and the quantum statistical model. The EOS based on the K‧ finite-strain theory due to Keane and Stacey are also discussed, emphasising the importance of K∞‧ , in the limit P→∞.

Vibrational energy transport in acetylbenzonitrile described by an ab initio-based quantum tier model

NASA Astrophysics Data System (ADS)

Fujisaki, Hiroshi; Yagi, Kiyoshi; Kikuchi, Hiroto; Takami, Toshiya; Stock, Gerhard

2017-01-01

Performing comprehensive quantum-chemical calculations, a vibrational Hamiltonian of acetylbenzonitrile is constructed, on the basis of which a quantum-mechanical "tier model" is developed that describes the vibrational dynamics following excitation of the CN stretch mode. Taking into account 36 vibrational modes and cubic and quartic anharmonic couplings between up to three different modes, the tier model calculations are shown to qualitatively reproduce the main findings of the experiments of Rubtsov and coworkers (2011), including the energy relaxation of the initially excited CN mode and the structure-dependent vibrational transport. Moreover, the calculations suggest that the experimentally measured cross-peak among the CN and CO modes does not correspond to direct excitation of the CO normal mode but rather reflects excited low-frequency vibrations that anharmonically couple to the CO mode. Complementary quasiclassical trajectory calculations are found to be in good overall agreement with the quantum calculations.

Distinguishability of stacks in ZnTe/ZnSe quantum dots via spectral analysis of Aharonov-Bohm oscillations

NASA Astrophysics Data System (ADS)

Roy, Bidisha; Ji, Haojie; Dhomkar, Siddharth; Cadieu, Fred J.; Peng, Le; Moug, Richard; Tamargo, Maria C.; Kuskovsky, Igor L.

2013-02-01

A spectral analysis of the Aharonov-Bohm (AB) oscillations in photoluminescence intensity was performed for stacked type-II ZnTe/ZnSe quantum dots (QDs) fabricated within multilayered Zn-Se-Te system with sub-monolayer insertions of Te. Robust AB oscillations allowed for fine probing of distinguishable QDs stacks within the ensemble of QDs. The AB transition magnetic field, B AB , changed from the lower energy side to the higher energy side of the PL spectra revealing the presence of different sets of QDs stacks. The change occurs within the spectral range, where the contributing green and blue bands of the spectra overlapped. "Bundling" in lifetime measurements is seen at transition spectral regions confirming the results.

Spins and photons: connecting quantum registers in diamond

NASA Astrophysics Data System (ADS)

Childress, Lily

2012-06-01

Long-lived electronic and nuclear spin states have made the nitrogen-vacancy (NV) defect in diamond a leading candidate for quantum information processing in the solid state. Multi-qubit quantum registers formed by single defects and nearby nuclear spins can currently be controlled and detected with high fidelity. Nevertheless, development of coherent connections between distant NVs remains an outstanding challenge. One advantage to working with solid-state defects is the opportunity to integrate them with microfabricated mechanical, electronic, or optical devices; in principle, such devices could mediate interactions between registers, turning them into nodes within a larger quantum network. In the last few months, several experiments have made key steps toward realizing a coherent quantum interface between individual NV centers using a mechanical quantum bus [1] or optical channels [2,3]. This talk will explore the current state of the art, and report on recent observation of two photon quantum interference between different gate-tunable defect centers [2]. These results pave the way towards measurement-based entanglement between remote NV centers and the realization of quantum networks with solid-state spins.[4pt] [1] Kolkowitz et al., Science 335, 1603 (2012)[2] Bernien et al., Phys. Rev. Lett. 108, 043604 (2012)[3] Sipahigil et al., http://lanl.arxiv.org/abs/1112.3975

Binding energies from diffusion Monte Carlo for the MB-pol H{sub 2}O and D{sub 2}O dimer: A comparison to experimental values

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

Mallory, Joel D.; Mandelshtam, Vladimir A.

2015-10-14

The diffusion Monte Carlo (DMC) method is applied to compute the ground state energies of the water monomer and dimer and their D{sub 2}O isotopomers using MB-pol; the most recent and most accurate ab inito-based potential energy surface (PES). MB-pol has already demonstrated excellent agreement with high level electronic structure data, as well as agreement with some experimental, spectroscopic, and thermodynamic data. Here, the DMC binding energies of (H{sub 2}O){sub 2} and (D{sub 2}O){sub 2} agree with the corresponding values obtained from velocity map imaging within, respectively, 0.01 and 0.02 kcal/mol. This work adds two more valuable data points thatmore » highlight the accuracy of the MB-pol PES.« less

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

Quantum Simulation of Helium Hydride Cation in a Solid-State Spin Register.

PubMed

Wang, Ya; Dolde, Florian; Biamonte, Jacob; Babbush, Ryan; Bergholm, Ville; Yang, Sen; Jakobi, Ingmar; Neumann, Philipp; Aspuru-Guzik, Alán; Whitfield, James D; Wrachtrup, Jörg

2015-08-25

Ab initio computation of molecular properties is one of the most promising applications of quantum computing. While this problem is widely believed to be intractable for classical computers, efficient quantum algorithms exist which have the potential to vastly accelerate research throughput in fields ranging from material science to drug discovery. Using a solid-state quantum register realized in a nitrogen-vacancy (NV) defect in diamond, we compute the bond dissociation curve of the minimal basis helium hydride cation, HeH(+). Moreover, we report an energy uncertainty (given our model basis) of the order of 10(-14) hartree, which is 10 orders of magnitude below the desired chemical precision. As NV centers in diamond provide a robust and straightforward platform for quantum information processing, our work provides an important step toward a fully scalable solid-state implementation of a quantum chemistry simulator.

Superpersistent currents and whispering gallery modes in relativistic quantum chaotic systems

PubMed Central

Xu, Hongya; Huang, Liang; Lai, Ying-Cheng; Grebogi, Celso

2015-01-01

Persistent currents (PCs), one of the most intriguing manifestations of the Aharonov-Bohm (AB) effect, are known to vanish for Schrödinger particles in the presence of random scatterings, e.g., due to classical chaos. But would this still be the case for Dirac fermions? Addressing this question is of significant value due to the tremendous recent interest in two-dimensional Dirac materials. We investigate relativistic quantum AB rings threaded by a magnetic flux and find that PCs are extremely robust. Even for highly asymmetric rings that host fully developed classical chaos, the amplitudes of PCs are of the same order of magnitude as those for integrable rings, henceforth the term superpersistent currents (SPCs). A striking finding is that the SPCs can be attributed to a robust type of relativistic quantum states, i.e., Dirac whispering gallery modes (WGMs) that carry large angular momenta and travel along the boundaries. We propose an experimental scheme using topological insulators to observe and characterize Dirac WGMs and SPCs, and speculate that these features can potentially be the base for a new class of relativistic qubit systems. Our discovery of WGMs in relativistic quantum systems is remarkable because, although WGMs are common in photonic systems, they are relatively rare in electronic systems. PMID:25758591

Superpersistent currents and whispering gallery modes in relativistic quantum chaotic systems.

PubMed

Xu, Hongya; Huang, Liang; Lai, Ying-Cheng; Grebogi, Celso

2015-03-11

Persistent currents (PCs), one of the most intriguing manifestations of the Aharonov-Bohm (AB) effect, are known to vanish for Schrödinger particles in the presence of random scatterings, e.g., due to classical chaos. But would this still be the case for Dirac fermions? Addressing this question is of significant value due to the tremendous recent interest in two-dimensional Dirac materials. We investigate relativistic quantum AB rings threaded by a magnetic flux and find that PCs are extremely robust. Even for highly asymmetric rings that host fully developed classical chaos, the amplitudes of PCs are of the same order of magnitude as those for integrable rings, henceforth the term superpersistent currents (SPCs). A striking finding is that the SPCs can be attributed to a robust type of relativistic quantum states, i.e., Dirac whispering gallery modes (WGMs) that carry large angular momenta and travel along the boundaries. We propose an experimental scheme using topological insulators to observe and characterize Dirac WGMs and SPCs, and speculate that these features can potentially be the base for a new class of relativistic qubit systems. Our discovery of WGMs in relativistic quantum systems is remarkable because, although WGMs are common in photonic systems, they are relatively rare in electronic systems.

Towards an ab-initio treatment of nonlocal electronic correlations with dynamical vertex approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten

Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.

Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

NASA Astrophysics Data System (ADS)

Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

2018-05-01

Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

Diode laser surgery. Ab interno and ab externo versus conventional surgery in rabbits.

PubMed

Karp, C L; Higginbotham, E J; Edward, D P; Musch, D C

1993-10-01

Fibroblastic proliferation of subconjunctival tissues remains a primary mechanism of failure in filtration surgery. Minimizing the surgical manipulation of episcleral tissues may reduce scarring. Laser sclerostomy surgery involves minimal tissue dissection, and is gaining attention as a method of potentially improving filter duration in high-risk cases. Twenty-five New Zealand rabbits underwent filtration surgery in one eye, and the fellow eye remained as the unoperated control. Ten rabbits underwent ab externo diode laser sclerostomy surgery, ten underwent ab interno diode sclerostomy surgery, and five had posterior sclerostomy procedures. Filtration failure was defined as a less-than-4-mmHg intraocular pressure (IOP) difference between the operative and control eyes. The mean time to failure for the ab externo, ab interno, and conventional posterior sclerostomy techniques measured 17.4 +/- 11.5, 13.1 +/- 6.7, and 6.0 +/- 3.1 days, respectively. In a comparison of the laser-treated groups with the conventional procedure, the time to failure was significantly longer (P = 0.02) for the ab externo filter. The mean ab interno sclerostomy duration was longer than the posterior lip procedure, but this difference was not statistically significant (P = 0.15). The overall level of IOP reduction was similar in the three groups. These data suggest that diode laser sclerostomy is a feasible technique in rabbits, and the ab externo approach resulted in longer filter duration than the conventional posterior lip procedure in this model.

Anti-GD2 mAbs and next-generation mAb-based agents for cancer therapy

PubMed Central

Perez Horta, Zulmarie; Goldberg, Jacob L; Sondel, Paul M

2016-01-01

Tumor-specific monoclonal antibodies (mAbs) have demonstrated efficacy in the clinic, becoming an important approach for cancer immunotherapy. Due to its limited expression on normal tissue, the GD2 disialogangloside expressed on neuroblastoma cells is an excellent candidate for mAb therapy. In 2015, dinutuximab (an anti-GD2 mAb) was approved by the US FDA and is currently used in a combination immunotherapeutic regimen for the treatment of children with high-risk neuroblastoma. Here, we review the extensive preclinical and clinical development of anti-GD2 mAbs and the different mechanisms by which they mediate tumor cell killing. In addition, we discuss different mAb-based strategies that capitalize on the targeting ability of anti-GD2 mAbs to potentially deliver, as monotherapy, or in combination with other treatments, improved antitumor efficacy. PMID:27485082

S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

PubMed

Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

2014-09-04

We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar

Introduction to the Neutrosophic Quantum Theory

NASA Astrophysics Data System (ADS)

Smarandache, Florentin

2014-10-01

Neutrosophic Quantum Theory (NQT) is the study of the principle that certain physical quantities can assume neutrosophic values, instead of discrete values as in quantum theory. These quantities are thus neutrosophically quantized. A neutrosophic values (neutrosophic amount) is expressed by a set (mostly an interval) that approximates (or includes) a discrete value. An oscillator can lose or gain energy by some neutrosophic amount (we mean neither continuously nor discretely, but as a series of integral sets: S, 2S, 3S, ..., where S is a set). In the most general form, one has an ensemble of sets of sets, i.e. R1S1 ,R2S2 ,R3S3 , ..., where all Rn and Sn are sets that may vary in function of time and of other parameters. Several such sets may be equal, or may be reduced to points, or may be empty. {The multiplication of two sets A and B is classically defined as: AB ={ab, a??A and b??B}. And similarly a number n times a set A is defined as: nA ={na, a??A}.} The unit of neutrosophic energy is Hν , where H is a set (in particular an interval) that includes Planck constant h, and ν is the frequency. Therefore, an oscillator could change its energy by a neutrosophic number of quanta: Hν , 2H ν, 3H ν, etc. For example, when H is an interval [h1 ,h2 ] , with 0 <=h1 <=h2 , that contains Planck constant h, then one has: [h1 ν ,h2 ν ], [2h1 ν , 2h2 ν ], [3h1 ν , 3h2 ν ],..., as series of intervals of energy change of the oscillator. The most general form of the units of neutrosophic energy is Hnνn , where all Hn and νn are sets that similarly as above may vary in function of time and of other oscillator and environment parameters. Neutrosophic quantum theory combines classical mechanics and quantum mechanics.

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

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.

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

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

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…

Multichannel-quantum-defect-theory treatment of preionized and predissociated triplet gerade levels of H2

NASA Astrophysics Data System (ADS)

Matzkin, A.; Jungen, Ch.; Ross, S. C.

2000-12-01

Multichannel quantum defect theory (MQDT) is used to calculate highly excited predissociated and preionized triplet gerade states of H2. The treatment is ab initio and is based on the clamped-nuclei quantum-defect matrices and dipole transition moments derived from quantum-chemical potential energy curves by Ross et al. [Can. J. Phys. (to be published)]. Level positions, predissociation or preionization widths and relative intensities are found to be in good agreement with those observed by Lembo et al. [Phys. Rev. A 38, 3447 (1988); J. Chem. Phys. 92, 2219 (1990)] by an optical-optical double resonance photoionization or depletion technique.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

PubMed

Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

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

Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it; Jackson, Bret; Hughes, Keith H.

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theorymore » for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.« less

R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter.

PubMed

Yang, Jing; Jin, Qi-Yu; Zhang, Biao; Shen, Hong-Bin

2016-08-15

Inter-residue contacts in proteins dictate the topology of protein structures. They are crucial for protein folding and structural stability. Accurate prediction of residue contacts especially for long-range contacts is important to the quality of ab inito structure modeling since they can enforce strong restraints to structure assembly. In this paper, we present a new Residue-Residue Contact predictor called R2C that combines machine learning-based and correlated mutation analysis-based methods, together with a two-dimensional Gaussian noise filter to enhance the long-range residue contact prediction. Our results show that the outputs from the machine learning-based method are concentrated with better performance on short-range contacts; while for correlated mutation analysis-based approach, the predictions are widespread with higher accuracy on long-range contacts. An effective query-driven dynamic fusion strategy proposed here takes full advantages of the two different methods, resulting in an impressive overall accuracy improvement. We also show that the contact map directly from the prediction model contains the interesting Gaussian noise, which has not been discovered before. Different from recent studies that tried to further enhance the quality of contact map by removing its transitive noise, we designed a new two-dimensional Gaussian noise filter, which was especially helpful for reinforcing the long-range residue contact prediction. Tested on recent CASP10/11 datasets, the overall top L/5 accuracy of our final R2C predictor is 17.6%/15.5% higher than the pure machine learning-based method and 7.8%/8.3% higher than the correlated mutation analysis-based approach for the long-range residue contact prediction. http://www.csbio.sjtu.edu.cn/bioinf/R2C/Contact:hbshen@sjtu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Revealing strategies of quorum sensing in Azospirillum brasilense strains Ab-V5 and Ab-V6.

PubMed

Fukami, Josiane; Abrantes, Julia Laura Fernandes; Del Cerro, Pablo; Nogueira, Marco Antonio; Ollero, Francisco Javier; Megías, Manuel; Hungria, Mariangela

2018-01-01

Azospirillum brasilense is an important plant-growth promoting bacterium (PGPB) that requires several critical steps for root colonization, including biofilm and exopolysaccharide (EPS) synthesis and cell motility. In several bacteria these mechanisms are mediated by quorum sensing (QS) systems that regulate the expression of specific genes mediated by the autoinducers N-acyl-homoserine lactones (AHLs). We investigated QS mechanisms in strains Ab-V5 and Ab-V6 of A. brasilense, which are broadly used in commercial inoculants in Brazil. Neither of these strains carries a luxI gene, but there are several luxR solos that might perceive AHL molecules. By adding external AHLs we verified that biofilm and EPS production and cell motility (swimming and swarming) were regulated via QS in Ab-V5, but not in Ab-V6. Differences were observed not only between strains, but also in the specificity of LuxR-type receptors to AHL molecules. However, Ab-V6 was outstanding in indole acetic acid (IAA) synthesis and this molecule might mimic AHL signals. We also applied the quorum quenching (QQ) strategy, obtaining transconjugants of Ab-V5 and Ab-V6 carrying a plasmid with acyl-homoserine lactonase. When maize (Zea mays L.) was inoculated with the wild-type and transconjugant strains, plant growth was decreased with the transconjugant of Ab-V5-confirming the importance of an AHL-mediated QS system-but did not affect plant growth promotion by Ab-V6.

Quantum Tunneling of Water in Beryl. A New State of the Water Molecule

DOE PAGES

Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani; ...

2016-04-22

When using neutron scattering and ab initio simulations, we document the discovery of a new “quantum tunneling state” of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. Additionally, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

Quantum Tunneling of Water in Beryl. A New State of the Water Molecule

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

Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani

When using neutron scattering and ab initio simulations, we document the discovery of a new “quantum tunneling state” of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. Additionally, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

An eigenvalue approach to quantum plasmonics based on a self-consistent hydrodynamics method

NASA Astrophysics Data System (ADS)

Ding, Kun; Chan, C. T.

2018-02-01

Plasmonics has attracted much attention not only because it has useful properties such as strong field enhancement, but also because it reveals the quantum nature of matter. To handle quantum plasmonics effects, ab initio packages or empirical Feibelman d-parameters have been used to explore the quantum correction of plasmonic resonances. However, most of these methods are formulated within the quasi-static framework. The self-consistent hydrodynamics model offers a reliable approach to study quantum plasmonics because it can incorporate the quantum effect of the electron gas into classical electrodynamics in a consistent manner. Instead of the standard scattering method, we formulate the self-consistent hydrodynamics method as an eigenvalue problem to study quantum plasmonics with electrons and photons treated on the same footing. We find that the eigenvalue approach must involve a global operator, which originates from the energy functional of the electron gas. This manifests the intrinsic nonlocality of the response of quantum plasmonic resonances. Our model gives the analytical forms of quantum corrections to plasmonic modes, incorporating quantum electron spill-out effects and electrodynamical retardation. We apply our method to study the quantum surface plasmon polariton for a single flat interface.

Ab Initio energetics of SiO bond cleavage.

PubMed

Hühn, Carolin; Erlebach, Andreas; Mey, Dorothea; Wondraczek, Lothar; Sierka, Marek

2017-10-15

A multilevel approach that combines high-level ab initio quantum chemical methods applied to a molecular model of a single, strain-free SiOSi bridge has been used to derive accurate energetics for SiO bond cleavage. The calculated SiO bond dissociation energy and the activation energy for water-assisted SiO bond cleavage of 624 and 163 kJ mol -1 , respectively, are in excellent agreement with values derived recently from experimental data. In addition, the activation energy for H 2 O-assisted SiO bond cleavage is found virtually independent of the amount of water molecules in the vicinity of the reaction site. The estimated reaction energy for this process including zero-point vibrational contribution is in the range of -5 to 19 kJ mol -1 . © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Ab Initio Values of the Thermophysical Properties of Helium as Standards

PubMed Central

Hurly, John J.; Moldover, Michael R.

2000-01-01

Recent quantum mechanical calculations of the interaction energy of pairs of helium atoms are accurate and some include reliable estimates of their uncertainty. We combined these ab initio results with earlier published results to obtain a helium-helium interatomic potential that includes relativistic retardation effects over all ranges of interaction. From this potential, we calculated the thermophysical properties of helium, i.e., the second virial coefficients, the dilute-gas viscosities, and the dilute-gas thermal conductivities of 3He, 4He, and their equimolar mixture from 1 K to 104 K. We also calculated the diffusion and thermal diffusion coefficients of mixtures of 3He and 4He. For the pure fluids, the uncertainties of the calculated values are dominated by the uncertainties of the potential; for the mixtures, the uncertainties of the transport properties also include contributions from approximations in the transport theory. In all cases, the uncertainties are smaller than the corresponding experimental uncertainties; therefore, we recommend the ab initio results be used as standards for calibrating instruments relying on these thermophysical properties. We present the calculated thermophysical properties in easy-to-use tabular form. PMID:27551630

Undoing Gender Through Legislation and Schooling: the Case of AB 537 and AB 394 IN California, USA

NASA Astrophysics Data System (ADS)

Knotts, Greg

2009-11-01

This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools have an unconscious acceptance of heteronormativity and gendered norms, which undermines both the spirit and language of these laws. This paper examines how California schools can both change standard practices and realise the transformative social change that laws like AB 537 and AB 394 can instigate. I assert that the systemic implementation of these laws, through the adoption, enforcement and evaluation of existing AB 537 Task Force Recommendations, is necessary for their success. My second assertion is that AB 537 and AB 394 have the potential to change and reconstitute gender-based and heteronormative standards at school sites.

Data and Analysis of the Double Stars STFA 10AB and STFA 1744AB

NASA Astrophysics Data System (ADS)

Arcilla, Marisa; Bowden, Sam; DeBlase, Jacqueline; Hall, Anthony; Hall, Corielyn; Hernandez, Alyssa; Renna, Danielle; Rodriguez, Fatima; Salazar, Cassandra; Sanchez, Andres; Teeter, Dayton; Brewer, Mark; Funk, Benjamin; Gillette, Travis; Sharpe, Scott

2017-04-01

Eighth grade students at Vanguard Preparatory School measured the double stars STFA 10AB and STFA 1744AB. A 22-inch Newtonian Alt/Az telescope and a 14-inch Celestron Schmidt Cassegrain telescope were used. The star Bellatrix was used as the calibration star to determine the scale constant of the 22-inch telescope to be 7.8 “/tick marks. The double star STFA 1744AB was used as the calibration star to determine the scale constant of the 14-inch telescope to be 5.1 “/tick marks. The separation and position angle of STFA 10AB was determined by the 22-inch telescope to be 347.9” and 339.3°. The separation and position angle of STFA 1744AB was determined by the 14-inch telescope to be 3.6” and 158.1°. The measurements that were calculated were compared to the most recent measurements listed in the Washington Double Star Catalog.

Quantum oscillation and the Aharonov-Bohm effect in a multiply connected normal-conductor loop

NASA Astrophysics Data System (ADS)

Takai, Daisuke; Ohta, Kuniichi

1994-12-01

The magnetostatic and electrostatic Aharonov-Bohm (AB) effects in multiply connected normal-conductor rings are studied. A previously developed model of a single mesoscopic ring is generalized to include an arbitrary number of rings, and the oscillatory behavior of the total transmission coefficients for the serially connected N (N is equal to integer) rings are derived as a function of the magnetic flux threading each ring and as a function of the electrostatic potential applied to the rings. It is shown that quantum oscillation of multiple rings exhibits greater variety of behavior than in periodic superlattices. We investigate the influence of the scattering at a junction and the number of atoms in the ring in both magnetostatic and electrostatic oscillation of multiring systems. For the electrostatic AB effects, when scattering occurs at the junctions between the connecting wire and the ring, the conductance in the AB oscillation is modified to an N-1 peaked shape. It is shown that this oscillatory behavior is greatly influenced by the number of atoms in the ring and is controlled by the electrostatic potential or magnetic flux that is applied to the ring. We discuss the behavior of the quantum oscillations upon varying the number of connected rings and the number of minibands.

Nuclear quantum dynamics in dense hydrogen

PubMed Central

Kang, Dongdong; Sun, Huayang; Dai, Jiayu; Chen, Wenbo; Zhao, Zengxiu; Hou, Yong; Zeng, Jiaolong; Yuan, Jianmin

2014-01-01

Nuclear dynamics in dense hydrogen, which is determined by the key physics of large-angle scattering or many-body collisions between particles, is crucial for the dynamics of planet's evolution and hydrodynamical processes in inertial confinement confusion. Here, using improved ab initio path-integral molecular dynamics simulations, we investigated the nuclear quantum dynamics regarding transport behaviors of dense hydrogen up to the temperatures of 1 eV. With the inclusion of nuclear quantum effects (NQEs), the ionic diffusions are largely higher than the classical treatment by the magnitude from 20% to 146% as the temperature is decreased from 1 eV to 0.3 eV at 10 g/cm3, meanwhile, electrical and thermal conductivities are significantly lowered. In particular, the ionic diffusion is found much larger than that without NQEs even when both the ionic distributions are the same at 1 eV. The significant quantum delocalization of ions introduces remarkably different scattering cross section between protons compared with classical particle treatments, which explains the large difference of transport properties induced by NQEs. The Stokes-Einstein relation, Wiedemann-Franz law, and isotope effects are re-examined, showing different behaviors in nuclear quantum dynamics. PMID:24968754

Quantum dot properties in the multiband envelope-function approximation using boundary conditions based upon first-principles quantum calculations

NASA Astrophysics Data System (ADS)

Flory, Curt A.; Musgrave, Charles B.; Zhang, Zhiyong

2008-05-01

A number of physical processes involving quantum dots depend critically upon the “evanescent” electron eigenstate wave function that extends outside of the material surface into the surrounding region. These processes include electron tunneling through quantum dots, as well as interactions between multiple quantum dot structures. In order to unambiguously determine these evanescent fields, appropriate boundary conditions have been developed to connect the electronic solutions interior to the semiconductor quantum dot to exterior vacuum solutions. In standard envelope function theory, the interior wave function consists of products of band edge and envelope functions, and both must be considered when matching to the external solution. While the envelope functions satisfy tractable equations, the band edge functions are generally not known. In this work, symmetry arguments in the spherically symmetric approximation are used in conjunction with the known qualitative behavior of bonding and antibonding orbitals to catalog the behavior of the band edge functions at the unit cell boundary. This physical approximation allows consolidation of the influence of the band edge functions to two simple surface parameters that are incorporated into the boundary conditions and are straightforwardly computed by using numerical first-principles quantum techniques. These new boundary conditions are employed to analyze an isolated spherically symmetric semiconductor quantum dot in vacuum within the analytical model of Sercel and Vahala [Phys. Rev. Lett. 65, 239 (1990); Phys. Rev. B 42, 3690 (1990)]. Results are obtained for quantum dots made of GaAs and InP, which are compared with ab initio calculations that have appeared in the literature.

Ab initio study of Pd carbonyls and CO/Pd(110)

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

Ramprasad, R.; Glassford, K.M.; Adams, J.B.

1994-12-31

Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and amore » plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.« less

CdSe/ZnS Quantum Dot-Labeled Lateral Flow Strips for Rapid and Quantitative Detection of Gastric Cancer Carbohydrate Antigen 72-4

NASA Astrophysics Data System (ADS)

Yan, Xinyu; Wang, Kan; Lu, Wenting; Qin, Weijian; Cui, Daxiang; He, Jinghua

2016-03-01

Carbohydrate antigen 72-4 (CA72-4) is an important biomarker associated closely with diagnosis and prognosis of early gastric cancer. How to realize quick, sensitive, specific, and quantitative detection of CA72-4 in clinical specimens has become a great requirement. Herein, we reported a CdSe/ZnS quantum dot-labeled lateral flow test strip combined with a charge-coupled device (CCD)-based reader was developed for rapid, sensitive, and quantitative detection of CA72-4. Two mouse monoclonal antibodies (mAbs) against CA72-4 were employed. One of them was coated as a test line, while another mAb was labeled with quantum dots and coated onto conjugate pad. The goat anti-mouse IgG was immobilized as a control line. After sample was added, a sandwich structure was formed with CA72-4 and these two mAbs. The fluorescent signal from quantum dots (QD)-labeled mAb in sandwich structure was related to the amount of detected CA72-4. A CCD-based reader was used to realize quantitative detection of CA72-4. Results showed that developed QD-labeled lateral flow strips to detect CA72-4 biomarker with the sensitivity of 2 IU/mL and 10 min detection time. One hundred sera samples from clinical patients with gastric cancer and healthy people were used to confirm specificity of this strip method; results showed that established strip method own 100 % reproducibility and 100 % specificity compared with Roche electrochemiluminescence assay results. In conclusion, CdSe/ZnS quantum dot-labeled lateral flow strips for detection of CA72-4 could realize rapid, sensitive, and specific detection of clinical samples and could own great potential in clinical translation in near future.

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

PubMed

Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

2006-05-24

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

N-H stretching modes of adenosine monomer in solution studied by ultrafast nonlinear infrared spectroscopy and ab initio calculations.

PubMed

Greve, Christian; Preketes, Nicholas K; Costard, Rene; Koeppe, Benjamin; Fidder, Henk; Nibbering, Erik T J; Temps, Friedrich; Mukamel, Shaul; Elsaesser, Thomas

2012-07-26

The N-H stretching vibrations of adenine, one of the building blocks of DNA, are studied by combining infrared absorption and nonlinear two-dimensional infrared spectroscopy with ab initio calculations. We determine diagonal and off-diagonal anharmonicities of N-H stretching vibrations in chemically modified adenosine monomer dissolved in chloroform. For the single-quantum excitation manifold, the normal mode picture with symmetric and asymmetric NH(2) stretching vibrations is fully appropriate. For the two-quantum excitation manifold, however, the interplay between intermode coupling and frequency shifts due to a large diagonal anharmonicity leads to a situation where strong mixing does not occur. We compare our findings with previously reported values obtained on overtone spectroscopy of coupled hydrogen stretching oscillators.

Molecular nanomagnets with switchable coupling for quantum simulation

DOE PAGES

Chiesa, Alessandro; Whitehead, George F. S.; Carretta, Stefano; ...

2014-12-11

Molecular nanomagnets are attractive candidate qubits because of their wide inter- and intra-molecular tunability. Uniform magnetic pulses could be exploited to implement one- and two-qubit gates in presence of a properly engineered pattern of interactions, but the synthesis of suitable and potentially scalable supramolecular complexes has proven a very hard task. Indeed, no quantum algorithms have ever been implemented, not even a proof-of-principle two-qubit gate. In this paper we show that the magnetic couplings in two supramolecular {Cr7Ni}-Ni-{Cr7Ni} assemblies can be chemically engineered to fit the above requisites for conditional gates with no need of local control. Microscopic parameters aremore » determined by a recently developed many-body ab-initio approach and used to simulate quantum gates. We find that these systems are optimal for proof-of-principle two-qubit experiments and can be exploited as building blocks of scalable architectures for quantum simulation.« less

Unified ab initio approaches to nuclear structure and reactions

DOE PAGES

Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...

2016-04-13

The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less

Determination of the electronic energy levels of colloidal nanocrystals using field-effect transistors and Ab-initio calculations.

PubMed

Bisri, Satria Zulkarnaen; Degoli, Elena; Spallanzani, Nicola; Krishnan, Gopi; Kooi, Bart Jan; Ghica, Corneliu; Yarema, Maksym; Heiss, Wolfgang; Pulci, Olivia; Ossicini, Stefano; Loi, Maria Antonietta

2014-08-27

Colloidal nanocrystals electronic energy levels are determined by strong size-dependent quantum confinement. Understanding the configuration of the energy levels of nanocrystal superlattices is vital in order to use them in heterostructures with other materials. A powerful method is reported to determine the energy levels of PbS nanocrystal assemblies by combining the utilization of electric-double-layer-gated transistors and advanced ab-initio theory. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oriented conjugates of monoclonal and single-domain antibodies with quantum dots for flow cytometry and immunohistochemistry diagnostic applications

NASA Astrophysics Data System (ADS)

Sukhanova, Alyona; Even-Desrumeaux, Klervi; Millot, Jean-Marc; Chames, Patrick; Baty, Daniel; Artemyev, Mikhail; Oleinikov, Vladimir; Cohen, Jacques H. M.; Nabiev, Igor

2012-03-01

Ideal diagnostic nanoprobes should not exceed 15 nm in size and should contain high-affinity homogeneously oriented capture molecules on their surface. An advanced procedure for antibody (Ab) reduction was used to cleave each Ab into two functional half-Abs, 75-kDa heavy-light chain fragments, each containing an intact antigen-binding site. Affinity purification of half-Abs followed by their linkage to quantum dots (QDs) yielded oriented QD-Ab conjugates whose functionality was considerably improved compared to those obtained using the standard protocols. Ultrasmall diagnostic nanoprobes were engineered through oriented conjugation of QDs with 13-kDa single-domain Abs (sdAbs) derived from llama IgG. sdAbs were tagged with QDs via an additional cysteine residue specifically integrated into the C-terminal region of sdAb using genetic engineering. This approach made it possible to obtain sdAb-QD nanoprobes <12 nm in diameter comprising four copies of sdAbs linked to the same QD in an oriented manner. sdAb-QD conjugates against carcinoembryonic antigen (CEA) and HER2 exhibited an extremely high specificity in flow cytometry; the quality of immunohistochemical labeling of biopsy samples was found to be superior to that of labeling according to the current "gold standard" protocols of anatomo-pathological practice. The nano-bioengineering approaches developed can be extended to oriented conjugation of Abs and sdAbs with different semiconductor, noble metal, or magnetic nanoparticles.

Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kumar, Sanjay

2007-12-01

State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.

Thermalization and its mechanism for generic quantum isolated systems

NASA Astrophysics Data System (ADS)

Olshanii, Maxim; Dunjko, Vanja; Rigol, Marcos

2008-05-01

Time dynamics of isolated many-body quantum systems has long been an elusive subject, perhaps most urgently needed in the foundations of quantum statistical mechanics. In generic systems, one expects the nonequilibrium dynamics to lead to thermalization: a relaxation to states where the values of macroscopic quantities are stationary, universal with respect to widely differing initial conditions, and predictable through the time-tested recipe of statistical mechanics. The relaxation mechanism is not obvious, however; dynamical chaos cannot play the key role as it does in classical systems since quantum evolution is linear. Here we demonstrateootnotetextM. Rigol, V. Dunjko, and M. Olshanii, to appear in Nature (2008), using the results of an ab initio numerical experiment with 5 hard-core bosons moving in a 5x5 lattice, that in quantum systems thermalization happens not in course of time evolution but instead at the level of individual eigenstates, as first proposed by DeutschootnotetextJ. M. Deutsch, Phys.Rev. A 43, 2046 (1991) and SrednickiootnotetextM. Srednicki, Phys. Rev. E 50, 888 (1994).

Ab initio calculation of transport properties between PbSe quantum dots facets with iodide ligands

NASA Astrophysics Data System (ADS)

Wang, B.; Patterson, R.; Chen, W.; Zhang, Z.; Yang, J.; Huang, S.; Shrestha, S.; Conibeer, G.

2018-01-01

The transport properties between Lead Selenide (PbSe) quantum dots decorated with iodide ligands has been studied using density functional theory (DFT). Quantum conductance at each selected energy levels has been calculated along with total density of states and projected density of states. The DFT calculation is carried on using a grid-based planar augmented wave (GPAW) code incorporated with the linear combination of atomic orbital (LCAO) mode and Perdew Burke Ernzerhof (PBE) exchange-correlation functional. Three iodide ligand attached low index facets including (001), (011), (111) are investigated in this work. P-orbital of iodide ligand majorly contributes to density of state (DOS) at near top valence band resulting a significant quantum conductance, whereas DOS of Pb p-orbital shows minor influence. Various values of quantum conductance observed along different planes are possibly reasoned from a combined effect electrical field over topmost surface and total distance between adjacent facets. Ligands attached to (001) and (011) planes possess similar bond length whereas it is significantly shortened in (111) plane, whereas transport between (011) has an overall low value due to newly formed electric field. On the other hand, (111) plane with a net surface dipole perpendicular to surface layers leading to stronger electron coupling suggests an apparent increase of transport probability. Apart from previously mentioned, the maximum transport energy levels located several eVs (1 2 eVs) from the edge of valence band top.

Entanglement entropy of 2D conformal quantum critical points: hearing the shape of a quantum drum.

PubMed

Fradkin, Eduardo; Moore, Joel E

2006-08-04

The entanglement entropy of a pure quantum state of a bipartite system A union or logical sumB is defined as the von Neumann entropy of the reduced density matrix obtained by tracing over one of the two parts. In one dimension, the entanglement of critical ground states diverges logarithmically in the subsystem size, with a universal coefficient that for conformally invariant critical points is related to the central charge of the conformal field theory. We find that the entanglement entropy of a standard class of z=2 conformal quantum critical points in two spatial dimensions, in addition to a nonuniversal "area law" contribution linear in the size of the AB boundary, generically has a universal logarithmically divergent correction, which is completely determined by the geometry of the partition and by the central charge of the field theory that describes the critical wave function.

Registration of nine sorghum seed parent (A/B) lines

USDA-ARS?s Scientific Manuscript database

Nine sorghum [Sorghum bicolor (L.) Moench] A1 cyto plasmic-genic male sterile seed parent (A) and their maintainer (B) lines [KS 133A/B, KS 134A/B, KS 135A/B, KS 136A/B, KS 137A/B, KS 138A/B, KS 139A/B, KS 140A/B and KS 141A/B] were released by the Kansas State University, Agricultural Research Cent...

mAbs: a business perspective.

PubMed

Scolnik, Pablo A

2009-01-01

The twenty two monoclonal antibodies (mAbs) currently marketed in the U.S. have captured almost half of the top-20 U.S. therapeutic biotechnology sales for 2007. Eight of these products have annual sales each of more than $1 B, were developed in the relatively short average period of six years, qualified for FDA programs designed to accelerate drug approval, and their cost has been reimbursed liberally by payers. With growth of the product class driven primarily by advancements in protein engineering and the low probability of generic threats, mAbs are now the largest class of biological therapies under development. The high cost of these drugs and the lack of generic competition conflict with a financially stressed health system, setting reimbursement by payers as the major limiting factor to growth. Advances in mAb engineering are likely to result in more effective mAb drugs and an expansion of the therapeutic indications covered by the class. The parallel development of biomarkers for identifying the patient subpopulations most likely to respond to treatment may lead to a more cost-effective use of these drugs. To achieve the success of the current top-tier mAbs, companies developing new mAb products must adapt to a significantly more challenging commercial environment.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

PubMed Central

2015-01-01

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. PMID:24803856

Spin-dependent Otto quantum heat engine based on a molecular substance

NASA Astrophysics Data System (ADS)

Hübner, W.; Lefkidis, G.; Dong, C. D.; Chaudhuri, D.; Chotorlishvili, L.; Berakdar, J.

2014-07-01

We explore the potential of single molecules for thermodynamic cycles. To this end we propose two molecular heat engines based on the Ni2 dimer in the presence of a static magnetic field: (a) a quantum Otto engine and (b) a modified quantum Otto engine for which optical excitations induced by a laser pulse substitute for one of the heat-exchange points. For reliable predictions and to inspect the role of spin and electronic correlations we perform fully correlated ab initio calculations of the molecular electronic structure including spin-orbital effects. We analyze the efficiency of the engines in dependence of the electronic level scheme and the entanglement and find a significant possible enhancement connected to the quantum nature and the heat capacity of the dimer, as well as to the zero-field triplet states splitting.

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

PubMed

Wang, Lu; Fried, Stephen D; Boxer, Steven G; Markland, Thomas E

2014-12-30

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results.

PubMed

Hahn, Seungsoo

2016-10-28

The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.

Structural and Biophysical Characterization of Bacillus thuringiensis Insecticidal Proteins Cry34Ab1 and Cry35Ab1

PubMed Central

Kelker, Matthew S.; Berry, Colin; Evans, Steven L.; Pai, Reetal; McCaskill, David G.; Wang, Nick X.; Russell, Joshua C.; Baker, Matthew D.; Yang, Cheng; Pflugrath, J. W.; Wade, Matthew; Wess, Tim J.; Narva, Kenneth E.

2014-01-01

Bacillus thuringiensis strains are well known for the production of insecticidal proteins upon sporulation and these proteins are deposited in parasporal crystalline inclusions. The majority of these insect-specific toxins exhibit three domains in the mature toxin sequence. However, other Cry toxins are structurally and evolutionarily unrelated to this three-domain family and little is known of their three dimensional structures, limiting our understanding of their mechanisms of action and our ability to engineer the proteins to enhance their function. Among the non-three domain Cry toxins, the Cry34Ab1 and Cry35Ab1 proteins from B. thuringiensis strain PS149B1 are required to act together to produce toxicity to the western corn rootworm (WCR) Diabrotica virgifera virgifera Le Conte via a pore forming mechanism of action. Cry34Ab1 is a protein of ∼14 kDa with features of the aegerolysin family (Pfam06355) of proteins that have known membrane disrupting activity, while Cry35Ab1 is a ∼44 kDa member of the toxin_10 family (Pfam05431) that includes other insecticidal proteins such as the binary toxin BinA/BinB. The Cry34Ab1/Cry35Ab1 proteins represent an important seed trait technology having been developed as insect resistance traits in commercialized corn hybrids for control of WCR. The structures of Cry34Ab1 and Cry35Ab1 have been elucidated to 2.15 Å and 1.80 Å resolution, respectively. The solution structures of the toxins were further studied by small angle X-ray scattering and native electrospray ion mobility mass spectrometry. We present here the first published structure from the aegerolysin protein domain family and the structural comparisons of Cry34Ab1 and Cry35Ab1 with other pore forming toxins. PMID:25390338

Single domain antibody-quantum dot conjugates for ricin detection by both fluoroimmunoassay and surface plasmon resonance.

PubMed

Anderson, George P; Glaven, Richard H; Algar, W Russ; Susumu, Kimihiro; Stewart, Michael H; Medintz, Igor L; Goldman, Ellen R

2013-07-05

The combination of stable biorecognition elements and robust quantum dots (QDs) has the potential to yield highly effective reporters for bioanalyses. Llama-derived single domain antibodies (sdAb) provide small thermostable recognition elements that can be easily manipulated using standard DNA methods. The sdAb was self-assembled on dihydrolipoic acid (DHLA) ligand-capped CdSe-ZnS core-shell QDs made in our laboratory through the polyhistidine tail of the protein, which coordinated to zinc ions on the QD surface. The sdAb-QD bioconjugates were then applied in both fluorometric and surface plasmon resonance (SPR) immunoassays for the detection of ricin, a potential biothreat agent. The sdAb-QD conjugates functioned in fluoroimmunoassays for the detection of ricin, providing equivalent limits of detection when compared to the same anti-ricin sdAb labeled with a conventional fluorophore. In addition, the DHLA-QD-sdAb conjugates were very effective reporter elements in SPR sandwich assays, providing more sensitive detection with a signal enhancement of ~10-fold over sdAb reporters and 2-4 fold over full sized antibody reporters. Commercially prepared streptavidin-modified polymer-coated QDs also amplified the SPR signal for the detection of ricin when applied to locations where biotinylated anti-ricin sdAb was bound to target; however, we observed a 4-fold greater amplification when using the DHLA-QD-sdAb conjugates in this format. Copyright © 2013. Published by Elsevier B.V.

Spin-Orbit Interactions and Quantum Spin Dynamics in Cold Ion-Atom Collisions

NASA Astrophysics Data System (ADS)

Tscherbul, Timur V.; Brumer, Paul; Buchachenko, Alexei A.

2016-09-01

We present accurate ab initio and quantum scattering calculations on a prototypical hybrid ion-atom system Yb+ -Rb, recently suggested as a promising candidate for the experimental study of open quantum systems, quantum information processing, and quantum simulation. We identify the second-order spin-orbit (SO) interaction as the dominant source of hyperfine relaxation in cold Yb+ -Rb collisions. Our results are in good agreement with recent experimental observations [L. Ratschbacher et al., Phys. Rev. Lett. 110, 160402 (2013)] of hyperfine relaxation rates of trapped Yb+ immersed in an ultracold Rb gas. The calculated rates are 4 times smaller than is predicted by the Langevin capture theory and display a weak T-0.3 temperature dependence, indicating significant deviations from statistical behavior. Our analysis underscores the deleterious nature of the SO interaction and implies that light ion-atom combinations such as Yb+ -Li should be used to minimize hyperfine relaxation and decoherence of trapped ions in ultracold atomic gases.

Solvent (acetone-butanol: ab) production

USDA-ARS?s Scientific Manuscript database

This article describes production of butanol [acetone-butanol-ethanol, (also called AB or ABE or solvent)] by fermentation using both traditional and current technologies. AB production from agricultural commodities, such as corn and molasses, was an important historical fermentation. Unfortunately,...

Multipartite quantum correlations and local recoverability

PubMed Central

Wilde, Mark M.

2015-01-01

Characterizing genuine multipartite quantum correlations in quantum physical systems has historically been a challenging problem in quantum information theory. More recently, however, the total correlation or multipartite information measure has been helpful in accomplishing this goal, especially with the multipartite symmetric quantum (MSQ) discord (Piani et al. 2008 Phys. Rev. Lett. 100, 090502. (doi:10.1103/PhysRevLett.100.090502)) and the conditional entanglement of multipartite information (CEMI) (Yang et al. 2008 Phys. Rev. Lett. 101, 140501. (doi:10.1103/PhysRevLett.101.140501)). Here, we apply a recent and significant improvement of strong subadditivity of quantum entropy (Fawzi & Renner 2014 (http://arxiv.org/abs/1410.0664)) in order to develop these quantities further. In particular, we prove that the MSQ discord is nearly equal to zero if and only if the multipartite state for which it is evaluated is approximately locally recoverable after performing measurements on each of its systems. Furthermore, we prove that the CEMI is a faithful entanglement measure, i.e. it vanishes if and only if the multipartite state for which it is evaluated is a fully separable state. Along the way, we provide an operational interpretation of the MSQ discord in terms of the partial state distribution protocol, which in turn, as a special case, gives an interpretation for the original discord quantity. Finally, we prove an inequality that could potentially improve upon the Fawzi–Renner inequality in the multipartite context, but it remains an open question to determine whether this is so. PMID:27547097

In Vitro Study of Bacteriophage AB3 Endolysin LysAB3 Activity Against Acinetobacter baumannii Biofilm and Biofilm-Bound A. baumannii.

PubMed

Zhang, Jie; Xu, Lu-Lu; Gan, Dan; Zhang, Xingping

2018-06-01

The increase in the prevalence of drug-resistant Acinetobacter baumannii is a serious public health concern, which is closely linked to the formation of biofilm. It is reported that the bacteriophage and its endolysin have a good ability to degrade biofilms. The goals of this study were to compare the ability of A. baumannii bacteriophage AB3, its endolysin AB3, and three antibiotics to degrade A. baumannii biofilm and biofilm-bound A. baumannii and to understand the antibacterial mechanism of LysAB3. The 558-bp sequence of the LysAB3 gene was amplified by polymerase chain reaction (PCR); the fragment was cloned into pET28a (+) to construct the recombinant plasmid pET28a-LysAB3, which was then expressed in E. coli BL21 (DE3) to obtain the LysAB3. Differences in A. baumannii biofilm and biofilm-bound A. baumannii after treatment with bacteriophage AB3, LysAB3 or three antibiotics were examined using the crystal violet staining method and an MTT (3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide) assay. Changes in biofilm morphology and thickness in each treatment group were observed by laser scanning confocal microscopy. In addition, a LysAB3 construct with the amphiphilic peptide structural region removed (LysAB3-D) was assessed for its antibacterial activity. After 24-hour treatment with either bacteriophage AB3 and its LysAB3, A. baumannii biofilms were significantly degraded, and the number of viable biofilm-bound A. baumannii were also significantly decreased. After removing the amphiphilic peptide structure motif from LysAB3, the antibacterial activity decreased from 95.8% to 33.3%. Thus, LysAB3 can effectively degrade A. baumannii biofilm and biofilm-bound A. baumannii in vitro. The antibacterial mechanism of LysAB3 may be associated with the ability of the amphiphilic peptide structural region to enhance the permeability of cytoplasmic membrane of A. baumannii by degradation of bacterial wall peptidoglycan.

Ab-initio calculation of electronic structure and optical properties of AB-stacked bilayer α-graphyne

NASA Astrophysics Data System (ADS)

Behzad, Somayeh

2016-09-01

Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.

Field Trial Performance of Herculex XTRA (Cry34Ab1/Cry35Ab1) and SmartStax (Cry34Ab1/Cry35Ab1 + Cry3Bb1) Hybrids and Soil Insecticides Against Western and Northern Corn Rootworms (Coleoptera: Chrysomelidae).

PubMed

Johnson, K D; Campbell, L A; Lepping, M D; Rule, D M

2017-06-01

Western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), and northern corn rootworm, Diabrotica barberi Smith and Lawrence (Coleoptera: Chrysomelidae), are important insect pests in corn, Zea mays L. For more than a decade, growers have been using transgenic plants expressing proteins from the bacterium Bacillus thuringiensis (Bt) to protect corn roots from feeding. In 2011, western corn rootworm populations were reported to have developed resistance to Bt hybrids expressing Cry3Bb1 and later found to be cross-resistant to hybrids expressing mCry3A and eCry3.1Ab. The identification of resistance to Cry3 (Cry3Bb1, mCry3A, and eCry3.1Ab) hybrids led to concerns about durability and efficacy of products with single traits and of products containing a pyramid of a Cry3 protein and the binary Bt proteins Cry34Ab1 and Cry35Ab1. From 2012 to 2014, 43 field trials were conducted across the central United States to estimate root protection provided by plants expressing Cry34Ab1/Cry35Ab1 alone (Herculex RW) or pyramided with Cry3Bb1 (SmartStax). These technologies were evaluated with and without soil-applied insecticides to determine if additional management measures provided benefit where Cry3 performance was reduced. Trials were categorized for analysis based on rootworm damage levels on Cry3-expressing hybrids and rootworm feeding pressure within each trial. Across scenarios, Cry34Ab1/Cry35Ab1 hybrids provided excellent root protection. Pyramided traits provided greater root and yield protection than non-Bt plus a soil-applied insecticide, and only in trials where larval feeding pressure exceeded two nodes of damage did Cry34Ab1/Cry35Ab1 single-trait hybrids and pyramided hybrids show greater root protection from the addition of soil-applied insecticides. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Photodissociation of phenol via nonadiabatic tunneling: Comparison of two ab initio based potential energy surfaces

NASA Astrophysics Data System (ADS)

Xie, Changjian; Guo, Hua

2017-09-01

The nonadiabatic tunneling-facilitated photodissociation of phenol is investigated using a reduced-dimensional quantum model on two ab initio-based coupled potential energy surfaces (PESs). Although dynamics occurs largely on the lower adiabat, the proximity to a conical intersection between the S1 and S2 states requires the inclusion of both the geometric phase (GP) and diagonal Born-Oppenheimer correction (DBOC). The lifetime of the lowest-lying vibronic state is computed using the diabatic and various adiabatic models. The GP and DBOC terms are found to be essential on one set of PESs, but have a small impact on the other.

Interaction between methyl glyoxal and ascorbic acid: experimental and theoretical aspects

NASA Astrophysics Data System (ADS)

Banerjee, D.; Koll, A.; Filarowski, A.; Bhattacharyya, S. P.; Mukherjee, S.

2004-06-01

The absorption spectral change of methyl glyoxal (MG) due to the interaction with ascorbic acid (AA or Vitamin C) has been investigated using steady-state spectroscopic technique. A plausible explanation for the spectral change has been discussed on the basis of hydrogen bonding interaction between the two interacting species. The equilibrium constant for the complex formation due to hydrogen bonding interaction between MG and AA has been obtained from absorption spectral changes. Ab inito calculations with DFT B3LYP/6/31G (d,p) basis sets have been used to find out the molecular structure of the hydrogen bonded complex. The O⋯H distance found in the OH⋯O hydrogen bond turns out to be quite short (1.974 Å) which is in conformity with the large value of the equilibrium constant determined experimentally.

On Predicting the Crystal Structure of Energetic Materials From Quantum Mechanics

DTIC Science & Technology

2008-12-01

DE ABSTRACT A quantum-mechanically-based potential energy function that describes interactions of dimers of the explosive ...method is capable of producing force fields for interactions of the molecular crystalline explosive RDX, and appears to be suitable to enable reliable...Ridge, TN. Byrd, E.F.C., Scuseria, G.E., Chabalowski, C.F., 2004: “An ab initio study of solid nitromethane , HMX, RDX and CL20: Successes and

Flux-dependent anti-crossing of resonances in parallel non-coupled double quantum dots

NASA Astrophysics Data System (ADS)

Joe, Yong S.; Hedin, Eric R.; Kim, Jiseok

2008-08-01

We present novel resonant phenomena through parallel non-coupled double quantum dots (QDs) embedded in each arm of an Aharonov-Bohm (AB) ring with magnetic flux passing through its center. The electron transmission through this AB ring with each QD formed by two short-range potential barriers is calculated using a scattering matrix at each junction and a transfer matrix in each arm. We show that as the magnetic flux modulates, a distortion of the grid-like square transmission occurs and an anti-crossing of the resonances appears. Hence, the modulation of magnetic flux in this system can have an equivalent effect to the control of inter-dot coupling between the two QDs.

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

PubMed Central

Wang, Lu; Fried, Stephen D.; Boxer, Steven G.; Markland, Thomas E.

2014-01-01

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds. PMID:25503367

On the Making of Quantum Chemistry in Germany

NASA Astrophysics Data System (ADS)

Karachalios, Andreas

During the 1990s several historians of science have studied the emergence of quantum chemistry as an autonomous discipline in different national contexts (Nye, 1993; Simões, 1993; Simões, forthcoming; Gavroglu and Simões, 1994; Karachalios, 1997a). Beyond these disciplinary studies, a number of contributions to special aspects of this theme have appeared (Schweber, 1990; Gavroglu, 1995; Simões and Gavroglu, 1997, 1999a,b; Schwarz et al., 1999). In this literature the birth of quantum chemistry has generally been associated with two dates: the 1927 paper of Walter Heitler and Fritz London and the year 1931 in which Linus Pauling and John Clarke Slater independently explained the tetrahedral orientation of the four bonds of the carbon atom. To these dates we might also add a third: in 1928 London published a paper, 'Zur Quantentheorie der homöopolaren Valenzzahlen' (London, 1928), in which he gave a quantum mechanical explanation of the classical chemical notion of valency. There he showed a relationship between the valency numbers and the spectroscopical multiplicity, namely that valency=multiplicity-1. This relation established a bridge between physical and chemical facts. Taken together, these developments constitute important events for the international development of quantum chemistry.

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

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

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

Dielectronic recombination of lowly charged tungsten ions Wq+(q = 5 - 10)

NASA Astrophysics Data System (ADS)

Kwon, Duck-Hee

2018-03-01

Dielectronic recombination (DR) rate coefficients for the ground levels of low ionization state Wq+ (q = 5 - 10) ions have been obtained by an ab-inito level-by-level calculation using the flexible atomic code (FAC) based on relativistic jj coupling scheme and independent process, isolated resonance, distorted wave approximation. The radiative transition calculation in the original FAC has been adapted into parallel programming for time effective dealing with so many resonance levels of the complex open 4f, 5p, or 5d-shell structure ion. Core excitations Δnc = 0 , 1 of 4f, 5p, and 5d (W5+), Δnc = 2 of 4f, and Δnc = 0 of 4d (W7+), and 5s (W8+) are included to the total DR rate coefficient. The core excitations Δnc = 0 , 5p → 5l and Δnc = 1 , 4f → 5l mainly contribute to the total DR rate coefficients. The strong resonances involved in the DR are analyzed and the total DR rate coefficients are compared with available previous ab-initio predictions and with ADAS data by a simple semiempirical formula.

HHV-6A/B Integration and the Pathogenesis Associated with the Reactivation of Chromosomally Integrated HHV-6A/B.

PubMed

Collin, Vanessa; Flamand, Louis

2017-06-26

Unlike other human herpesviruses, human herpesvirus 6A and 6B (HHV-6A/B) infection can lead to integration of the viral genome in human chromosomes. When integration occurs in germinal cells, the integrated HHV-6A/B genome can be transmitted to 50% of descendants. Such individuals, carrying one copy of the HHV-6A/B genome in every cell, are referred to as having inherited chromosomally-integrated HHV-6A/B (iciHHV-6) and represent approximately 1% of the world's population. Interestingly, HHV-6A/B integrate their genomes in a specific region of the chromosomes known as telomeres. Telomeres are located at chromosomes' ends and play essential roles in chromosomal stability and the long-term proliferative potential of cells. Considering that the integrated HHV-6A/B genome is mostly intact without any gross rearrangements or deletions, integration is likely used for viral maintenance into host cells. Knowing the roles played by telomeres in cellular homeostasis, viral integration in such structure is not likely to be without consequences. At present, the mechanisms and factors involved in HHV-6A/B integration remain poorly defined. In this review, we detail the potential biological and medical impacts of HHV-6A/B integration as well as the possible chromosomal integration and viral excision processes.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Impact of Antibody Bioconjugation on Emission and Energy Band Profile of CdSeTe/ZnS Quantum Dots

NASA Astrophysics Data System (ADS)

Torchynska, T. V.; Gomez, J. A. Jaramillo; Polupan, G.; Macotela, L. G. Vega

2018-03-01

The variation of the photoluminescence (PL) and Raman scattering spectra of CdSeTe/ZnS quantum dots (QDs) on conjugation to an antibody has been investigated. Two types of CdSeTe/ZnS QD with different emission wavelength (705 nm and 800 nm) were studied comparatively before and after conjugation to anti-pseudorabies virus antibody (AB). Nonconjugated QDs were characterized by Gaussian-type PL bands. PL shifts to higher energy and asymmetric shape of PL bands was detected in PL spectra of bioconjugated QDs. The surface-enhanced Raman scattering effect was exhibited by the bioconjugated CdSeTe/ZnS QDs, indicating that the excitation light used in the Raman study generated electric dipoles in the AB molecules. The optical bandgap of the CdSeTe core was calculated numerically as a function of its radius based on an effective mass approximation model. The energy band diagrams for non- and bioconjugated CdSeTe/ZnS QDs were obtained, revealing a type II quantum well in the CdSeTe core. The calculations show that AB dipoles, excited in the bioconjugated QDs, stimulate a change in the energy band diagram of the QDs that alters the PL spectrum. These results could be useful for improving the sensitivity of QD biosensors.

Nuclear quantum effects on adsorption of H2 and isotopologues on metal ions

NASA Astrophysics Data System (ADS)

Savchenko, Ievgeniia; Gu, Bing; Heine, Thomas; Jakowski, Jacek; Garashchuk, Sophya

2017-02-01

The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of H2 and isotopologues on metal ions, are examined using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. The lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions. Analysis of the nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) performed for complexes of Li+ and Cu+2 with H2/D2/HD shows that the PES anharmonicity changes the ZPE by up to 9%.

SdAb heterodimer formation using leucine zippers

NASA Astrophysics Data System (ADS)

Goldman, Ellen R.; Anderson, George P.; Brozozog-Lee, P. Audrey; Zabetakis, Dan

2013-05-01

Single domain antibodies (sdAb) are variable domains cloned from camel, llama, or shark heavy chain only antibodies, and are among the smallest known naturally derived antigen binding fragments. SdAb derived from immunized llamas are able to bind antigens with high affinity, and most are capable of refolding after heat or chemical denaturation to bind antigen again. We hypothesized that the ability to produce heterodimeric sdAb would enable reagents with the robust characteristics of component sdAb, but with dramatically improved overall affinity through increased avidity. Previously we had constructed multimeric sdAb by genetically linking sdAb that bind non-overlapping epitopes on the toxin, ricin. In this work we explored a more flexible approach; the construction of multivalent binding reagents using multimerization domains. We expressed anti-ricin sdAb that recognize different epitopes on the toxin as fusions with differently charged leucine zippers. When the initially produced homodimers are mixed the leucine zipper domains will pair to produce heterodimers. We used fluorescence resonance energy transfer to confirm heterodimer formation. Surface plasmon resonance, circular dichroism, enzyme linked immunosorbent assays, and fluid array assays were used to characterize the multimer constructs, and evaluate their utility in toxin detection.

Finding Effective Models in Transition Metals using Quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Williams, Kiel; Wagner, Lucas K.

There is a gap between high-accuracy ab-initio calculations, like those produced from Quantum Monte Carlo (QMC), and effective lattice models such as the Hubbard model. We have developed a method that combines data produced from QMC with fitting techniques taken from data science, allowing us to determine which degrees of freedom are required to connect ab-initio and model calculations. We test this approach for transition metal atoms, where spectroscopic reference data exists. We report on the accuracy of several derived effective models that include different degrees of freedom, and comment on the quality of the parameter values we obtain from our fitting procedure. We gratefully acknowledge funding from the National Science Foundation Graduate Research Fellowship Program under Grant Number DGE-1144245 (K.T.W.) and from SciDAC Grant DE-FG02-12ER46875 (L.K.W.).

Ab Initio Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1996-01-01

Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

Computations and interpretations: The growth of quantum chemistry, 1927-1967

NASA Astrophysics Data System (ADS)

Park, Buhm Soon

1999-10-01

This dissertation is a contribution to the historical study of scientific disciplines in the twentieth century. It seeks to examine the development of quantum chemistry during the four decades after its inception in 1927. This development was manifest in theories, tools, scientists, and institutions, all of which constituted the disciplinary identity of quantum chemistry. To characterize its identity, I deal with the origins of key ideas and concepts; the change of computational tools from desk calculators to digital computers; the formation of a network among research groups and individuals; and the institutionalization of annual meetings. The dissertation's thesis is three-fold. First, in the pre- World War II years, there were individual contributions to the development of theories in quantum chemistry, but the founding fathers worked in their disciplinary contexts of physics or chemistry with little interest in building a quantum chemistry community. Second, the introduction of electronic digital computers in the postwar years affected the resurgence of the ab initio approach-the attempt to solve the Schrödinger equation without recourse to empirical data-and also the emergence of a community of quantum chemists. But the use of computers did not give rise to a consensus over the aims, methods, or content of the discipline. Third, quantum chemistry exerted a significant influence upon the transformation of chemical education and research in general, thanks to ``chemical translators,'' who sought to explain the gist of quantum chemistry in a language that chemists could understand. In sum, quantum chemistry has been a discipline characterized by diverse traditions, and the whole of chemistry has been under the influence of computations and interpretations made by quantum chemists.

40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

Code of Federal Regulations, 2011 CFR

2011-07-01

... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

Code of Federal Regulations, 2013 CFR

2013-07-01

... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

Code of Federal Regulations, 2014 CFR

2014-07-01

... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

Code of Federal Regulations, 2012 CFR

2012-07-01

... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

Antibiotic stewardship through the EU project "ABS International".

PubMed

Allerberger, Franz; Frank, Annegret; Gareis, Roland

2008-01-01

The increasing problem of antimicrobial resistance requires implementation of antibiotic stewardship (ABS) programs. The project "ABS International--implementing antibiotic strategies for appropriate use of antibiotics in hospitals in member states of the European Union" was started in September 2006 in Austria, Belgium, the Czech Republic, Germany, Hungary, Italy, Poland, Slovenia and Slovakia. A training program for national ABS trainers was prepared and standard templates for ABS tools (antibiotic list, guides for antibiotic treatment and surgical prophylaxis, antibiotic-related organization) and valid process measures, as well as quality indicators for antibiotic use were developed. Specific ABS tools are being implemented in up to five healthcare facilities in each country. Although ABS International clearly focuses on healthcare institutions, future antimicrobial stewardship programs must also cover public education and antibiotic prescribing in primary care.

Ab-initio study of the energetics and thermodynamics of the reaction CH3H + O( 3P) → CF3H … O → CF3 + OH

NASA Astrophysics Data System (ADS)

Kreye, W. C.

1996-07-01

Ab-initio computations at 298.15 K were made of the activation quantities ΔH ‡, ΔS ‡, and ΔG ‡ and of the reaction quantities ΔHr and ΔSr for CF3H + O( 3P) → CF3H … O → .CF3.OH. CF 3H … O is the transition state (TS). GAUSSIAN92 was used and energies computed at a slightly modified Gaussian-2 level. Two potential surfaces for the TS had symmetries 3A' and 3A″. The two rate constants included a semi-classical, quantum-mechanical-tunneling transmission coefficient. The ab-initio ΔH ‡and ΔH r values were in excellent agreement (± 1 kcal/mol) with experiment; but the ΔS ‡, ΔG ‡, and ΔS r values yielded somewhat poorer agreement. Experimental and ab-initio structures were in excellent agreement.

Non-adiabatic quantum reactive scattering in hyperspherical coordinates

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

Kendrick, Brian K.

A new electronically non-adiabatic quantum reactive scattering methodology is presented based on a time-independent coupled channel formalism and the adiabatically adjusting principal axis hyperspherical coordinates of Pack and Parker [J. Chem. Phys. 87, 3888 (1987)]. The methodology computes the full state-to-state scattering matrix for A + B 2(v, j) ↔ AB(v', j') + B and A + AB(v, j) → A + AB(v', j') reactions that involve two coupled electronic states which exhibit a conical intersection. The methodology accurately treats all six degrees of freedom relative to the center-of-mass which includes non-zero total angular momentum J and identical particle exchangemore » symmetry. The new methodology is applied to the ultracold hydrogen exchange reaction for which large geometric phase effects have been recently reported [B. K. Kendrick et al., Phys. Rev. Lett. 115, 153201 (2015)]. Rate coefficients for the H/D + HD(v = 4, j = 0) → H/D + HD(v', j') reactions are reported for collision energies between 1 μK and 100 K (total energy ≈1.9 eV). A new diabatic potential energy matrix is developed based on the Boothroyd, Keogh, Martin, and Peterson (BKMP2) and double many body expansion plus single-polynomial (DSP) adiabatic potential energy surfaces for the ground and first excited electronic states of H 3, respectively. The rate coefficients computed using the new non-adiabatic methodology and diabatic potential matrix reproduce the recently reported rates that include the geometric phase and are computed using a single adiabatic ground electronic state potential energy surface (BKMP2). The dramatic enhancement and suppression of the ultracold rates due to the geometric phase are confirmed as well as its effects on several shape resonances near 1 K. In conclusion, the results reported here represent the first fully non-adiabatic quantum reactive scattering calculation for an ultracold reaction and validate the importance of the geometric phase on the Wigner

Non-adiabatic quantum reactive scattering in hyperspherical coordinates

NASA Astrophysics Data System (ADS)

Kendrick, Brian K.

