Sample records for quantum mechanical-molecular mechanical

  1. Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations.

    PubMed

    Lin, Hai; Zhao, Yan; Tishchenko, Oksana; Truhlar, Donald G

    2006-09-01

    The multiconfiguration molecular mechanics (MCMM) method is a general algorithm for generating potential energy surfaces for chemical reactions by fitting high-level electronic structure data with the help of molecular mechanical (MM) potentials. It was previously developed as an extension of standard MM to reactive systems by inclusion of multidimensional resonance interactions between MM configurations corresponding to specific valence bonding patterns, with the resonance matrix element obtained from quantum mechanical (QM) electronic structure calculations. In particular, the resonance matrix element is obtained by multidimensional interpolation employing a finite number of geometries at which electronic-structure calculations of the energy, gradient, and Hessian are carried out. In this paper, we present a strategy for combining MCMM with hybrid quantum mechanical molecular mechanical (QM/MM) methods. In the new scheme, electronic-structure information for obtaining the resonance integral is obtained by means of hybrid QM/MM calculations instead of fully QM calculations. As such, the new strategy can be applied to the studies of very large reactive systems. The new MCMM scheme is tested for two hydrogen-transfer reactions. Very encouraging convergence is obtained for rate constants including tunneling, suggesting that the new MCMM method, called QM/MM-MCMM, is a very general, stable, and efficient procedure for generating potential energy surfaces for large reactive systems. The results are found to converge well with respect to the number of Hessians. The results are also compared to calculations in which the resonance integral data are obtained by pure QM, and this illustrates the sensitivity of reaction rate calculations to the treatment of the QM-MM border. For the smaller of the two systems, comparison is also made to direct dynamics calculations in which the potential energies are computed quantum mechanically on the fly.

  2. Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM)

    NASA Astrophysics Data System (ADS)

    Sinitskiy, Anton V.; Voth, Gregory A.

    2018-01-01

    Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

  3. Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).

    PubMed

    Sinitskiy, Anton V; Voth, Gregory A

    2018-01-07

    Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

  4. Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism.

    PubMed

    Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

    2016-10-11

    The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S N 1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

  5. Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

    PubMed

    Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

    2016-09-13

    We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

  6. Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

    PubMed

    Tvaroška, Igor

    2015-02-11

    Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Combined quantum and molecular mechanics (QM/MM).

    PubMed

    Friesner, Richard A

    2004-12-01

    We describe the current state of the art of mixed quantum mechanics/molecular mechanics (QM/MM) methodology, with a particular focus on modeling of enzymatic reactions. Over the past decade, the effectiveness of these methods has increased dramatically, based on improved quantum chemical methods, advances in the description of the QM/MM interface, and reductions in the cost/performance of computing hardware. Two examples of pharmaceutically relevant applications, cytochrome P450 and class C β-lactamase, are presented.: © 2004 Elsevier Ltd . All rights reserved.

  8. A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1.

    PubMed

    Zhu, Kongkai; Lu, Junyan; Liang, Zhongjie; Kong, Xiangqian; Ye, Fei; Jin, Lu; Geng, Heji; Chen, Yong; Zheng, Mingyue; Jiang, Hualiang; Li, Jun-Qian; Luo, Cheng

    2013-03-01

    New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a major global threat to human health for its rapid rate of dissemination and ability to make pathogenic microbes resistant to almost all known β-lactam antibiotics. In addition, effective NDM-1 inhibitors have not been identified to date. In spite of the plethora of structural and kinetic data available, the accurate molecular characteristics of and details on the enzymatic reaction of NDM-1 hydrolyzing β-lactam antibiotics remain incompletely understood. In this study, a combined computational approach including molecular docking, molecular dynamics simulations and quantum mechanics/molecular mechanics calculations was performed to characterize the catalytic mechanism of meropenem catalyzed by NDM-1. The quantum mechanics/molecular mechanics results indicate that the ionized D124 is beneficial to the cleavage of the C-N bond within the β-lactam ring. Meanwhile, it is energetically favorable to form an intermediate if no water molecule coordinates to Zn2. Moreover, according to the molecular dynamics results, the conserved residue K211 plays a pivotal role in substrate binding and catalysis, which is quite consistent with previous mutagenesis data. Our study provides detailed insights into the catalytic mechanism of NDM-1 hydrolyzing meropenem β-lactam antibiotics and offers clues for the discovery of new antibiotics against NDM-1 positive strains in clinical studies.

  9. Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

    PubMed

    Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

    2017-07-21

    In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

  10. Simulation with quantum mechanics/molecular mechanics for drug discovery.

    PubMed

    Barbault, Florent; Maurel, François

    2015-10-01

    Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

  11. Simulation with quantum mechanics/molecular mechanics for drug discovery.

    PubMed

    Barbault, Florent; Maurel, François

    2015-08-08

    Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. Areas covered: In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. Expert opinion: QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

  12. Exact and Optimal Quantum Mechanics/Molecular Mechanics Boundaries.

    PubMed

    Sun, Qiming; Chan, Garnet Kin-Lic

    2014-09-09

    Motivated by recent work in density matrix embedding theory, we define exact link orbitals that capture all quantum mechanical (QM) effects across arbitrary quantum mechanics/molecular mechanics (QM/MM) boundaries. Exact link orbitals are rigorously defined from the full QM solution, and their number is equal to the number of orbitals in the primary QM region. Truncating the exact set yields a smaller set of link orbitals optimal with respect to reproducing the primary region density matrix. We use the optimal link orbitals to obtain insight into the limits of QM/MM boundary treatments. We further analyze the popular general hybrid orbital (GHO) QM/MM boundary across a test suite of molecules. We find that GHOs are often good proxies for the most important optimal link orbital, although there is little detailed correlation between the detailed GHO composition and optimal link orbital valence weights. The optimal theory shows that anions and cations cannot be described by a single link orbital. However, expanding to include the second most important optimal link orbital in the boundary recovers an accurate description. The second optimal link orbital takes the chemically intuitive form of a donor or acceptor orbital for charge redistribution, suggesting that optimal link orbitals can be used as interpretative tools for electron transfer. We further find that two optimal link orbitals are also sufficient for boundaries that cut across double bonds. Finally, we suggest how to construct "approximately" optimal link orbitals for practical QM/MM calculations.

  13. An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent.

    PubMed

    Watanabe, Hiroshi C; Banno, Misa; Sakurai, Minoru

    2016-03-14

    Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method". In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.

  14. Application of high level wavefunction methods in quantum mechanics/molecular mechanics hybrid schemes.

    PubMed

    Mata, Ricardo A

    2010-05-21

    In this Perspective, several developments in the field of quantum mechanics/molecular mechanics (QM/MM) approaches are reviewed. Emphasis is placed on the use of correlated wavefunction theory and new state of the art methods for the treatment of large quantum systems. Until recently, computational chemistry approaches to large/complex chemical problems have seldom been considered as tools for quantitative predictions. However, due to the tremendous development of computational resources and new quantum chemical methods, it is nowadays possible to describe the electronic structure of biomolecules at levels of theory which a decade ago were only possible for system sizes of up to 20 atoms. These advances are here outlined in the context of QM/MM. The article concludes with a short outlook on upcoming developments and possible bottlenecks for future applications.

  15. Quantum mechanical/molecular mechanical/continuum style solvation model: time-dependent density functional theory.

    PubMed

    Thellamurege, Nandun M; Cui, Fengchao; Li, Hui

    2013-08-28

    A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state.

  16. Quantum Mechanical Studies of Molecular Hyperpolarizabilities.

    DTIC Science & Technology

    1980-04-30

    exponent , reflects the screening of an electron in a given orbital by the interior electrons in the atom or molecule. In practice, when studying...Basis sets have evolved over the years in molecular quantum mechanics until sets of orbital exponents for the different atoms composing the molecule have...and R. P. Hurst , J. Chem. Phys. 46, 2356 (1967); S. P. LickmannI and J. W. Moskowitz, J. Chem. Phys. 54, 3622 7T971). 26. T. H. Dunning, J. Chem. Phys

  17. 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.

  18. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    PubMed

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  19. 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.

  20. Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations.

    PubMed

    Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino

    2016-06-27

    This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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.

  2. Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

    PubMed

    Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao

    2013-09-10

    Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

  3. Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

    NASA Astrophysics Data System (ADS)

    Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

    2017-12-01

    In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

  4. Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

    PubMed

    Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

    2017-12-28

    In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

  5. Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling.

    PubMed

    Lodola, Alessio; Mor, Marco; Sirirak, Jitnapa; Mulholland, Adrian J

    2009-04-01

    FAAH (fatty acid amide hydrolase) is a promising target for the treatment of several central nervous system and peripheral disorders. Combined QM/MM (quantum mechanics/molecular mechanics) calculations have elucidated the role of its unusual catalytic triad in the hydrolysis of oleamide and oleoylmethyl ester substrates, and have identified the productive inhibitor-binding orientation for the carbamoylating compound URB524. These are potentially crucial insights for designing new covalent inhibitors of this drug target.

  6. Water Assisted Reaction Mechanism of OH- with CCl4 in Aqueous Solution - Hybrid Quantum Mechanical and Molecular Mechanics Investigation

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

    Chen, Jie; Yin, Hongyun; Wang, Dunyou

    2013-02-20

    The OH- (H2O) + CCl4 reaction in aqueous solution was investigated using the combined quantum mechanical and molecular mechanics approach. The reaction mechanism of OH- (H2O) + CCl4 consists of two concerted steps - formation of OH- in the favorable attack conformation via the proton transfer process, and the nucleophilic substitution process in which the newly formed OH- attacks the CCl4. The free energy activation barrier is 38.2 kcal/mol at CCSD(T)/MM level of theory for this reaction, which is about 10.3 kcal/mol higher than that of the direct nucleophilic substitution mechanism of the OH- + CCl4 reaction in aqueous solution.

  7. 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

  8. Epigenetics: Biology's Quantum Mechanics

    PubMed Central

    Jorgensen, Richard A.

    2011-01-01

    The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920s and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene – the molecular biological view and the epigenetic view – are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider. PMID:22639577

  9. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  10. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.

    PubMed

    Quesne, Matthew G; Borowski, Tomasz; de Visser, Sam P

    2016-02-18

    Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations.

    PubMed

    Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco

    2016-09-13

    The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.

  12. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

    PubMed

    Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

    2015-01-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations of the thiopurine S-methyltransferase reaction with 6-mercaptopurine.

    PubMed

    Pan, Xiao-Liang; Cui, Feng-Chao; Liu, Jing-Yao

    2011-06-23

    Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the methylation of 6-mercaptopurine catalyzed by thiopurine S-methyltransferase. Several setups with different tautomeric forms and orientations of the substrate were considered. It is found that, with the orientation in chain A of the X-ray structure, the substrate can form an ideal near-attack configuration for the methylation reaction, which may take place after the deprotonation of the substrate by the conserved residue Asp23 through a water chain. The potential of mean force (PMF) of the methyl-transfer step for the most favorable pathway is 19.6 kcal/mol, which is in good agreement with the available experimental rate constant data.

  14. Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

    PubMed

    Świderek, Katarzyna; Arafet, Kemel; Kohen, Amnon; Moliner, Vicent

    2017-03-14

    Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid quantum mechanics/molecular mechanics (QM/MM) potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE). Dynamics and quantum-tunneling effects are revealed to have little effect on the reaction rate, but are significant in determining the KIEs and their temperature dependence. A good agreement with experiments is found, especially when computed for RM1/MM simulations. The small temperature dependence of quantum tunneling corrections and the quasiclassical contribution term cancel each other, while the recrossing transmission coefficient seems to be temperature-independent over the interval of 5-40 °C.

  15. Insights into the catalytic mechanism of dehydrogenase BphB: A quantum mechanics/molecular mechanics study.

    PubMed

    Zhang, Ruiming; Shi, Xiangli; Sun, Yanhui; Zhang, Qingzhu; Wang, Wenxing

    2018-05-17

    The present study delineated the dehydrogenation mechanism of cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) and cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl (2,3-DD-4,4'-DBPH) by Pandoraea pnomenusa strain B-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) in atomistic detail. The enzymatic process was investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Five different snapshots were extracted and calculated, which revealed that the Boltzmann-weighted average barriers of 2,3-DDBPH and 2,3-DD-4,4'-DBPH dehydrogenation processes are 10.7 and 11.5 kcal mol -1 , respectively. The established dehydrogenation mechanism provides new insight into the degradation processes of other chlorinated 2,3-DDBPH. In addition to Asn115, Ser142, and Lys149, the importance of Ile 89, Asn143, Pro184, Met 187, Thr189, and Lue 191 during the dehydrogenation process of 2,3-DDBPH and 2,3-DD-4,4'-DBPH were also highlighted to search for promising mutation targets for improving the catalytic efficiency of BphB. Copyright © 2018. Published by Elsevier Ltd.

  16. Phosphorylation Reaction in cAPK Protein Kinase - Free Energy Quantum Mechanic/Molecular Mechanics Simulations.

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

    Valiev, Marat; Yang, Jie; Adams, Joseph

    2007-11-29

    Protein kinases catalyze the transfer of the γ-phosphoryl group from ATP, a key regulatory process governing signalling pathways in eukaryotic cells. The structure of the active site in these enzymes is highly conserved implying common catalytic mechanism. In this work we investigate the reaction process in cAPK protein kinase (PKA) using a combined quantum mechanics and molecular mechanics approach. The novel computational features of our work include reaction pathway determination with nudged elastic band methodology and calculation of free energy profiles of the reaction process taking into account finite temperature fluctuations of the protein environment. We find that the transfermore » of the γ-phosphoryl group in the protein environment is an exothermic reaction with the reaction barrier of 15 kcal/mol.« less

  17. Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations.

    PubMed

    Rosnik, Andreana M; Curutchet, Carles

    2015-12-08

    Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.

  18. Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations.

    PubMed

    Zou, Yi; Wang, Fang; Wang, Yan; Guo, Wenjie; Zhang, Yihua; Xu, Qiang; Lai, Yisheng

    2017-05-05

    Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations. Secondly, molecular dynamics (MD) simulations and MM/PBSA free energy calculations were employed to determine the dynamic binding process and crucial residues were confirmed through close contact analysis, hydrogen-bond analysis and binding free energy decomposition calculations. Subsequent quantum mechanics and nonbonding interaction analysis were carried out to provide in-depth explanations on the critical role of those key residues, and Arg231 and 7-propionate of the heme group were major contributors to ligand binding, which lowed a great amount of interaction energy. We anticipate that these findings will be valuable for enzymatic studies and rational drug design. Copyright © 2017. Published by Elsevier Masson SAS.

  19. A quantum-mechanics molecular-mechanics scheme for extended systems

    NASA Astrophysics Data System (ADS)

    Hunt, Diego; Sanchez, Veronica M.; Scherlis, Damián A.

    2016-08-01

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

  20. A quantum-mechanics molecular-mechanics scheme for extended systems.

    PubMed

    Hunt, Diego; Sanchez, Veronica M; Scherlis, Damián A

    2016-08-24

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

  1. Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations.

    PubMed

    Álvarez-Barcia, Sonia; Kästner, Johannes

    2017-06-01

    Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe═O cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value.

  2. Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase.

    PubMed

    Jitonnom, Jitrayut; Mujika, Jon I; van der Kamp, Marc W; Mulholland, Adrian J

    2017-12-05

    Creatininase catalyzes the conversion of creatinine (a biosensor for kidney function) to creatine via a two-step mechanism: water addition followed by ring opening. Water addition is common to other known cyclic amidohydrolases, but the precise mechanism for ring opening is still under debate. The proton donor in this step is either His178 or a water molecule bound to one of the metal ions, and the roles of His178 and Glu122 are unclear. Here, the two possible reaction pathways have been fully examined by means of combined quantum mechanics/molecular mechanics simulations at the SCC-DFTB/CHARMM22 level of theory. The results indicate that His178 is the main catalytic residue for the whole reaction and explain its role as proton shuttle during the ring-opening step. In the first step, His178 provides electrostatic stabilization to the gem-diolate tetrahedral intermediate. In the second step, His178 abstracts the hydroxyl proton of the intermediate and delivers it to the cyclic amide nitrogen, leading to ring opening. The latter is the rate-limiting step with a free energy barrier of 18.5 kcal/mol, in agreement with the experiment. We find that Glu122 must be protonated during the enzyme reaction, so that it can form a stable hydrogen bond with its neighboring water molecule. Simulations of the E122Q mutant showed that this replacement disrupts the H-bond network formed by three conserved residues (Glu34, Ser78, and Glu122) and water, increasing the energy barrier. Our computational studies provide a comprehensive explanation for previous structural and kinetic observations, including why the H178A mutation causes a complete loss of activity but the E122Q mutation does not.

  3. Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study.

    PubMed

    Mondal, Padmabati; Granucci, Giovanni; Rastädter, Dominique; Persico, Maurizio; Burghardt, Irene

    2018-05-28

    The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans -to- cis isomerization is slowed down to a time scale of ∼10-15 picoseconds, in contrast to 500 femtoseconds in vacuo , with a quantum yield reduced by a factor of two. By contrast, cis -to- trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis -azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

  4. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

    DOE PAGES

    Huang, Jing; Mei, Ye; König, Gerhard; ...

    2017-01-24

    Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

  5. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

    PubMed

    Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

    2017-02-14

    In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

  6. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

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

    Huang, Jing; Mei, Ye; König, Gerhard

    Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

  7. A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) study on Ornithine Cyclodeaminase (OCD): a tale of two iminiums.

    PubMed

    Ion, Bogdan F; Bushnell, Eric A C; Luna, Phil De; Gauld, James W

    2012-10-11

    Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine's C(α)-H group to the NAD+ cofactor with concomitant formation of a C(α)=NH(2)+ Schiff base with a barrier of 90.6 kJ mol-1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the C(α)=NH(2)+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the C(α)-position. This is then followed by cleavage and loss of the α-NH(2) group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.

  8. A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

    PubMed Central

    Ion, Bogdan F.; Bushnell, Eric A. C.; De Luna, Phil; Gauld, James W.

    2012-01-01

    Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2 + Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2 + intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. PMID:23202934

  9. Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

    PubMed

    Bayse, Craig A; Merz, Kenneth M

    2014-08-05

    Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.

  10. Inactivation of TEM-1 by avibactam (NXL-104): insights from quantum mechanics/molecular mechanics metadynamics simulations.

    PubMed

    Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco; Colombo, Giorgio

    2014-08-12

    The fast and constant development of drug-resistant bacteria represents a serious medical emergence. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this context, avibactam represents a promising, innovative inhibitor of beta-lactamases with a novel molecular structure compared to previously developed inhibitors, showing a promising inhibitory activity toward a significant number of beta-lactamase enzymes. In this work, we studied, at the atomistic level, the mechanisms of formation of the covalent complex between avibactam and TEM-1, an experimentally well-characterized class A beta-lactamase, using classical and quantum mechanics/molecular mechanics (QM/MM) simulations combined with metadynamics. Our simulations provide a detailed structural and energetic picture of the molecular steps leading to the formation of the avibactam/TEM-1 covalent adduct. In particular, they support a mechanism in which the rate-determining step is the water-assisted Glu166 deprotonation by Ser70. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements. Additionally, our simulations highlight the important role of Lys73 in assisting the Ser70 and Ser130 deprotonations. While based on the specific case of the avibactam/TEM-1, the simple protocol we present here can be immediately extended and applied to the study of covalent complex formation in different enzyme-inhibitor pairs.

  11. Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution.

    PubMed

    Melkikh, Alexey V; Khrennikov, Andrei

    2017-11-01

    A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Enzymatic studies using quantum mechanical and molecular mechanical techniques

    NASA Astrophysics Data System (ADS)

    Faulder, Paul F.

    Enzymes have evolved to increase the rate of biological reactions using fundamental physical processes. Until recently, the nature of catalysis has been based upon a classical model but it has since been considered that certain aspects of catalysis, particularly those concerning the transfer of a hydrogen species, may be accounted for using the theory of quantum mechanics. This thesis reports the use of reaction paths obtained using QMMM (combined quantum mechanics-molecular mechanics), combined with canonical variational transition state theory and multidimensional tunnelling corrections, to study two dehydrogenase enzymes, Liver Alcohol Dehydrogenase (LADH) and Methylamine Dehydrogenase (MADH). These methods are used to investigate the nature of these models in explaining reported experimental data indicative of quantum mechanical tunnelling within these enzymes. The results obtained are in good agreement with experimental data indicating the presence of tunnelling in LADH and, to a greater degree, in MADH, reflected in the magnitude of the calculated kinetic isotope effects (KIEs). For LADH, a primary tritium KIE of 5.6 is reported, calculated using transition state theory (TST) with a Wigner tunnelling correction, and compares favourably with an experimental value of 7.1. For MADH, a KIE of 11.1 was determined using canonical variational theory (CVT) with a small curvature tunnelling (SCT) correction, and compared favourably with an experimental value of 16.8. In addition, a relationship is observed between the contribution due to tunnelling in each system and the geometric positioning of the donating and accepting atoms of the transferring species, and is in qualitative agreement with current opinion concerning tunnelling and the dynamic nature of catalysis. Potential energy barriers have been obtained for both systems using QMMM. For LADH, barriers of 8.2 kcal mol-1 and 22.0 kcal mol-1, and reaction energies of -25.7 kcal mol-1 and +3.4 kcal mol-1, are

  13. Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2.