2018-01-01

A new electronically non-adiabatic quantum reactive scattering methodology is presented based on a time-independent coupled channel formalism and the adiabatically adjusting principal axis hyperspherical coordinates of Pack and Parker [J. Chem. Phys. 87, 3888 (1987)]. The methodology computes the full state-to-state scattering matrix for A + B2(v , j) ↔ AB(v ', j') + B and A + AB(v , j) → A + AB(v ', j') reactions that involve two coupled electronic states which exhibit a conical intersection. The methodology accurately treats all six degrees of freedom relative to the center-of-mass which includes non-zero total angular momentum J and identical particle exchange symmetry. The new methodology is applied to the ultracold hydrogen exchange reaction for which large geometric phase effects have been recently reported [B. K. Kendrick et al., Phys. Rev. Lett. 115, 153201 (2015)]. Rate coefficients for the H/D + HD(v = 4, j = 0) → H/D + HD(v ', j') reactions are reported for collision energies between 1 μK and 100 K (total energy ≈1.9 eV). A new diabatic potential energy matrix is developed based on the Boothroyd, Keogh, Martin, and Peterson (BKMP2) and double many body expansion plus single-polynomial (DSP) adiabatic potential energy surfaces for the ground and first excited electronic states of H3, respectively. The rate coefficients computed using the new non-adiabatic methodology and diabatic potential matrix reproduce the recently reported rates that include the geometric phase and are computed using a single adiabatic ground electronic state potential energy surface (BKMP2). The dramatic enhancement and suppression of the ultracold rates due to the geometric phase are confirmed as well as its effects on several shape resonances near 1 K. The results reported here represent the first fully non-adiabatic quantum reactive scattering calculation for an ultracold reaction and validate the importance of the geometric phase on the Wigner threshold behavior.

The quantum null energy condition in curved space

NASA Astrophysics Data System (ADS)

Fu, Zicao; Koeller, Jason; Marolf, Donald

2017-11-01

The quantum null energy condition (QNEC) is a conjectured bound on components (Tkk = Tab ka k^b) of the stress tensor along a null vector k a at a point p in terms of a second k-derivative of the von Neumann entropy S on one side of a null congruence N through p generated by k a . The conjecture has been established for super-renormalizeable field theories at points p that lie on a bifurcate Killing horizon with null tangent k a and for large-N holographic theories on flat space. While the Koeller-Leichenauer holographic argument clearly yields an inequality for general ( p, k^a) , more conditions are generally required for this inequality to be a useful QNEC. For d≤slant 3 , for arbitrary backgroud metric we show that the QNEC is naturally finite and independent of renormalization scheme when the expansion θ of N at the point p vanishes. This is consistent with the original QNEC conjecture which required θ and the shear σab to satisfy θ \\vert _p= \\dotθ\\vert p =0 , σab\\vert _p=0 . But for d=4, 5 more conditions than even these are required. In particular, we also require the vanishing of additional derivatives and a dominant energy condition. In the above cases the holographic argument does indeed yield a finite QNEC, though for d≥slant6 we argue these properties to fail even for weakly isolated horizons (where all derivatives of θ, σab vanish) that also satisfy a dominant energy condition. On the positive side, a corrollary to our work is that, when coupled to Einstein-Hilbert gravity, d ≤slant 3 holographic theories at large N satisfy the generalized second law (GSL) of thermodynamics at leading order in Newton’s constant G. This is the first GSL proof which does not require the quantum fields to be perturbations to a Killing horizon.

Non-adiabatic quantum reactive scattering in hyperspherical coordinates

DOE PAGES

Kendrick, Brian K.

2018-01-28

A new electronically non-adiabatic quantum reactive scattering methodology is presented based on a time-independent coupled channel formalism and the adiabatically adjusting principal axis hyperspherical coordinates of Pack and Parker [J. Chem. Phys. 87, 3888 (1987)]. The methodology computes the full state-to-state scattering matrix for A + B 2(v, j) ↔ AB(v', j') + B and A + AB(v, j) → A + AB(v', j') reactions that involve two coupled electronic states which exhibit a conical intersection. The methodology accurately treats all six degrees of freedom relative to the center-of-mass which includes non-zero total angular momentum J and identical particle exchangemore » symmetry. The new methodology is applied to the ultracold hydrogen exchange reaction for which large geometric phase effects have been recently reported [B. K. Kendrick et al., Phys. Rev. Lett. 115, 153201 (2015)]. Rate coefficients for the H/D + HD(v = 4, j = 0) → H/D + HD(v', j') reactions are reported for collision energies between 1 μK and 100 K (total energy ≈1.9 eV). A new diabatic potential energy matrix is developed based on the Boothroyd, Keogh, Martin, and Peterson (BKMP2) and double many body expansion plus single-polynomial (DSP) adiabatic potential energy surfaces for the ground and first excited electronic states of H 3, respectively. The rate coefficients computed using the new non-adiabatic methodology and diabatic potential matrix reproduce the recently reported rates that include the geometric phase and are computed using a single adiabatic ground electronic state potential energy surface (BKMP2). The dramatic enhancement and suppression of the ultracold rates due to the geometric phase are confirmed as well as its effects on several shape resonances near 1 K. In conclusion, the results reported here represent the first fully non-adiabatic quantum reactive scattering calculation for an ultracold reaction and validate the importance of the geometric phase on the Wigner

Photoionization cross section and binding energy of single dopant in hollow cylindrical core/shell quantum dot

NASA Astrophysics Data System (ADS)

Feddi, E.; El-Yadri, M.; Dujardin, F.; Restrepo, R. L.; Duque, C. A.

2017-02-01

In this study, we have investigated the confined donor impurity in a hollow cylindrical-shell quantum dot. The charges are assumed to be completely confined to the interior of the shell with rigid walls. Within the framework of the effective-mass approximation and by using a simple variational approach, we have computed the donor binding energy as a function of the shell sizes in order to study the behavior of the electron-impurity attraction for a very small thickness. Our results show that the binding energy of a donor impurity placed at the center of cylindrical core/shell dots depends strongly on the shell size. The binding energy increases when the shell-wideness becomes smaller and shows the same behavior as in a simple cylindrical quantum dot. A special case has been studied, which corresponds to the ratio between the inner and outer radii near to one (a/b → 1) for which our model gives a non-significant behavior of the impurity binding energy. This fact implies the existence of a critical value (a/b) for which the binding energy of the donor impurity tends to the limit value of 4 effective Rydbergs as in a 2D quantum well. We also analyse the photoionization cross section considering only the in-plane incident radiation polarization. We determine its behavior as a function of photon energy, shell size, and donor position. The measurement of photoionization in such systems would be of great interest to understand the optical properties of carriers in quantum dots.

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

PubMed

Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

Quantum information generation, storage and transmission based on nuclear spins

NASA Astrophysics Data System (ADS)

Zaharov, V. V.; Makarov, V. I.

2018-05-01

A new approach to quantum information generation, storage and transmission is proposed. It is shown that quantum information generation and storage using an ensemble of N electron spins encounter unresolvable implementation problems (at least at the present time). As an alternative implementation we discuss two promising radical systems, one with N equivalent nuclear spins and another with N nonequivalent nuclear spins. Detailed analysis shows that only the radical system containing N nonequivalent nuclei is perfectly matched for quantum information generation, storage and transmission. We develop a procedure based on pulsed electron paramagnetic resonance (EPR) and we apply it to the radical system with the set of nonequivalent nuclei. The resulting EPR spectrum contains 2N transition lines, where N is the number of the atoms with the nuclear spin 1/2, and each of these lines may be encoded with a determined qudit sequence. For encoding the EPR lines we propose to submit the radical system to two magnetic pulses in the direction perpendicular to the z axis of the reference frame. As a result, the radical system impulse response may be measured, stored and transmitted through the communications channel. Confirming our development, the ab initio analysis of the system with three anion radicals was done showing matching between the simulations and the theoretical predictions. The developed method may be easily adapted for quantum information generation, storage, processing and transmission in quantum computing and quantum communications applications.

A QUANTUM MECHANICAL STUDY OF THE PROTONATION AND COVALENT HYDRATION OF QUINAZOLINE IN THE PRESENCE OF METAL CATIONS

EPA Science Inventory

We have investigated the protonation and reversible covalent hydration of quinazoline in the presence of Li+, Na+, and Ca2+ ions using ab initio quantum mechanical calculations at the MP2/6-31G**//HF/6-31G*level of theory. Proton affinities, enthalpies of hydration at 298.15K (DH...

Quantum anomalous Hall phase and half-metallic phase in ferromagnetic (111) bilayers of 4 d and 5 d transition metal perovskites

NASA Astrophysics Data System (ADS)

Chandra, Hirak Kumar; Guo, Guang-Yu

2017-04-01

Extraordinary electronic phases can form in artificial oxide heterostructures, which will provide a fertile ground for new physics and also give rise to novel device functions. Based on a systematic first-principles density functional theory study of the magnetic and electronic properties of the (111) superlattices (ABO3) 2/(AB'O3)10 of 4 d and 5 d transition metal perovskite (B = Ru, Rh, Ag, Re, Os, Ir, Au; AB'O3=LaAlO3 , SrTiO3) , we demonstrate that due to quantum confinement, bilayers (LaBO3)2 (B = Ru, Re, Os) and (SrBO3)2 (B = Rh, Os, Ir) are ferromagnetic with ordering temperatures up to room temperature. In particular, bilayer (LaOsO3)2 is an exotic spin-polarized quantum anomalous Hall insulator, while the other ferromagnetic bilayers are metallic with large Hall conductances comparable to the conductance quantum. Furthermore, bilayers (LaRuO3)2 and (SrRhO3)2 are half metallic, while the bilayer (SrIrO3)2 exhibits a peculiar colossal magnetic anisotropy. Our findings thus show that 4 d and 5 d metal perovskite (111) bilayers are a class of quasi-two-dimensional materials for exploring exotic quantum phases and also for advanced applications such as low-power nanoelectronics and oxide spintronics.

Theory-restricted resonant x-ray reflectometry of quantum materials

NASA Astrophysics Data System (ADS)

Fürsich, Katrin; Zabolotnyy, Volodymyr B.; Schierle, Enrico; Dudy, Lenart; Kirilmaz, Ozan; Sing, Michael; Claessen, Ralph; Green, Robert J.; Haverkort, Maurits W.; Hinkov, Vladimir

2018-04-01

The delicate interplay of competing phases in quantum materials is dominated by parameters such as the crystal field potential, the spin-orbit coupling, and, in particular, the electronic correlation strength. Whereas small quantitative variations of the parameter values can thus qualitatively change the material, these values can hitherto hardly be obtained with reasonable precision, be it theoretically or experimentally. Here we propose a solution combining resonant x-ray reflectivity (RXR) with multiplet ligand field theory (MLFT). We first perform ab initio DFT calculations within the MLFT framework to get initial parameter values, which we then use in a fit of the theoretical model to RXR. To validate our method, we apply it to NiO and SrTiO3 and obtain parameter values, which are amended by as much as 20 % compared to the ab initio results. Our approach is particularly useful to investigate topologically trivial and nontrivial correlated insulators, staggered moments in magnetically or orbitally ordered materials, and reconstructed interfaces.

Role of Quantum Vibrations on the Structural, Electronic, and Optical Properties of 9-Methylguanine.

PubMed

Law, Yu Kay; Hassanali, Ali A

2015-11-05

In this work, we report theoretical predictions of the UV-absorption spectra of 9-methylguanine using time dependent density functional theory (TDDFT). Molecular dynamics simulations of the hydrated DNA base are peformed using an empirical force field, Born-Oppenheimer ab initio molecular dynamics (AIMD), and finally path-integral AIMD to understand the role of the underlying electronic potential, solvation, and nuclear quantum vibrations on the absorption spectra. It is shown that the conformational distributions, including hydrogen bonding interactions, are perturbed by the inclusion of nuclear quantum effects, leading to significant changes in the total charge and dipole fluctuations of the DNA base. The calculated absorption spectra using the different sampling protocols shows that the inclusion of nuclear quantum effects causes a significant broadening and red shift of the spectra bringing it into closer agreement with experiments.

Quantum fluctuations of a fullerene cage modulate its internal magnetic environment.

PubMed

Kawatsu, Tsutomu; Tachikawa, Masanori

2018-01-17

To investigate the effect of quantum fluctuations on the magnetic environment inside a C 60 fullerene cage, we have calculated the nuclear magnetic shielding constant of protons in H 2 @C 60 and HD@C 60 systems by on-the-fly ab initio path integral simulation, including both thermal and nuclear quantum effects. The most dominant upfield from an isolated hydrogen molecule occurs due to the diamagnetic current of the C 60 cage, which is partly cancelled by the paramagnetic current, where the paramagnetic contribution is enlarged by the zero-point vibrational fluctuation of the C 60 carbon backbone structure via a widely distributed HOMO-LUMO gap. This quantum modulation mechanism of the nuclear magnetic shielding constant is newly proposed. Because this quantum effect is independent of the difference between H 2 and HD, the H 2 /HD isotope shift occurs in spite of the C 60 cage. The nuclear magnetic constants computed for H 2 @C 60 and HD@C 60 are 32.047 and 32.081 ppm, respectively, which are in reasonable agreement with the corresponding values of 32.19 and 32.23 ppm estimated from the experimental values of the chemical shifts.

Ground and excited states of NH4: Electron propagator and quantum defect analysis

NASA Astrophysics Data System (ADS)

Ortiz, J. V.; Martín, I.; Velasco, A. M.; Lavín, C.

2004-05-01

Vertical excitation energies of the Rydberg radical NH4 are inferred from ab initio electron propagator calculations on the electron affinities of NH4+. The adiabatic ionization energy of NH4 is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine Einstein emission coefficients and radiative lifetimes. Comparisons with spectroscopic data and previous calculations are discussed.

Path integral Monte Carlo determination of the fourth-order virial coefficient for unitary two-component Fermi gas with zero-range interactions

NASA Astrophysics Data System (ADS)

Yan, Yangqian; Blume, D.

2016-05-01

The unitary equal-mass Fermi gas with zero-range interactions constitutes a paradigmatic model system that is relevant to atomic, condensed matter, nuclear, particle, and astro physics. This work determines the fourth-order virial coefficient b4 of such a strongly-interacting Fermi gas using a customized ab inito path integral Monte Carlo (PIMC) algorithm. In contrast to earlier theoretical results, which disagreed on the sign and magnitude of b4, our b4 agrees with the experimentally determined value, thereby resolving an ongoing literature debate. Utilizing a trap regulator, our PIMC approach determines the fourth-order virial coefficient by directly sampling the partition function. An on-the-fly anti-symmetrization avoids the Thomas collapse and, combined with the use of the exact two-body zero-range propagator, establishes an efficient general means to treat small Fermi systems with zero-range interactions. We gratefully acknowledge support by the NSF.

Quantum-Chemical ab initio Calculations on the Three Isomers of Diborabenzene (C4H4B2)

NASA Astrophysics Data System (ADS)

Singh, Jaswinder; Wang, Yuekui; Raabe, Gerhard

2010-01-01

Quantum-chemical ab initio calculations up to the ZPE+CCSD(T)/aug-cc-pVTZ//MP2/6- 311++G** level were performed on three possible structural isomers of diborabenzene (C4H4B2). All three molecules were found to be local minima on the C4H4B2 energy surface and to have closed shell singlet ground states. While the ground states of the 1,3- and 1,4-isomer are planar and of C2v and D2h symmetry, respectively, 1,2-diborabenzene is non-planar with a C2 axis passing through the center of the BB bond and the middle of the opposite carbon-carbon bond as the only symmetry element. The energetically most favourable 1,3-diborabenzene was found to be about 19 and 36 kcal/mol lower in energy than the 1,2- and the 1,4-isomer. Planar 1,3- and 1,4-diborabenzene have three doubly occupied π orbitals while non-planar 1,2-diborabenzene has also three doubly occupied orbitals which can be derived from the π orbitals of its 3.7 kcal/mol energetically less favourable planar form ("π-like" orbitals). The lowest unoccupied orbitals of all three isomers have σ symmetry with large coefficients at the two boron atoms. These orbitals are lower in energy than the lowest unoccupied molecular orbitals (LUMOs) of e. g. benzene and pyridine and might cause pronounced acceptor properties which could be one of the reasons for the elusiveness of the title compounds. The results of bond separation reactions show that cyclic conjugation stabilizes all three diborabenzenes relative to their isolated fragments. The most effective stabilization energy of about 24 kcal/mol was found for the energetically lowest 1,3-isomer. This value amounts to approximately one third of the experimental value for the bond separation energy of pyridine. In all cases the energetically lowest triplet states are significantly (16 - 24 kcal/mol) higher in energy than the singlet ground states. Also among the triplets the 1,3-isomer is the energetically most fabourable species.

Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

NASA Astrophysics Data System (ADS)

Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

2017-01-01

Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

Effect of monoclonal antibodies (MoAb) to class I and class II HLA antigens on lectin- and MoAb OKT3-induced lymphocyte proliferation.

PubMed

Akiyama, Y; Zicht, R; Ferrone, S; Bonnard, G D; Herberman, R B

1985-04-01

We have examined the effect of several monoclonal antibodies (MoAb) to monomorphic determinants of class II HLA antigens, and MoAb to monomorphic determinants of class I HLA antigens and to beta-2-microglobulin (beta 2-mu) on lectin- and MoAb OKT3-induced proliferation of human peripheral blood mononuclear cells (PBMNC) and cultured T cells (CTC). Some, but not all, anti-class II HLA MoAb inhibited the proliferative response of PBMNC to MoAb OKT3 and pokeweed mitogen (PWM). The degree of inhibitory effect varied considerably. This effect was not limited to anti-class II HLA MoAb since anti-class I HLA MoAb and anti-beta 2-mu MoAb also inhibited MoAb OKT3- or PWM-induced proliferative responses. In contrast, the response of PBMNC to phytohemagglutinin (PHA) and concanavalin A (Con A) was not blocked by any anti-class II HLA MoAb. However, some anti-class II HLA MoAb also inhibited the proliferative response of CTC plus allogeneic peripheral blood adherent accessory cells (AC) to PHA or Con A as well as to MoAb OKT3 or PWM. This may be attributable to the substantially greater class II HLA antigen expression by CTC than by fresh lymphocytes. Pretreatment of either CTC or AC with anti-class II HLA MoAb inhibited OKT3-induced proliferation. In contrast, pretreatment of CTC, but not AC, with anti-class I HLA MoAb inhibited the proliferative response of CTC to OKT3. Pretreatment of CTC with anti-class I HLA MoAb inhibited PHA-, Con A and PWM-induced proliferation, to a greater degree than the anti-class II HLA MoAb. It appears as if lymphocyte activation by different mitogens exhibits variable requirements for the presence of cells expressing major histocompatibility determinants. Binding of Ab to membrane markers may interfere with lymphocyte-AC cooperation, perhaps by inhibiting binding of mitogens to their receptors or by interfering with lymphocyte and AC function. We also have examined the role of class II HLA antigens on CTC by depleting class II HLA-positive cells

Protective mAbs and Cross-Reactive mAbs Raised by Immunization with Engineered Marburg Virus GPs.

PubMed

Fusco, Marnie L; Hashiguchi, Takao; Cassan, Robyn; Biggins, Julia E; Murin, Charles D; Warfield, Kelly L; Li, Sheng; Holtsberg, Frederick W; Shulenin, Sergey; Vu, Hong; Olinger, Gene G; Kim, Do H; Whaley, Kevin J; Zeitlin, Larry; Ward, Andrew B; Nykiforuk, Cory; Aman, M Javad; Berry, Jody D; Berry, Jody; Saphire, Erica Ollmann

2015-06-01

The filoviruses, which include the marburg- and ebolaviruses, have caused multiple outbreaks among humans this decade. Antibodies against the filovirus surface glycoprotein (GP) have been shown to provide life-saving therapy in nonhuman primates, but such antibodies are generally virus-specific. Many monoclonal antibodies (mAbs) have been described against Ebola virus. In contrast, relatively few have been described against Marburg virus. Here we present ten mAbs elicited by immunization of mice using recombinant mucin-deleted GPs from different Marburg virus (MARV) strains. Surprisingly, two of the mAbs raised against MARV GP also cross-react with the mucin-deleted GP cores of all tested ebolaviruses (Ebola, Sudan, Bundibugyo, Reston), but these epitopes are masked differently by the mucin-like domains themselves. The most efficacious mAbs in this panel were found to recognize a novel "wing" feature on the GP2 subunit that is unique to Marburg and does not exist in Ebola. Two of these anti-wing antibodies confer 90 and 100% protection, respectively, one hour post-exposure in mice challenged with MARV.

Masses and activity of AB Doradus B a/b. The age of the AB Dor quadruple system revisited

NASA Astrophysics Data System (ADS)

Wolter, U.; Czesla, S.; Fuhrmeister, B.; Robrade, J.; Engels, D.; Wieringa, M.; Schmitt, J. H. M. M.

2014-10-01

We present a multiwavelength study of the close binary AB Dor Ba/b (Rst137B). Our study comprises astrometric orbit measurements, optical spectroscopy, X-ray and radio observations. Using all available adaptive optics images of AB Dor B taken with VLT/NACO from 2004 to 2009, we tightly constrain its orbital period to 360.6 ± 1.5 days. We present the first orbital solution of Rst 137B and estimate the combined mass of AB Dor Ba+b as 0.69+0.02-0.24 M⊙, slightly exceeding previous estimates based on IR photometry. Our determined orbital inclination of Rst 137B is close to the axial inclination of AB Dor A inferred from Doppler imaging. Our VLT/UVES spectra yield high rotational velocities of ≥30 km s-1 for both components Ba and Bb, in accord with previous measurements, which corresponds to rotation periods significantly shorter than one day. Our combined spectral model, using PHOENIX spectra, yields an effective temperature of 3310 ± 50 K for the primary and approximately 60 K less for the secondary. The optical spectra presumably cover a chromospheric flare and show that at least one component of Rst 137B is significantly active. Activity and weak variations are also found in our simultaneous XMM-Newton observations, while our ATCA radio data yield constant fluxes at the level of previous measurements. Using evolutionary models, our newly determined stellar parameters confirm that the age of Rst 137B is between 50 and 100 Myr. Based on observations collected at the European Southern Observatory, Paranal, Chile, 383.D-1002(A) and the ESO Science Archive Facility. Using data obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member states and NASA. Using data obtained with the Australia Telescope Compact Array (ATCA) operated by the Commonwealth Scientific and Industrial Research Organisation (CSIRO).

Controlling the thermoelectric effect by mechanical manipulation of the electron's quantum phase in atomic junctions.

PubMed

Aiba, Akira; Demir, Firuz; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Tsukagoshi, Kazuhito; Saffarzadeh, Alireza; Kirczenow, George; Kiguchi, Manabu

2017-08-11

The thermoelectric voltage developed across an atomic metal junction (i.e., a nanostructure in which one or a few atoms connect two metal electrodes) in response to a temperature difference between the electrodes, results from the quantum interference of electrons that pass through the junction multiple times after being scattered by the surrounding defects. Here we report successfully tuning this quantum interference and thus controlling the magnitude and sign of the thermoelectric voltage by applying a mechanical force that deforms the junction. The observed switching of the thermoelectric voltage is reversible and can be cycled many times. Our ab initio and semi-empirical calculations elucidate the detailed mechanism by which the quantum interference is tuned. We show that the applied strain alters the quantum phases of electrons passing through the narrowest part of the junction and hence modifies the electronic quantum interference in the device. Tuning the quantum interference causes the energies of electronic transport resonances to shift, which affects the thermoelectric voltage. These experimental and theoretical studies reveal that Au atomic junctions can be made to exhibit both positive and negative thermoelectric voltages on demand, and demonstrate the importance and tunability of the quantum interference effect in the atomic-scale metal nanostructures.

Montelukast photodegradation: elucidation of Ф-order kinetics, determination of quantum yields and application to actinometry.

PubMed

Maafi, Mounir; Maafi, Wassila

2014-08-25

A recently developed Ф-order semi-emperical integrated rate-law for photoreversible AB(2Ф) reactions has been successfully applied to investigate Montelukast sodium (Monte) photodegradation kinetics in ethanol. The model equations also served to propose a new stepwise kinetic elucidation method valid for any AB(2Ф) system and its application to the determination of Monte's forward (Ф(λ(irr))(A-->B)) and reverse (Ф(λ(irr))(B-->A)) quantum yields at various irradiation wavelengths. It has been found that Ф(λ(irr))(A-->B) undergoes a 15-fold increase with wavelength between 220 and 360 nm, with the spectral section 250-360 nm representing Monte effective photodegradation causative range. The reverse quantum yield values were generally between 12 and 54% lower than those recorded for Ф(λ(irr))(A-->B), with the trans-isomer (Monte) converting almost completely to its cis-counterpart at high irradiation wavelengths. Furthermore, the potential use of Monte as an actinometer has been investigated, and an actinometric method was proposed. This study demonstrated the usefulness of Monte for monochromatic light actinometry for the dynamic range 258-380 nm. Copyright © 2014 Elsevier B.V. All rights reserved.

Endo-Fullerene and Doped Diamond Nanocrystallite Based Models of Qubits for Solid-State Quantum Computers

NASA Technical Reports Server (NTRS)

Park, Seongjun; Srivastava, Deepak; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

Models of encapsulated 1/2 nuclear spin H-1 and P-31 atoms in fullerene and diamond nanocrystallite, respectively, are proposed and examined with ab-initio local density functional method for possible applications as single quantum bits (qubits) in solid-state quantum computers. A H-1 atom encapsulated in a fully deuterated fullerene, C(sub 20)D(sub 20), forms the first model system and ab-initio calculation shows that H-1 atom is stable in atomic state at the center of the fullerene with a barrier of about 1 eV to escape. A P-31 atom positioned at the center of a diamond nanocrystallite is the second model system, and 3 1P atom is found to be stable at the substitutional site relative to interstitial sites by 15 eV, Vacancy formation energy is 6 eV in diamond so that substitutional P-31 atom will be stable against diffusion during the formation mechanisms within the nanocrystallite. The coupling between the nuclear spin and weakly bound (valance) donor electron coupling in both systems is found to be suitable for single qubit applications, where as the spatial distributions of (valance) donor electron wave functions are found to be preferentially spread along certain lattice directions facilitating two or more qubit applications. The feasibility of the fabrication pathways for both model solid-state qubit systems within practical quantum computers is discussed with in the context of our proposed solid-state qubits.

Modeling study of the ABS relay valve

NASA Astrophysics Data System (ADS)

Lei, Ming; Lin, Min; Guo, Bin; Luo, Zai; Xu, Weidong

2011-05-01

The ABS (anti-lock braking system) relay valve is the key component of anti-lock braking system in most commercial vehicles such as trucks, tractor-trailers, etc. In this paper, structure of ABS relay valve and its work theory were analyzed. Then a mathematical model of ABS relay valve, which was investigated by dividing into electronic part, magnetic part, pneumatic part and mechanical part, was set up. The displacement of spools and the response of pressure increasing, holding, releasing of ABS relay valve were simulated and analyzed under conditions of control pressure 500 KPa, braking pressure 600 KPa, atmospheric pressure 100 KPa and air temperature 310 K. Thisarticle provides reliable theory for improving the performance and efficiency of anti-lock braking system of vehicles.

Photoluminescent graphene quantum dots for in vivo imaging of apoptotic cells

NASA Astrophysics Data System (ADS)

Roy, Prathik; Periasamy, Arun Prakash; Lin, Chiu-Ya; Her, Guor-Mour; Chiu, Wei-Jane; Li, Chi-Lin; Shu, Chia-Lun; Huang, Chih-Ching; Liang, Chi-Te; Chang, Huan-Tsung

2015-01-01

Apoptosis (programmed cell death) is linked to many incurable neurodegenerative, cardiovascular and cancer causing diseases. Numerous methods have been developed for imaging apoptotic cells in vitro; however, there are few methods available for imaging apoptotic cells in live animals (in vivo). Here we report a novel method utilizing the unique photoluminescence properties of plant leaf-derived graphene quantum dots (GQDs) modified with annexin V antibody (AbA5) to form (AbA5)-modified GQDs (AbA5-GQDs) enabling us to label apoptotic cells in live zebrafish (Danio rerio). The key is that zebrafish shows bright red photoluminescence in the presence of apoptotic cells. The toxicity of the GQDs has also been investigated with the GQDs exhibiting high biocompatibility as they were excreted from the zebrafish's body without affecting its growth significantly at a concentration lower than 2 mg mL-1 over a period of 4 to 72 hour post fertilization. The GQDs have further been used to image human breast adenocarcinoma cell line (MCF-7 cells), human cervical cancer cell line (HeLa cells), and normal human mammary epithelial cell line (MCF-10A). These results are indispensable to further the advance of graphene-based nanomaterials for biomedical applications.Apoptosis (programmed cell death) is linked to many incurable neurodegenerative, cardiovascular and cancer causing diseases. Numerous methods have been developed for imaging apoptotic cells in vitro; however, there are few methods available for imaging apoptotic cells in live animals (in vivo). Here we report a novel method utilizing the unique photoluminescence properties of plant leaf-derived graphene quantum dots (GQDs) modified with annexin V antibody (AbA5) to form (AbA5)-modified GQDs (AbA5-GQDs) enabling us to label apoptotic cells in live zebrafish (Danio rerio). The key is that zebrafish shows bright red photoluminescence in the presence of apoptotic cells. The toxicity of the GQDs has also been investigated with

Ab initio predictions of the symmetry energy and recent constraints

NASA Astrophysics Data System (ADS)

Sammarruca, Francesca

2017-01-01

The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

FTA-ABS test

MedlinePlus

... rule out a possible false-negative result. Normal Results A negative or nonreactive result means that you ... meaning of your specific test results. What Abnormal Results Mean A positive FTA-ABS is often a ...

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

NASA Astrophysics Data System (ADS)

Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

2017-10-01

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

Ab initio perspective on the Mollwo-Ivey relation for F centers in alkali halides

NASA Astrophysics Data System (ADS)

Tiwald, Paul; Karsai, Ferenc; Laskowski, Robert; Gräfe, Stefanie; Blaha, Peter; Burgdörfer, Joachim; Wirtz, Ludger

2015-10-01

We revisit the well-known Mollwo-Ivey relation that describes the "universal" dependence of the absorption energies of F-type color centers on the lattice constant a of alkali-halide crystals, Eabs∝a-n. We perform both state-of-the-art ab initio quantum chemistry and post-DFT calculations of F-center absorption spectra. By "tuning" independently the lattice constant and the atomic species we show that the scaling with the lattice constant alone (keeping the elements fixed) would yield n =2 in agreement with the "particle-in-the-box" model. Keeping the lattice constant fixed and changing the atomic species enables us to quantify the ion-size effects which are shown to be responsible for the exponent n ≈1.8 .

Substituent Inductive Effects on the Electrochemical Oxidation of Flavonoids Studied by Square Wave Voltammetry and Ab Initio Calculations.

PubMed

Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo

2016-10-27

Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.

Undoing Gender through Legislation and Schooling: The Case of AB 537 and AB 394 in California, USA

ERIC Educational Resources Information Center

Knotts, Greg

2009-01-01

This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools…

Nuclear quantum effects on adsorption of H 2 and isotopologues on metal ions

DOE PAGES

Savchenko, Ievgeniia; Gu, Bing; Heine, Thomas; ...

2017-01-03

The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of Hmore » $$_2$$ and isotopologues on metal ions, are examined in this study using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. To estimate for the anharmonicity, a nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) have been employed for complexes of Li$^+$ and Cu$$^{+2}$$ with H$$_2$$, D$$_2$$, HD. The dynamics analysis shows that incorporation of the PES anharmonicity changes the ZPE by up to 9%. Finally, the lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions.« less

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

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

Ab initio calculation of infrared intensities for hydrogen peroxide

NASA Technical Reports Server (NTRS)

Rogers, J. D.; Hillman, J. J.

1982-01-01

Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

Ab initio calculation of infrared intensities for hydrogen peroxide

NASA Astrophysics Data System (ADS)

Rogers, J. D.; Hillman, J. J.

1982-04-01

Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

An ab initio study of ion induced charge transfer dynamics in collision of carbon ions with thymine.