    PubMed

    Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik; Harvey, Jeremy N; Mulholland, Adrian J

    2016-06-20

    The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site, but this is not a prerequisite for reaction via either mechanism. Several active site residues play a role in the binding of mexiletine in the active site, including Thr124 and Phe226. This work reveals key details of the N-hydroxylation of mexiletine and further demonstrates that mechanistic studies using QM/MM methods are useful for understanding drug metabolism.

  14. Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II.

    PubMed

    Sproviero, Eduardo M; Gascón, José A; McEvoy, James P; Brudvig, Gary W; Batista, Victor S

    2007-04-01

    The annual production of 260 Gtonnes of oxygen, during the process of photosynthesis, sustains life on earth. Oxygen is produced in the thylakoid membranes of green-plant chloroplasts and the internal membranes of cyanobacteria by photocatalytic water oxidation at the oxygen-evolving complex (OEC) of photosystem II (PSII). Recent breakthroughs in X-ray crystallography and advances in quantum mechanics/molecular mechanics (QM/MM) hybrid methods have enabled the construction of chemically sensible models of the OEC of PSII. The resulting computational structural models suggest the complete ligation of the catalytic center by amino acid residues, water, hydroxide and chloride, as determined from the intrinsic electronic properties of the oxomanganese core and the perturbational influence of the surrounding protein environment. These structures are found to be consistent with available mechanistic data, and are also compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements. It is therefore conjectured that these OEC models are particularly relevant for the elucidation of the catalytic mechanism of water oxidation.

  15. Combined quantum mechanical and molecular mechanical method for metal-organic frameworks: proton topologies of NU-1000.

    PubMed

    Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

    2018-01-17

    Metal-organic frameworks (MOFs) are materials with applications in catalysis, gas separations, and storage. Quantum mechanical (QM) calculations can provide valuable guidance to understand and predict their properties. In order to make the calculations faster, rather than modeling these materials as periodic (infinite) systems, it is useful to construct finite models (called cluster models) and use subsystem methods such as fragment methods or combined quantum mechanical and molecular mechanical (QM/MM) methods. Here we employ a QM/MM methodology to study one particular MOF that has been of widespread interest because of its wide pores and good solvent and thermal stability, namely NU-1000, which contains hexanuclear zirconium nodes and 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy 4- ) linkers. A modified version of the Bristow-Tiana-Walsh transferable force field has been developed to allow QM/MM calculations on NU-1000; we call the new parametrization the NU1T force field. We consider isomeric structures corresponding to various proton topologies of the [Zr 6 (μ 3 -O) 8 O 8 H 16 ] 8+ node of NU-1000, and we compute their relative energies using a QM/MM scheme designed for the present kind of problem. We compared the results to full quantum mechanical (QM) energy calculations and found that the QM/MM models can reproduce the full QM relative energetics (which span a range of 334 kJ mol -1 ) with a mean unsigned deviation (MUD) of only 2 kJ mol -1 . Furthermore, we found that the structures optimized by QM/MM are nearly identical to their full QM optimized counterparts.

  16. Role of Arg228 in the phosphorylation of galactokinase: the mechanism of GHMP kinases by quantum mechanics/molecular mechanics studies.

    PubMed

    Huang, Meilan; Li, Xiaozhou; Zou, Jian-Wei; Timson, David J

    2013-07-16

    GHMP kinases are a group of structurally related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalyzing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical, and biotechnological importance, the mechanism of GHMP kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the γ-phosphate of ATP close to an aspartate residue; however, for one GHMP family member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it was proposed by some authors that all the GHMP kinases function by a similar mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of the GHMP kinase family, was investigated using molecular dynamics simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using an adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 in the proximity of the α-phosphate of ATP, forming a H-bond network; therefore, the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the β,γ-bridging oxygen of the ATP during bond cleavage. The reaction occurs via a direct phosphorylation mechanism, and the Asp186 in the proximity of ATP does not directly participate in the reaction pathway. Because Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation, may be developed into potential selective inhibitors for galactokinase.

  17. Quantum mechanical/molecular mechanical/continuum style solvation model: second order Møller-Plesset perturbation theory.

    PubMed

    Thellamurege, Nandun M; Si, Dejun; Cui, Fengchao; Li, Hui

    2014-05-07

    A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

  18. Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

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

    Thellamurege, Nandun M.; Si, Dejun; Cui, Fengchao

    A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths ofmore » the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.« less

  19. Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl- + CH3I Reaction in Water.

    PubMed

    Liu, Peng; Li, Chen; Wang, Dunyou

    2017-10-19

    The Cl - + CH 3 I → CH 3 Cl + I - reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.

  20. Lorentz quantum mechanics

    NASA Astrophysics Data System (ADS)

    Zhang, Qi; Wu, Biao

    2018-01-01

    We present a theoretical framework for the dynamics of bosonic Bogoliubov quasiparticles. We call it Lorentz quantum mechanics because the dynamics is a continuous complex Lorentz transformation in complex Minkowski space. In contrast, in usual quantum mechanics, the dynamics is the unitary transformation in Hilbert space. In our Lorentz quantum mechanics, three types of state exist: space-like, light-like and time-like. Fundamental aspects are explored in parallel to the usual quantum mechanics, such as a matrix form of a Lorentz transformation, and the construction of Pauli-like matrices for spinors. We also investigate the adiabatic evolution in these mechanics, as well as the associated Berry curvature and Chern number. Three typical physical systems, where bosonic Bogoliubov quasi-particles and their Lorentz quantum dynamics can arise, are presented. They are a one-dimensional fermion gas, Bose-Einstein condensate (or superfluid), and one-dimensional antiferromagnet.

  1. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

    PubMed

    Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

    2015-03-05

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

  2. Quantum mechanical force field for water with explicit electronic polarization.

    PubMed

    Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

    2013-08-07

    A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across

  3. Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

    PubMed Central

    2015-01-01

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

  4. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

    DOE PAGES

    Sodt, Alexander J.; Mei, Ye; Konig, Gerhard; ...

    2014-10-16

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completelymore » avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.« less

  5. Autonomy, explanation, and theoretical values: physicists and chemists on molecular quantum mechanics.

    PubMed

    Hendry, Robin Findlay

    2003-05-01

    The emergence of quantum chemistry in the early twentieth century was an international as well as an interdisciplinary affair, involving dialogue between physicists and chemists in Germany, the United States, and Britain. Historians of science have recently documented both the causes and effects of this internationalism and interdisciplinarity. Chemists and physicists involved in the development of quantum chemistry in its first few decades tended to argue for opposing views on acceptable standards of explanation in their field, although the debate did not divide along disciplinary lines. The purpose of this paper is to investigate these different positions, through the methodological reflections of John Clarke Slater, Linus Pauling, and Charles Coulson. Slater tended to argue for quantum-mechanical rigor and the application of fundamental principles as the values guiding models of molecular bonding. Although they were on different sides of the debate between the valence-bond and molecular-orbital approaches, Pauling and Coulson both emphasized the recovery of traditional chemical explanations and systematic explanatory power within chemistry.

  6. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

    PubMed

    Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José

    2016-11-03

    The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

  7. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

    PubMed

    Ferenczy, György G

    2013-04-05

    The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem. Copyright © 2013 Wiley Periodicals, Inc.

  8. Hybrid Quantum Mechanical/Molecular Mechanics Study of the SN2 Reaction of CH3Cl+OH- in Water

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

    Yin, Hongyun; Wang, Dunyou; Valiev, Marat

    2011-11-03

    The SN2 mechanism for the reaction of CH3Cl + OH- in aqueous solution was investigated using combined quantum mechanical and molecular mechanics methodology. We analyzed structures of reactant, transition and product states along the reaction pathway. The free energy profile was calculated using the multi-layered representation with the DFT and CCSD(T) level of theory for the quantum-mechanical description of the reactive region. Our results show that the aqueous environment has a significant impact on the reaction process. We find that solvation energy contribution raises the reaction barrier by ~18.9 kcal/mol and the reaction free energy by ~24.5 kcal/mol. The presencemore » of the solvent also induces perturbations in the electronic structure of the solute leading to an increase of 3.5 kcal/mol for the reaction barrier and a decrease of 5.6 kcal/mol for the reaction free energy respectively. Combining the results of two previous calculation results on CHCl3 + OH- and CH2Cl2 + OH- reactions in water, we demonstrate that increase in the chlorination of the methyl group (from CH3Cl to CHCl3) is accompanied by the decrease in the free energy reaction barrier, with the CH3Cl + OH- having the largest barrier among the three reactions.« less

  9. 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.

  10. Testing Nonassociative Quantum Mechanics.

    PubMed

    Bojowald, Martin; Brahma, Suddhasattwa; Büyükçam, Umut

    2015-11-27

    The familiar concepts of state vectors and operators in quantum mechanics rely on associative products of observables. However, these notions do not apply to some exotic systems such as magnetic monopoles, which have long been known to lead to nonassociative algebras. Their quantum physics has remained obscure. This Letter presents the first derivation of potentially testable physical results in nonassociative quantum mechanics, based on effective potentials. They imply new effects which cannot be mimicked in usual quantum mechanics with standard magnetic fields.

  11. Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

    PubMed

    Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

    2015-12-03

    Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.

  12. Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

    PubMed

    Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

    2018-04-10

    Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of

  13. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

    PubMed

    Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; Luo, Ray; Lee, Taisung; Caldwell, James; Wang, Junmei; Kollman, Peter

    2003-12-01

    Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999-2012, 2003

  14. Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

    PubMed

    Ferrer, Silvia; Ruiz-Pernía, Javier; Martí, Sergio; Moliner, Vicent; Tuñón, Iñaki; Bertrán, Juan; Andrés, Juan

    2011-01-01

    The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary science that allows one to reach the molecular design of tailor-made enzyme catalysts. This is even more so when one refers to enzyme catalysts, for which the detailed structure and composition are known and can be manipulated to introduce well-defined residues which can be implicated in the chemical rearrangements taking place in the active site. The methods and techniques of theoretical and computational chemistry are becoming more and more important in both understanding the fundamental biological roles of enzymes and facilitating their utilization in biotechnology. Improvement of the catalytic function of enzymes is important from scientific and industrial viewpoints, and to put this fact in the actual perspective as well as the potentialities, we recommend the very recent report of Sanderson [Sanderson, K. (2011). Chemistry: enzyme expertise. Nature 471, 397.]. Great fundamental advances have been made toward the ab initio design of enzyme catalysts based on molecular modeling. This has been based on the molecular mechanistic knowledge of the reactions to be catalyzed, together with the development of advanced synthesis and characterization techniques. The corresponding molecular mechanism can be studied by means of powerful quantum chemical calculations. The catalytic

  15. Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms.

    PubMed

    Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

    2018-05-30

    Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

  16. 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

  17. Questioning quantum mechanics

    NASA Astrophysics Data System (ADS)

    Frappier, Mélanie

    2018-03-01

    A century after its inception, quantum mechanics continues to puzzle us with dead-and-alive cats, waves "collapsing" into particles, and "spooky action at a distance." In his first book, What Is Real?, science writer and astrophysicist Adam Becker sets out to explore why the physics community is still arguing today about quantum mechanics's true meaning.

  18. 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

  19. Quantum Mechanics From the Cradle?

    ERIC Educational Resources Information Center

    Martin, John L.

    1974-01-01

    States that the major problem in learning quantum mechanics is often the student's ignorance of classical mechanics and that one conceptual hurdle in quantum mechanics is its statistical nature, in contrast to the determinism of classical mechanics. (MLH)

  20. Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions

    NASA Astrophysics Data System (ADS)

    Ngaojampa, C.; Nimmanpipug, P.; Yu, L. D.; Anuntalabhochai, S.; Lee, V. S.

    2011-02-01

    In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation.

  1. Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study.

    PubMed

    Xu, Yulong; Zhang, Jingxue; Wang, Dunyou

    2015-06-28

    The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

  2. Investigation of the CH3Cl + CN- reaction in water: Multilevel quantum mechanics/molecular mechanics study

    NASA Astrophysics Data System (ADS)

    Xu, Yulong; Zhang, Jingxue; Wang, Dunyou

    2015-06-01

    The CH3Cl + CN- reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ˜11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

  3. Speakable and Unspeakable in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Bell, J. S.; Aspect, Introduction by Alain

    2004-06-01

    List of papers on quantum philosophy by J. S. Bell; Preface; Acknowledgements; Introduction by Alain Aspect; 1. On the problem of hidden variables in quantum mechanics; 2. On the Einstein-Rosen-Podolsky paradox; 3. The moral aspects of quantum mechanics; 4. Introduction to the hidden-variable question; 5. Subject and object; 6. On wave packet reduction in the Coleman-Hepp model; 7. The theory of local beables; 8. Locality in quantum mechanics: reply to critics; 9. How to teach special relativity; 10. Einstein-Podolsky-Rosen experiments; 11. The measurement theory of Everett and de Broglie's pilot wave; 12. Free variables and local causality; 13. Atomic-cascade photons and quantum-mechanical nonlocality; 14. de Broglie-Bohm delayed choice double-slit experiments and density matrix; 15. Quantum mechanics for cosmologists; 16. Bertlmann's socks and the nature of reality; 17. On the impossible pilot wave; 18. Speakable and unspeakable in quantum mechanics; 19. Beables for quantum field theory; 20. Six possible worlds of quantum mechanics; 21. EPR correlations and EPR distributions; 22. Are there quantum jumps?; 23. Against 'measurement'; 24. La Nouvelle cuisine.

  4. Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

    PubMed

    Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

    2014-11-20

    Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  5. Quantum mechanics/molecular mechanics study of the catalytic cycle of water splitting in photosystem II.

    PubMed

    Sproviero, Eduardo M; Gascón, José A; McEvoy, James P; Brudvig, Gary W; Batista, Victor S

    2008-03-19

    This paper investigates the mechanism of water splitting in photosystem II (PSII) as described by chemically sensible models of the oxygen-evolving complex (OEC) in the S0-S4 states. The reaction is the paradigm for engineering direct solar fuel production systems since it is driven by solar light and the catalyst involves inexpensive and abundant metals (calcium and manganese). Molecular models of the OEC Mn3CaO4Mn catalytic cluster are constructed by explicitly considering the perturbational influence of the surrounding protein environment according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, in conjunction with the X-ray diffraction (XRD) structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The resulting models are validated through direct comparisons with high-resolution extended X-ray absorption fine structure spectroscopic data. Structures of the S3, S4, and S0 states include an additional mu-oxo bridge between Mn(3) and Mn(4), not present in XRD structures, found to be essential for the deprotonation of substrate water molecules. The structures of reaction intermediates suggest a detailed mechanism of dioxygen evolution based on changes in oxidization and protonation states and structural rearrangements of the oxomanganese cluster and surrounding water molecules. The catalytic reaction is consistent with substrate water molecules coordinated as terminal ligands to Mn(4) and calcium and requires the formation of an oxyl radical by deprotonation of the substrate water molecule ligated to Mn(4) and the accumulation of four oxidizing equivalents. The oxyl radical is susceptible to nucleophilic attack by a substrate water molecule initially coordinated to calcium and activated by two basic species, including CP43-R357 and the mu-oxo bridge between Mn(3) and Mn(4). The reaction is concerted with water ligand exchange, swapping the activated water by a water molecule in the second coordination shell of

  6. Advanced Concepts in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Esposito, Giampiero; Marmo, Giuseppe; Miele, Gennaro; Sudarshan, George

    2014-11-01

    Preface; 1. Introduction: the need for a quantum theory; 2. Experimental foundations of quantum theory; 3. Waves and particles; 4. Schrödinger picture, Heisenberg picture and probabilistic aspects; 5. Integrating the equations of motion; 6. Elementary applications: 1-dimensional problems; 7. Elementary applications: multidimensional problems; 8. Coherent states and related formalism; 9. Introduction to spin; 10. Symmetries in quantum mechanics; 11. Approximation methods; 12. Modern pictures of quantum mechanics; 13. Formulations of quantum mechanics and their physical implications; 14. Exam problems; Glossary of geometric concepts; References; Index.

  7. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

    PubMed

    Ferenczy, György G

    2013-04-05

    Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods. Copyright © 2012 Wiley Periodicals, Inc.

  8. Locality and quantum mechanics.

    PubMed

    Unruh, W G

    2018-07-13

    It is argued that it is best not to think of quantum mechanics as non-local, but rather that it is non-realistic.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'. © 2018 The Author(s).

  9. Gaussian effective potential: Quantum mechanics

    NASA Astrophysics Data System (ADS)

    Stevenson, P. M.

    1984-10-01

    We advertise the virtues of the Gaussian effective potential (GEP) as a guide to the behavior of quantum field theories. Much superior to the usual one-loop effective potential, the GEP is a natural extension of intuitive notions familiar from quantum mechanics. A variety of quantum-mechanical examples are studied here, with an eye to field-theoretic analogies. Quantum restoration of symmetry, dynamical mass generation, and "quantum-mechanical resuscitation" are among the phenomena discussed. We suggest how the GEP could become the basis of a systematic approximation procedure. A companion paper will deal with scalar field theory.

  10. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

    PubMed

    Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

    2018-03-22

    Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

  11. Quantum mechanical tunneling in the automerization of cyclobutadiene

    NASA Astrophysics Data System (ADS)

    Schoonmaker, R.; Lancaster, T.; Clark, S. J.

    2018-03-01

    Cyclobutadiene has a four-membered carbon ring with two double bonds, but this highly strained molecular configuration is almost square and, via a coordinated motion, the nuclei quantum mechanically tunnels through the high-energy square state to a configuration equivalent to the initial configuration under a 90° rotation. This results in a square ground state, comprising a superposition of two molecular configurations, that is driven by quantum tunneling. Using a quantum mechanical model, and an effective nuclear potential from density functional theory, we calculate the vibrational energy spectrum and the accompanying wavefunctions. We use the wavefunctions to identify the motions of the molecule and detail how different motions can enhance or suppress the tunneling rate. This is relevant for kinematics of tunneling-driven reactions, and we discuss these implications. We are also able to provide a qualitative account of how the molecule will respond to an external perturbation and how this may enhance or suppress infra-red-active vibrational transitions.

  12. Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical-Molecular Mechanical Simulations of Proton Transfer in DNA.

    PubMed

    Das, Susanta; Nam, Kwangho; Major, Dan Thomas

    2018-03-13

    In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. ±1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

  13. Development and validation of an achievement test in introductory quantum mechanics: The Quantum Mechanics Visualization Instrument (QMVI)

    NASA Astrophysics Data System (ADS)

    Cataloglu, Erdat

    The purpose of this study was to construct a valid and reliable multiple-choice achievement test to assess students' understanding of core concepts of introductory quantum mechanics. Development of the Quantum Mechanics Visualization Instrument (QMVI) occurred across four successive semesters in 1999--2001. During this time 213 undergraduate and graduate students attending the Pennsylvania State University (PSU) at University Park and Arizona State University (ASU) participated in this development and validation study. Participating students were enrolled in four distinct groups of courses: Modern Physics, Undergraduate Quantum Mechanics, Graduate Quantum Mechanics, and Chemistry Quantum Mechanics. Expert panels of professors of physics experienced in teaching quantum mechanics courses and graduate students in physics and science education established the core content and assisted in the validating of successive versions of the 24-question QMVI. Instrument development was guided by procedures outlined in the Standards for Educational and Psychological Testing (AERA-APA-NCME, 1999). Data gathered in this study provided information used in the development of successive versions of the QMVI. Data gathered in the final phase of administration of the QMVI also provided evidence that the intended score interpretation of the QMVI achievement test is valid and reliable. A moderate positive correlation coefficient of 0.49 was observed between the students' QMVI scores and their confidence levels. Analyses of variance indicated that students' scores in Graduate Quantum Mechanics and Undergraduate Quantum Mechanics courses were significantly higher than the mean scores of students in Modern Physics and Chemistry Quantum Mechanics courses (p < 0.05). That finding is consistent with the additional understanding and experience that should be anticipated in graduate students and junior-senior level students over sophomore physics majors and majors in another field. The moderate

  14. Transfer of Learning in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Singh, Chandralekha

    2005-09-01

    We investigate the difficulties that undergraduate students in quantum mechanics courses have in transferring learning from previous courses or within the same course from one context to another by administering written tests and conducting individual interviews. Quantum mechanics is abstract and its paradigm is very different from the classical one. A good grasp of the principles of quantum mechanics requires creating and organizing a knowledge structure consistent with the quantum postulates. Previously learned concepts such as the principle of superposition and probability can be useful in quantum mechanics if students are given opportunity to build associations between new and prior knowledge. We also discuss the need for better alignment between quantum mechanics and modern physics courses taken previously because semi-classical models can impede internalization of the quantum paradigm in more advanced courses.