PubMed

Bacchus-Montabonel, Marie-Christine; Tergiman, Yvette Suzanne

2011-05-28

Charge transfer in collisions of carbon ions on a thymine target has been studied theoretically in a wide collision range by means of ab initio quantum chemistry molecular methods. The process appears markedly anisotropic in the whole energy domain, significantly favoured in the perpendicular orientation. A specific decrease of the charge transfer cross sections at low collision energies may be pointed out and could induce an enhancement of the complementary fragmentation processes for collision energies down to about 10 eV, as observed for the low-electron fragmentation process. Such feature may be of important interest in ion-induced biomolecular radiation damage. This journal is © the Owner Societies 2011

Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen

2016-03-01

On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.

Evolving trends in mAb production processes

PubMed Central

Wolfe, Leslie S.; Mostafa, Sigma S.; Norman, Carnley

2017-01-01

Abstract Monoclonal antibodies (mAbs) have established themselves as the leading biopharmaceutical therapeutic modality. The establishment of robust manufacturing platforms are key for antibody drug discovery efforts to seamlessly translate into clinical and commercial successes. Several drivers are influencing the design of mAb manufacturing processes. The advent of biosimilars is driving a desire to achieve lower cost of goods and globalize biologics manufacturing. High titers are now routinely achieved for mAbs in mammalian cell culture. These drivers have resulted in significant evolution in process platform approaches. Additionally, several new trends in bioprocessing have arisen in keeping with these needs. These include the consideration of alternative expression systems, continuous biomanufacturing and non‐chromatographic separation formats. This paper discusses these drivers in the context of the kinds of changes they are driving in mAb production processes. PMID:29313024

Bound state potential energy surface construction: ab initio zero-point energies and vibrationally averaged rotational constants.

PubMed

Bettens, Ryan P A

2003-01-15

Collins' method of interpolating a potential energy surface (PES) from quantum chemical calculations for reactive systems (Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. J. Chem. Phys. 1995, 102, 5647. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 8302. Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 1999, 111, 816) has been applied to a bound state problem. The interpolation method has been combined for the first time with quantum diffusion Monte Carlo calculations to obtain an accurate ground state zero-point energy, the vibrationally average rotational constants, and the vibrationally averaged internal coordinates. In particular, the system studied was fluoromethane using a composite method approximating the QCISD(T)/6-311++G(2df,2p) level of theory. The approach adopted in this work (a) is fully automated, (b) is fully ab initio, (c) includes all nine nuclear degrees of freedom, (d) requires no assumption of the functional form of the PES, (e) possesses the full symmetry of the system, (f) does not involve fitting any parameters of any kind, and (g) is generally applicable to any system amenable to quantum chemical calculations and Collins' interpolation method. The calculated zero-point energy agrees to within 0.2% of its current best estimate. A0 and B0 are within 0.9 and 0.3%, respectively, of experiment.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores.

PubMed

Law, Y K; Hassanali, A A

2018-03-14

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores

NASA Astrophysics Data System (ADS)

Law, Y. K.; Hassanali, A. A.

2018-03-01

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

PubMed Central

2016-01-01

Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

Defect states and charge transport in quantum dot solids

DOE PAGES

Brawand, Nicholas P.; Goldey, Matthew B.; Vörös, Márton; ...

2017-01-16

Defects at the surface of semiconductor quantum dots (QDs) give rise to electronic states within the gap, which are detrimental to charge transport properties of QD devices. We investigated charge transport in silicon quantum dots with deep and shallow defect levels, using ab initio calculations and constrained density functional theory. We found that shallow defects may be more detrimental to charge transport than deep ones, with associated transfer rates differing by up to 5 orders of magnitude for the small dots (1-2 nm) considered here. Hence, our results indicate that the common assumption, that the ability of defects to trapmore » charges is determined by their position in the energy gap of the QD, is too simplistic, and our findings call for a reassessment of the role played by shallow defects in QD devices. Altogether, our results highlight the key importance of taking into account the atomistic structural properties of QD surfaces when investigating transport properties.« less

Quantum molecular dynamics simulation of shock-wave experiments in aluminum

NASA Astrophysics Data System (ADS)

Minakov, D. V.; Levashov, P. R.; Khishchenko, K. V.; Fortov, V. E.

2014-06-01

We present quantum molecular dynamics calculations of principal, porous, and double shock Hugoniots, release isentropes, and sound velocity behind the shock front for aluminum. A comprehensive analysis of available shock-wave data is performed; the agreement and discrepancies of simulation results with measurements are discussed. Special attention is paid to the melting region of aluminum along the principal Hugoniot; the boundaries of the melting zone are estimated using the self-diffusion coefficient. Also, we make a comparison with a high-quality multiphase equation of state for aluminum. Independent semiempirical and first-principle models are very close to each other in caloric variables (pressure, density, particle velocity, etc.) but the equation of state gives higher temperature on the principal Hugoniot and release isentropes than ab initio calculations. Thus, the quantum molecular dynamics method can be used for calibration of semiempirical equations of state in case of lack of experimental data.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations.

PubMed

Schiffmann, Christoph; Sebastiani, Daniel

2011-05-10

We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules.

Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures

NASA Astrophysics Data System (ADS)

Clay, Raymond; Morales, Miguel

2017-06-01

In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Single-domain antibody bioconjugated near-IR quantum dots for targeted cellular imaging of pancreatic cancer.

PubMed

Zaman, Md Badruz; Baral, Toya Nath; Jakubek, Zygmunt J; Zhang, Jianbing; Wu, Xiaohua; Lai, Edward; Whitfield, Dennis; Yu, Kui

2011-05-01

Successful targeted imaging of BxPC3 human pancreatic cancer cells is feasible with near-IR CdTeSe/CdS quantum dots (QDs) functionalized with single-domain antibody (sdAb) 2A3. For specific targeting, sdAbs are superior to conventional antibodies, especially in terms of stability, aggregation, and production cost. The bright CdTeSe/CdS QDs were synthesized to emit in the diagnostic window of 650-900 nm with a narrow emission band. 2A3 was derived from llama and is small in size of 13 kDa, but with fully-functional recognition to the target carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6), a possible biomarker as a therapeutic target of pancreatic cancer. For compelling imaging, optical may be the most sensible among the various imaging modalities, regarding the sensitivity and cost. This first report on sdAb-conjugated near-IR QDs with high signal to background sensitivity for targeted cellular imaging brings insights into the development of optical molecular imaging for early stage cancer diagnosis.

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

PubMed Central

Müller, Albert Leopold; Kjeldsen, Kasper Urup; Rattei, Thomas; Pester, Michael; Loy, Alexander

2015-01-01

The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods. PMID:25343514

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

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

Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only atmore » a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.« less

reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

PubMed

Müller, Julian; Hartke, Bernd

2016-08-09

Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.

Clinical performance of the novel DiaSorin LIAISON(®) XL murex: HBsAg Quant, HCV-Ab, HIV-Ab/Ag assays.

PubMed

Krawczyk, Adalbert; Hintze, Christian; Ackermann, Jessica; Goitowski, Birgit; Trippler, Martin; Grüner, Nico; Neumann-Fraune, Maria; Verheyen, Jens; Fiedler, Melanie

2014-01-01

The fully automated and closed LIAISON(®)XL platform was developed for reliable detection of infection markers like hepatitis B virus (HBV) surface antigen (HBsAg), hepatitis C virus (HCV) antibodies (Ab) or human immunodeficiency virus (HIV)-Ag/Ab. To date, less is known about the diagnostic performance of this system in direct comparison to the common Abbott ARCHITECT(®) platform. We compared the diagnostic performance and usability of the DiaSorin LIAISON(®)XL with the commonly used Abbott ARCHITECT(®) system. The qualitative performance of the above mentioned assays was compared in about 500 sera. Quantitative tests were performed for HBsAg-positive samples from patients under therapy (n=289) and in vitro expressed mutants (n=37). For HCV-Ab, a total number of 155 selected samples from patients chronically infected with different HCV genotypes were tested. The concordance between both systems was 99.4% for HBsAg, 98.81% for HCV-Ab, and 99.6% for HIV-Ab/Ag. The quantitative LIAISON(®)XL murex HBsAg assay detected all mutants in comparable amounts to the HBsAg wild type and yielded highly reliable HBsAg kinetics in patients treated with antiviral drugs. Dilution experiments using the 2nd International Standard for HBsAg (WHO) showed a high accuracy of this test. HCV-Ab from patients infected with genotypes 1-3 were equally detected in both systems. Interestingly, S/CO levels of HCV-Ab from patients infected with genotype 3 seem to be relatively low using both systems. The LIAISON(®)XL platform proved to be an excellent system for diagnostics of HBV, HCV, and HIV with equal performance compared to the ARCHITECT(®) system. Copyright © 2013 Elsevier B.V. All rights reserved.

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses.

PubMed

Baral, Khagendra; Li, Aize; Ching, Wai-Yim

2017-10-12

A density functional theory (DFT)-based ab initio molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li-Na and Na-K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li-O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations.

Quantum phases for point-like charged particles and for electrically neutral dipoles in an electromagnetic field

NASA Astrophysics Data System (ADS)

Kholmetskii, A. L.; Missevitch, O. V.; Yarman, T.

2018-05-01

We point out that the known quantum phases for an electric/magnetic dipole moving in an electromagnetic (EM) field must be presented as the superposition of more fundamental quantum phases emerging for elementary charges. Using this idea, we find two new fundamental quantum phases for point-like charges, next to the known electric and magnetic Aharonov-Bohm (A-B) phases, named by us as the complementary electric and magnetic phases, correspondingly. We further demonstrate that these new phases can indeed be derived via the Schrödinger equation for a particle in an EM field, where however the operator of momentum is re-defined via the replacement of the canonical momentum of particle by the sum of its mechanical momentum and interactional field momentum for a system "charged particle and a macroscopic source of EM field". The implications of the obtained results are discussed.

Quantum molecular dynamics simulation of shock-wave experiments in aluminum

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

Minakov, D. V.; Khishchenko, K. V.; Fortov, V. E.

2014-06-14

We present quantum molecular dynamics calculations of principal, porous, and double shock Hugoniots, release isentropes, and sound velocity behind the shock front for aluminum. A comprehensive analysis of available shock-wave data is performed; the agreement and discrepancies of simulation results with measurements are discussed. Special attention is paid to the melting region of aluminum along the principal Hugoniot; the boundaries of the melting zone are estimated using the self-diffusion coefficient. Also, we make a comparison with a high-quality multiphase equation of state for aluminum. Independent semiempirical and first-principle models are very close to each other in caloric variables (pressure, density,more » particle velocity, etc.) but the equation of state gives higher temperature on the principal Hugoniot and release isentropes than ab initio calculations. Thus, the quantum molecular dynamics method can be used for calibration of semiempirical equations of state in case of lack of experimental data.« less

Towards an ab initio description of correlated materials

NASA Astrophysics Data System (ADS)

Yee, Chuck-Hou

Strongly-correlated materials are a rich playground for physical phenomena, exhibiting complex phase diagrams with many competing orders. Ab initio insights into materials combined with physical ideas provide the ability to identify the organizing principles driving the correlated electronic behavior and pursue first-principles design of new compounds. Realistic modeling of correlated materials is an active area of research, especially with the recent merger of density functional theory (DFT) with dynamical mean-field theory (DMFT). This thesis is structured in two parts. The first describes the methods and algorithmic developments which drive advances in DFT+DMFT. In Ch. 2 and 3, we provide an overview of the two foundational theories, DMFT and DFT. In the second half of Ch. 3, we describe some of the principles guiding the combination of the two theories to form DFT+DMFT. In Ch. 4, we describe the algorithm lying at the heart of modern DFT+DMFT implementations, the hybridization expansion formulation of continuous-time quantum monte carlo (CTQMC) for the general Anderson impurity problem, as well as a fast rejection algorithm for speeding-up the local trace evaluation. The final chapter in the methods section describes an algorithm for direct sampling of the partition function, and thus the free energy and entropy, of simple Anderson impurity models within CTQMC. The second part of the thesis is a collection of applications of our ab initio approach to key correlated materials. We first apply our method to plutonium binary alloys (Ch. 6), which when supplemented with slave-boson mean-field theory, allows us to understand the observed photoemission spectra. Ch. 7 describes the computation of spectra and optical conductivity for rare-earth nickelates grown as epitaxial thin films. In the final two chapters, we turn our attention to the high-temperature superconductors. In the first, we show that the charge-transfer energy is a key chemical variable which controls

[Kidney allotransplantation from the AB0-incompatible donors].

PubMed

Goriaĭnov, V A; Kaabak, M M; Babenko, N N; Shishlo, L A; Morozova, M M; Ragimov, A A; Dazhkova, N G; Salimov, E L

2013-01-01

The experience of 28 kidney allotransplantations from the AB0-incompatible donors was analyzed. The comparative group consisted of 38 patients, who received the AB0-compatible organ. The results were assessed using the following parameters: renal function, morphology of the biopsy samples of the transplanted kidney and actuary survival of the recipients with functioning transplants in both groups. The comparative analysis showed no significant difference between the two groups, giving the right to consider the kidney allotransplantation from the AB0-incompatible donors safe and effective.

ABO Mistyping of cis-AB Blood Group by the Automated Microplate Technique.

PubMed

Chun, Sejong; Ryu, Mi Ra; Cha, Seung-Yeon; Seo, Ji-Young; Cho, Duck

2018-01-01

The cis -AB phenotype, although rare, is the relatively most frequent of ABO subgroups in Koreans. To prevent ABO mistyping of cis -AB samples, our hospital has applied a combination of the manual tile method with automated devices. Herein, we report cases of ABO mistyping detected by the combination testing system. Cases that showed discrepant results by automated devices and the manual tile method were evaluated. These samples were also tested by the standard tube method. The automated devices used in this study were a QWALYS-3 and Galileo NEO. Exons 6 and 7 of the ABO gene were sequenced. 13 cases that had the cis -AB allele showed results suggestive of the cis -AB subgroup by manual methods, but were interpreted as AB by either automated device. This happened in 87.5% of these cases by QWALYS-3 and 70.0% by Galileo NEO. Genotyping results showed that 12 cases were ABO*cis-AB01/ABO*O01 or ABO*cis-AB01/ABO*O02 , and one case was ABO*cis-AB01/ ABO*A102. Cis -AB samples were mistyped as AB by the automated microplate technique in some cases. We suggest that the manual tile method can be a simple supplemental test for the detection of the cis -AB phenotype, especially in countries with relatively high cis- AB prevalence.

Dynamics of Photoexcited State of Semiconductor Quantum Dots

NASA Astrophysics Data System (ADS)

Trivedi, Dhara J.

In this thesis, non-adiabatic molecular dynamics (NAMD) of excited states in semiconductor quantum dots are investigated. Nanoscale systems provide important opportunities for theory and computation for research because the experimental tools often provide an incomplete picture of the structure and/or function of nanomaterials, and theory can often fill in missing features crucial in understanding what is being measured. The simulation of NAMD is an indispensable tool for understanding complex ultrafast photoinduced processes such as charge and energy transfer, thermal relaxation, and charge recombination. Based on the state-of-the-art ab initio approaches in both the energy and time domains, the thesis presents a comprehensive discussion of the dynamical processes in quantum dots, ranging from the initial photon absorption to the final emission. We investigate the energy relaxation and transfer rates in pure and surface passivated quantum dots of different sizes. The study establishes the fundamental mechanisms of the electron and hole relaxation processes with and without hole traps. We develop and implement more accurate and efficient methods for NAMD. These methods are advantageous over the traditional ones when one encounters classically forbidden transitions. We also explore the effect of decoherence and non-adiabatic couplings on the dynamics. The results indicate significant influence on the accuracy and related computational cost of the simulated dynamics.

Compact quantum dot-antibody conjugates for FRET immunoassays with subnanomolar detection limits

NASA Astrophysics Data System (ADS)

Mattera, Lucia; Bhuckory, Shashi; Wegner, K. David; Qiu, Xue; Agnese, Fabio; Lincheneau, Christophe; Senden, Tim; Djurado, David; Charbonnière, Loïc J.; Hildebrandt, Niko; Reiss, Peter

2016-05-01

A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields ultra-compact, stable, and highly luminescent antibody-QD conjugates suitable for use in FRET immunoassays. Hydrophobic InPZnS/ZnSe/ZnS (emission wavelength: 530 nm), CdSe/ZnS (605 nm), and CdSeTe/ZnS (705 nm) QDs were surface functionalized with zwitterionic penicillamine, enabling aqueous phase transfer under conservation of the photoluminescence properties. Post-functionalization with a heterobifunctional crosslinker, containing a lipoic acid group and a maleimide function, enabled the subsequent coupling to sulfhydryl groups of proteins. This was demonstrated by QD conjugation with fragmented antibodies (F(ab)). The obtained F(ab)-QD conjugates range among the smallest antibody-functionalized nanoprobes ever reported, with a hydrodynamic diameter <13 nm, PL quantum yield up to 66% at 705 nm, and colloidal stability of several months in various buffers. They were applied as FRET acceptors in homogeneous, time-gated immunoassays using Tb-antibodies as FRET donors, both coupled by an immunological sandwich complex between the two antibodies and a PSA (prostate specific antigen) biomarker. The advantages of the compact surface coating for FRET could be demonstrated by an 6.2 and 2.5 fold improvement of the limit of detection (LOD) for PSA compared to commercially available hydrophilic QDs emitting at 605 and 705 nm, respectively. While the commercial QDs contain identical inorganic cores responsible for their fluorescence, they are coated with a comparably thick amphiphilic polymer layer leading to much larger hydrodynamic diameters (>26 nm without biomolecules). The LODs of 0.8 and 3.7 ng mL-1 obtained in 50 μL serum samples are below the clinical cut-off level of PSA (4 ng mL-1) and demonstrate their direct applicability in clinical diagnostics.A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields

Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

2011-01-01

Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

Scattering study of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction on an ab initio based analytical potential energy surface

NASA Astrophysics Data System (ADS)

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N.

2016-01-01

Initial state selected dynamics of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]+ structure lying 0.72 eV below the Ne + NeH+ asymptote is found to be the most stable geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.

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

Nanostructures based on quantum dots for application in promising methods of single- and multiphoton imaging and diagnostics

NASA Astrophysics Data System (ADS)

Nabiev, I. R.

2017-01-01

Molecules recognizing biomarkers of diseases (monoclonal antibodies (monoABs)) are often too large for biomedical applications, and the conditions that are used to bind them with nanolabels lead to disordered orientation of monoABs with respect to the nanoparticle surface. Extremely small nanoprobes, designed via oriented conjugation of quantum dots (QDs) with single-domain antibodies (sdABs) derived from the immunoglobulin of llama and produced in the E. coli culture, have a hydrodynamic diameter less than 12 nm and contain equally oriented sdAB molecules on the surface of each QD. These nanoprobes exhibit excellent specificity and sensitivity in quantitative determination of a small number of cells expressing biomarkers. In addition, the higher diffusion coefficient of sdABs makes it possible to perform immunohistochemical analysis in bulk tissue, inaccessible for conventional monoABs. The necessary conditions for implementing high-quality immunofluorescence diagnostics are a high specificity of labeling and clear differences between the fluorescence of nanoprobes and the autofluorescence of tissues. Multiphoton micros-copy with excitation in the near-IR spectral range, which is remote from the range of tissue autofluorescence excitation, makes it possible to solve this problem and image deep layers in biological tissues. The two-photon absorption cross sections of CdSe/ZnS QDs conjugated with sdABs exceed the corresponding values for organic fluorophores by several orders of magnitude. These nanoprobes provide clear discrimination between the regions of tumor and normal tissues with a ratio of the sdAB fluorescence to the tissue autofluorescence upon two-photon excitation exceeding that in the case of single-photon excitation by a factor of more than 40. The data obtained indicate that the sdAB-QD conjugates used as labels provide the same, or even better, quality as the "gold standard" of immunohistochemical diagnostics. The developed nanoprobes are expected to

Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Quantum learning of classical stochastic processes: The completely positive realization problem

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

Monràs, Alex; Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543; Winter, Andreas

2016-01-15

machine learning, device-independent characterization and reverse-engineering of stochastic processes and quantum processors, and more generally, of dynamical processes with quantum memory [M. Guţă, Phys. Rev. A 83(6), 062324 (2011); M. Guţă and N. Yamamoto, e-print http://arxiv.org/abs/1303.3771 (2013)].« less

Fully ab initio calculation of the resonant one-phonon Raman intensity of graphene

NASA Astrophysics Data System (ADS)

Reichardt, Sven; Wirtz, Ludger

We developed a fully ab initio, many-body perturbation theory approach for the calculation of resonant, one-phonon Raman spectra. Our general approach is applicable to any material and here we present its application to the case of graphene. Our diagrammatic, first-principles approach allows us to go beyond and improve on an earlier theoretical study by Basko, which relied on an analytical calculation in certain limits. We investigate the dependence of the G peak intensity on both the excitation energy and Fermi level. Furthermore, our method allows us to identify the relevant electronic quantum pathways and to demonstrate the importance of the contributions from non-resonant electronic transitions. We also applied our approach to the calculation of the resonant one-phonon Raman spectrum of MoS2, with our results being in good agreement with experimental data. SR acknowledges financial support from the National Research Fund (FNR) Luxembourg.

Ab Initio Computation of Dynamical Properties: Pressure Broadening

NASA Astrophysics Data System (ADS)

Wiesenfeld, Laurent; Drouin, Brian

2014-06-01

Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into

Development of Anti-lock Braking System (ABS) for Vehicles Braking

NASA Astrophysics Data System (ADS)

Minh, Vu Trieu; Oamen, Godwin; Vassiljeva, Kristina; Teder, Leo

2016-11-01

This paper develops a real laboratory of anti-lock braking system (ABS) for vehicle and conducts real experiments to verify the ability of this ABS to prevent the vehicle wheel from being locked while braking. Two controllers of PID and fuzzy logic are tested for analysis and comparison. This ABS laboratory is designed for bachelor and master students to simulate and analyze performances of ABS with different control techniques on various roads and load conditions. This paper provides educational theories and practices on the design of control for system dynamics.

[VDRL and FTA-ABS reactivity in cerebrospinal fluid: our experience].

PubMed

García-Rodríguez, J A; Martín-Sánchez, A M; Canut, A; García-García, L; Cacho, J

1990-01-01

The reactivity of 194 samples of CSF against VDRL and FTA-ABS was studied in patients attending the Clinical Hospital in Salamanca over a five years period. This laboratory was asked to rule out an etiology of syphilis. Twelve samples of CSF proved to be reactive (6.2%) against VDRL and/or FTA-ABS. Seven of these corresponded to six adults diagnosed as suffering from neurosyphilis and one to an infant with early congenital syphilis without neurological alterations; these had in common the presence of active syphilis and a reactive FTA-ABS in serum. In the CSF of the six cases of neurosyphilis, VDRL was reactive in two patients (33.3%) and FTA-ABS in five (83.3%). One minimally reactive VDRL and four FTA-ABS were detected in the remaining five patients, with no known previous history of syphilis, that were suffering from different neurological alterations and that had a nonreactive FTA-ABS in serum. The results obtained in this study point to inappropriate use in CSF of VDRL and FTA-ABS to exclude neurosyphilis in our hospital since only 3.6% of the CSF studied corresponded to patients diagnosed as suffering from neurosyphilis and also to the need for improving the criteria for patient selection.

Quantum Monte Carlo tunneling from quantum chemistry to quantum annealing

NASA Astrophysics Data System (ADS)

Mazzola, Guglielmo; Smelyanskiy, Vadim N.; Troyer, Matthias

2017-10-01

Quantum tunneling is ubiquitous across different fields, from quantum chemical reactions and magnetic materials to quantum simulators and quantum computers. While simulating the real-time quantum dynamics of tunneling is infeasible for high-dimensional systems, quantum tunneling also shows up in quantum Monte Carlo (QMC) simulations, which aim to simulate quantum statistics with resources growing only polynomially with the system size. Here we extend the recent results obtained for quantum spin models [Phys. Rev. Lett. 117, 180402 (2016), 10.1103/PhysRevLett.117.180402], and we study continuous-variable models for proton transfer reactions. We demonstrate that QMC simulations efficiently recover the scaling of ground-state tunneling rates due to the existence of an instanton path, which always connects the reactant state with the product. We discuss the implications of our results in the context of quantum chemical reactions and quantum annealing, where quantum tunneling is expected to be a valuable resource for solving combinatorial optimization problems.

Time-Domain Ab Initio Analysis of Excitation Dynamics in a Quantum Dot/Polymer Hybrid: Atomistic Description Rationalizes Experiment.

PubMed

Long, Run; Prezhdo, Oleg V

2015-07-08

Hybrid organic/inorganic polymer/quantum dot (QD) solar cells are an attractive alternative to the traditional cells. The original, simple models postulate that one-dimensional polymers have continuous energy levels, while zero-dimensional QDs exhibit atom-like electronic structure. A realistic, atomistic viewpoint provides an alternative description. Electronic states in polymers are molecule-like: finite in size and discrete in energy. QDs are composed of many atoms and have high, bulk-like densities of states. We employ ab initio time-domain simulation to model the experimentally observed ultrafast photoinduced dynamics in a QD/polymer hybrid and show that an atomistic description is essential for understanding the time-resolved experimental data. Both electron and hole transfers across the interface exhibit subpicosecond time scales. The interfacial processes are fast due to strong electronic donor-acceptor, as evidenced by the densities of the photoexcited states which are delocalized between the donor and the acceptor. The nonadiabatic charge-phonon coupling is also strong, especially in the polymer, resulting in rapid energy losses. The electron transfer from the polymer is notably faster than the hole transfer from the QD, due to a significantly higher density of acceptor states. The stronger molecule-like electronic and charge-phonon coupling in the polymer rationalizes why the electron-hole recombination inside the polymer is several orders of magnitude faster than in the QD. As a result, experiments exhibit multiple transfer times for the long-lived hole inside the QD, ranging from subpicoseconds to nanoseconds. In contrast, transfer of the short-lived electron inside the polymer does not occur beyond the first picosecond. The energy lost by the hole on its transit into the polymer is accommodated by polymer's high-frequency vibrations. The energy lost by the electron injected into the QD is accommodated primarily by much lower-frequency collective and

Summary of workshop 'Theory Meets Industry'—the impact of ab initio solid state calculations on industrial materials research

NASA Astrophysics Data System (ADS)

Wimmer, E.

2008-02-01

A workshop, 'Theory Meets Industry', was held on 12-14 June 2007 in Vienna, Austria, attended by a well balanced number of academic and industrial scientists from America, Europe, and Japan. The focus was on advances in ab initio solid state calculations and their practical use in industry. The theoretical papers addressed three dominant themes, namely (i) more accurate total energies and electronic excitations, (ii) more complex systems, and (iii) more diverse and accurate materials properties. Hybrid functionals give some improvements in energies, but encounter difficulties for metallic systems. Quantum Monte Carlo methods are progressing, but no clear breakthrough is on the horizon. Progress in order-N methods is steady, as is the case for efficient methods for exploring complex energy hypersurfaces and large numbers of structural configurations. The industrial applications were dominated by materials issues in energy conversion systems, the quest for hydrogen storage materials, improvements of electronic and optical properties of microelectronic and display materials, and the simulation of reactions on heterogeneous catalysts. The workshop is a clear testimony that ab initio computations have become an industrial practice with increasingly recognized impact.

Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature.

PubMed

Litman, Yair; Donadio, Davide; Ceriotti, Michele; Rossi, Mariana

2018-03-14

Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQEs) influence the structural stability and the dynamical properties of these systems. In this work, we explore the impact of NQEs on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We thus perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account the conformational entropy and anharmonicities at finite temperatures. We propose that when adsorption is weak and NQEs on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We then calculate the full contribution of NQEs to the free energies, including also anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared with the harmonic estimates. We also find that the dissociation process has a negligible contribution from tunneling but is dominated by zero point energies, which can enhance the rate of dissociation by three orders of magnitude. Finally we highlight how both temperature and NQEs indirectly impact dipoles and the redistribution of electron density, causing work function changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in the work function provides a possible approach to determine experimentally the most stable configurations of water

Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature

NASA Astrophysics Data System (ADS)

Litman, Yair; Donadio, Davide; Ceriotti, Michele; Rossi, Mariana

2018-03-01

Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQEs) influence the structural stability and the dynamical properties of these systems. In this work, we explore the impact of NQEs on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We thus perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account the conformational entropy and anharmonicities at finite temperatures. We propose that when adsorption is weak and NQEs on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We then calculate the full contribution of NQEs to the free energies, including also anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared with the harmonic estimates. We also find that the dissociation process has a negligible contribution from tunneling but is dominated by zero point energies, which can enhance the rate of dissociation by three orders of magnitude. Finally we highlight how both temperature and NQEs indirectly impact dipoles and the redistribution of electron density, causing work function changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in the work function provides a possible approach to determine experimentally the most stable configurations of water

Visualization of Current and Mapping of Elements in Quantum Dot Solar Cells

DOE PAGES

Niezgoda, J. Scott; Ng, Amy; Poplawsky, Jonathan D.; ...

2015-12-17

The delicate influence of properties such as high surface state density and organic-inorganic boundaries on the individual quantum dot electronic structure complicates pursuits toward forming quantitative models of quantum dot thin films ab initio. Our report describes the application of electron beam-induced current (EBIC) microscopy to depleted-heterojunction colloidal quantum dot photovoltaics (DH-CQD PVs), a technique which affords one a map of current production within the active layer of a PV device. The effects of QD sample size polydispersity as well as layer thickness in CQD active layers as they pertain to current production within these PVs are imaged and explained.more » The results from these experiments compare well with previous estimations, and confirm the ability of EBIC to function as a valuable empirical tool for the design and betterment of DH-CQD PVs. Lastly, extensive and unexpected PbS QD penetration into the mesoporous TiO 2 layer is observed through imaging of device cross sections by energy-dispersive X-ray spectroscopy combined with scanning transmission electron microscopy. Finally, the effects of this finding are discussed and corroborated with the EBIC studies on similar devices.« less

Ab initio theory and modeling of water.

PubMed

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

2017-10-10

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Quantum games as quantum types

NASA Astrophysics Data System (ADS)

Delbecque, Yannick

In this thesis, we present a new model for higher-order quantum programming languages. The proposed model is an adaptation of the probabilistic game semantics developed by Danos and Harmer [DH02]: we expand it with quantum strategies which enable one to represent quantum states and quantum operations. Some of the basic properties of these strategies are established and then used to construct denotational semantics for three quantum programming languages. The first of these languages is a formalisation of the measurement calculus proposed by Danos et al. [DKP07]. The other two are new: they are higher-order quantum programming languages. Previous attempts to define a denotational semantics for higher-order quantum programming languages have failed. We identify some of the key reasons for this and base the design of our higher-order languages on these observations. The game semantics proposed in this thesis is the first denotational semantics for a lambda-calculus equipped with quantum types and with extra operations which allow one to program quantum algorithms. The results presented validate the two different approaches used in the design of these two new higher-order languages: a first one where quantum states are used through references and a second one where they are introduced as constants in the language. The quantum strategies presented in this thesis allow one to understand the constraints that must be imposed on quantum type systems with higher-order types. The most significant constraint is the fact that abstraction over part of the tensor product of many unknown quantum states must not be allowed. Quantum strategies are a new mathematical model which describes the interaction between classical and quantum data using system-environment dialogues. The interactions between the different parts of a quantum system are described using the rich structure generated by composition of strategies. This approach has enough generality to be put in relation with other

Core molecule dependence of energy migration in phenylacetylene nanostar dendrimers: Ab initio molecular orbital-configuration interaction based quantum master equation study

NASA Astrophysics Data System (ADS)

Kishi, Ryohei; Minami, Takuya; Fukui, Hitoshi; Takahashi, Hideaki; Nakano, Masayoshi

2008-06-01

The core molecule dependence of energy (exciton) migration in phenylacetylene nanostar dendrimers is investigated using the ab initio molecular orbital (MO)-configuration interaction based quantum master equation approach. We examine three kinds of core molecular species, i.e., benzene, anthracene, and pentacene, with different highest occupied MO-lowest unoccupied MO (HOMO-LUMO) gaps, which lead to different orbital interactions between the dendron parts and the core molecule. The nanostars bearing anthracene and pentacene cores are characterized by multistep exciton states with spatially well-segmented distributions: The exciton distributions of high-lying exciton states are spatially localized well in the periphery region, whereas those of low-lying exciton states are done in the core region. On the other hand, for the nanostar bearing benzene core, which also has multistep exciton states, the spatial exciton distributions of low-lying exciton states are delocalized over the dendron and the core regions. It is found that the former nanostars exhibit nearly complete exciton migration from the periphery to the core molecule in contrast to the latter one, in which significant exciton distribution remains in the dendron parts attached to the core after the exciton relaxation, although all these dendrimers exhibit fast exciton relaxation from the initially populated states. It is predicted from the analysis based on the MO correlation diagrams and the relative relaxation factor that the complete exciton migration to the core occurs not only when the HOMO-LUMO gap of the core molecule is nearly equal to that of the dendron parts attached to the core (anthracene case) but also when fairly smaller than that (pentacene case), whereas the complete migration is not achieved when the HOMO-LUMO gap of the core is larger than that of the dendron parts (benzene case). These results suggest that the fast and complete exciton migration of real dendrimers could be realized by

Quantum dynamics of tunneling dominated reactions at low temperatures

NASA Astrophysics Data System (ADS)

Hazra, Jisha; Balakrishnan, N.

2015-05-01

We report a quantum dynamics study of the Li + HF → LiF + H reaction at low temperatures of interest to cooling and trapping experiments. Contributions from non-zero partial waves are analyzed and results show narrow resonances in the energy dependence of the cross section that survive partial wave summation. The computations are performed using the ABC code and a simple modification of the ABC code that enables separate energy cutoffs for the reactant and product rovibrational energy levels is found to dramatically reduce the basis set size and computational expense. Results obtained using two ab initio electronic potential energy surfaces for the LiHF system show strong sensitivity to the choice of the potential. In particular, small differences in the barrier heights of the two potential surfaces are found to dramatically influence the reaction cross sections at low energies. Comparison with recent measurements of the reaction cross section (Bobbenkamp et al 2011 J. Chem. Phys. 135 204306) shows similar energy dependence in the threshold regime and an overall good agreement with experimental data compared to previous theoretical results. Also, usefulness of a recently introduced method for ultracold reactions that employ the quantum close-coupling method at short-range and the multichannel quantum defect theory at long-range, is demonstrated in accurately evaluating product state-resolved cross sections for D + H2 and H + D2 reactions.

Ab initio calculation of resonant Raman intensities of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Reichardt, Sven; Molina-Sanchez, Alejandro; Wirtz, Ludger

Raman spectroscopy is used to characterize optical and vibrational properties of materials. Its computational simulation is important for the interpretation of experimental results. Two approaches are the bond polarizability model and density functional perturbation theory. However, both are known to not capture resonance effects. These resonances and quantum interference effects are important to correctly reproduce the intensities as a function of laser energy as, e.g., reported for the case of multi-layer MoTe21.We present two fully ab initio approaches that overcome this limitation. In the first, we calculate finite difference derivatives of the dielectric susceptibility with the phonon displacements2. In the second we calculate electron-light and electron-phonon matrix elements from density functional theory and use them to evaluate expressions for the Raman intensity derived from time-dependent perturbation theory. These expressions are implemented in a computer code that performs the calculations as a post-processing step. We compare both methods and study the case of triple-layer MoTe2. Luxembourg National Research Fund (FNR).

A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

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

Ho, T.; Rabitz, H.

1996-02-01

A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easilymore » extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}« less

MicroRNA-23a/b and microRNA-27a/b suppress Apaf-1 protein and alleviate hypoxia-induced neuronal apoptosis.

PubMed

Chen, Q; Xu, J; Li, L; Li, H; Mao, S; Zhang, F; Zen, K; Zhang, C-Y; Zhang, Q

2014-03-20

Expression of apoptotic protease activating factor-1 (Apaf-1) gradually decreases during brain development, and this decrease is likely responsible for the decreased sensitivity of brain tissue to apoptosis. However, the mechanism by which Apaf-1 expression is decreased remains elusive. In the present study, we found that four microRNAs (miR-23a/b and miR-27a/b) of miR-23a-27a-24 and miR-23b-27b-24 clusters play key roles in modulating the expression of Apaf-1. First, we found that miR-23a/b and miR-27a/b suppressed the expression of Apaf-1 in vitro. Interestingly, the expression of the miR-23-27-24 clusters in the mouse cortex gradually increased in a manner that was inversely correlated with the pattern of Apaf-1 expression. Second, hypoxic injuries during fetal distress caused reduced expression of the miR-23b and miR-27b that was inversely correlated with an elevation of Apaf-1 expression during neuronal apoptosis. Third, we made neuronal-specific transgenic mice and found that overexpressing the miR-23b and miR-27b in mouse neurons inhibited the neuronal apoptosis induced by intrauterine hypoxia. In conclusion, our results demonstrate, in central neural system, that miR-23a/b and miR-27a/b are endogenous inhibitory factors of Apaf-1 expression and regulate the sensitivity of neurons to apoptosis. Our findings may also have implications for the potential target role of microRNAs in the treatment of neuronal apoptosis-related diseases.

Deletion of nfnAB in Thermoanaerobacterium saccharolyticum and Its Effect on Metabolism

DOE PAGES

Lo, Jonathan; Zheng, Tianyong; Olson, Daniel G.; ...

2015-06-29

NfnAB catalyzes the reversible transfer of electrons from reduced ferredoxin and NADH to 2 NADP +. The NfnAB complex has been hypothesized to be the main enzyme for ferredoxin oxidization in strains of Thermoanaerobacterium saccharolyticum engineered for increased ethanol production. NfnAB complex activity was detectable in crude cell extracts of T. saccharolyticum. In this paper, activity was also detected using activity staining of native PAGE gels. The nfnAB gene was deleted in different strains of T. saccharolyticum to determine its effect on end product formation. In wild-type T. saccharolyticum, deletion of nfnAB resulted in a 46% increase in H 2more » formation but otherwise little change in other fermentation products. In two engineered strains with 80% theoretical ethanol yield, loss of nfnAB caused two different responses: in one strain, ethanol yield decreased to about 30% of the theoretical value, while another strain had no change in ethanol yield. Biochemical analysis of cell extracts showed that the ΔnfnAB strain with decreased ethanol yield had NADPH-linked alcohol dehydrogenase (ADH) activity, while the ΔnfnAB strain with unchanged ethanol yield had NADH-linked ADH activity. Deletion of nfnAB caused loss of NADPH-linked ferredoxin oxidoreductase activity in all cell extracts. Significant NADH-linked ferredoxin oxidoreductase activity was seen in all cell extracts, including those that had lost nfnAB. This suggests that there is an unidentified NADH:ferredoxin oxidoreductase (distinct from nfnAB) playing a role in ethanol formation. The NfnAB complex plays a key role in generating NADPH in a strain that had become reliant on NADPH-ADH activity. Importance: Thermophilic anaerobes that can convert biomass-derived sugars into ethanol have been investigated as candidates for biofuel formation. Many anaerobes have been genetically engineered to increase biofuel formation; however, key aspects of metabolism remain unknown and poorly understood. One

Cell Culture Systems To Study Human Herpesvirus 6A/B Chromosomal Integration.

PubMed

Gravel, Annie; Dubuc, Isabelle; Wallaschek, Nina; Gilbert-Girard, Shella; Collin, Vanessa; Hall-Sedlak, Ruth; Jerome, Keith R; Mori, Yasuko; Carbonneau, Julie; Boivin, Guy; Kaufer, Benedikt B; Flamand, Louis

2017-07-15

Human herpesviruses 6A/B (HHV-6A/B) can integrate their viral genomes in the telomeres of human chromosomes. The viral and cellular factors contributing to HHV-6A/B integration remain largely unknown, mostly due to the lack of efficient and reproducible cell culture models to study HHV-6A/B integration. In this study, we characterized the HHV-6A/B integration efficiencies in several human cell lines using two different approaches. First, after a short-term infection (5 h), cells were processed for single-cell cloning and analyzed for chromosomally integrated HHV-6A/B (ciHHV-6A/B). Second, cells were infected with HHV-6A/B and allowed to grow in bulk for 4 weeks or longer and then analyzed for the presence of ciHHV-6. Using quantitative PCR (qPCR), droplet digital PCR, and fluorescent in situ hybridization, we could demonstrate that HHV-6A/B integrated in most human cell lines tested, including telomerase-positive (HeLa, MCF-7, HCT-116, and HEK293T) and telomerase-negative cell lines (U2OS and GM847). Our results also indicate that inhibition of DNA replication, using phosphonoacetic acid, did not affect HHV-6A/B integration. Certain clones harboring ciHHV-6A/B spontaneously express viral genes and proteins. Treatment of cells with phorbol ester or histone deacetylase inhibitors triggered the expression of many viral genes, including U39 , U90 , and U100 , without the production of infectious virus, suggesting that the tested stimuli were not sufficient to trigger full reactivation. In summary, both integration models yielded comparable results and should enable the identification of viral and cellular factors contributing to HHV-6A/B integration and the screening of drugs influencing viral gene expression, as well as the release of infectious HHV-6A/B from the integrated state. IMPORTANCE The analysis and understanding of HHV-6A/B genome integration into host DNA is currently limited due to the lack of reproducible and efficient viral integration systems. In the

Quantum space and quantum completeness

NASA Astrophysics Data System (ADS)

Jurić, Tajron

2018-05-01

Motivated by the question whether quantum gravity can "smear out" the classical singularity we analyze a certain quantum space and its quantum-mechanical completeness. Classical singularity is understood as a geodesic incompleteness, while quantum completeness requires a unique unitary time evolution for test fields propagating on an underlying background. Here the crucial point is that quantum completeness renders the Hamiltonian (or spatial part of the wave operator) to be essentially self-adjoint in order to generate a unique time evolution. We examine a model of quantum space which consists of a noncommutative BTZ black hole probed by a test scalar field. We show that the quantum gravity (noncommutative) effect is to enlarge the domain of BTZ parameters for which the relevant wave operator is essentially self-adjoint. This means that the corresponding quantum space is quantum complete for a larger range of BTZ parameters rendering the conclusion that in the quantum space one observes the effect of "smearing out" the singularity.

AB-CHMINACA, AB-PINACA, and FUBIMINA: Affinity and Potency of Novel Synthetic Cannabinoids in Producing Δ9-Tetrahydrocannabinol–Like Effects in Mice

PubMed Central

Marusich, Julie A.; Lefever, Timothy W.; Antonazzo, Kateland R.; Wallgren, Michael T.; Cortes, Ricardo A.; Patel, Purvi R.; Grabenauer, Megan; Moore, Katherine N.

2015-01-01

Diversion of synthetic cannabinoids for abuse began in the early 2000s. Despite legislation banning compounds currently on the drug market, illicit manufacturers continue to release new compounds for recreational use. This study examined new synthetic cannabinoids, AB-CHMINACA (N-[1-amino-3-methyl-oxobutan-2-yl]-1-[cyclohexylmethyl]-1H-indazole-3-carboxamide), AB-PINACA [N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-pentyl-1H-indazole-3-carboxamide], and FUBIMINA [(1-(5-fluoropentyl)-1H-benzo[d]imadazol-2-yl)(naphthalen-1-yl)methanone], with the hypothesis that these compounds, like those before them, would be highly susceptible to abuse. Cannabinoids were examined in vitro for binding and activation of CB1 receptors, and in vivo for pharmacological effects in mice and in Δ9-tetrahydrocannabinol (Δ9-THC) discrimination. AB-CHMINACA, AB-PINACA, and FUBIMINA bound to and activated CB1 and CB2 receptors, and produced locomotor suppression, antinociception, hypothermia, and catalepsy. Furthermore, these compounds, along with JWH-018 [1-pentyl-3-(1-naphthoyl)indole], CP47,497 [rel-5-(1,1-dimethylheptyl)-2-[(1R,3S)-3-hydroxycyclohexyl]-phenol], and WIN55,212-2 ([(3R)-2,3-dihydro-5-methyl-3-(4-morpholinylmethyl)pyrrolo[1,2,3-de]-1,4-benzoxazin-6-yl]-1-naphthalenyl-methanone, monomethanesulfonate), substituted for Δ9-THC in Δ9-THC discrimination. Rank order of potency correlated with CB1 receptor-binding affinity, and all three compounds were full agonists in [35S]GTPγS binding, as compared with the partial agonist Δ9-THC. Indeed, AB-CHMINACA and AB-PINACA exhibited higher efficacy than most known full agonists of the CB1 receptor. Preliminary analysis of urinary metabolites of the compounds revealed the expected hydroxylation. AB-PINACA and AB-CHMINACA are of potential interest as research tools due to their unique chemical structures and high CB1 receptor efficacies. Further studies on these chemicals are likely to include research on understanding cannabinoid receptors

Fluorescence dye-based detection of mAb aggregates in CHO culture supernatants.

PubMed

Paul, Albert Jesuran; Schwab, Karen; Prokoph, Nina; Haas, Elena; Handrick, René; Hesse, Friedemann

2015-06-01

Product yields, efficacy, and safety of monoclonal antibodies (mAbs) are reduced by the formation of higher molecular weight aggregates during upstream processing. In-process characterization of mAb aggregate formation is a challenge since there is a lack of a fast detection method to identify mAb aggregates in cell culture. In this work, we present a rapid method to characterize mAb aggregate-containing Chinese hamster ovary (CHO) cell culture supernatants. The fluorescence dyes thioflavin T (ThT) and 4-4-bis-1-phenylamino-8-naphthalene sulfonate (Bis-ANS) enabled the detection of soluble as well as large mAb aggregates. Partial least square (PLS) regression models were used to evaluate the linearity of the dye-based mAb aggregate detection in buffer down to a mAb aggregate concentration of 2.4 μg mL(-1). Furthermore, mAb aggregates were detected in bioprocess medium using Bis-ANS and ThT. Dye binding to aggregates was stable for 60 min, making the method robust and reliable. Finally, the developed method using 10 μmol L(-1) Bis-ANS enabled discrimination between CHO cell culture supernatants containing different levels of mAb aggregates. The method can be adapted for high-throughput screening, e.g., to screen for cell culture conditions influencing mAb product quality, and hence can contribute to the improvement of production processes of biopharmaceuticals in mammalian cell culture.

[Find your way in the jungle of mAbs].

PubMed

Watier, H

2017-09-01

The rapidly increasing number of approved monoclonal antibodies (mAbs) and the huge number of mAbs in clinical development are a matter of concern for who wants to easily identify targets, indications, mechanisms of action and possible adverse effects. The current nomenclature being of limited interest, simple rationales will be presented for helping practitioners in rapidly classify mAbs depending on their structure-pharmacology relationship and in evaluating their potential effects, particularly in transfusion medicine. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Quantum correlations in multipartite quantum systems

NASA Astrophysics Data System (ADS)

Jafarizadeh, M. A.; Heshmati, A.; Karimi, N.; Yahyavi, M.

2018-03-01

Quantum entanglement is the most famous type of quantum correlation between elements of a quantum system that has a basic role in quantum communication protocols like quantum cryptography, teleportation and Bell inequality detection. However, it has already been shown that various applications in quantum information theory do not require entanglement. Quantum discord as a new kind of quantum correlations beyond entanglement, is the most popular candidate for general quantum correlations. In this paper, first we find the entanglement witness in a particular multipartite quantum system which consists of a N-partite system in 2 n -dimensional space. Then we give an exact analytical formula for the quantum discord of this system. At the end of the paper, we investigate the additivity relation of the quantum correlation and show that this relation is satisfied for a N-partite system with 2 n -dimensional space.

Ab initio theory and modeling of water

PubMed Central

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

2017-01-01

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

Ab initio study of the chlorine nitrate protonation reaction - Implications for loss of ClONO2 in the stratosphere

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1993-01-01

Ab initio quantum mechanical methods, including coupled-cluster theory, are used to determine the equilibrium geometries, dipole moments, and harmonic vibrational frequencies of ClONO2, NO2(+), and four isomers of protonated ClONO2. It was found that, for the equilibrium structures and harmonic frequencies of ClONO2, HOCl, and NO2(+), the highest-level theoretical predictions are consistent with the available experimental information concerning the reactions of ClONO2 and HOCl with HCl on the surface of polar stratospheric clouds (PSCs). The study supports a recent hypothesis that the reaction of ClONO2 on the surface of PSCs is proton catalyzed, although the mechanism is different.

Quantum Dot-Based Hybrid Nanostructures and Energy Transfer on the Nanoscale for Single- and Multi-Photon Imaging and Cancer Diagnostics

NASA Astrophysics Data System (ADS)

Nabiev, Igor

2017-01-01

An ideal single-photon (1P) or multiphoton fluorescent nanoprobe should combine a nanocrystal with the largest possible 1P or two-photon (2P) absorption cross section and the smallest possible highly specific recognition molecules conjugated with the nanoparticle in an oriented manner. However, the conditions used for conjugation of typical recognition molecules (conventional antibodies, Abs) with nanoparticles often provoke their unfolding and/or yield nanoprobes with irregular orientation of Abs on the nanoparticle surface. Conjugation of smaller Ab fragments, such as single-domain antibodies (sdAbs), with quantum dots (QDs) in an oriented manner can be considered as an attractive approach to engineering of ultrasmall diagnostic nanoprobes. QDs conjugated to 13-kDa sdAbs derived from camelid IgG or streptavidin have been used as efficient 1P or 2P excitation probes for imaging of cancer markers. The 2P absorption cross sections (TPACSs) for some conjugates are higher than 49,000 GM (Goeppert-Mayer units), which is close to the theoretical value calculated for CdSe QDs and considerably exceeds that of organic dyes. A further step in advanced QD-based cancer diagnostics has been made through implementation of efficient FRET-based imaging with 2P excitation, which has been demonstrated for double immunostaining complexes formed on the surface of cancer cells from sdAb-QD conjugates (donor) and a combination of monoclonal Abs and secondary antibodies labeled with the AlexaFluor dye (acceptor). The proposed approach permits obtaining an exceptional contrast of 2P imaging of cancer biomarkers without any contribution of cell and tissue autofluorescence in the recorded images.

Statistics of transmission eigenvalues in two-dimensional quantum cavities: Ballistic versus stochastic scattering

NASA Astrophysics Data System (ADS)

Rotter, Stefan; Aigner, Florian; Burgdörfer, Joachim

2007-03-01

We investigate the statistical distribution of transmission eigenvalues in phase-coherent transport through quantum dots. In two-dimensional ab initio simulations for both clean and disordered two-dimensional cavities, we find markedly different quantum-to-classical crossover scenarios for these two cases. In particular, we observe the emergence of “noiseless scattering states” in clean cavities, irrespective of sharp-edged entrance and exit lead mouths. We find the onset of these “classical” states to be largely independent of the cavity’s classical chaoticity, but very sensitive with respect to bulk disorder. Our results suggest that for weakly disordered cavities, the transmission eigenvalue distribution is determined both by scattering at the disorder potential and the cavity walls. To properly account for this intermediate parameter regime, we introduce a hybrid crossover scheme, which combines previous models that are valid in the ballistic and the stochastic limit, respectively.

Giant photocurrent enhancement by transition metal doping in quantum dot sensitized solar cells

NASA Astrophysics Data System (ADS)

Rimal, Gaurab; Pimachev, Artem K.; Yost, Andrew J.; Poudyal, Uma; Maloney, Scott; Wang, Wenyong; Chien, TeYu; Dahnovsky, Yuri; Tang, Jinke

2016-09-01

A huge enhancement in the incident photon-to-current efficiency of PbS quantum dot (QD) sensitized solar cells by manganese doping is observed. In the presence of Mn dopants with relatively small concentration (4 at. %), the photoelectric current increases by an average of 300% (up to 700%). This effect cannot be explained by the light absorption mechanism because both the experimental and theoretical absorption spectra demonstrate several times decreases in the absorption coefficient. To explain such dramatic increase in the photocurrent we propose the electron tunneling mechanism from the LUMO of the QD excited state to the Zn2SnO4 (ZTO) semiconductor photoanode. This change is due to the presence of the Mn instead of Pb atom at the QD/ZTO interface. The ab initio calculations confirm this mechanism. This work proposes an alternative route for a significant improvement of the efficiency for quantum dot sensitized solar cells.

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

Quantum dynamical simulation of the scattering of Ar from a frozen LiF(100) surface based on a first principles interaction potential

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

Azuri, Asaf; Pollak, Eli, E-mail: eli.pollak@weizmann.ac.il

2015-07-07

In-plane two and three dimensional diffraction patterns are computed for the vertical scattering of an Ar atom from a frozen LiF(100) surface. Suitable collimation of the incoming wavepacket serves to reveal the quantum mechanical diffraction. The interaction potential is based on a fit to an ab initio potential calculated using density functional theory with dispersion corrections. Due to the potential coupling found between the two horizontal surface directions, there are noticeable differences between the quantum angular distributions computed for two and three dimensional scattering. The quantum results are compared to analogous classical Wigner computations on the same surface and withmore » the same conditions. The classical dynamics largely provides the envelope for the quantum diffractive scattering. The classical results also show that the corrugation along the [110] direction of the surface is smaller than along the [100] direction, in qualitative agreement with experimental observations of unimodal and bimodal scattering for the [110] and [100] directions, respectively.« less

Comparing Vibrationally Averaged Nuclear Shielding Constants by Quantum Diffusion Monte Carlo and Second-Order Perturbation Theory.

PubMed

Ng, Yee-Hong; Bettens, Ryan P A

2016-03-03

Using the method of modified Shepard's interpolation to construct potential energy surfaces of the H2O, O3, and HCOOH molecules, we compute vibrationally averaged isotropic nuclear shielding constants ⟨σ⟩ of the three molecules via quantum diffusion Monte Carlo (QDMC). The QDMC results are compared to that of second-order perturbation theory (PT), to see if second-order PT is adequate for obtaining accurate values of nuclear shielding constants of molecules with large amplitude motions. ⟨σ⟩ computed by the two approaches differ for the hydrogens and carbonyl oxygen of HCOOH, suggesting that for certain molecules such as HCOOH where big displacements away from equilibrium happen (internal OH rotation), ⟨σ⟩ of experimental quality may only be obtainable with the use of more sophisticated and accurate methods, such as quantum diffusion Monte Carlo. The approach of modified Shepard's interpolation is also extended to construct shielding constants σ surfaces of the three molecules. By using a σ surface with the equilibrium geometry as a single data point to compute isotropic nuclear shielding constants for each descendant in the QDMC ensemble representing the ground state wave function, we reproduce the results obtained through ab initio computed σ to within statistical noise. Development of such an approach could thereby alleviate the need for any future costly ab initio σ calculations.

Optimization of Antibiotic Use in Hospitals – Antimicrobial Stewardship and the EU Project ABS International

PubMed Central

Allerberger, Franz; Lechner, Arno; Wechsler-Fördös, Agnes; Gareis, Roland

2008-01-01

Background The problem of antimicrobial resistance requires common strategies at the European level. Methods We report on an EU initiative fostering antibiotic (AB) stewardship (ABS) in hospitals. Results The project ‘ABS International: implementing antibiotic strategies for appropriate use of antibiotics in hospitals in member states of the EU’ started in September 2006 in Austria, Belgium, the Czech Republic, Germany, Hungary, Italy, Poland, Slovenia and Slovakia. A training program for national ABS trainers was prepared and standard templates for ABS tools (AB list, guidelines for AB treatment and surgical prophylaxis, and AB-related organization) and valid process measures as well as quality indicators for AB use were developed. Specific ABS tools are being implemented in up to five health care facilities per country. Conclusion ABS International is the first EU-funded initiative focusing on the implementation of structural measures in hospitals to promote the prudent use of ABs. PMID:18667815

Quantumness-generating capability of quantum dynamics

NASA Astrophysics Data System (ADS)

Li, Nan; Luo, Shunlong; Mao, Yuanyuan

2018-04-01

We study quantumness-generating capability of quantum dynamics, where quantumness refers to the noncommutativity between the initial state and the evolving state. In terms of the commutator of the square roots of the initial state and the evolving state, we define a measure to quantify the quantumness-generating capability of quantum dynamics with respect to initial states. Quantumness-generating capability is absent in classical dynamics and hence is a fundamental characteristic of quantum dynamics. For qubit systems, we present an analytical form for this measure, by virtue of which we analyze several prototypical dynamics such as unitary dynamics, phase damping dynamics, amplitude damping dynamics, and random unitary dynamics (Pauli channels). Necessary and sufficient conditions for the monotonicity of quantumness-generating capability are also identified. Finally, we compare these conditions for the monotonicity of quantumness-generating capability with those for various Markovianities and illustrate that quantumness-generating capability and quantum Markovianity are closely related, although they capture different aspects of quantum dynamics.

Staphylococcus aureus Biofilms Induce Macrophage Dysfunction Through Leukocidin AB and Alpha-Toxin

PubMed Central

Scherr, Tyler D.; Hanke, Mark L.; Huang, Ouwen; James, David B. A.; Horswill, Alexander R.; Bayles, Kenneth W.; Fey, Paul D.; Torres, Victor J.

2015-01-01

ABSTRACT The macrophage response to planktonic Staphylococcus aureus involves the induction of proinflammatory microbicidal activity. However, S. aureus biofilms can interfere with these responses in part by polarizing macrophages toward an anti-inflammatory profibrotic phenotype. Here we demonstrate that conditioned medium from mature S. aureus biofilms inhibited macrophage phagocytosis and induced cytotoxicity, suggesting the involvement of a secreted factor(s). Iterative testing found the active factor(s) to be proteinaceous and partially agr-dependent. Quantitative mass spectrometry identified alpha-toxin (Hla) and leukocidin AB (LukAB) as critical molecules secreted by S. aureus biofilms that inhibit murine macrophage phagocytosis and promote cytotoxicity. A role for Hla and LukAB was confirmed by using hla and lukAB mutants, and synergy between the two toxins was demonstrated with a lukAB hla double mutant and verified by complementation. Independent confirmation of the effects of Hla and LukAB on macrophage dysfunction was demonstrated by using an isogenic strain in which Hla was constitutively expressed, an Hla antibody to block toxin activity, and purified LukAB peptide. The importance of Hla and LukAB during S. aureus biofilm formation in vivo was assessed by using a murine orthopedic implant biofilm infection model in which the lukAB hla double mutant displayed significantly lower bacterial burdens and more macrophage infiltrates than each single mutant. Collectively, these findings reveal a critical synergistic role for Hla and LukAB in promoting macrophage dysfunction and facilitating S. aureus biofilm development in vivo. PMID:26307164

Intrinsic quantum anomalous Hall effect in the kagome lattice Cs 2LiMn 3F 12

DOE PAGES

Xu, Gang; Lian, Biao; Zhang, Shou -Cheng

2015-10-27

In a kagome lattice, the time reversal symmetry can be broken by a staggered magnetic flux emerging from ferromagnetic ordering and intrinsic spin-orbit coupling, leading to several well-separated nontrivial Chern bands and intrinsic quantum anomalous Hall effect. Based on this idea and ab initio calculations, we propose the realization of the intrinsic quantum anomalous Hall effect in the single layer Cs 2Mn 3F 12 kagome lattice and on the (001) surface of a Cs 2LiMn 3F 12 single crystal by modifying the carrier coverage on it, where the band gap is around 20 meV. Furthermore, a simplified tight binding modelmore » based on the in-plane ddσ antibonding states is constructed to understand the topological band structures of the system.« less

Quantum computer games: quantum minesweeper

NASA Astrophysics Data System (ADS)

Gordon, Michal; Gordon, Goren

2010-07-01

The computer game of quantum minesweeper is introduced as a quantum extension of the well-known classical minesweeper. Its main objective is to teach the unique concepts of quantum mechanics in a fun way. Quantum minesweeper demonstrates the effects of superposition, entanglement and their non-local characteristics. While in the classical minesweeper the goal of the game is to discover all the mines laid out on a board without triggering them, in the quantum version there are several classical boards in superposition. The goal is to know the exact quantum state, i.e. the precise layout of all the mines in all the superposed classical boards. The player can perform three types of measurement: a classical measurement that probabilistically collapses the superposition; a quantum interaction-free measurement that can detect a mine without triggering it; and an entanglement measurement that provides non-local information. The application of the concepts taught by quantum minesweeper to one-way quantum computing are also presented.

Quantum ensembles of quantum classifiers.

PubMed

Schuld, Maria; Petruccione, Francesco

2018-02-09

Quantum machine learning witnesses an increasing amount of quantum algorithms for data-driven decision making, a problem with potential applications ranging from automated image recognition to medical diagnosis. Many of those algorithms are implementations of quantum classifiers, or models for the classification of data inputs with a quantum computer. Following the success of collective decision making with ensembles in classical machine learning, this paper introduces the concept of quantum ensembles of quantum classifiers. Creating the ensemble corresponds to a state preparation routine, after which the quantum classifiers are evaluated in parallel and their combined decision is accessed by a single-qubit measurement. This framework naturally allows for exponentially large ensembles in which - similar to Bayesian learning - the individual classifiers do not have to be trained. As an example, we analyse an exponentially large quantum ensemble in which each classifier is weighed according to its performance in classifying the training data, leading to new results for quantum as well as classical machine learning.

Quantum Foundations of Quantum Information

NASA Astrophysics Data System (ADS)

Griffiths, Robert

2009-03-01

The main foundational issue for quantum information is: What is quantum information about? What does it refer to? Classical information typically refers to physical properties, and since classical is a subset of quantum information (assuming the world is quantum mechanical), quantum information should--and, it will be argued, does--refer to quantum physical properties represented by projectors on appropriate subspaces of a quantum Hilbert space. All sorts of microscopic and macroscopic properties, not just measurement outcomes, can be represented in this way, and are thus a proper subject of quantum information. The Stern-Gerlach experiment illustrates this. When properties are compatible, which is to say their projectors commute, Shannon's classical information theory based on statistical correlations extends without difficulty or change to the quantum case. When projectors do not commute, giving rise to characteristic quantum effects, a foundation for the subject can still be constructed by replacing the ``measurement and wave-function collapse'' found in textbooks--an efficient calculational tool, but one giving rise to numerous conceptual difficulties--with a fully consistent and paradox free stochastic formulation of standard quantum mechanics. This formulation is particularly helpful in that it contains no nonlocal superluminal influences; the reason the latter carry no information is that they do not exist.

An optimum A-B scale of psychotherapist effectiveness.

PubMed

Stephens, J H; Shaffer, J W; Zlotowitz, H I

1975-04-01

On the basis of the original Whitehorn-Betz data collected over a 16-year period, it is shown that all previously derived A-B scales of psychotherapist effectiveness using Strong Vocational Interest Blank (SVIB) items are deficient in terms of correlation with the original criterion and, frequently, in terms of reliability as well. The reasons for these deficiencies are discussed, and a new experimental A-B scale is formulated and tested for adequacy. This scale is shown to possess substantial internal consistency reliability and to have a high degree of correlation with the criterion even after the removal of possible contaminating factors such as use ofancillary teatments, differences in patient prognosis, and changing practices and interest over time. It is further shown that none of the A-B scales has any validity with respect to female therapists in the original data pool. Exploration of the factor-analytic structure of this new scale and two other widely used A-B measures in terms of the occupationa scales of the SVIB reveals differential loadings on four dimensions labeled verbal/comceptual vs. manual/practical, scientific vs. sales, social concern, and artistic vs. business-oriented. It is concluded that although male therapists' scores on the best of the A-B scales may , under certain circumstances,be related to short term judged improvement in patients treated, there is little evidence that high scoring therapists are more likey than low scoring ones to have a favorable, long range impact on diagnosed schizophrenics.

Stacking stability of MoS2 bilayer: An ab initio study

NASA Astrophysics Data System (ADS)

Tao, Peng; Guo, Huai-Hong; Yang, Teng; Zhang, Zhi-Dong

2014-10-01

The study of the stacking stability of bilayer MoS2 is essential since a bilayer has exhibited advantages over single layer MoS2 in many aspects for nanoelectronic applications. We explored the relative stability, optimal sliding path between different stacking orders of bilayer MoS2, and (especially) the effect of inter-layer stress, by combining first-principles density functional total energy calculations and the climbing-image nudge-elastic-band (CI-NEB) method. Among five typical stacking orders, which can be categorized into two kinds (I: AA, AB and II: AA', AB', A'B), we found that stacking orders with Mo and S superposing from both layers, such as AA' and AB, is more stable than the others. With smaller computational efforts than potential energy profile searching, we can study the effect of inter-layer stress on the stacking stability. Under isobaric condition, the sliding barrier increases by a few eV/(ucGPa) from AA' to AB', compared to 0.1 eV/(ucGPa) from AB to [AB]. Moreover, we found that interlayer compressive stress can help enhance the transport properties of AA'. This study can help understand why inter-layer stress by dielectric gating materials can be an effective means to improving MoS2 on nanoelectronic applications.

Impact-induced fracture mechanisms of immiscible PC/ABS (50/50) blends

NASA Astrophysics Data System (ADS)

Machmud, M. N.; Omiya, M.; Inoue, H.; Kishimoto, K.

2018-03-01

This paper presents a study on fracture mechanisms of polycarbonate (PC)/acrylonitrile-butadiene-styrene (ABS) (50/50) blends with different ABS types under a drop weight impact test (DWIT) using a circular sheet specimen. Formation of secondary crack indicated by a stress-whitening layer on the mid-plane of scattered specimens and secondary surface of fracture perpendicular to primary fracture surface were captured under scanning electron microscope (SEM). Although the both blends finally failed in brittle modes, SEM observation showed that their secondary fracture mechanisms were completely different. Observation through the thickness of the etched PC/ABS specimen samples using SEM also clearly showed that PC and ABS were immiscible. The immiscibility between PC and ABS was indicated by presence of their layer structures through the thickness of the blends. It was revealed that layer of ABS structure was influenced by size of rubber particle and this latter parameter then affected microstructure and fracture mechanisms of the blends. Impact-induced fracture mechanisms of the blends due to such microstructures are discussed in this paper. It was also pointed out that the secondary cracking was likely caused by interface delamination between PC and ABS layers in the core due to transverse shear stress generated during the impact test.