  15. Quantum Mechanics and Molecular Mechanics Study of the Catalytic Mechanism of Human AMSH-LP Domain Deubiquitinating Enzymes.

    PubMed

    Zhu, Wenyou; Liu, Yongjun; Ling, Baoping

    2015-08-25

    Deubiquitinating enzymes (DUBs) catalyze the cleavage of the isopeptide bond in polyubiquitin chains to control and regulate the deubiquitination process in all known eukaryotic cells. The human AMSH-LP DUB domain specifically cleaves the isopeptide bonds in the Lys63-linked polyubiquitin chains. In this article, the catalytic mechanism of AMSH-LP has been studied using a combined quantum mechanics and molecular mechanics method. Two possible hydrolysis processes (Path 1 and Path 2) have been considered. Our calculation results reveal that the activation of Zn(2+)-coordinated water molecule is the essential step for the hydrolysis of isopeptide bond. In Path 1, the generated hydroxyl first attacks the carbonyl group of Gly76, and then the amino group of Lys63 is protonated, which is calculated to be the rate limiting step with an energy barrier of 13.1 kcal/mol. The energy barrier of the rate limiting step and the structures of intermediate and product are in agreement with the experimental results. In Path 2, the protonation of amino group of Lys63 is prior to the nucleophilic attack of activated hydroxyl. The two proton transfer processes in Path 2 correspond to comparable overall barriers (33.4 and 36.1 kcal/mol), which are very high for an enzymatic reaction. Thus, Path 2 can be ruled out. During the reaction, Glu292 acts as a proton transfer mediator, and Ser357 mainly plays a role in stabilizing the negative charge of Gly76. Besides acting as a Lewis acid, Zn(2+) also influences the reaction by coordinating to the reaction substrates (W1 and Gly76).

  16. MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.

    PubMed

    Perdih, Andrej; Hodoscek, Milan; Solmajer, Tom

    2009-02-15

    MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase), a three-domain bacterial protein, catalyses a highly specific incorporation of D-glutamate to the cytoplasmic intermediate UDP-N-acetyl-muramoyl-L-alanine (UMA) utilizing ATP hydrolysis to ADP and P(i). This reaction is part of a biosynthetic path yielding bacterial peptidoglycan. On the basis of structural studies of MurD complexes, a stepwise catalytic mechanism was proposed that commences with a formation of the acyl-phosphate intermediate, followed by a nucleophilic attack of D-glutamate that, through the formation of a tetrahedral reaction intermediate and subsequent phosphate dissociation, affords the final product, UDP-N-acetyl-muramoyl-L-alanine-D-glutamate (UMAG). A hybrid quantum mechanical/molecular mechanical (QM/MM) molecular modeling approach was utilized, combining the B3LYP QM level of theory with empirical force field simulations to evaluate three possible reaction pathways leading to tetrahedral intermediate formation. Geometries of the starting structures based on crystallographic experimental data and tetrahedral intermediates were carefully examined together with a role of crucial amino acids and water molecules. The replica path method was used to generate the reaction pathways between the starting structures and the corresponding tetrahedral reaction intermediates, offering direct comparisons with a sequential kinetic mechanism and the available structural data for this enzyme. The acquired knowledge represents new and valuable information to assist in the ongoing efforts leading toward novel inhibitors of MurD as potential antibacterial drugs. (c) 2008 Wiley-Liss, Inc.

  17. Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

    PubMed

    Faheem, Muhammad; Heyden, Andreas

    2014-08-12

    We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

  18. Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution.

    PubMed

    Liu, Peng; Wang, Qiong; Niu, Meixing; Wang, Dunyou

    2017-08-10

    Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.

  19. Improving students' understanding of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Zhu, Guangtian

    2011-12-01

    Learning physics is challenging at all levels. Students' difficulties in the introductory level physics courses have been widely studied and many instructional strategies have been developed to help students learn introductory physics. However, research shows that there is a large diversity in students' preparation and skills in the upper-level physics courses and it is necessary to provide scaffolding support to help students learn advanced physics. This thesis explores issues related to students' common difficulties in learning upper-level undergraduate quantum mechanics and how these difficulties can be reduced by research-based learning tutorials and peer instruction tools. We investigated students' difficulties in learning quantum mechanics by administering written tests and surveys to many classes and conducting individual interviews with a subset of students. Based on these investigations, we developed Quantum Interactive Learning Tutorials (QuILTs) and peer instruction tools to help students build a hierarchical knowledge structure of quantum mechanics through a guided approach. Preliminary assessments indicate that students' understanding of quantum mechanics is improved after using the research-based learning tools in the junior-senior level quantum mechanics courses. We also designed a standardized conceptual survey that can help instructors better probe students' understanding of quantum mechanics concepts in one spatial dimension. The validity and reliability of this quantum mechanics survey is discussed.

  20. Bell's theorem and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Rosen, Nathan

    1994-02-01

    Bell showed that assuming locality leads to a disagreement with quantum mechanics. Here the nature of the nonlocality that follows from quantum mechanics is investigated. Note by the Editor—Readers will recognize Professor Rosen, author of this paper, as one of the co-authors of the famous EPR paper, Albert Einstein, Boris Podolsky, and Nathan Rosen, ``Can Quantum-Mechanical Description of Physical Reality be considered Complete?'', Phys. Rev. 47, 770-780 (1935). Robert H. Romer, Editor

  1. Quantum mechanics/molecular mechanics studies on the mechanism of action of cofactor pyridoxal 5'-phosphate in ornithine 4,5-aminomutase.

    PubMed

    Pang, Jiayun; Scrutton, Nigel S; Sutcliffe, Michael J

    2014-09-01

    A computational study was performed on the experimentally elusive cyclisation step in the cofactor pyridoxal 5'-phosphate (PLP)-dependent D-ornithine 4,5-aminomutase (OAM)-catalysed reaction. Calculations using both model systems and a combined quantum mechanics/molecular mechanics approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor PLP and the active site of the enzyme. The captodative effect of PLP is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff-base nitrogen atom (N2). Furthermore, electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial "strain" energy on the orientation of the cyclic intermediate to control its trajectory. In addition the "strain" energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state. Our results provide new insights into several aspects of the radical mechanism in aminomutase catalysis and broaden our understanding of cofactor PLP-dependent reactions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Quantum mechanics/molecular mechanics modeling of covalent addition between EGFR-cysteine 797 and N-(4-anilinoquinazolin-6-yl) acrylamide.

    PubMed

    Capoferri, Luigi; Lodola, Alessio; Rivara, Silvia; Mor, Marco

    2015-03-23

    Irreversible epidermal growth factor receptor (EGFR) inhibitors can circumvent resistance to first-generation ATP-competitive inhibitors in the treatment of nonsmall-cell lung cancer. They covalently bind a noncatalytic cysteine (Cys797) at the surface of EGFR active site by an acrylamide warhead. Herein, we used a hybrid quantum mechanics/molecular mechanics (QM/MM) potential in combination with umbrella sampling in the path-collective variable space to investigate the mechanism of alkylation of Cys797 by the prototypical covalent inhibitor N-(4-anilinoquinazolin-6-yl) acrylamide. Calculations show that Cys797 reacts with the acrylamide group of the inhibitor through a direct addition mechanism, with Asp800 acting as a general base/general acid in distinct steps of the reaction. The obtained reaction free energy is negative (ΔA = -12 kcal/mol) consistent with the spontaneous and irreversible alkylation of Cys797 by N-(4-anilinoquinazolin-6-yl) acrylamide. Our calculations identify desolvation of Cys797 thiolate anion as a key step of the alkylation process, indicating that changes in the intrinsic reactivity of the acrylamide would have only a minor impact on the inhibitor potency.

  3. Insights into the Lactonase Mechanism of Serum Paraoxonase 1 (PON1): Experimental and Quantum Mechanics/Molecular Mechanics (QM/MM) Studies.

    PubMed

    Le, Quang Anh Tuan; Kim, Seonghoon; Chang, Rakwoo; Kim, Yong Hwan

    2015-07-30

    Serum paraoxonase 1 (PON1) is a versatile enzyme for the hydrolysis of various substrates (e.g., lactones, phosphotriesters) and for the formation of a promising chemical platform γ-valerolactone. Elucidation of the PON1-catalyzed lactonase reaction mechanism is very important for understanding the enzyme function and for engineering this enzyme for specific applications. Kinetic study and hybrid quantum mechanics/molecular mechanics (QM/MM) method were used to investigate the PON1-catalyzed lactonase reaction of γ-butyrolactone (GBL) and (R)-γ-valerolactone (GVL). The activation energies obtained from the QM/MM calculations were in good agreement with the experiments. Interestingly, the QM/MM energy barriers at MP2/3-21G(d,p) level for the lactonase of GVL and GBL were respectively 14.3-16.2 and 11.5-13.1 kcal/mol, consistent with the experimental values (15.57 and 14.73 kcal/mol derived from respective kcat values of 36.62 and 147.21 s(-1)). The QM/MM energy barriers at MP2/6-31G(d) and MP2/6-31G(d,p) levels were also in relatively good agreements with the experiments. Importantly, the difference in the QM/MM energy barriers at MP2 level with all investigated basis sets for the lactonase of GVL and GBL were in excellent agreement with the experiments (0.9-3.1 and 0.8 kcal/mol, respectively). A detailed mechanism for the PON1-catalyzed lactonase reaction was also proposed in this study.

  4. Tunneling time in space fractional quantum mechanics

    NASA Astrophysics Data System (ADS)

    Hasan, Mohammad; Mandal, Bhabani Prasad

    2018-02-01

    We calculate the time taken by a wave packet to travel through a classically forbidden region of space in space fractional quantum mechanics. We obtain the close form expression of tunneling time from a rectangular barrier by stationary phase method. We show that tunneling time depends upon the width b of the barrier for b → ∞ and therefore Hartman effect doesn't exist in space fractional quantum mechanics. Interestingly we found that the tunneling time monotonically reduces with increasing b. The tunneling time is smaller in space fractional quantum mechanics as compared to the case of standard quantum mechanics. We recover the Hartman effect of standard quantum mechanics as a special case of space fractional quantum mechanics.

  5. Supersymmetric symplectic quantum mechanics

    NASA Astrophysics Data System (ADS)

    de Menezes, Miralvo B.; Fernandes, M. C. B.; Martins, Maria das Graças R.; Santana, A. E.; Vianna, J. D. M.

    2018-02-01

    Symplectic Quantum Mechanics SQM considers a non-commutative algebra of functions on a phase space Γ and an associated Hilbert space HΓ to construct a unitary representation for the Galilei group. From this unitary representation the Schrödinger equation is rewritten in phase space variables and the Wigner function can be derived without the use of the Liouville-von Neumann equation. In this article we extend the methods of supersymmetric quantum mechanics SUSYQM to SQM. With the purpose of applications in quantum systems, the factorization method of the quantum mechanical formalism is then set within supersymmetric SQM. A hierarchy of simpler hamiltonians is generated leading to new computation tools for solving the eigenvalue problem in SQM. We illustrate the results by computing the states and spectra of the problem of a charged particle in a homogeneous magnetic field as well as the corresponding Wigner function.

  6. First-Principles Quantum Dynamics of Singlet Fission: Coherent versus Thermally Activated Mechanisms Governed by Molecular π Stacking

    NASA Astrophysics Data System (ADS)

    Tamura, Hiroyuki; Huix-Rotllant, Miquel; Burghardt, Irene; Olivier, Yoann; Beljonne, David

    2015-09-01

    Singlet excitons in π -stacked molecular crystals can split into two triplet excitons in a process called singlet fission that opens a route to carrier multiplication in photovoltaics. To resolve controversies about the mechanism of singlet fission, we have developed a first principles nonadiabatic quantum dynamical model that reveals the critical role of molecular stacking symmetry and provides a unified picture of coherent versus thermally activated singlet fission mechanisms in different acenes. The slip-stacked equilibrium packing structure of pentacene derivatives is found to enhance ultrafast singlet fission mediated by a coherent superexchange mechanism via higher-lying charge transfer states. By contrast, the electronic couplings for singlet fission strictly vanish at the C2 h symmetric equilibrium π stacking of rubrene. In this case, singlet fission is driven by excitations of symmetry-breaking intermolecular vibrations, rationalizing the experimentally observed temperature dependence. Design rules for optimal singlet fission materials therefore need to account for the interplay of molecular π -stacking symmetry and phonon-induced coherent or thermally activated mechanisms.

  7. Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F- + CH3I reaction in aqueous solution.

    PubMed

    Liu, Peng; Zhang, Jingxue; Wang, Dunyou

    2017-06-07

    A double-inversion mechanism of the F - + CH 3 I reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state. The potentials of mean force were calculated with both the DFT/MM and CCSD(T)/MM levels of theory. Our calculated free energy barrier of the abstraction-induced inversion is 69.5 kcal mol -1 at the CCSD(T)/MM level of theory, which agrees with the one at 72.9 kcal mol -1 calculated using the Born solvation model and gas-phase data; and our calculated free energy barrier of the Walden inversion is 24.2 kcal mol -1 , which agrees very well with the experimental value at 25.2 kcal mol -1 in aqueous solution. The calculations show that the aqueous solution makes significant contributions to the potentials of mean force and exerts a big impact on the molecular-level evolution along the reaction pathway.

  8. Emergent quantum mechanics without wavefunctions

    NASA Astrophysics Data System (ADS)

    Mesa Pascasio, J.; Fussy, S.; Schwabl, H.; Grössing, G.

    2016-03-01

    We present our model of an Emergent Quantum Mechanics which can be characterized by “realism without pre-determination”. This is illustrated by our analytic description and corresponding computer simulations of Bohmian-like “surreal” trajectories, which are obtained classically, i.e. without the use of any quantum mechanical tool such as wavefunctions. However, these trajectories do not necessarily represent ontological paths of particles but rather mappings of the probability density flux in a hydrodynamical sense. Modelling emergent quantum mechanics in a high-low intesity double slit scenario gives rise to the “quantum sweeper effect” with a characteristic intensity pattern. This phenomenon should be experimentally testable via weak measurement techniques.

  9. Macro-mechanics controls quantum mechanics: mechanically controllable quantum conductance switching of an electrochemically fabricated atomic-scale point contact.

    PubMed

    Staiger, Torben; Wertz, Florian; Xie, Fangqing; Heinze, Marcel; Schmieder, Philipp; Lutzweiler, Christian; Schimmel, Thomas

    2018-01-12

    Here, we present a silver atomic-scale device fabricated and operated by a combined technique of electrochemical control (EC) and mechanically controllable break junction (MCBJ). With this EC-MCBJ technique, we can perform mechanically controllable bistable quantum conductance switching of a silver quantum point contact (QPC) in an electrochemical environment at room temperature. Furthermore, the silver QPC of the device can be controlled both mechanically and electrochemically, and the operating mode can be changed from 'electrochemical' to 'mechanical', which expands the operating mode for controlling QPCs. These experimental results offer the perspective that a silver QPC may be used as a contact for a nanoelectromechanical relay.

  10. Contact geometry and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Herczeg, Gabriel; Waldron, Andrew

    2018-06-01

    We present a generally covariant approach to quantum mechanics in which generalized positions, momenta and time variables are treated as coordinates on a fundamental "phase-spacetime". We show that this covariant starting point makes quantization into a purely geometric flatness condition. This makes quantum mechanics purely geometric, and possibly even topological. Our approach is especially useful for time-dependent problems and systems subject to ambiguities in choices of clock or observer. As a byproduct, we give a derivation and generalization of the Wigner functions of standard quantum mechanics.

  11. Search for violations of quantum mechanics

    DOE PAGES

    Ellis, John; Hagelin, John S.; Nanopoulos, D. V.; ...

    1984-07-01

    The treatment of quantum effects in gravitational fields indicates that pure states may evolve into mixed states, and Hawking has proposed modification of the axioms of field theory which incorporate the corresponding violation of quantum mechanics. In this study we propose a modified hamiltonian equation of motion for density matrices and use it to interpret upper bounds on the violation of quantum mechanics in different phenomenological situations. We apply our formalism to the K 0-K 0 system and to long baseline neutron interferometry experiments. In both cases we find upper bounds of about 2 × 10 -21 GeV on contributionsmore » to the single particle “hamiltonian” which violate quantum mechanical coherence. We discuss how these limits might be improved in the future, and consider the relative significance of other successful tests of quantum mechanics. Finally, an appendix contains model estimates of the magnitude of effects violating quantum mechanics.« less

  12. Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations

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

    Ojeda-May, Pedro; Pu, Jingzhi, E-mail: jpu@iupui.edu

    The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r{sup −1} term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as amore » Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN{sub 2} reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN{sub 2} reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of

  13. Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations.

    PubMed

    Ojeda-May, Pedro; Pu, Jingzhi

    2015-11-07

    The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.

  14. Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations

    NASA Astrophysics Data System (ADS)

    Ojeda-May, Pedro; Pu, Jingzhi

    2015-11-01

    The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r-1 term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.

  15. Grassmann matrix quantum mechanics

    DOE PAGES

    Anninos, Dionysios; Denef, Frederik; Monten, Ruben

    2016-04-21

    We explore quantum mechanical theories whose fundamental degrees of freedom are rectangular matrices with Grassmann valued matrix elements. We study particular models where the low energy sector can be described in terms of a bosonic Hermitian matrix quantum mechanics. We describe the classical curved phase space that emerges in the low energy sector. The phase space lives on a compact Kähler manifold parameterized by a complex matrix, of the type discovered some time ago by Berezin. The emergence of a semiclassical bosonic matrix quantum mechanics at low energies requires that the original Grassmann matrices be in the long rectangular limit.more » In conclusion, we discuss possible holographic interpretations of such matrix models which, by construction, are endowed with a finite dimensional Hilbert space.« less

  16. Progress in post-quantum mechanics

    NASA Astrophysics Data System (ADS)

    Sarfatti, Jack

    2017-05-01

    Newton's mechanics in the 17th century increased the lethality of artillery. Thermodynamics in the 19th led to the steam-powered industrial revolution. Maxwell's unification of electricity, magnetism and light gave us electrical power, the telegraph, radio and television. The discovery of quantum mechanics in the 20th century by Planck, Bohr, Einstein, Schrodinger, Heisenberg led to the creation of the atomic and hydrogen bombs as well as computer chips, the world-wide-web and Silicon Valley's multibillion dollar corporations. The lesson is that breakthroughs in fundamental physics, both theoretical and experimental, have always led to profound technological wealth-creating industries and will continue to do so. There is now a new revolution brewing in quantum mechanics that can be divided into three periods. The first quantum revolution was from 1900 to about 1975. The second quantum information/computer revolution was from about 1975 to 2015. (The early part of this story is told by Kaiser in his book, How the Hippies Saved Physics, how a small group of Berkeley/San Francisco physicists triggered that second revolution.) The third quantum revolution is how an extension of quantum mechanics may lead to the understanding of consciousness as a natural physical phenomenon that can emerge in many material substrates, not only in our carbon-based biochemistry. In particular, this new post-quantum mechanics may lead to naturally conscious artificial intelligence in nano-electronic machines, as well as perhaps extending human life spans to hundreds of years and more.