Quantum memory Quantum memory

NASA Astrophysics Data System (ADS)

Le Gouët, Jean-Louis; Moiseev, Sergey

2012-06-01

Interaction of quantum radiation with multi-particle ensembles has sparked off intense research efforts during the past decade. Emblematic of this field is the quantum memory scheme, where a quantum state of light is mapped onto an ensemble of atoms and then recovered in its original shape. While opening new access to the basics of light-atom interaction, quantum memory also appears as a key element for information processing applications, such as linear optics quantum computation and long-distance quantum communication via quantum repeaters. Not surprisingly, it is far from trivial to practically recover a stored quantum state of light and, although impressive progress has already been accomplished, researchers are still struggling to reach this ambitious objective. This special issue provides an account of the state-of-the-art in a fast-moving research area that makes physicists, engineers and chemists work together at the forefront of their discipline, involving quantum fields and atoms in different media, magnetic resonance techniques and material science. Various strategies have been considered to store and retrieve quantum light. The explored designs belong to three main—while still overlapping—classes. In architectures derived from photon echo, information is mapped over the spectral components of inhomogeneously broadened absorption bands, such as those encountered in rare earth ion doped crystals and atomic gases in external gradient magnetic field. Protocols based on electromagnetic induced transparency also rely on resonant excitation and are ideally suited to the homogeneous absorption lines offered by laser cooled atomic clouds or ion Coulomb crystals. Finally off-resonance approaches are illustrated by Faraday and Raman processes. Coupling with an optical cavity may enhance the storage process, even for negligibly small atom number. Multiple scattering is also proposed as a way to enlarge the quantum interaction distance of light with matter. The

From quantum coherence to quantum correlations

NASA Astrophysics Data System (ADS)

Sun, Yuan; Mao, Yuanyuan; Luo, Shunlong

2017-06-01

In quantum mechanics, quantum coherence of a state relative to a quantum measurement can be identified with the quantumness that has to be destroyed by the measurement. In particular, quantum coherence of a bipartite state relative to a local quantum measurement encodes quantum correlations in the state. If one takes minimization with respect to the local measurements, then one is led to quantifiers which capture quantum correlations from the perspective of coherence. In this vein, quantum discord, which quantifies the minimal correlations that have to be destroyed by quantum measurements, can be identified as the minimal coherence, with the coherence measured by the relative entropy of coherence. To advocate and formulate this idea in a general context, we first review coherence relative to Lüders measurements which extends the notion of coherence relative to von Neumann measurements (or equivalently, orthonomal bases), and highlight the observation that quantum discord arises as minimal coherence through two prototypical examples. Then, we introduce some novel measures of quantum correlations in terms of coherence, illustrate them through examples, investigate their fundamental properties and implications, and indicate their applications to quantum metrology.

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

PubMed Central

2016-01-01

Semiempirical (SE) methods can be derived from either Hartree–Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems. PMID:27074247

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

A Kine-chemical Investigation of the AB Dor Moving Group "Stream"

NASA Astrophysics Data System (ADS)

Barenfeld, Scott A.; Bubar, Eric J.; Mamajek, Eric E.; Young, Patrick A.

2013-03-01

The AB Dor Moving Group consists of a "nucleus" of ~10 stars at d ~= 20 pc, along with dozens of purported "stream" members distributed across the sky. We perform a chemical and kinematic analysis of a subsample of AB Dor stream stars to test whether they constitute a physical stellar group. We use the NEMO Galactic kinematic code to investigate the orbits of the stream members, and perform a chemical abundance analysis using high resolution spectra taken with the Magellan Clay 6.5 m telescope. Using a χ2 test with the measured abundances for 10 different elements, we find that only half of the purported AB Dor stream members could possibly constitute a statistically chemically homogeneous sample. Some stream members with three-dimensional velocities were hundreds of parsecs from the AB Dor nucleus ~108 yr ago, and hence were unlikely to share a common origin. We conclude that the published lists of AB Dor moving group stream members are unlikely to represent the dispersed remnant of a single star formation episode. A subsample of the stream stars appears to be both statistically chemically homogeneous and in the vicinity of the AB Dor nucleus at birth. Their mean metallicity is [Fe/H] = 0.02 ± 0.02 dex, which we consider representative for the AB Dor group. Finally, we report a strong lower limit on the age of the AB Dor nucleus of >110 Myr based on the pre-main sequence contraction times for K-type members which have reached the main sequence.

Ab initio thermal rate calculations of HO + HO = O(3P) + H2O reaction and isotopologues.

PubMed

Nguyen, Thanh Lam; Stanton, John F

2013-04-04

The forward and reverse reactions, HO + HO ⇌ O((3)P) + H2O, which play roles in both combustion and laboratory studies, were theoretically characterized with a master equation approach to compute thermal reaction rate constants at both the low and high pressure limits. Our ab initio k(T) results for the title reaction and two isotopic variants agree very well with experiments (within 15%) over a wide temperature range. The calculated reaction rate shows a distinctly non-Arrhenius behavior and a strong curvature consistent with the experiment. This characteristic behavior is due to effects of positive barrier height and quantum mechanical tunneling. Tunneling is very important and contributes more than 70% of total reaction rate at room temperature. A prereactive complex is also important in the overall reaction scheme.

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

What is quantum in quantum randomness?

PubMed

Grangier, P; Auffèves, A

2018-07-13

It is often said that quantum and classical randomness are of different nature, the former being ontological and the latter epistemological. However, so far the question of 'What is quantum in quantum randomness?', i.e. what is the impact of quantization and discreteness on the nature of randomness, remains to be answered. In a first part, we make explicit the differences between quantum and classical randomness within a recently proposed ontology for quantum mechanics based on contextual objectivity. In this view, quantum randomness is the result of contextuality and quantization. We show that this approach strongly impacts the purposes of quantum theory as well as its areas of application. In particular, it challenges current programmes inspired by classical reductionism, aiming at the emergence of the classical world from a large number of quantum systems. In a second part, we analyse quantum physics and thermodynamics as theories of randomness, unveiling their mutual influences. We finally consider new technological applications of quantum randomness that have opened up in the emerging field of quantum thermodynamics.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'. © 2018 The Author(s).

Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection from a PbSe quantum dot into the TiO2 surface.

PubMed

Long, Run; Prezhdo, Oleg V

2011-11-30

Following recent experiments [Science 2010, 328, 1543; PNAS 2011, 108, 965], we report an ab initio nonadiabatic molecular dynamics (NAMD) simulation of the ultrafast photoinduced electron transfer (ET) from a PbSe quantum dot (QD) into the rutile TiO(2) (110) surface. The system forms the basis for QD-sensitized semiconductor solar cells and demonstrates that ultrafast interfacial ET is instrumental for achieving high efficiencies in solar-to-electrical energy conversion. The simulation supports the observation that the ET successfully competes with energy losses due to electron-phonon relaxation. The ET proceeds by the adiabatic mechanism because of strong donor-acceptor coupling. High frequency polar vibrations of both QD and TiO(2) promote the ET, since these modes can rapidly influence the donor-acceptor state energies and coupling. Low frequency vibrations generate a distribution of initial conditions for ET, which shows a broad variety of scenarios at the single-molecule level. Compared to the molecule-TiO(2) interfaces, the QD-TiO(2) system exhibits pronounced differences that arise due to the larger size and higher rigidity of QDs relative to molecules. Both donor and acceptor states are more delocalized in the QD system, and the ET is promoted by optical phonons, which have relatively low frequencies in the QD materials composed of heavy elements. In contrast, in molecular systems, optical phonons are not thermally accessible under ambient conditions. Meanwhile, TiO(2) acceptor states resemble surface impurities due to the local influence of molecular chromophores. At the same time, the photoinduced ET at both QD-TiO(2) and molecule-TiO(2) interfaces is ultrafast and occurs by the adiabatic mechanism, as a result of strong donor-acceptor coupling. The reported state-of-the-art simulation generates a detailed time-domain atomistic description of the interfacial ET process that is fundamental to a wide variety of applications.

A novel cry2Ab gene from the indigenous isolate Bacillus thuringiensis subsp. kurstaki.

PubMed

Sevim, Ali; Eryüzlü, Emine; Demirbağ, Zihni; Demir, Ismail

2012-01-01

A novel cry2Ab gene was cloned and sequenced from the indigenous isolate of Bacillus thuringiensis subsp. kurstaki. This gene was designated as cry2Ab25 and its sequence revealed an open reading frame of 1,902 bp encoding a 633 aa protein with calculated molecular mass of 70 kDa and pI value of 8.98. The amino acid sequence of the Cry2Ab25 protein was compared with previously known Cry2Ab toxins, and the phylogenetic relationships among them were determined. The deduced amino acid sequence of the Cry2Ab25 protein showed 99% homology to the known Cry2Ab proteins, except for Cry2Ab10 and Cry2Ab12 with 97% homology, and a variation in one amino acid residue in comparison with all known Cry2Ab proteins. The cry2Ab25 gene was expressed in Escherichia coli BL21(DE3) cells. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) revealed that the Cry2Ab25 protein is about 70 kDa. The toxin expressed in BL21(DE3) exhibited high toxicity against Malacosoma neustria and Rhagoletis cerasi with 73% and 75% mortality after 5 days of treatment, respectively.

7 CFR Exhibits A-B to Subpart G... - [Reserved

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 12 2013-01-01 2013-01-01 false [Reserved] A Exhibits A-B to Subpart G to Part 1822 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS..., Procedures, and Authorizations Exhibits A-B to Subpart G to Part 1822 [Reserved] ...

Creep Behavior of ABS Polymer in Temperature-Humidity Conditions

NASA Astrophysics Data System (ADS)

An, Teagen; Selvaraj, Ramya; Hong, Seokmoo; Kim, Naksoo

2017-04-01

Acrylonitrile-Butadiene-Styrene (ABS), also known as a thermoplastic polymer, is extensively utilized for manufacturing home appliances products as it possess impressive mechanical properties, such as, resistance and toughness. However, the aforementioned properties are affected by operating temperature and atmosphere humidity due to the viscoelasticity property of an ABS polymer material. Moreover, the prediction of optimum working conditions are the little challenging task as it influences the final properties of product. This present study aims to develop the finite element (FE) models for predicting the creep behavior of an ABS polymeric material. In addition, the material constants, which represent the creep properties of an ABS polymer material, were predicted with the help of an interpolation function. Furthermore, a comparative study has been made with experiment and simulation results to verify the accuracy of developed FE model. The results showed that the predicted value from FE model could agree well with experimental data as well it can replicate the actual creep behavior flawlessly.

AB toxins: a paradigm switch from deadly to desirable.

PubMed

Odumosu, Oludare; Nicholas, Dequina; Yano, Hiroshi; Langridge, William

2010-07-01

To ensure their survival, a number of bacterial and plant species have evolved a common strategy to capture energy from other biological systems. Being imperfect pathogens, organisms synthesizing multi-subunit AB toxins are responsible for the mortality of millions of people and animals annually. Vaccination against these organisms and their toxins has proved rather ineffective in providing long-term protection from disease. In response to the debilitating effects of AB toxins on epithelial cells of the digestive mucosa, mechanisms underlying toxin immunomodulation of immune responses have become the focus of increasing experimentation. The results of these studies reveal that AB toxins may have a beneficial application as adjuvants for the enhancement of immune protection against infection and autoimmunity. Here, we examine similarities and differences in the structure and function of bacterial and plant AB toxins that underlie their toxicity and their exceptional properties as immunomodulators for stimulating immune responses against infectious disease and for immune suppression of organ-specific autoimmunity.

AB Toxins: A Paradigm Switch from Deadly to Desirable

PubMed Central

Odumosu, Oludare; Nicholas, Dequina; Yano, Hiroshi; Langridge, William

2010-01-01

To ensure their survival, a number of bacterial and plant species have evolved a common strategy to capture energy from other biological systems. Being imperfect pathogens, organisms synthesizing multi-subunit AB toxins are responsible for the mortality of millions of people and animals annually. Vaccination against these organisms and their toxins has proved rather ineffective in providing long-term protection from disease. In response to the debilitating effects of AB toxins on epithelial cells of the digestive mucosa, mechanisms underlying toxin immunomodulation of immune responses have become the focus of increasing experimentation. The results of these studies reveal that AB toxins may have a beneficial application as adjuvants for the enhancement of immune protection against infection and autoimmunity. Here, we examine similarities and differences in the structure and function of bacterial and plant AB toxins that underlie their toxicity and their exceptional properties as immunomodulators for stimulating immune responses against infectious disease and for immune suppression of organ-specific autoimmunity. PMID:22069653

Ab interno trabeculectomy: patient selection and perspectives

PubMed Central

Vinod, Kateki; Gedde, Steven J

2016-01-01

Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm’s canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries. PMID:27574396

From ab Initio Potential Energy Surfaces to State-Resolved Reactivities: X + H 2O ↔ HX + OH [X = F, Cl, and O( 3P)] Reactions

DOE PAGES

Li, Jun; Jiang, Bin; Song, Hongwei; ...

2015-04-17

Here, we survey the recent advances in theoretical understanding of quantum state resolved dynamics, using the title reactions as examples. It is shown that the progress was made possible by major developments in two areas. First, an accurate analytical representation of many high-level ab initio points over a large configuration space can now be made with high fidelity and the necessary permutation symmetry. The resulting full-dimensional global potential energy surfaces enable dynamical calculations using either quasi-classical trajectory or more importantly quantum mechanical methods. The second advance is the development of accurate and efficient quantum dynamical methods, which are necessary formore » providing a reliable treatment of quantum effects in reaction dynamics such as tunneling, resonances, and zero-point energy. The powerful combination of the two advances has allowed us to achieve a quantitatively accurate characterization of the reaction dynamics, which unveiled rich dynamical features such as steric steering, strong mode specificity, and bond selectivity. The dependence of reactivity on reactant modes can be rationalized by the recently proposed sudden vector projection model, which attributes the mode specificity and bond selectivity to the coupling of reactant modes with the reaction coordinate at the relevant transition state. The deeper insights provided by these theoretical studies have advanced our understanding of reaction dynamics to a new level.« less

Femtosecond two-photon photoassociation of hot magnesium atoms: A quantum dynamical study using thermal random phase wavefunctions

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kosloff, Ronnie; Tomza, Michał; Skomorowski, Wojciech; Pawłowski, Filip; Moszynski, Robert; Rybak, Leonid; Levin, Liat; Amitay, Zohar; Berglund, J. Martin; Reich, Daniel M.; Koch, Christiane P.

2013-10-01

Two-photon photoassociation of hot magnesium atoms by femtosecond laser pulses, creating electronically excited magnesium dimer molecules, is studied from first principles, combining ab initio quantum chemistry and molecular quantum dynamics. This theoretical framework allows for rationalizing the generation of molecular rovibrational coherence from thermally hot atoms [L. Rybak, S. Amaran, L. Levin, M. Tomza, R. Moszynski, R. Kosloff, C. P. Koch, and Z. Amitay, Phys. Rev. Lett. 107, 273001 (2011)]. Random phase thermal wavefunctions are employed to model the thermal ensemble of hot colliding atoms. Comparing two different choices of basis functions, random phase wavefunctions built from eigenstates are found to have the fastest convergence for the photoassociation yield. The interaction of the colliding atoms with a femtosecond laser pulse is modeled non-perturbatively to account for strong-field effects.

34 CFR Appendixes A-B to Part 682 - [Reserved

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 3 2010-07-01 2010-07-01 false [Reserved] A Appendixes A-B to Part 682 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION FEDERAL FAMILY EDUCATION LOAN (FFEL) PROGRAM Appendixes A-B to Part 682 [Reserved] ...

Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis.

PubMed

Schmidt, Andrea; Gruber, Karl; Kratky, Christoph; Lamzin, Victor S

2008-08-01

Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Ab initio treatment of ion-induced charge transfer dynamics of isolated 2-deoxy-D-ribose.

PubMed

Bacchus-Montabonel, Marie-Christine

2014-08-21

Modeling-induced radiation damage in biological systems, in particular, in DNA building blocks, is of major concern in cancer therapy studies. Ion-induced charge-transfer dynamics may indeed be involved in proton and hadrontherapy treatments. We have thus performed a theoretical approach of the charge-transfer dynamics in collision of C(4+) ions and protons with isolated 2-deoxy-D-ribose in a wide collision energy range by means of ab initio quantum chemistry molecular methods. The comparison of both projectile ions has been performed with regard to previous theoretical and experimental results. The charge transfer appears markedly less efficient with the 2-deoxy-D-ribose target than that with pyrimidine nucleobases, which would induce an enhancement of the fragmentation process in agreement with experimental measurements. The mechanism has been analyzed with regard to inner orbital excitations, and qualitative tendencies have been pointed out for studies on DNA buiding block damage.

Neutron matter with Quantum Monte Carlo: chiral 3N forces and static response

DOE PAGES

Buraczynski, M.; Gandolfi, S.; Gezerlis, A.; ...

2016-03-14

Neutron matter is related to the physics of neutron stars and that of neutron-rich nuclei. Moreover, Quantum Monte Carlo (QMC) methods offer a unique way of solving the many-body problem non-perturbatively, providing feedback on features of nuclear interactions and addressing scenarios that are inaccessible to other approaches. Our contribution goes over two recent accomplishments in the theory of neutron matter: a) the fusing of QMC with chiral effective field theory interactions, focusing on local chiral 3N forces, and b) the first attempt to find an ab initio solution to the problem of static response.

Quantum Computer Games: Quantum Minesweeper

ERIC Educational Resources Information Center

Gordon, Michal; Gordon, Goren

2010-01-01

The computer game of quantum minesweeper is introduced as a quantum extension of the well-known classical minesweeper. Its main objective is to teach the unique concepts of quantum mechanics in a fun way. Quantum minesweeper demonstrates the effects of superposition, entanglement and their non-local characteristics. While in the classical…

A KINE-CHEMICAL INVESTIGATION OF THE AB DOR MOVING GROUP 'STREAM'

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

Barenfeld, Scott A.; Bubar, Eric J.; Mamajek, Eric E.

2013-03-20

The AB Dor Moving Group consists of a 'nucleus' of {approx}10 stars at d {approx_equal} 20 pc, along with dozens of purported 'stream' members distributed across the sky. We perform a chemical and kinematic analysis of a subsample of AB Dor stream stars to test whether they constitute a physical stellar group. We use the NEMO Galactic kinematic code to investigate the orbits of the stream members, and perform a chemical abundance analysis using high resolution spectra taken with the Magellan Clay 6.5 m telescope. Using a {chi}{sup 2} test with the measured abundances for 10 different elements, we findmore » that only half of the purported AB Dor stream members could possibly constitute a statistically chemically homogeneous sample. Some stream members with three-dimensional velocities were hundreds of parsecs from the AB Dor nucleus {approx}10{sup 8} yr ago, and hence were unlikely to share a common origin. We conclude that the published lists of AB Dor moving group stream members are unlikely to represent the dispersed remnant of a single star formation episode. A subsample of the stream stars appears to be both statistically chemically homogeneous and in the vicinity of the AB Dor nucleus at birth. Their mean metallicity is [Fe/H] = 0.02 {+-} 0.02 dex, which we consider representative for the AB Dor group. Finally, we report a strong lower limit on the age of the AB Dor nucleus of >110 Myr based on the pre-main sequence contraction times for K-type members which have reached the main sequence.« less

ABS 3D printed solutions for cryogenic applications

NASA Astrophysics Data System (ADS)

Bartolomé, E.; Bozzo, B.; Sevilla, P.; Martínez-Pasarell, O.; Puig, T.; Granados, X.

2017-03-01

3D printing has become a common, inexpensive and rapid prototyping technique, enabling the ad hoc fabrication of complex shapes. In this paper, we demonstrate that 3D printed objects in ABS can be used at cryogenic temperatures, offering flexible solutions in different fields. Firstly, a thermo-mechanical characterization of ABS 3D printed specimens at 77 K is reported, which allowed us to delimit the type of cryogenic uses where 3D printed pieces may be implemented. Secondly, we present three different examples where ABS 3D printed objects working at low temperatures have provided specific solutions: (i) SQUID inserts for angular magnetometry (low temperature material characterization field); (ii) a cage support for a metamaterial ;magnetic concentrator; (superconductivity application), and (iii) dedicated tools for cryopreservation in assisted reproductive techniques (medicine field).

Ab Initio Vibrational Levels For HO2 and Vibrational Splittings for Hydrogen Atom Transfer

NASA Technical Reports Server (NTRS)

Barclay, V. J.; Dateo, Christopher E.; Hamilton, I. P.; Arnold, James O. (Technical Monitor)

1994-01-01

We calculate vibrational levels and wave functions for HO2 using the recently reported ab initio potential energy surface of Walch and Duchovic. There is intramolecular hydrogen atom transfer when the hydrogen atom tunnels through a T-shaped saddle point separating two equivalent equilibrium geometries, and correspondingly, the energy levels are split. We focus on vibrational levels and wave functions with significant splitting. The first three vibrational levels with splitting greater than 2/cm are (15 0), (0 7 1) and (0 8 0) where V(sub 2) is the O-O-H bend quantum number. We discuss the dynamics of hydrogen atom transfer; in particular, the O-O distances at which hydrogen atom transfer is most probable for these vibrational levels. The material of the proposed presentation was reviewed and the technical content will not reveal any information not already in the public domain and will not give any foreign industry or government a competitive advantage.

Quantum Chess: Making Quantum Phenomena Accessible

NASA Astrophysics Data System (ADS)

Cantwell, Christopher

Quantum phenomena have remained largely inaccessible to the general public. There tends to be a scare factor associated with the word ``Quantum''. This is in large part due to the alien nature of phenomena such as superposition and entanglement. However, Quantum Computing is a very active area of research and one day we will have games that run on those quantum computers. Quantum phenomena such as superposition and entanglement will seem as normal as gravity. Is it possible to create such games today? Can we make games that are built on top of a realistic quantum simulation and introduce players of any background to quantum concepts in a fun and mentally stimulating way? One of the difficulties with any quantum simulation run on a classical computer is that the Hilbert space grows exponentially, making simulations of an appreciable size physically impossible due largely to memory restrictions. Here we will discuss the conception and development of Quantum Chess, and how to overcome some of the difficulties faced. We can then ask the question, ``What's next?'' What are some of the difficulties Quantum Chess still faces, and what is the future of quantum games?

History of California's AB 1725 and Its Major Provisions.

ERIC Educational Resources Information Center

Livingston, Tab

This paper addresses the history of California's Assembly Bill 1725 (AB 1725) legislation and describes its major provisions. Signed in 1988 by Governor George Deukmejian, AB 1725's focus is to emphasize the new role of California community colleges as postsecondary institutions committed to transferring students, offering remedial courses, and…

Full-dimensional quantum dynamics study of the H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} reaction on an ab initio potential energy surface

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

Chen, Liuyang; University of Chinese Academy of Sciences, Beijing 100049; Shao, Kejie

2016-05-21

This work performs a time-dependent wavepacket study of the H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} reaction on a new ab initio potential energy surface (PES). The PES is constructed using neural network method based on 68 478 geometries with energies calculated at UCCSD(T)-F12a/aug-cc-pVTZ level and covers H{sub 2} + C{sub 2}H↔H + C{sub 2}H{sub 2}, H + C{sub 2}H{sub 2} → HCCH{sub 2}, and HCCH{sub 2} radial isomerization reaction regions. The reaction dynamics of H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} are investigated using full-dimensional quantum dynamics method. The initial-state selected reactionmore » probabilities are calculated for reactants in eight vibrational states. The calculated results showed that the H{sub 2} vibrational excitation predominantly enhances the reactivity while the excitation of bending mode of C{sub 2}H slightly inhibits the reaction. The excitations of two stretching modes of C{sub 2}H molecule have negligible effect on the reactivity. The integral cross section is calculated with J-shift approximation and the mode selectivity in this reaction is discussed. The rate constants over 200-2000 K are calculated and agree well with the experimental measured values.« less

Expected number of quantum channels in quantum networks.

PubMed

Chen, Xi; Wang, He-Ming; Ji, Dan-Tong; Mu, Liang-Zhu; Fan, Heng

2015-07-15

Quantum communication between nodes in quantum networks plays an important role in quantum information processing. Here, we proposed the use of the expected number of quantum channels as a measure of the efficiency of quantum communication for quantum networks. This measure quantified the amount of quantum information that can be teleported between nodes in a quantum network, which differs from classical case in that the quantum channels will be consumed if teleportation is performed. We further demonstrated that the expected number of quantum channels represents local correlations depicted by effective circles. Significantly, capacity of quantum communication of quantum networks quantified by ENQC is independent of distance for the communicating nodes, if the effective circles of communication nodes are not overlapped. The expected number of quantum channels can be enhanced through transformations of the lattice configurations of quantum networks via entanglement swapping. Our results can shed lights on the study of quantum communication in quantum networks.

Expected number of quantum channels in quantum networks

PubMed Central

Chen, Xi; Wang, He-Ming; Ji, Dan-Tong; Mu, Liang-Zhu; Fan, Heng

2015-01-01

Quantum communication between nodes in quantum networks plays an important role in quantum information processing. Here, we proposed the use of the expected number of quantum channels as a measure of the efficiency of quantum communication for quantum networks. This measure quantified the amount of quantum information that can be teleported between nodes in a quantum network, which differs from classical case in that the quantum channels will be consumed if teleportation is performed. We further demonstrated that the expected number of quantum channels represents local correlations depicted by effective circles. Significantly, capacity of quantum communication of quantum networks quantified by ENQC is independent of distance for the communicating nodes, if the effective circles of communication nodes are not overlapped. The expected number of quantum channels can be enhanced through transformations of the lattice configurations of quantum networks via entanglement swapping. Our results can shed lights on the study of quantum communication in quantum networks. PMID:26173556

Radiolytic Synthesis of Pt-Particle/ABS Catalysts for H₂O₂ Decomposition in Contact Lens Cleaning.

PubMed

Ohkubo, Yuji; Aoki, Tomonori; Seino, Satoshi; Mori, Osamu; Ito, Issaku; Endo, Katsuyoshi; Yamamura, Kazuya

2017-08-23

A container used in contact lens cleaning requires a Pt plating weight of 1.5 mg for H₂O₂ decomposition although Pt is an expensive material. Techniques that decrease the amount of Pt are therefore needed. In this study, Pt nanoparticles instead of Pt plating film were supported on a substrate of acrylonitrile-butadiene-styrene copolymer (ABS). This was achieved by the reduction of Pt ions in an aqueous solution containing the ABS substrate using high-energy electron-beam irradiation. Pt nanoparticles supported on the ABS substrate (Pt-particle/ABS) had a size of 4-10 nm. The amount of Pt required for Pt-particle/ABS was 250 times less than that required for an ABS substrate covered with Pt plating film (Pt-film/ABS). The catalytic activity for H₂O₂ decomposition was estimated by measuring the residual H₂O₂ concentration after immersing the catalyst for 360 min. The Pt-particle/ABS catalyst had a considerably higher specific catalytic activity for H₂O₂ decomposition than the Pt-film/ABS catalyst. In addition, sterilization performance was estimated from the initial rate of H₂O₂ decomposition over 60 min. The Pt-particle/ABS catalyst demonstrated a better sterilization performance than the Pt-film/ABS catalyst. The difference between Pt-particle/ABS and Pt-film/ABS was shown to reflect the size of the O₂ bubbles formed during H₂O₂ decomposition.

Blind Quantum Signature with Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Li, Wei; Shi, Ronghua; Guo, Ying

2017-04-01

Blind quantum computation allows a client without quantum abilities to interact with a quantum server to perform a unconditional secure computing protocol, while protecting client's privacy. Motivated by confidentiality of blind quantum computation, a blind quantum signature scheme is designed with laconic structure. Different from the traditional signature schemes, the signing and verifying operations are performed through measurement-based quantum computation. Inputs of blind quantum computation are securely controlled with multi-qubit entangled states. The unique signature of the transmitted message is generated by the signer without leaking information in imperfect channels. Whereas, the receiver can verify the validity of the signature using the quantum matching algorithm. The security is guaranteed by entanglement of quantum system for blind quantum computation. It provides a potential practical application for e-commerce in the cloud computing and first-generation quantum computation.

On the origin of the gauche effect. A quantum chemical study of 1,2-difluoroethane

NASA Astrophysics Data System (ADS)

Engkvist, O.; Karlström, G.; Widmark, P.-O.

1997-01-01

The conformational equilibrium of 1,2-difluoroethane has been investigated using ab initio quantum chemical calculations at the SCF, MP2 and CCSD(T) levels, with ANO basis sets. The relative stability of the gauche-conformation of 1,2-difluoroethane is found to be a consequence of the nodal structure of the singly occupied orbital in the CFH 2 radical. It is also shown that the nodal structure of the singly occupied orbitals in the CFH biradical can explain the stability of the cis conformation of 1,2-difluoroethene.

A note on AB INITIO semiconductor band structures

NASA Astrophysics Data System (ADS)

Fiorentini, Vincenzo

1992-09-01

We point out that only the internal features of the DFT ab initio theoretical picture of a crystal should be used in a consistent ab initio calculation of the band structure. As a consequence, we show that ground-state band structure calculations should be performed for the system in equilibrium at zero pressure, i.e. at the computed equilibrium cell volume ω th. Examples of consequences of this attitude are considered.

Identification of Bacillus thuringiensis Cry1AbMod binding-proteins from Spodoptera frugiperda.

PubMed

Martínez de Castro, Diana L; García-Gómez, Blanca I; Gómez, Isabel; Bravo, Alejandra; Soberón, Mario

2017-12-01

Bacillus thuringiensis Cry toxins are currently used for pest control in transgenic crops but evolution of resistance by the insect pests threatens the use of this technology. The Cry1AbMod toxin was engineered to lack the alpha helix-1 of the parental Cry1Ab toxin and was shown to counter resistance to Cry1Ab and Cry1Ac toxins in different insect species including the fall armyworm Spodoptera frugiperda. In addition, Cry1AbMod showed enhanced toxicity to Cry1Ab-susceptible S. frugiperda populations. To gain insights into the mechanisms of this Cry1AbMod-enhanced toxicity, we isolated the Cry1AbMod toxin binding proteins from S. frugiperda brush border membrane vesicles (BBMV), which were identified by pull-down assay and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The LC-MS/MS results indicated that Cry1AbMod toxin could bind to four classes of aminopeptidase (N1, N3, N4 y N5) and actin, with the highest amino acid sequence coverage acquired for APN 1 and APN4. In addition to these proteins, we found other proteins not previously described as Cry toxin binding proteins. This is the first report that suggests the interaction between Cry1AbMod and APN in S. frugiperda. Copyright © 2017 Elsevier Inc. All rights reserved.

Macrolide resistance in Legionella pneumophila: the role of LpeAB efflux pump.

PubMed

Massip, Clémence; Descours, Ghislaine; Ginevra, Christophe; Doublet, Patricia; Jarraud, Sophie; Gilbert, Christophe

2017-05-01

A previous study on 12 in vitro -selected azithromycin-resistant Legionella pneumophila lineages showed that ribosomal mutations were major macrolide resistance determinants. In addition to these mechanisms that have been well described in many species, mutations upstream of lpeAB operon, homologous to acrAB in Escherichia coli , were identified in two lineages. In this study, we investigated the role of LpeAB and of these mutations in macrolide resistance of L. pneumophila . The role of LpeAB was studied by testing the antibiotic susceptibility of WT, deleted and complemented L. pneumophila Paris strains. Translational fusion experiments using GFP as a reporter were conducted to investigate the consequences of the mutations observed in the upstream sequence of lpeAB operon. We demonstrated the involvement of LpeAB in an efflux pump responsible for a macrolide-specific reduced susceptibility of L. pneumophila Paris strain. Mutations in the upstream sequence of lpeAB operon were associated with an increased protein expression. Increased expression was also observed under sub-inhibitory macrolide concentrations in strains with both mutated and WT promoting regions. LpeAB are components of an efflux pump, which is a macrolide resistance determinant in L. pneumophila Paris strain. Mutations observed in the upstream sequence of lpeAB operon in resistant lineages led to an overexpression of this efflux pump. Sub-inhibitory concentrations of macrolides themselves participated in upregulating this efflux and could constitute a first step in the acquisition of a high macrolide resistance level. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Quantum machine learning for quantum anomaly detection

NASA Astrophysics Data System (ADS)

Liu, Nana; Rebentrost, Patrick

2018-04-01

Anomaly detection is used for identifying data that deviate from "normal" data patterns. Its usage on classical data finds diverse applications in many important areas such as finance, fraud detection, medical diagnoses, data cleaning, and surveillance. With the advent of quantum technologies, anomaly detection of quantum data, in the form of quantum states, may become an important component of quantum applications. Machine-learning algorithms are playing pivotal roles in anomaly detection using classical data. Two widely used algorithms are the kernel principal component analysis and the one-class support vector machine. We find corresponding quantum algorithms to detect anomalies in quantum states. We show that these two quantum algorithms can be performed using resources that are logarithmic in the dimensionality of quantum states. For pure quantum states, these resources can also be logarithmic in the number of quantum states used for training the machine-learning algorithm. This makes these algorithms potentially applicable to big quantum data applications.

Quantum Walk Schemes for Universal Quantum Computation

NASA Astrophysics Data System (ADS)

Underwood, Michael S.

Random walks are a powerful tool for the efficient implementation of algorithms in classical computation. Their quantum-mechanical analogues, called quantum walks, hold similar promise. Quantum walks provide a model of quantum computation that has recently been shown to be equivalent in power to the standard circuit model. As in the classical case, quantum walks take place on graphs and can undergo discrete or continuous evolution, though quantum evolution is unitary and therefore deterministic until a measurement is made. This thesis considers the usefulness of continuous-time quantum walks to quantum computation from the perspectives of both their fundamental power under various formulations, and their applicability in practical experiments. In one extant scheme, logical gates are effected by scattering processes. The results of an exhaustive search for single-qubit operations in this model are presented. It is shown that the number of distinct operations increases exponentially with the number of vertices in the scattering graph. A catalogue of all graphs on up to nine vertices that implement single-qubit unitaries at a specific set of momenta is included in an appendix. I develop a novel scheme for universal quantum computation called the discontinuous quantum walk, in which a continuous-time quantum walker takes discrete steps of evolution via perfect quantum state transfer through small 'widget' graphs. The discontinuous quantum-walk scheme requires an exponentially sized graph, as do prior discrete and continuous schemes. To eliminate the inefficient vertex resource requirement, a computation scheme based on multiple discontinuous walkers is presented. In this model, n interacting walkers inhabiting a graph with 2n vertices can implement an arbitrary quantum computation on an input of length n, an exponential savings over previous universal quantum walk schemes. This is the first quantum walk scheme that allows for the application of quantum error correction

Quantum information. Unconditional quantum teleportation between distant solid-state quantum bits.

PubMed

Pfaff, W; Hensen, B J; Bernien, H; van Dam, S B; Blok, M S; Taminiau, T H; Tiggelman, M J; Schouten, R N; Markham, M; Twitchen, D J; Hanson, R

2014-08-01

Realizing robust quantum information transfer between long-lived qubit registers is a key challenge for quantum information science and technology. Here we demonstrate unconditional teleportation of arbitrary quantum states between diamond spin qubits separated by 3 meters. We prepare the teleporter through photon-mediated heralded entanglement between two distant electron spins and subsequently encode the source qubit in a single nuclear spin. By realizing a fully deterministic Bell-state measurement combined with real-time feed-forward, quantum teleportation is achieved upon each attempt with an average state fidelity exceeding the classical limit. These results establish diamond spin qubits as a prime candidate for the realization of quantum networks for quantum communication and network-based quantum computing. Copyright © 2014, American Association for the Advancement of Science.

Communication: XFAIMS—eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses

DOE PAGES

Mignolet, Benoit; Curchod, Basile F. E.; Martinez, Todd J.

2016-11-17

Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments “on-the-fly,” from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. As a result, we then show the ability of XFAIMS to model the dynamics inmore » polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H 2CSO).« less

QSAR models based on quantum topological molecular similarity.

PubMed

Popelier, P L A; Smith, P J

2006-07-01

A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

Valley- and spin-polarized oscillatory magneto-optical absorption in monolayer MoS2 quantum rings

NASA Astrophysics Data System (ADS)

Oliveira, D.; Villegas-Lelovsky, L.; Soler, M. A. G.; Qu, Fanyao

2018-03-01

Besides optical valley selectivity, strong spin-orbit interaction along with Berry curvature effects also leads to unconventional valley- and spin-polarized Landau levels in monolayer transition metal dichalcogenides (TMDCs) under a perpendicular magnetic field. We find that these unique properties are inherited to the magneto-optical absorption spectrum of the TMDC quantum rings (QRs). In addition, it is robust against variation of the magnetic flux and of the QR geometry. In stark contrast to the monolayer bulk material, the MoS2 QRs manifest themselves in both the optical valley selectivity and unprecedented size tunability of the frequency of the light absorbed. We also find that when the magnetic field setup is changed, the phase transition from Aharonov-Bohm (AB) quantum interference to aperiodic oscillation of magneto-optical absorption spectrum takes place. The exciton spectrum in a realistic finite thickness MoS2 QR is also discussed.

Determination of lateral size distribution of type-II ZnTe/ZnSe stacked submonolayer quantum dots via spectral analysis of optical signature of the Aharanov-Bohm excitons

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

Ji, Haojie; Dhomkar, Siddharth; Roy, Bidisha

2014-10-28

For submonolayer quantum dot (QD) based photonic devices, size and density of QDs are critical parameters, the probing of which requires indirect methods. We report the determination of lateral size distribution of type-II ZnTe/ZnSe stacked submonolayer QDs, based on spectral analysis of the optical signature of Aharanov-Bohm (AB) excitons, complemented by photoluminescence studies, secondary-ion mass spectroscopy, and numerical calculations. Numerical calculations are employed to determine the AB transition magnetic field as a function of the type-II QD radius. The study of four samples grown with different tellurium fluxes shows that the lateral size of QDs increases by just 50%, evenmore » though tellurium concentration increases 25-fold. Detailed spectral analysis of the emission of the AB exciton shows that the QD radii take on only certain values due to vertical correlation and the stacked nature of the QDs.« less

Heats of Segregation of BCC Metals Using Ab Initio and Quantum Approximate Methods

NASA Technical Reports Server (NTRS)

Good, Brian; Chaka, Anne; Bozzolo, Guillermo

2003-01-01

Many multicomponent alloys exhibit surface segregation, in which the composition at or near a surface may be substantially different from that of the bulk. A number of phenomenological explanations for this tendency have been suggested, involving, among other things, differences among the components' surface energies, molar volumes, and heats of solution. From a theoretical standpoint, the complexity of the problem has precluded a simple, unified explanation, thus preventing the development of computational tools that would enable the identification of the driving mechanisms for segregation. In that context, we investigate the problem of surface segregation in a variety of bcc metal alloys by computing dilute-limit heats of segregation using both the quantum-approximate energy method of Bozzolo, Ferrante and Smith (BFS), and all-electron density functional theory. In addition, the composition dependence of the heats of segregation is investigated using a BFS-based Monte Carlo procedure, and, for selected cases of interest, density functional calculations. Results are discussed in the context of a simple picture that describes segregation behavior as the result of a competition between size mismatch and alloying effects

Ab-initio quantum transport simulation of self-heating in single-layer 2-D materials

NASA Astrophysics Data System (ADS)

Stieger, Christian; Szabo, Aron; Bunjaku, Teutë; Luisier, Mathieu

2017-07-01

Through advanced quantum mechanical simulations combining electron transport and phonon transport from first-principles, self-heating effects are investigated in n-type transistors with single-layer MoS2, WS2, and black phosphorus as channel materials. The selected 2-D crystals all exhibit different phonon-limited mobility values, as well as electron and phonon properties, which have a direct influence on the increase in their lattice temperature and on the power dissipated inside their channel as a function of the applied gate voltage and electrical current magnitude. This computational study reveals (i) that self-heating plays a much more important role in 2-D materials than in Si nanowires, (ii) that it could severely limit the performance of 2-D devices at high current densities, and (iii) that black phosphorus appears less sensitive to this phenomenon than transition metal dichalcogenides.

Parametric Quantum Search Algorithm as Quantum Walk: A Quantum Simulation

NASA Astrophysics Data System (ADS)

Ellinas, Demosthenes; Konstandakis, Christos

2016-02-01

Parametric quantum search algorithm (PQSA) is a form of quantum search that results by relaxing the unitarity of the original algorithm. PQSA can naturally be cast in the form of quantum walk, by means of the formalism of oracle algebra. This is due to the fact that the completely positive trace preserving search map used by PQSA, admits a unitarization (unitary dilation) a la quantum walk, at the expense of introducing auxiliary quantum coin-qubit space. The ensuing QW describes a process of spiral motion, chosen to be driven by two unitary Kraus generators, generating planar rotations of Bloch vector around an axis. The quadratic acceleration of quantum search translates into an equivalent quadratic saving of the number of coin qubits in the QW analogue. The associated to QW model Hamiltonian operator is obtained and is shown to represent a multi-particle long-range interacting quantum system that simulates parametric search. Finally, the relation of PQSA-QW simulator to the QW search algorithm is elucidated.

Quantum demultiplexer of quantum parameter-estimation information in quantum networks

NASA Astrophysics Data System (ADS)

Xie, Yanqing; Huang, Yumeng; Wu, Yinzhong; Hao, Xiang

2018-05-01

The quantum demultiplexer is constructed by a series of unitary operators and multipartite entangled states. It is used to realize information broadcasting from an input node to multiple output nodes in quantum networks. The scheme of quantum network communication with respect to phase estimation is put forward through the demultiplexer subjected to amplitude damping noises. The generalized partial measurements can be applied to protect the transferring efficiency from environmental noises in the protocol. It is found out that there are some optimal coherent states which can be prepared to enhance the transmission of phase estimation. The dynamics of state fidelity and quantum Fisher information are investigated to evaluate the feasibility of the network communication. While the state fidelity deteriorates rapidly, the quantum Fisher information can be enhanced to a maximum value and then decreases slowly. The memory effect of the environment induces the oscillations of fidelity and quantum Fisher information. The adjustment of the strength of partial measurements is helpful to increase quantum Fisher information.

Importance of nonlocal electron correlation in the BaNiS2 semimetal from quantum oscillations studies

NASA Astrophysics Data System (ADS)

Klein, Yannick; Casula, Michele; Santos-Cottin, David; Audouard, Alain; Vignolles, David; Fève, Gwendal; Freulon, Vincent; Plaçais, Bernard; Verseils, Marine; Yang, Hancheng; Paulatto, Lorenzo; Gauzzi, Andrea

2018-02-01

By means of Shubnikov-de Haas and de Haas-van Alphen oscillations, and ab initio calculations, we have studied the Fermi surface of high-quality BaNiS2 single crystals, with mean free path l ˜400 Å . The angle and temperature dependence of quantum oscillations indicates a quasi-two-dimensional Fermi surface, made of an electronlike tube centered at Γ , and of four holelike cones, generated by Dirac bands, weakly dispersive in the out-of-plane direction. Ab initio electronic structure calculations, in the density functional theory framework, show that the inclusion of screened exchange is necessary to account for the experimental Fermi pockets. Therefore, the choice of the functional becomes crucial. A modified HSE hybrid functional with 7% of exact exchange outperforms both GGA and GGA +U density functionals, signaling the importance of nonlocal screened-exchange interactions in BaNiS2, and, more generally, in 3 d compensated semimetals.

Research progress on quantum informatics and quantum computation

NASA Astrophysics Data System (ADS)

Zhao, Yusheng

2018-03-01

Quantum informatics is an emerging interdisciplinary subject developed by the combination of quantum mechanics, information science, and computer science in the 1980s. The birth and development of quantum information science has far-reaching significance in science and technology. At present, the application of quantum information technology has become the direction of people’s efforts. The preparation, storage, purification and regulation, transmission, quantum coding and decoding of quantum state have become the hotspot of scientists and technicians, which have a profound impact on the national economy and the people’s livelihood, technology and defense technology. This paper first summarizes the background of quantum information science and quantum computer and the current situation of domestic and foreign research, and then introduces the basic knowledge and basic concepts of quantum computing. Finally, several quantum algorithms are introduced in detail, including Quantum Fourier transform, Deutsch-Jozsa algorithm, Shor’s quantum algorithm, quantum phase estimation.

[In vitro hepatic targeting tendency of galactosyl-anti CD3 McAb-TILS].

PubMed

Jiang, P; He, S; Zhang, C

1999-03-01

This study was undertaken to enhance the hepatic targeting tendency of tumor infiltrating lymphocytes (TILs) and hence to lower the recurrence rate of primary liver cancer after hepatectomy. Galactosyl-anti CD3McAb-TILs were prepared and then were incubated together with hepatocytes. Their interaction through asialoglycoprotein receptor-mediated mechanism was observed under the inverted phase contrast microscope. The carbohydrate density of galactosyl-anti CD3McAb and the combining rate of galactosyl-anti CD3McAb with TILs were measured. The results revealed that galactosyl-anti CD3 McAb-TIL obviously were adhered to hepatocytes. The carbohydrate density of galactosyl-anti CD3McAb was 62.18, and the combining rate of galactosyl-anti CD3McAb with TILs was 97.9%. The results suggested that in vitro hepatic targeting tendency of galactosyl-anti CD3McAb-TILs was satisfactory, and that the carbohydrate density of 62.18 and the combining rate of 97.9% ensured the effective use of TILs.

SEER Abstracting Tool (SEER*Abs)

Cancer.gov

With this customizable tool, registrars can collect and store data abstracted from medical records. Download the software and find technical support and reference manuals. SEER*Abs has features for creating records, managing abstracting work and data, accessing reference data, and integrating edits.

Quantum probability and quantum decision-making.

PubMed

Yukalov, V I; Sornette, D

2016-01-13

A rigorous general definition of quantum probability is given, which is valid not only for elementary events but also for composite events, for operationally testable measurements as well as for inconclusive measurements, and also for non-commuting observables in addition to commutative observables. Our proposed definition of quantum probability makes it possible to describe quantum measurements and quantum decision-making on the same common mathematical footing. Conditions are formulated for the case when quantum decision theory reduces to its classical counterpart and for the situation where the use of quantum decision theory is necessary. © 2015 The Author(s).

Radioiodine Labeled Anti-MIF McAb: A Potential Agent for Inflammation Imaging

PubMed Central

Zhang, Chao; Hou, Gui-hua; Han, Jian-kui; Song, Jing; Liang, Ting

2007-01-01

Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that may play a role in the pathogenesis of inflammation. Radiolabeled anti-MIF McAb can be used to detect in vivo inflammatory changes. The objective of this study was to investigate in vivo biology of radioiodinated anti-MIF McAb using the inflammation model mice. Anti-MIF McAb was radioiodinated with NaI125 by Iodogen method. Animal models were induced in the mice by intramuscular injection of S. aureus, E. coli, and turpentine oil. The biodistribution studies with radioiodinated anti-MIF McAb were performed on inflammation mice. The relationship between inflammatory lesions and anti-MIF McAb binding was investigated using the percent of injected dose per gram tissue (% ID/g) of tissue samples and whole-body autoradiography. The radioactivity of I125-anti-MIF McAb in the inflammatory tissue increased gradually for three inflammation models. The highest uptake was found in S. aureus group and the lowest was in E. coli group. The uptake in turpentine oil group was average. Whole-body autoradiography showed that all inflammation foci could be visualized clearly from 24 hours after injection, but 48 hours images were much clearer in accordance with the high T/NT ratio. These results demonstrate the ability of radioiodinated anti-MIF McAb to measure in vivo inflammatory events represented by high expression of MIF and suggests that radiolabeled anti-MIF McAb warrants further investigation as a potential inflammation-seeking agent for imaging to detect inflammatory disorders. PMID:18317509

Fermionic entanglement via quantum walks in quantum dots

NASA Astrophysics Data System (ADS)

Melnikov, Alexey A.; Fedichkin, Leonid E.

2018-02-01

Quantum walks are fundamentally different from random walks due to the quantum superposition property of quantum objects. Quantum walk process was found to be very useful for quantum information and quantum computation applications. In this paper we demonstrate how to use quantum walks as a tool to generate high-dimensional two-particle fermionic entanglement. The generated entanglement can survive longer in the presence of depolorazing noise due to the periodicity of quantum walk dynamics. The possibility to create two distinguishable qudits in a system of tunnel-coupled semiconductor quantum dots is discussed.

Efficient quantum walk on a quantum processor

PubMed Central

Qiang, Xiaogang; Loke, Thomas; Montanaro, Ashley; Aungskunsiri, Kanin; Zhou, Xiaoqi; O'Brien, Jeremy L.; Wang, Jingbo B.; Matthews, Jonathan C. F.

2016-01-01

The random walk formalism is used across a wide range of applications, from modelling share prices to predicting population genetics. Likewise, quantum walks have shown much potential as a framework for developing new quantum algorithms. Here we present explicit efficient quantum circuits for implementing continuous-time quantum walks on the circulant class of graphs. These circuits allow us to sample from the output probability distributions of quantum walks on circulant graphs efficiently. We also show that solving the same sampling problem for arbitrary circulant quantum circuits is intractable for a classical computer, assuming conjectures from computational complexity theory. This is a new link between continuous-time quantum walks and computational complexity theory and it indicates a family of tasks that could ultimately demonstrate quantum supremacy over classical computers. As a proof of principle, we experimentally implement the proposed quantum circuit on an example circulant graph using a two-qubit photonics quantum processor. PMID:27146471

Emergent mechanics, quantum and un-quantum

NASA Astrophysics Data System (ADS)

Ralston, John P.

2013-10-01

There is great interest in quantum mechanics as an "emergent" phenomenon. The program holds that nonobvious patterns and laws can emerge from complicated physical systems operating by more fundamental rules. We find a new approach where quantum mechanics itself should be viewed as an information management tool not derived from physics nor depending on physics. The main accomplishment of quantum-style theory comes in expanding the notion of probability. We construct a map from macroscopic information as data" to quantum probability. The map allows a hidden variable description for quantum states, and efficient use of the helpful tools of quantum mechanics in unlimited circumstances. Quantum dynamics via the time-dependent Shroedinger equation or operator methods actually represents a restricted class of classical Hamiltonian or Lagrangian dynamics, albeit with different numbers of degrees of freedom. We show that under wide circumstances such dynamics emerges from structureless dynamical systems. The uses of the quantum information management tools are illustrated by numerical experiments and practical applications

Comparative study of thiophilic functionalised matrices for polyclonal F(ab')2 purification.

PubMed

Kumpalume, Peter; Slater, Nigel K H

2004-01-02

Thiophilic adsorbents have been developed using divinyl sulfone or epoxy activated Streamline quartz base matrix. Their capacity and selectivity for binding polyclonal F(ab')2 fragments generated by whole serum proteolysis was tested. Except for epoxy activated guanidine, all the adsorbents displayed high selectivity for F(ab')2 with dynamic binding capacities ranging from 3 to 10 mg/ml of adsorbent. Thiol immobilised ligands adsorbed more F(ab')2 and the recovery was equal to or more than that from amino immobilised ligands. All adsorbents showed good selectivity for IgG and the dynamic binding capacities were better than for F(ab')2.

Radiator-induced erythema ab igne in 8-year-old girl.

PubMed

Brzezinski, Piotr; Ismail, Samir; Chiriac, Anca

2014-04-01

The cutaneous lesion of erythema ab Igne are characterized by a reticulate erythema, hyperpigmentation, fine scaling, epidermal atrophy and telangiectasias, and reticulated erythema. We report a case of erythema ab igne on the hands of a 8-year-old girl, induced by classic homemade radiator.

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

NASA Astrophysics Data System (ADS)

Turi, László

2016-04-01

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

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

Turi, László, E-mail: turi@chem.elte.hu

2016-04-21

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions withmore » n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.« less

Experimental quantum forgery of quantum optical money

NASA Astrophysics Data System (ADS)

Bartkiewicz, Karol; Černoch, Antonín; Chimczak, Grzegorz; Lemr, Karel; Miranowicz, Adam; Nori, Franco

2017-03-01

Unknown quantum information cannot be perfectly copied (cloned). This statement is the bedrock of quantum technologies and quantum cryptography, including the seminal scheme of Wiesner's quantum money, which was the first quantum-cryptographic proposal. Surprisingly, to our knowledge, quantum money has not been tested experimentally yet. Here, we experimentally revisit the Wiesner idea, assuming a banknote to be an image encoded in the polarization states of single photons. We demonstrate that it is possible to use quantum states to prepare a banknote that cannot be ideally copied without making the owner aware of only unauthorized actions. We provide the security conditions for quantum money by investigating the physically-achievable limits on the fidelity of 1-to-2 copying of arbitrary sequences of qubits. These results can be applied as a security measure in quantum digital right management.

Wave packet and statistical quantum calculations for the He + NeH⁺ → HeH⁺ + Ne reaction on the ground electronic state.

PubMed

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N

2014-09-21

A real wave packet based time-dependent method and a statistical quantum method have been used to study the He + NeH(+) (v, j) reaction with the reactant in various ro-vibrational states, on a recently calculated ab initio ground state potential energy surface. Both the wave packet and statistical quantum calculations were carried out within the centrifugal sudden approximation as well as using the exact Hamiltonian. Quantum reaction probabilities exhibit dense oscillatory pattern for smaller total angular momentum values, which is a signature of resonances in a complex forming mechanism for the title reaction. Significant differences, found between exact and approximate quantum reaction cross sections, highlight the importance of inclusion of Coriolis coupling in the calculations. Statistical results are in fairly good agreement with the exact quantum results, for ground ro-vibrational states of the reactant. Vibrational excitation greatly enhances the reaction cross sections, whereas rotational excitation has relatively small effect on the reaction. The nature of the reaction cross section curves is dependent on the initial vibrational state of the reactant and is typical of a late barrier type potential energy profile.

Scattering study of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction on an ab initio based analytical potential energy surface

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

Koner, Debasish; Panda, Aditya N., E-mail: adi07@iitg.ernet.in; Barrios, Lizandra

2016-01-21

Initial state selected dynamics of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]{sup +} structure lying 0.72 eV below the Ne + NeH{sup +} asymptote is found to be the most stablemore » geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.« less

Quasiparticle Interference Studies of Quantum Materials.

PubMed

Avraham, Nurit; Reiner, Jonathan; Kumar-Nayak, Abhay; Morali, Noam; Batabyal, Rajib; Yan, Binghai; Beidenkopf, Haim

2018-06-03

Exotic electronic states are realized in novel quantum materials. This field is revolutionized by the topological classification of materials. Such compounds necessarily host unique states on their boundaries. Scanning tunneling microscopy studies of these surface states have provided a wealth of spectroscopic characterization, with the successful cooperation of ab initio calculations. The method of quasiparticle interference imaging proves to be particularly useful for probing the dispersion relation of the surface bands. Herein, how a variety of additional fundamental electronic properties can be probed via this method is reviewed. It is demonstrated how quasiparticle interference measurements entail mesoscopic size quantization and the electronic phase coherence in semiconducting nanowires; helical spin protection and energy-momentum fluctuations in a topological insulator; and the structure of the Bloch wave function and the relative insusceptibility of topological electronic states to surface potential in a topological Weyl semimetal. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum thermodynamic cycles and quantum heat engines. II.

PubMed

Quan, H T

2009-04-01

We study the quantum-mechanical generalization of force or pressure, and then we extend the classical thermodynamic isobaric process to quantum-mechanical systems. Based on these efforts, we are able to study the quantum version of thermodynamic cycles that consist of quantum isobaric processes, such as the quantum Brayton cycle and quantum Diesel cycle. We also consider the implementation of the quantum Brayton cycle and quantum Diesel cycle with some model systems, such as single particle in a one-dimensional box and single-mode radiation field in a cavity. These studies lay the microscopic (quantum-mechanical) foundation for Szilard-Zurek single-molecule engine.

Ab initio prediction of the vibration-rotation-tunneling spectrum of HCl-(H2O)2

NASA Astrophysics Data System (ADS)

Wormer, P. E. S.; Groenenboom, G. C.; van der Avoird, A.

2001-08-01

Quantum calculations of the vibration-rotation-tunneling (VRT) levels of the trimer HCl-(H2O)2 are presented. Two internal degrees of freedom are considered—the rotation angles of the two nonhydrogen-bonded (flipping) hydrogens in the complex—together with the overall rotation of the trimer in space. The kinetic energy expression of van der Avoird et al. [J. Chem. Phys. 105, 8034 (1996)] is used in a slightly modified form. The experimental microwave geometry of Kisiel et al. [J. Chem. Phys. 112, 5767 (2000)] served as input in the generation of a planar reference structure. The two-dimensional potential energy surface is generated ab initio by the iterative coupled-cluster method based on singly and doubly excited states with triply excited states included noniteratively [CCSD(T)]. Frequencies of vibrations and tunnel splittings are predicted for two isotopomers. The effect of the nonadditive three-body forces is considered and found to be important.

The Quantum Steganography Protocol via Quantum Noisy Channels

NASA Astrophysics Data System (ADS)

Wei, Zhan-Hong; Chen, Xiu-Bo; Niu, Xin-Xin; Yang, Yi-Xian

2015-08-01

As a promising branch of quantum information hiding, Quantum steganography aims to transmit secret messages covertly in public quantum channels. But due to environment noise and decoherence, quantum states easily decay and change. Therefore, it is very meaningful to make a quantum information hiding protocol apply to quantum noisy channels. In this paper, we make the further research on a quantum steganography protocol for quantum noisy channels. The paper proved that the protocol can apply to transmit secret message covertly in quantum noisy channels, and explicity showed quantum steganography protocol. In the protocol, without publishing the cover data, legal receivers can extract the secret message with a certain probability, which make the protocol have a good secrecy. Moreover, our protocol owns the independent security, and can be used in general quantum communications. The communication, which happen in our protocol, do not need entangled states, so our protocol can be used without the limitation of entanglement resource. More importantly, the protocol apply to quantum noisy channels, and can be used widely in the future quantum communication.

Quantum random oracle model for quantum digital signature

NASA Astrophysics Data System (ADS)

Shang, Tao; Lei, Qi; Liu, Jianwei

2016-10-01

The goal of this work is to provide a general security analysis tool, namely, the quantum random oracle (QRO), for facilitating the security analysis of quantum cryptographic protocols, especially protocols based on quantum one-way function. QRO is used to model quantum one-way function and different queries to QRO are used to model quantum attacks. A typical application of quantum one-way function is the quantum digital signature, whose progress has been hampered by the slow pace of the experimental realization. Alternatively, we use the QRO model to analyze the provable security of a quantum digital signature scheme and elaborate the analysis procedure. The QRO model differs from the prior quantum-accessible random oracle in that it can output quantum states as public keys and give responses to different queries. This tool can be a test bed for the cryptanalysis of more quantum cryptographic protocols based on the quantum one-way function.

Four-electron model for singlet and triplet excitation energy transfers with inclusion of coherence memory, inelastic tunneling and nuclear quantum effects

NASA Astrophysics Data System (ADS)

Suzuki, Yosuke; Ebina, Kuniyoshi; Tanaka, Shigenori

2016-08-01

A computational scheme to describe the coherent dynamics of excitation energy transfer (EET) in molecular systems is proposed on the basis of generalized master equations with memory kernels. This formalism takes into account those physical effects in electron-bath coupling system such as the spin symmetry of excitons, the inelastic electron tunneling and the quantum features of nuclear motions, thus providing a theoretical framework to perform an ab initio description of EET through molecular simulations for evaluating the spectral density and the temporal correlation function of electronic coupling. Some test calculations have then been carried out to investigate the dependence of exciton population dynamics on coherence memory, inelastic tunneling correlation time, magnitude of electronic coupling, quantum correction to temporal correlation function, reorganization energy and energy gap.

In vitro and in vivo evaluation of osteoinductivity and bone fusion ability of an activin a/BMP2 chimera (AB204): a comparison study between AB204 and rhBMP-2.

PubMed

Zheng, Guang Bin; Lee, Jae Hyup; Jin, Yuan-Zhe

2017-12-01

This study compared osteoinductivity and osteogenic capacity between AB204 and rhBMP-2 using hMSCs in vitro and a beagle's posterolateral spinal fusion model. Cultured hMSCs were treated with AB204 or rhBMP-2 with low to high doses. Three male beagles were performed posterolateral spinal fusion with biphasic calcium phosphate (2 ml) + AB204 or rhBMP-2 (20, 50 or 200 µg). They were euthanized after 8 weeks. The fusion rate and bone formation of spine samples were examined. AB204 had higher alkaline phosphatase activity, mineralization and osteogenic-related gene expression than rhBMP-2. Fusion rates in all rhBMP-2 groups were 0. They were 100% for 50 μg and 200 μg AB204 groups. Therefore, AB204 showed higher osteogenicity than rhBMP-2. It could be a better bone graft substitute.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

FeP(Im)–AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O2)

PubMed Central

Liao, Meng-Sheng; Huang, Ming-Ju; Watts, John D.

2011-01-01

Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (Ebond) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O2). The results indicate that an accurate prediction of Ebond for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield Ebond values of ca.1.1, 1.2, and 0.4 eV for AB = CO, NO, and O2, respectively, which are in reasonable agreement with experimental data (0.78 – 0.85 eV for CO, 0.99 eV for NO, and 0.44 – 0.53 eV for O2). The other functionals show more or less deficiency for one or two of the systems. The performances of the various functionals in describing the spin-state energetics of the five-coordinate FeP(Im) complex were also examined. PMID:22228914

Production and characterization of monoclonal antibodies (mAbs) against human serum albumin (HSA) for the development of an immunoaffinity system with oriented anti-HSA mAbs as immobilized ligand.

PubMed

Rajak, Poonam; Vijayalakshmi, M A; Jayaprakash, N S

2013-05-05

Proteins present in human serum are of immense importance in the field of biomarker discovery. But, the presence of high-abundant proteins like albumin makes the analysis more challenging because of masking effect on low-abundant proteins. Therefore, removal of albumin using highly specific monoclonal antibodies (mAbs) can potentiate the discovery of low-abundant proteins. In the present study, mAbs against human serum albumin (HSA) were developed and integrated in to an immunoaffinity based system for specific removal of albumin from the serum. Hybridomas were obtained by fusion of Sp2/0 mouse myeloma cells with spleen cells from the mouse immunized with HSA. Five clones (AHSA1-5) producing mAbs specific to HSA were established and characterized by enzyme linked immunosorbent assay (ELISA) and immunoblotting for specificity, sensitivity and affinity in terms of antigen binding. The mAbs were able to bind to both native albumin as well as its glycated isoform. Reactivity of mAbs with different mammalian sera was tested. The affinity constant of the mAbs ranged from 10(8) to 10(9)M(-1). An approach based on oriented immobilization was followed to immobilize purified anti-HSA mAbs on hydrazine activated agarose gel and the dynamic binding capacity of the column was determined. Copyright © 2013 Elsevier B.V. All rights reserved.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Quantum technology past, present, future: quantum energetics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Choi, Sang H.

2017-04-01

Since the development of quantum physics in the early part of the 1900s, this field of study has made remarkable contributions to our civilization. Some of these advances include lasers, light-emitting diodes (LED), sensors, spectroscopy, quantum dots, quantum gravity and quantum entanglements. In 1998, the NASA Langley Research Center established a quantum technology committee to monitor the progress in this area and initiated research to determine the potential of quantum technology for future NASA missions. The areas of interest in quantum technology at NASA included fundamental quantum-optics materials associated with quantum dots and quantum wells, device-oriented photonic crystals, smart optics, quantum conductors, quantum information and computing, teleportation theorem, and quantum energetics. A brief review of the work performed, the progress made in advancing these technologies, and the potential NASA applications of quantum technology will be presented.

Quantum teleportation between remote atomic-ensemble quantum memories

PubMed Central

Bao, Xiao-Hui; Xu, Xiao-Fan; Li, Che-Ming; Yuan, Zhen-Sheng; Lu, Chao-Yang; Pan, Jian-Wei

2012-01-01

Quantum teleportation and quantum memory are two crucial elements for large-scale quantum networks. With the help of prior distributed entanglement as a “quantum channel,” quantum teleportation provides an intriguing means to faithfully transfer quantum states among distant locations without actual transmission of the physical carriers [Bennett CH, et al. (1993) Phys Rev Lett 70(13):1895–1899]. Quantum memory enables controlled storage and retrieval of fast-flying photonic quantum bits with stationary matter systems, which is essential to achieve the scalability required for large-scale quantum networks. Combining these two capabilities, here we realize quantum teleportation between two remote atomic-ensemble quantum memory nodes, each composed of ∼108 rubidium atoms and connected by a 150-m optical fiber. The spin wave state of one atomic ensemble is mapped to a propagating photon and subjected to Bell state measurements with another single photon that is entangled with the spin wave state of the other ensemble. Two-photon detection events herald the success of teleportation with an average fidelity of 88(7)%. Besides its fundamental interest as a teleportation between two remote macroscopic objects, our technique may be useful for quantum information transfer between different nodes in quantum networks and distributed quantum computing. PMID:23144222

Quantum teleportation between remote atomic-ensemble quantum memories.