  17. Quantum Mechanical Earth: Where Orbitals Become Orbits

    ERIC Educational Resources Information Center

    Keeports, David

    2012-01-01

    Macroscopic objects, although quantum mechanical by nature, conform to Newtonian mechanics under normal observation. According to the quantum mechanical correspondence principle, quantum behavior is indistinguishable from classical behavior in the limit of very large quantum numbers. The purpose of this paper is to provide an example of the…

  18. A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid.

    PubMed

    Alves, Cláudio Nahum; Martí, Sergio; Castillo, Raquel; Andrés, Juan; Moliner, Vicent; Tuñón, Iñaki; Silla, Estanislao

    2008-04-01

    Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral resistance to diketo acids (DKAs) appears when some amino acid residues of the IN active site are mutated. Mutations represent a fascinating experimental challenge, and we invite theoretical simulations for the disclosure of still unexplored features of enzyme reactions. The aim of this work is to understand the molecular mechanisms of HIV-1 IN drug resistance, which will be useful for designing anti-HIV inhibitors with unique resistance profiles. In this study, we use molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy for wild-type and N155S mutant HIV-1 IN, both complexed with a DKA. This hybrid methodology has the advantage of the inclusion of quantum effects such as ligand polarization upon binding, which can be very important when highly polarizable groups are embedded in anisotropic environments, for example in metal-containing active sites. Furthermore, an energy terms decomposition analysis was performed to determine contributions of individual residues to the enzyme-inhibitor interactions. The results reveal that there is a strong interaction between the Lys-159, Lys-156, and Asn-155 residues and Mg(2+) cation and the DKA inhibitor. Our calculations show that the binding energy is higher in wild-type than in the N155S mutant, in accordance with the experimental results. The role of the mutated residue has thus been checked as maintaining the structure of the ternary complex formed by the protein, the Mg(2+) cation, and the inhibitor. These results might be useful to design compounds with more interesting anti-HIV-1 IN activity on the basis of its three-dimensional structure.

  19. QUANTUM MECHANICS. Quantum squeezing of motion in a mechanical resonator.

    PubMed

    Wollman, E E; Lei, C U; Weinstein, A J; Suh, J; Kronwald, A; Marquardt, F; Clerk, A A; Schwab, K C

    2015-08-28

    According to quantum mechanics, a harmonic oscillator can never be completely at rest. Even in the ground state, its position will always have fluctuations, called the zero-point motion. Although the zero-point fluctuations are unavoidable, they can be manipulated. Using microwave frequency radiation pressure, we have manipulated the thermal fluctuations of a micrometer-scale mechanical resonator to produce a stationary quadrature-squeezed state with a minimum variance of 0.80 times that of the ground state. We also performed phase-sensitive, back-action evading measurements of a thermal state squeezed to 1.09 times the zero-point level. Our results are relevant to the quantum engineering of states of matter at large length scales, the study of decoherence of large quantum systems, and for the realization of ultrasensitive sensing of force and motion. Copyright © 2015, American Association for the Advancement of Science.

  20. A perspective on quantum mechanics calculations in ADMET predictions.

    PubMed

    Bowen, J Phillip; Güner, Osman F

    2013-01-01

    Understanding the molecular basis of drug action has been an important objective for pharmaceutical scientists. With the increasing speed of computers and the implementation of quantum chemistry methodologies, pharmacodynamic and pharmacokinetic problems have become more computationally tractable. Historically the former has been the focus of drug design, but within the last two decades efforts to understand the latter have increased. It takes about fifteen years and over $1 billion dollars for a drug to go from laboratory hit, through lead optimization, to final approval by the U.S. Food and Drug Administration. While the costs have increased substantially, the overall clinical success rate for a compound to emerge from clinical trials is approximately 10%. Most of the attrition rate can be traced to ADMET (absorption, distribution, metabolism, excretion, and toxicity) problems, which is a powerful impetus to study these issues at an earlier stage in drug discovery. Quantum mechanics offers pharmaceutical scientists the opportunity to investigate pharmacokinetic problems at the molecular level prior to laboratory preparation and testing. This review will provide a perspective on the use of quantum mechanics or a combination of quantum mechanics coupled with other classical methods in the pharmacokinetic phase of drug discovery. A brief overview of the essential features of theory will be discussed, and a few carefully selected examples will be given to highlight the computational methods.

  1. 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.

  2. DNA Damage: Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

    PubMed Central

    Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

    2014-01-01

    AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N1-methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ-and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained. PMID:24339041

  3. Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

    PubMed

    Lonsdale, Richard; Hoyle, Simon; Grey, Daniel T; Ridder, Lars; Mulholland, Adrian J

    2012-02-28

    Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.

  4. Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes.

    PubMed

    Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

    2014-01-07

    AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N(1) -methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)-oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ- and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained. © 2013 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  5. Noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Gamboa, J.; Loewe, M.; Rojas, J. C.

    2001-09-01

    A general noncommutative quantum mechanical system in a central potential V=V(r) in two dimensions is considered. The spectrum is bounded from below and, for large values of the anticommutative parameter θ, we find an explicit expression for the eigenvalues. In fact, any quantum mechanical system with these characteristics is equivalent to a commutative one in such a way that the interaction V(r) is replaced by V=V(HHO,Lz), where HHO is the Hamiltonian of the two-dimensional harmonic oscillator and Lz is the z component of the angular momentum. For other finite values of θ the model can be solved by using perturbation theory.

  6. Molecular Quantum Mechanics 2010: From Methylene to DNA and Beyond Conference Support

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

    None, None

    This grant was $12500 for partial support of an international conference, Molecular Quantum Mechanics 2010, which was held on the campus of the University of California, Berkeley, from 24 to 29 May 2010. The conference involved more than 250 participants. The conference schedule ran from as early as 8:00 AM to as late as 10:30 PM at night, in order to accommodate six historical lectures, 16 plenary lectures, 42 invited talks and two very strong poster sessions containing 143 contributed posters. Since 1989, the Molecular Quantum Mechanics (MQM) series of international conferences has show- cased the frontiers of research inmore » quantum chemistry with a strong focus on basic theory and algorithms, as well as highlights of topical applications. Both were strongly in evidence at MQM 2010. At the same time as embracing the future, the MQM conferences also honour the lifetime contributions of some of the most prominent scientists in the field of theoretical and computational quantum chemistry. MQM 2010 recognised the work of Prof. Henry F. ‘Fritz’ Schaefer of the Center for Computational Chemistry at the University of Georgia, who was previously on the faculty at Berkeley The travel of invited speakers was partially covered by sponsorships from Dell Computer, Hewlett-Packard, Journal of Chemical Theory and Computation, Virginia Tech College of Science, Molecular Physics, Q-Chem Inc and the American Institute of Physics. By contrast, the conference grant from the Department of Energy was used to provide fellowships and scholarships to enable graduate students and postdoctoral fellows to attend the meeting, and thereby broaden the participation of young scientists at a meeting where in the past most of the attendees have been more senior faculty researchers. We believe that we were very successful in this regard: 118 students and postdocs attended out of the total of 256 participants. In detail, the DOE sponsorship money was partially used for dormitory

  7. Statistical mechanics based on fractional classical and quantum mechanics

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

    Korichi, Z.; Meftah, M. T., E-mail: mewalid@yahoo.com

    2014-03-15

    The purpose of this work is to study some problems in statistical mechanics based on the fractional classical and quantum mechanics. At first stage we have presented the thermodynamical properties of the classical ideal gas and the system of N classical oscillators. In both cases, the Hamiltonian contains fractional exponents of the phase space (position and momentum). At the second stage, in the context of the fractional quantum mechanics, we have calculated the thermodynamical properties for the black body radiation, studied the Bose-Einstein statistics with the related problem of the condensation and the Fermi-Dirac statistics.

  8. Geochemical Reaction Mechanism Discovery from Molecular Simulation

    DOE PAGES

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

  9. Macro-mechanics controls quantum mechanics: mechanically controllable quantum conductance switching of an electrochemically fabricated atomic-scale point contact

    NASA Astrophysics Data System (ADS)

    Staiger, Torben; Wertz, Florian; Xie, Fangqing; Heinze, Marcel; Schmieder, Philipp; Lutzweiler, Christian; Schimmel, Thomas

    2018-01-01

    Here, we present a silver atomic-scale device fabricated and operated by a combined technique of electrochemical control (EC) and mechanically controllable break junction (MCBJ). With this EC-MCBJ technique, we can perform mechanically controllable bistable quantum conductance switching of a silver quantum point contact (QPC) in an electrochemical environment at room temperature. Furthermore, the silver QPC of the device can be controlled both mechanically and electrochemically, and the operating mode can be changed from ‘electrochemical’ to ‘mechanical’, which expands the operating mode for controlling QPCs. These experimental results offer the perspective that a silver QPC may be used as a contact for a nanoelectromechanical relay.

  10. A multiscale quantum mechanics/electromagnetics method for device simulations.

    PubMed

    Yam, ChiYung; Meng, Lingyi; Zhang, Yu; Chen, GuanHua

    2015-04-07

    Multiscale modeling has become a popular tool for research applying to different areas including materials science, microelectronics, biology, chemistry, etc. In this tutorial review, we describe a newly developed multiscale computational method, incorporating quantum mechanics into electronic device modeling with the electromagnetic environment included through classical electrodynamics. In the quantum mechanics/electromagnetics (QM/EM) method, the regions of the system where active electron scattering processes take place are treated quantum mechanically, while the surroundings are described by Maxwell's equations and a semiclassical drift-diffusion model. The QM model and the EM model are solved, respectively, in different regions of the system in a self-consistent manner. Potential distributions and current densities at the interface between QM and EM regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. The method is illustrated in the simulation of several realistic systems. In the case of junctionless field-effect transistors, transfer characteristics are obtained and a good agreement between experiments and simulations is achieved. Optical properties of a tandem photovoltaic cell are studied and the simulations demonstrate that multiple QM regions are coupled through the classical EM model. Finally, the study of a carbon nanotube-based molecular device shows the accuracy and efficiency of the QM/EM method.

  11. Theoretical Modeling of Hydrogen Bonding in omolecular Solutions: The Combination of Quantum Mechanics and Molecular Mechanics

    NASA Astrophysics Data System (ADS)

    Ma, Jing; Jiang, Nan; Li, Hui

    Hydrogen bonding interaction takes an important position in solutions. The non-classic nature of hydrogen bonding requires the resource-demanding quantum mechanical (QM) calculations. The molecular mechanics (MM) method, with much lower computational load, is applicable to the large-sized system. The combination of QM and MM is an efficient way in the treatment of solution. Taking advantage of the low-cost energy-based fragmentation QM approach (in which the o-molecule is divided into several subsystems, and QM calculation is carried out on each subsystem that is embedded in the environment of background charges of distant parts), the fragmentation-based QM/MM and polarization models have been implemented for the modeling of o-molecule in aqueous solutions, respectively. Within the framework of the fragmentation-based QM/MM hybrid model, the solute is treated by the fragmentation QM calculation while the numerous solvent molecules are described by MM. In the polarization model, the polarizability is considered by allowing the partial charges and fragment-centered dipole moments to be variables, with values coming from the energy-based fragmentation QM calculations. Applications of these two methods to the solvated long oligomers and cyclic peptides have demonstrated that the hydrogen bonding interaction affects the dynamic change in chain conformations of backbone.