PubMed

Bao, Xiao-Hui; Xu, Xiao-Fan; Li, Che-Ming; Yuan, Zhen-Sheng; Lu, Chao-Yang; Pan, Jian-Wei

2012-12-11

Quantum teleportation and quantum memory are two crucial elements for large-scale quantum networks. With the help of prior distributed entanglement as a "quantum channel," quantum teleportation provides an intriguing means to faithfully transfer quantum states among distant locations without actual transmission of the physical carriers [Bennett CH, et al. (1993) Phys Rev Lett 70(13):1895-1899]. Quantum memory enables controlled storage and retrieval of fast-flying photonic quantum bits with stationary matter systems, which is essential to achieve the scalability required for large-scale quantum networks. Combining these two capabilities, here we realize quantum teleportation between two remote atomic-ensemble quantum memory nodes, each composed of ∼10(8) rubidium atoms and connected by a 150-m optical fiber. The spin wave state of one atomic ensemble is mapped to a propagating photon and subjected to Bell state measurements with another single photon that is entangled with the spin wave state of the other ensemble. Two-photon detection events herald the success of teleportation with an average fidelity of 88(7)%. Besides its fundamental interest as a teleportation between two remote macroscopic objects, our technique may be useful for quantum information transfer between different nodes in quantum networks and distributed quantum computing.

Ab Initio Crystal Field for Lanthanides.

PubMed

Ungur, Liviu; Chibotaru, Liviu F

2017-03-13

An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc) 2 ] - (Pc=phthalocyanine) and Dy 4 K 2 ([Dy 4 K 2 O(OtBu) 12 ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H 3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aggregating quantum repeaters for the quantum internet

NASA Astrophysics Data System (ADS)

Azuma, Koji; Kato, Go

2017-09-01

The quantum internet holds promise for accomplishing quantum teleportation and unconditionally secure communication freely between arbitrary clients all over the globe, as well as the simulation of quantum many-body systems. For such a quantum internet protocol, a general fundamental upper bound on the obtainable entanglement or secret key has been derived [K. Azuma, A. Mizutani, and H.-K. Lo, Nat. Commun. 7, 13523 (2016), 10.1038/ncomms13523]. Here we consider its converse problem. In particular, we present a universal protocol constructible from any given quantum network, which is based on running quantum repeater schemes in parallel over the network. For arbitrary lossy optical channel networks, our protocol has no scaling gap with the upper bound, even based on existing quantum repeater schemes. In an asymptotic limit, our protocol works as an optimal entanglement or secret-key distribution over any quantum network composed of practical channels such as erasure channels, dephasing channels, bosonic quantum amplifier channels, and lossy optical channels.

Quantum Secure Direct Communication with Quantum Memory

NASA Astrophysics Data System (ADS)

Zhang, Wei; Ding, Dong-Sheng; Sheng, Yu-Bo; Zhou, Lan; Shi, Bao-Sen; Guo, Guang-Can

2017-06-01

Quantum communication provides an absolute security advantage, and it has been widely developed over the past 30 years. As an important branch of quantum communication, quantum secure direct communication (QSDC) promotes high security and instantaneousness in communication through directly transmitting messages over a quantum channel. The full implementation of a quantum protocol always requires the ability to control the transfer of a message effectively in the time domain; thus, it is essential to combine QSDC with quantum memory to accomplish the communication task. In this Letter, we report the experimental demonstration of QSDC with state-of-the-art atomic quantum memory for the first time in principle. We use the polarization degrees of freedom of photons as the information carrier, and the fidelity of entanglement decoding is verified as approximately 90%. Our work completes a fundamental step toward practical QSDC and demonstrates a potential application for long-distance quantum communication in a quantum network.

Quantifying quantum coherence with quantum Fisher information.

PubMed

Feng, X N; Wei, L F

2017-11-14

Quantum coherence is one of the old but always important concepts in quantum mechanics, and now it has been regarded as a necessary resource for quantum information processing and quantum metrology. However, the question of how to quantify the quantum coherence has just been paid the attention recently (see, e.g., Baumgratz et al. PRL, 113. 140401 (2014)). In this paper we verify that the well-known quantum Fisher information (QFI) can be utilized to quantify the quantum coherence, as it satisfies the monotonicity under the typical incoherent operations and the convexity under the mixing of the quantum states. Differing from most of the pure axiomatic methods, quantifying quantum coherence by QFI could be experimentally testable, as the bound of the QFI is practically measurable. The validity of our proposal is specifically demonstrated with the typical phase-damping and depolarizing evolution processes of a generic single-qubit state, and also by comparing it with the other quantifying methods proposed previously.

Quantum Secure Direct Communication with Quantum Memory.

PubMed

Zhang, Wei; Ding, Dong-Sheng; Sheng, Yu-Bo; Zhou, Lan; Shi, Bao-Sen; Guo, Guang-Can

2017-06-02

Quantum communication provides an absolute security advantage, and it has been widely developed over the past 30 years. As an important branch of quantum communication, quantum secure direct communication (QSDC) promotes high security and instantaneousness in communication through directly transmitting messages over a quantum channel. The full implementation of a quantum protocol always requires the ability to control the transfer of a message effectively in the time domain; thus, it is essential to combine QSDC with quantum memory to accomplish the communication task. In this Letter, we report the experimental demonstration of QSDC with state-of-the-art atomic quantum memory for the first time in principle. We use the polarization degrees of freedom of photons as the information carrier, and the fidelity of entanglement decoding is verified as approximately 90%. Our work completes a fundamental step toward practical QSDC and demonstrates a potential application for long-distance quantum communication in a quantum network.

Anharmonic effects in the quantum cluster equilibrium method

NASA Astrophysics Data System (ADS)

von Domaros, Michael; Perlt, Eva

2017-03-01

The well-established quantum cluster equilibrium (QCE) model provides a statistical thermodynamic framework to apply high-level ab initio calculations of finite cluster structures to macroscopic liquid phases using the partition function. So far, the harmonic approximation has been applied throughout the calculations. In this article, we apply an important correction in the evaluation of the one-particle partition function and account for anharmonicity. Therefore, we implemented an analytical approximation to the Morse partition function and the derivatives of its logarithm with respect to temperature, which are required for the evaluation of thermodynamic quantities. This anharmonic QCE approach has been applied to liquid hydrogen chloride and cluster distributions, and the molar volume, the volumetric thermal expansion coefficient, and the isobaric heat capacity have been calculated. An improved description for all properties is observed if anharmonic effects are considered.

Diffusion quantum Monte Carlo and density functional calculations of the structural stability of bilayer arsenene

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Santana, Juan A.; Özaydin, H. Duygu; Ersan, Fatih; Aktürk, O. Üzengi; Aktürk, Ethem; Reboredo, Fernando A.

2018-06-01

We have studied the structural stability of monolayer and bilayer arsenene (As) in the buckled (b) and washboard (w) phases with diffusion quantum Monte Carlo (DMC) and density functional theory (DFT) calculations. DMC yields cohesive energies of 2.826(2) eV/atom for monolayer b-As and 2.792(3) eV/atom for w-As. In the case of bilayer As, DMC and DFT predict that AA-stacking is the more stable form of b-As, while AB is the most stable form of w-As. The DMC layer-layer binding energies for b-As-AA and w-As-AB are 30(1) and 53(1) meV/atom, respectively. The interlayer separations were estimated with DMC at 3.521(1) Å for b-As-AA and 3.145(1) Å for w-As-AB. A comparison of DMC and DFT results shows that the van der Waals density functional method yields energetic properties of arsenene close to DMC, while the DFT + D3 method closely reproduced the geometric properties from DMC. The electronic properties of monolayer and bilayer arsenene were explored with various DFT methods. The bandgap values vary significantly with the DFT method, but the results are generally qualitatively consistent. We expect the present work to be useful for future experiments attempting to prepare multilayer arsenene and for further development of DFT methods for weakly bonded systems.

Properties of Type-II ZnTe/ZnSe Submonolayer Quantum Dots Studied via Excitonic Aharonov- Bohm Effect and Polarized Optical Spectroscopy

NASA Astrophysics Data System (ADS)

Ji, Haojie

In this thesis I develop understanding of the fundamental physical and material properties of type-II ZnTe/ZnSe submonolayer quantum dots (QDs), grown via combination of molecular beam epitaxy (MBE) and migration enhanced epitaxy (MEE). I use magneto-photoluminescence, including excitonic Aharonov-Bohm (AB) effect and polarized optical spectroscopy as the primary tools in this work. I present previous studies as well as the background of optical and magneto-optical processes in semiconductor nanostructures and introduce the experimental methods in Chapters 1 - 3. In Chapter 4 I focus on the excitonic AB effect in the type-II QDs. I develop a lateral tightly-bound exciton model for ZnTe/ZnSe type-II QDs, using analytical methods and numerical calculations. This explained the magneto-PL observation and allowed for establishing the size and density of the QDs in each sample based on the results of PL and magneto-PL measurements. For samples with larger QDs, I observe behaviors that fall between properties of quantum-dot and quantum-well-like systems due to increased QD densities and their type-II nature. Finally, the decoherence mechanisms of the AB excitons are investigated via the temperature dependent studies of the magneto-PL. It is determined that the AB exciton decoherence is due to transport-like (acoustic phonon) scattering of the electrons moving in the ZnSe barriers, but with substantially smaller magnitude of electron-phonon coupling constant due to relatively strong electron-hole coupling within these type-II QDs. In Chapter 5 I discuss the results of circularly polarized magneto-PL measurements. A model with ultra-long spin-flip time of holes confined to submonolayer QDs is proposed. The g-factor of type-II excitons was extracted from the Zeeman splitting and the g-factor of electrons was obtained by fitting the temperature dependence of the degree of circular polarization (DCP), from which g-factor of holes confined within ZnTe QDs was found. It is shown

Quantum capacity of quantum black holes

NASA Astrophysics Data System (ADS)

Adami, Chris; Bradler, Kamil

2014-03-01

The fate of quantum entanglement interacting with a black hole has been an enduring mystery, not the least because standard curved space field theory does not address the interaction of black holes with matter. We discuss an effective Hamiltonian of matter interacting with a black hole that has a precise analogue in quantum optics and correctly reproduces both spontaneous and stimulated Hawking radiation with grey-body factors. We calculate the quantum capacity of this channel in the limit of perfect absorption, as well as in the limit of a perfectly reflecting black hole (a white hole). We find that the white hole is an optimal quantum cloner, and is isomorphic to the Unruh channel with positive quantum capacity. The complementary channel (across the horizon) is entanglement-breaking with zero capacity, avoiding a violation of the quantum no-cloning theorem. The black hole channel on the contrary has vanishing capacity, while its complement has positive capacity instead. Thus, quantum states can be reconstructed faithfully behind the black hole horizon, but not outside. This work sheds new light on black hole complementarity because it shows that black holes can both reflect and absorb quantum states without violating the no-cloning theorem, and makes quantum firewalls obsolete.

Duality quantum algorithm efficiently simulates open quantum systems

PubMed Central

Wei, Shi-Jie; Ruan, Dong; Long, Gui-Lu

2016-01-01

Because of inevitable coupling with the environment, nearly all practical quantum systems are open system, where the evolution is not necessarily unitary. In this paper, we propose a duality quantum algorithm for simulating Hamiltonian evolution of an open quantum system. In contrast to unitary evolution in a usual quantum computer, the evolution operator in a duality quantum computer is a linear combination of unitary operators. In this duality quantum algorithm, the time evolution of the open quantum system is realized by using Kraus operators which is naturally implemented in duality quantum computer. This duality quantum algorithm has two distinct advantages compared to existing quantum simulation algorithms with unitary evolution operations. Firstly, the query complexity of the algorithm is O(d3) in contrast to O(d4) in existing unitary simulation algorithm, where d is the dimension of the open quantum system. Secondly, By using a truncated Taylor series of the evolution operators, this duality quantum algorithm provides an exponential improvement in precision compared with previous unitary simulation algorithm. PMID:27464855

Car and Parrinello meet Green and Kubo: simulating atomic heat transport from equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Baroni, Stefano

Modern simulation methods based on electronic-structure theory have long been deemed unfit to compute heat transport coefficients within the Green-Kubo formalism. This is so because the quantum-mechanical energy density from which the heat flux is derived is inherently ill defined, thus allegedly hampering the use of the Green-Kubo formula. While this objection would actually apply to classical systems as well, I will demonstrate that the thermal conductivity is indeed independent of the specific microscopic expression for the energy density and current from which it is derived. This fact results from a kind of gauge invariance stemming from energy conservation and extensivity, which I will illustrate numerically for a classical Lennard-Jones fluid. I will then introduce an expression for the adiabatic energy flux, derived within density-functional theory, that allows simulating atomic heat transport using equilibrium ab initio molecular dynamics. The resulting methodology is demonstrated by comparing results from ab-initio and classical molecular-dynamics simulations of a model liquid-Argon system, for which accurate inter-atomic potentials are derived by the force-matching method, and applied to compute the thermal conductivity of heavy water at ambient conditions. The problem of evaluating transport coefficients along with their accuracy from relatively short trajectories is finally addressed and discussed with a few representative examples. Partially funded by the European Union through the MaX Centre of Excellence (Grant No. 676598).

Interfacing External Quantum Devices to a Universal Quantum Computer

PubMed Central

Lagana, Antonio A.; Lohe, Max A.; von Smekal, Lorenz

2011-01-01

We present a scheme to use external quantum devices using the universal quantum computer previously constructed. We thereby show how the universal quantum computer can utilize networked quantum information resources to carry out local computations. Such information may come from specialized quantum devices or even from remote universal quantum computers. We show how to accomplish this by devising universal quantum computer programs that implement well known oracle based quantum algorithms, namely the Deutsch, Deutsch-Jozsa, and the Grover algorithms using external black-box quantum oracle devices. In the process, we demonstrate a method to map existing quantum algorithms onto the universal quantum computer. PMID:22216276

Interfacing external quantum devices to a universal quantum computer.

PubMed

Lagana, Antonio A; Lohe, Max A; von Smekal, Lorenz

2011-01-01

We present a scheme to use external quantum devices using the universal quantum computer previously constructed. We thereby show how the universal quantum computer can utilize networked quantum information resources to carry out local computations. Such information may come from specialized quantum devices or even from remote universal quantum computers. We show how to accomplish this by devising universal quantum computer programs that implement well known oracle based quantum algorithms, namely the Deutsch, Deutsch-Jozsa, and the Grover algorithms using external black-box quantum oracle devices. In the process, we demonstrate a method to map existing quantum algorithms onto the universal quantum computer. © 2011 Lagana et al.

Quantum algorithms for quantum field theories.

PubMed

Jordan, Stephen P; Lee, Keith S M; Preskill, John

2012-06-01

Quantum field theory reconciles quantum mechanics and special relativity, and plays a central role in many areas of physics. We developed a quantum algorithm to compute relativistic scattering probabilities in a massive quantum field theory with quartic self-interactions (φ(4) theory) in spacetime of four and fewer dimensions. Its run time is polynomial in the number of particles, their energy, and the desired precision, and applies at both weak and strong coupling. In the strong-coupling and high-precision regimes, our quantum algorithm achieves exponential speedup over the fastest known classical algorithm.

SatR Is a Repressor of Fluoroquinolone Efflux Pump SatAB

PubMed Central

Escudero, Jose Antonio; San Millan, Alvaro; Montero, Natalia; Gutierrez, Belen; Ovejero, Cristina Martinez; Carrilero, Laura

2013-01-01

Streptococcus suis is an emerging zoonotic agent responsible for high-mortality outbreaks among the human population in China. In this species, the ABC transporter SatAB mediates fluoroquinolone resistance when overexpressed. Here, we describe and characterize satR, an open reading frame (ORF) encoding a MarR superfamily regulator that acts as a repressor of satAB. satR is cotranscribed with satAB, and its interruption entails the overexpression of the pump, leading to a clinically relevant increase in resistance to fluoroquinolones. PMID:23650171

Process for treating ab5 nickel-metal hydride battery scrap

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

Lyman, J.W.; Palmer, G.R.

1994-12-31

A process for treating an AB5 Ni-MH battery to recover purified positive and negative electrode components of the battery is disclosed. An AB5 Ni-MH battery is placed in a mineral acid leach solution to cause the positive and negative electrode components of the battery to separate.

Abstract quantum computing machines and quantum computational logics

NASA Astrophysics Data System (ADS)

Chiara, Maria Luisa Dalla; Giuntini, Roberto; Sergioli, Giuseppe; Leporini, Roberto

2016-06-01

Classical and quantum parallelism are deeply different, although it is sometimes claimed that quantum Turing machines are nothing but special examples of classical probabilistic machines. We introduce the concepts of deterministic state machine, classical probabilistic state machine and quantum state machine. On this basis, we discuss the question: To what extent can quantum state machines be simulated by classical probabilistic state machines? Each state machine is devoted to a single task determined by its program. Real computers, however, behave differently, being able to solve different kinds of problems. This capacity can be modeled, in the quantum case, by the mathematical notion of abstract quantum computing machine, whose different programs determine different quantum state machines. The computations of abstract quantum computing machines can be linguistically described by the formulas of a particular form of quantum logic, termed quantum computational logic.

Cis-trans photoisomerization of azobenzene upon excitation to the S1 state: an ab initio molecular dynamics and QM/MM study

NASA Astrophysics Data System (ADS)

Pederzoli, Marek; Pittner, Jiří; Barbatti, Mario; Lischka, Hans

2012-10-01

The cis-trans isomerization of azobenzene upon S1(n,π*) excitation is studied both in gas phase and in solution. Our study is based on ab initio non-adiabatic dynamics simulations with the non-adiabatic effects included via the fewest-switches surface hopping method with potential-energy surfaces and couplings determined on the fly. The non-adiabatic couplings have been computed based on overlaps of CASSCF wave functions. The solvent is described using classical molecular dynamics employing the quantum mechanics/molecular mechanics (QM/MM) approach. Azobenzene photoisomerization upon S1(n,π*) excitation occurs purely as a rotational motion of the central CNNC moiety. Two non-equivalent rotational pathways, corresponding to clockwise or counterclockwise rotation, are available. The course of the rotational motion is strongly dependent on the initial conditions. The internal conversion occurs via a S0/S1 crossing seam located near the midpoint of both of these rotational pathways. Based on statistical analysis it is shown that the occurrence of one or other pathways can be completely controlled by selecting adequate initial conditions. The effect of the solvent on the reaction mechanism is small. The lifetime of the S1 state is marginally lowered; the effect does not depend on the polarity, but rather on the viscosity of the solvent. The quantum yield is solvent dependent; the simulations in water give smaller quantum yield than those obtained in n-hexane and in gas phase.

Compact quantum dot-antibody conjugates for FRET immunoassays with subnanomolar detection limits.

PubMed

Mattera, Lucia; Bhuckory, Shashi; Wegner, K David; Qiu, Xue; Agnese, Fabio; Lincheneau, Christophe; Senden, Tim; Djurado, David; Charbonnière, Loïc J; Hildebrandt, Niko; Reiss, Peter

2016-06-07

A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields ultra-compact, stable, and highly luminescent antibody-QD conjugates suitable for use in FRET immunoassays. Hydrophobic InPZnS/ZnSe/ZnS (emission wavelength: 530 nm), CdSe/ZnS (605 nm), and CdSeTe/ZnS (705 nm) QDs were surface functionalized with zwitterionic penicillamine, enabling aqueous phase transfer under conservation of the photoluminescence properties. Post-functionalization with a heterobifunctional crosslinker, containing a lipoic acid group and a maleimide function, enabled the subsequent coupling to sulfhydryl groups of proteins. This was demonstrated by QD conjugation with fragmented antibodies (F(ab)). The obtained F(ab)-QD conjugates range among the smallest antibody-functionalized nanoprobes ever reported, with a hydrodynamic diameter <13 nm, PL quantum yield up to 66% at 705 nm, and colloidal stability of several months in various buffers. They were applied as FRET acceptors in homogeneous, time-gated immunoassays using Tb-antibodies as FRET donors, both coupled by an immunological sandwich complex between the two antibodies and a PSA (prostate specific antigen) biomarker. The advantages of the compact surface coating for FRET could be demonstrated by an 6.2 and 2.5 fold improvement of the limit of detection (LOD) for PSA compared to commercially available hydrophilic QDs emitting at 605 and 705 nm, respectively. While the commercial QDs contain identical inorganic cores responsible for their fluorescence, they are coated with a comparably thick amphiphilic polymer layer leading to much larger hydrodynamic diameters (>26 nm without biomolecules). The LODs of 0.8 and 3.7 ng mL(-1) obtained in 50 μL serum samples are below the clinical cut-off level of PSA (4 ng mL(-1)) and demonstrate their direct applicability in clinical diagnostics.

Quantum coherence and correlations in quantum system

PubMed Central

Xi, Zhengjun; Li, Yongming; Fan, Heng

2015-01-01

Criteria of measure quantifying quantum coherence, a unique property of quantum system, are proposed recently. In this paper, we first give an uncertainty-like expression relating the coherence and the entropy of quantum system. This finding allows us to discuss the relations between the entanglement and the coherence. Further, we discuss in detail the relations among the coherence, the discord and the deficit in the bipartite quantum system. We show that, the one-way quantum deficit is equal to the sum between quantum discord and the relative entropy of coherence of measured subsystem. PMID:26094795

Dissipative quantum computing with open quantum walks

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

Sinayskiy, Ilya; Petruccione, Francesco

An open quantum walk approach to the implementation of a dissipative quantum computing scheme is presented. The formalism is demonstrated for the example of an open quantum walk implementation of a 3 qubit quantum circuit consisting of 10 gates.

Student Measurements of STFA 10AB (Theta Tauri)

NASA Astrophysics Data System (ADS)

Gillette, Sean; Estrada, Chris; Estrada, Reed; Aguilera, Sophia; Chavez, Valerie; Givens, Jalynn; Lindorfer, Sarah; Michels, Kaylie; Mobley, Makenzie; Reder, Gabriel; Renteria, Kayla; Shattles, Jenna; Wilkin, Aiden; Woodbury, Maisy; Rhoades, Breauna; Rhoades, Mark

2017-04-01

Eighth grade students at Vanguard Preparatory School measured the double star STFA 10AB using a 22-inch Newtonian Alt/Az telescope and a Celestron Micro Guide eyepiece. Bellatrix was used as the calibration star. The calculated means of multiple observations of STFA 10AB resulted in a separation of 45.18,” a scale constant of 7.88 arcseconds per division, and position angle of 257.9°. These measurements were compared to the most recent values in the Washington Double Star Catalog.

Full Wave Function Optimization with Quantum Monte Carlo and Its Effect on the Dissociation Energy of FeS.

PubMed

Haghighi Mood, Kaveh; Lüchow, Arne

2017-08-17

Diffusion quantum Monte Carlo calculations with partial and full optimization of the guide function are carried out for the dissociation of the FeS molecule. For the first time, quantum Monte Carlo orbital optimization for transition metal compounds is performed. It is demonstrated that energy optimization of the orbitals of a complete active space wave function in the presence of a Jastrow correlation function is required to obtain agreement with the experimental dissociation energy. Furthermore, it is shown that orbital optimization leads to a 5 Δ ground state, in agreement with experiments but in disagreement with other high-level ab initio wave function calculations which all predict a 5 Σ + ground state. The role of the Jastrow factor in DMC calculations with pseudopotentials is investigated. The results suggest that a large Jastrow factor may improve the DMC accuracy substantially at small additional cost.

Prediction of folding preference of 10 kDa silk-like proteins using a Lego approach and ab initio calculations.

PubMed

Pohl, Gábor; Beke, Tamás; Borbély, János; Perczel, András

2006-11-15

Because of their great flexibility and strength resistance, both spider silks and silkworm silks are of increasing scientific and commercial interest. Despite numerous spectroscopic and theoretical studies, several structural properties at the atomic level have yet to be identified. The present theoretical investigation focuses on these issues by studying three silk-like model peptides: (AG)(64), [(AG)(4)EG](16), and [(AG)(4)PEG](16), using a Lego-type approach to construct these polypeptides. On the basis of these examples it is shown that thermoneutral isodesmic reactions and ab initio calculations provide a capable method to investigate structural properties of repetitive polypeptides. The most probable overall fold schema of these molecules with respect to the type of embedded hairpin structures were determined at the ab initio level of theory (RHF/6-311++G(d,p)//RHF/3-21G). Further on, analysis is carried out on the possible hairpin and turn regions and on their effect on the global fold. In the case of the (AG)(64) model peptide, the optimal beta-sheet/turn ratio was also determined, which provided good support for experimental observations. In addition, lateral shearing of a hairpin "folding unit" was investigated at the quantum chemical level to explain the mechanical properties of spider silk. The unique mechanical characteristics of silk bio-compounds are now investigated at the atomic level.

Quantum mechanical force fields for condensed phase molecular simulations

NASA Astrophysics Data System (ADS)

Giese, Timothy J.; York, Darrin M.

2017-09-01

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

(abstract) Studies on AB(sub 5) Metal Hydride Alloys with Sn Additives

NASA Technical Reports Server (NTRS)

Ratnakumar, B. V.; Surampudi, S.; Stefano, S. Di; Halpert, G.; Witham, C.; Fultz, B.

1994-01-01

The use of metal hydrides as negative electrodes in alkaline rechargeable cells is becoming increasingly popular, due to several advantages offered by the metal hydrides over conventional anode materials (such as Zn, Cd) in terms of specific energy environmental cycle life and compatibility. Besides, the similarities in the cell voltage pressure characteristics, and charge control methods of the Ni-MH cells to the commonly used Ni-Cd point to a projected take over of 25% of the Ni-Cd market for consumer electronics by the Ni-MH cells in the next couple of years. Two classes of metal hydrides alloys based on rare earth metals (AB(sub 5)) and titanium (AB(sub 2)) are being currently developed at various laboratories. AB(sub 2) alloys exhibit higher specific energy than the AB(sub 5) alloys but the state of the art commercial Ni-MH cells are predominately manufactured using AB(sub 5) alloys.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Overexpression of the ABC transporter AvtAB increases avermectin production in Streptomyces avermitilis.

PubMed

Qiu, Jingfan; Zhuo, Ying; Zhu, Dongqing; Zhou, Xiufen; Zhang, Lixin; Bai, Linquan; Deng, Zixin

2011-10-01

Avermectins are 16-membered macrocyclic polyketides with potent antiparasitic activities, produced by Streptomyces avermitilis. Upstream of the avermectin biosynthetic gene cluster, there is the avtAB operon encoding the ABC transporter AvtAB, which is highly homologous to the mammalian multidrug efflux pump P-glycoprotein (Pgp). Inactivation of avtAB had no effect, but increasing the concentration of avtAB mRNA 30-500-fold, using a multi-copy plasmid in S. avermitilis, enhanced avermectin production about two-fold both in the wild-type and in a high-yield producer strain on agar plates. In liquid industrial fermentation medium, the overall productivity of avermectin B1a in the engineered high-yield producer was improved for about 50%, from 3.3 to 4.8 g/l. In liquid YMG medium, moreover, the ratio of intracellular to extracellular accumulation of avermectin B1a was dropped from 6:1 to 4.5:1 in response to multiple copies of avtAB. Additionally, the overexpression of avtAB did not cause any increased expression of the avermectin biosynthetic genes through RT-PCR analysis. We propose that the AvtAB transporter exports avermectin, and thus reduces the feedback inhibition on avermectin production inside the cell. This strategy may be useful for enhancing the production of other antibiotics.

Towards Accurate Ab Initio Predictions of the Spectrum of Methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Kwak, Dochan (Technical Monitor)

2001-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

The adnAB Locus, Encoding a Putative Helicase-Nuclease Activity, Is Essential in Streptomyces

PubMed Central

Zhang, Lingli; Nguyen, Hoang Chuong; Chipot, Ludovic; Piotrowski, Emilie; Bertrand, Claire

2014-01-01

Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB, and newly discovered Mycobacterium tuberculosis AdnAB. Here we show that in Streptomyces, neither recBCD nor addAB homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to M. tuberculosis adnAB genes. These genes are conserved as a single copy in all sequenced genomes of Streptomyces. The disruption of adnAB in Streptomyces ambofaciens and Streptomyces coelicolor could not be achieved unless an ectopic copy was provided, indicating that adnAB is essential for growth. Both adnA and adnB genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of S. ambofaciens adnAB genes in an E. coli recB mutant restored viability and resistance to UV light, suggesting that Streptomyces AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance. PMID:24837284

AB 1725: A Comprehensive Analysis.

ERIC Educational Resources Information Center

California Community Colleges, Sacramento. Board of Governors.

A summary and analysis is provided of California Assembly Bill (AB) 1725, a reform bill that provides new direction and support for the state's community colleges. The analysis addresses each of the eight sections of the bill: (1) mission, highlighting reforms related to mission statements, transfer core curriculum, remedial limits, articulation…

Pseudosymmetric features of non-centrosymmetric AB type crystals

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

Gazhulina, A.P., E-mail: asyagazhulina@yandex.ru; Marychev, M.O.

2016-07-15

This work is supplement to our previous investigation (Gazhulina and Marychev, 2015) [1]. We have considered pseudosymmetric features with respect to the operation of inversion (pseudoinversion) for 340 non-centrosymmetric AB type crystals. Analysis of the features of particular structure types allowed us to determine the positions of pseudoinversion centers, subdivide them into separate types, and classify the entire set of crystals studied with respect to the types of pseudoinversion centers and peculiarities of the behavior of the degree of pseudoinversion depending on the ratio of atomic numbers of A and B components. For each group of crystals, average values andmore » lower boundaries of the maximum pseudoinversion are determined and distribution with respect to the degree of pseudoinversion is constructed. - Graphical abstract: A group of 340 non-centrosymmetric AB type crystals have been considered for their pseudosymmetry features with respect to the operation of inversion. Positions of pseudoinversion centers, subdivision of them into separate types, classification of the entire set of crystals studied with respect to the types of pseudoinversion centers and peculiarities of the behavior of the degree of pseudoinversion are established and discussed. Display Omitted - Highlights: • We consider pseudoinversion of 340 non-centrosymmetric AB type crystals. • AB type crystals are divided into three groups with respect to pseudoinversion. • Positions and types of pseudoinversion centers are determined. • Lower boundaries of the maximum pseudoinversion are determined.« less

Quantum molecular dynamics simulation of structural and thermodynamic properties of NiAl

NASA Astrophysics Data System (ADS)

Karchevskaya, E. S.; Minakov, D. V.; Levashov, P. R.

2018-01-01

In this work, structural and thermodynamic properties of a solid and liquid Ni-Al compound are studied using an ab initio method of quantum molecular dynamics (QMD). Simulations were carried out in 700-3000 K temperature range at atmospheric pressure. Radial distribution functions are analyzed to determine the presence of Ni-Al chemical bonds. Diffusion coefficients for individual components are also calculated. Another goal of this work is the investigation of the reaction propagation in thermally-initiated Ni-Al foils. For this purpose, we performed QMD simulations of Ni-Al layers in the microcanonical ensemble. An exothermic reaction between the solid Ni-Al layers is observed in our simulations at temperature less than the melting temperatures of the components.

QUANTUM: The Exhibition - quantum at the museum

NASA Astrophysics Data System (ADS)

Laforest, Martin; Olano, Angela; Day-Hamilton, Tobi

Distilling the essence of quantum phenomena, and how they are being harnessed to develop powerful quantum technologies, into a series of bite-sized, elementary-school-level pieces is what the scientific outreach team at the University of Waterloo's Institute for Quantum Computing was tasked with. QUANTUM: The Exhibition uses a series of informational panels, multimedia and interactive displays to introduce visitors to quantum phenomena and how they will revolutionize computing, information security and sensing. We'll discuss some of the approaches we took to convey the essence and impact of quantum mechanics and technologies to a lay audience while ensuring scientific accuracy.

Quantum thermodynamics of general quantum processes.

PubMed

Binder, Felix; Vinjanampathy, Sai; Modi, Kavan; Goold, John

2015-03-01

Accurately describing work extraction from a quantum system is a central objective for the extension of thermodynamics to individual quantum systems. The concepts of work and heat are surprisingly subtle when generalizations are made to arbitrary quantum states. We formulate an operational thermodynamics suitable for application to an open quantum system undergoing quantum evolution under a general quantum process by which we mean a completely positive and trace-preserving map. We derive an operational first law of thermodynamics for such processes and show consistency with the second law. We show that heat, from the first law, is positive when the input state of the map majorizes the output state. Moreover, the change in entropy is also positive for the same majorization condition. This makes a strong connection between the two operational laws of thermodynamics.

Quantum simulations with noisy quantum computers

NASA Astrophysics Data System (ADS)

Gambetta, Jay

Quantum computing is a new computational paradigm that is expected to lie beyond the standard model of computation. This implies a quantum computer can solve problems that can't be solved by a conventional computer with tractable overhead. To fully harness this power we need a universal fault-tolerant quantum computer. However the overhead in building such a machine is high and a full solution appears to be many years away. Nevertheless, we believe that we can build machines in the near term that cannot be emulated by a conventional computer. It is then interesting to ask what these can be used for. In this talk we will present our advances in simulating complex quantum systems with noisy quantum computers. We will show experimental implementations of this on some small quantum computers.