  12. Role of the Active Site Guanine in the glmS Ribozyme Self-Cleavage Mechanism: Quantum Mechanical/Molecular Mechanical Free Energy Simulations

    PubMed Central

    2015-01-01

    The glmS ribozyme catalyzes a self-cleavage reaction at the phosphodiester bond between residues A-1 and G1. This reaction is thought to occur by an acid–base mechanism involving the glucosamine-6-phosphate cofactor and G40 residue. Herein quantum mechanical/molecular mechanical free energy simulations and pKa calculations, as well as experimental measurements of the rate constant for self-cleavage, are utilized to elucidate the mechanism, particularly the role of G40. Our calculations suggest that an external base deprotonates either G40(N1) or possibly A-1(O2′), which would be followed by proton transfer from G40(N1) to A-1(O2′). After this initial deprotonation, A-1(O2′) starts attacking the phosphate as a hydroxyl group, which is hydrogen-bonded to deprotonated G40, concurrent with G40(N1) moving closer to the hydroxyl group and directing the in-line attack. Proton transfer from A-1(O2′) to G40 is concomitant with attack of the scissile phosphate, followed by the remainder of the cleavage reaction. A mechanism in which an external base does not participate, but rather the proton transfers from A-1(O2′) to a nonbridging oxygen during nucleophilic attack, was also considered but deemed to be less likely due to its higher effective free energy barrier. The calculated rate constant for the favored mechanism is in agreement with the experimental rate constant measured at biological Mg2+ ion concentration. According to these calculations, catalysis is optimal when G40 has an elevated pKa rather than a pKa shifted toward neutrality, although a balance among the pKa’s of A-1, G40, and the nonbridging oxygen is essential. These results have general implications, as the hammerhead, hairpin, and twister ribozymes have guanines at a similar position as G40. PMID:25526516

  13. Quantum mechanical calculations related to ionization and charge transfer in DNA

    NASA Astrophysics Data System (ADS)

    Cauët, E.; Valiev, M.; Weare, J. H.; Liévin, J.

    2012-07-01

    Ionization and charge migration in DNA play crucial roles in mechanisms of DNA damage caused by ionizing radiation, oxidizing agents and photo-irradiation. Therefore, an evaluation of the ionization properties of the DNA bases is central to the full interpretation and understanding of the elementary reactive processes that occur at the molecular level during the initial exposure and afterwards. Ab initio quantum mechanical (QM) methods have been successful in providing highly accurate evaluations of key parameters, such as ionization energies (IE) of DNA bases. Hence, in this study, we performed high-level QM calculations to characterize the molecular energy levels and potential energy surfaces, which shed light on ionization and charge migration between DNA bases. In particular, we examined the IEs of guanine, the most easily oxidized base, isolated and embedded in base clusters, and investigated the mechanism of charge migration over two and three stacked guanines. The IE of guanine in the human telomere sequence has also been evaluated. We report a simple molecular orbital analysis to explain how modifications in the base sequence are expected to change the efficiency of the sequence as a hole trap. Finally, the application of a hybrid approach combining quantum mechanics with molecular mechanics brings an interesting discussion as to how the native aqueous DNA environment affects the IE threshold of nucleobases.

  14. Reduction of α,β-Unsaturated Ketones by Old Yellow Enzymes: Mechanistic Insights from Quantum Mechanics/Molecular Mechanics Calculations.

    PubMed

    Lonsdale, Richard; Reetz, Manfred T

    2015-11-25

    Enoate reductases catalyze the reduction of activated C═C bonds with high enantioselectivity. The oxidative half-reaction, which involves the addition of a hydride and a proton to opposite faces of the C═C bond, has been studied for the first time by hybrid quantum mechanics/molecular mechanics (QM/MM). The reduction of 2-cyclohexen-1-one by YqjM from Bacillus subtilis was selected as the model system. Two-dimensional QM/MM (B3LYP-D/OPLS2005) reaction pathways suggest that the hydride and proton are added as distinct steps, with the former step preceding the latter. Furthermore, we present interesting insights into the reactivity of this enzyme, including the weak binding of the substrate in the active site, the role of the two active site histidine residues for polarization of the substrate C═O bond, structural details of the transition states to hydride and proton transfer, and the role of Tyr196 as proton donor. The information presented here will be useful for the future design of enantioselective YqjM mutants for other substrates.

  15. Phase space quantum mechanics - Direct

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

    Nasiri, S.; Sobouti, Y.; Taati, F.

    2006-09-15

    Conventional approach to quantum mechanics in phase space (q,p), is to take the operator based quantum mechanics of Schroedinger, or an equivalent, and assign a c-number function in phase space to it. We propose to begin with a higher level of abstraction, in which the independence and the symmetric role of q and p is maintained throughout, and at once arrive at phase space state functions. Upon reduction to the q- or p-space the proposed formalism gives the conventional quantum mechanics, however, with a definite rule for ordering of factors of noncommuting observables. Further conceptual and practical merits of themore » formalism are demonstrated throughout the text.« less

  16. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.

    PubMed

    Ganguly, Abir; Thaplyal, Pallavi; Rosta, Edina; Bevilacqua, Philip C; Hammes-Schiffer, Sharon

    2014-01-29

    The hepatitis delta virus (HDV) ribozyme catalyzes a self-cleavage reaction using a combination of nucleobase and metal ion catalysis. Both divalent and monovalent ions can catalyze this reaction, although the rate is slower with monovalent ions alone. Herein, we use quantum mechanical/molecular mechanical (QM/MM) free energy simulations to investigate the mechanism of this ribozyme and to elucidate the roles of the catalytic metal ion. With Mg(2+) at the catalytic site, the self-cleavage mechanism is observed to be concerted with a phosphorane-like transition state and a free energy barrier of ∼13 kcal/mol, consistent with free energy barrier values extrapolated from experimental studies. With Na(+) at the catalytic site, the mechanism is observed to be sequential, passing through a phosphorane intermediate, with free energy barriers of 2-4 kcal/mol for both steps; moreover, proton transfer from the exocyclic amine of protonated C75 to the nonbridging oxygen of the scissile phosphate occurs to stabilize the phosphorane intermediate in the sequential mechanism. To explain the slower rate observed experimentally with monovalent ions, we hypothesize that the activation of the O2' nucleophile by deprotonation and orientation is less favorable with Na(+) ions than with Mg(2+) ions. To explore this hypothesis, we experimentally measure the pKa of O2' by kinetic and NMR methods and find it to be lower in the presence of divalent ions rather than only monovalent ions. The combined theoretical and experimental results indicate that the catalytic Mg(2+) ion may play three key roles: assisting in the activation of the O2' nucleophile, acidifying the general acid C75, and stabilizing the nonbridging oxygen to prevent proton transfer to it.

  17. Facets of contextual realism in quantum mechanics

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

    Pan, Alok Kumar; Home, Dipankar

    2011-09-23

    In recent times, there is an upsurge of interest in demonstrating the quantum contextuality. In this proceedings, we explore the two different forms of arguments that have been used for showing the contextual character of quantum mechanics. First line of study concerns the violations of the noncontextual realist models by quantum mechanics, where second line of study that is qualitatively distinct from the earlier one, demonstrates the contextuality within the formalism of quantum mechanics.

  18. Computational applications of the many-interacting-worlds interpretation of quantum mechanics.

    PubMed

    Sturniolo, Simone

    2018-05-01

    While historically many quantum-mechanical simulations of molecular dynamics have relied on the Born-Oppenheimer approximation to separate electronic and nuclear behavior, recently a great deal of interest has arisen in quantum effects in nuclear dynamics as well. Due to the computational difficulty of solving the Schrödinger equation in full, these effects are often treated with approximate methods. In this paper, we present an algorithm to tackle these problems using an extension to the many-interacting-worlds approach to quantum mechanics. This technique uses a kernel function to rebuild the probability density, and therefore, in contrast with the approximation presented in the original paper, it can be naturally extended to n-dimensional systems. This opens up the possibility of performing quantum ground-state searches with steepest-descent methods, and it could potentially lead to real-time quantum molecular-dynamics simulations. The behavior of the algorithm is studied in different potentials and numbers of dimensions and compared both to the original approach and to exact Schrödinger equation solutions whenever possible.

  19. Time Asymmetric Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Bohm, Arno R.; Gadella, Manuel; Kielanowski, Piotr

    2011-09-01

    The meaning of time asymmetry in quantum physics is discussed. On the basis of a mathematical theorem, the Stone-von Neumann theorem, the solutions of the dynamical equations, the Schrödinger equation (1) for states or the Heisenberg equation (6a) for observables are given by a unitary group. Dirac kets require the concept of a RHS (rigged Hilbert space) of Schwartz functions; for this kind of RHS a mathematical theorem also leads to time symmetric group evolution. Scattering theory suggests to distinguish mathematically between states (defined by a preparation apparatus) and observables (defined by a registration apparatus (detector)). If one requires that scattering resonances of width Γ and exponentially decaying states of lifetime τ=h/Γ should be the same physical entities (for which there is sufficient evidence) one is led to a pair of RHS's of Hardy functions and connected with it, to a semigroup time evolution t0≤t<∞, with the puzzling result that there is a quantum mechanical beginning of time, just like the big bang time for the universe, when it was a quantum system. The decay of quasi-stable particles is used to illustrate this quantum mechanical time asymmetry. From the analysis of these processes, we show that the properties of rigged Hilbert spaces of Hardy functions are suitable for a formulation of time asymmetry in quantum mechanics.

  20. Combined spectroscopic, molecular docking and quantum mechanics study of β-casein and p-coumaric acid interactions following thermal treatment.

    PubMed

    Kaur, Jasmeet; Katopo, Lita; Hung, Andrew; Ashton, John; Kasapis, Stefan

    2018-06-30

    The molecular nature of interactions between β-casein and p-coumaric acid was studied following exposure of their solutions to ultra-high temperature (UHT at 145 °C). Interactions were characterised by employing multi-spectroscopic methods, molecular docking and quantum mechanics calculations. FTIR demonstrates that the ligand lies in the vicinity of the protein, hence inverting the absorbance spectrum of the complex. This outcome changes the conformational characteristics of the protein leading to a flexible and open structure that accommodates the phenolic microconstituent. Results are supported by UV-vis, CD and fluorescence quenching showing considerable shifts in spectra with complexation. Molecular docking indicates that there is at least a hydrogen bond between p-coumaric acid and the peptide backbone of isoleucine (Ile27). Quantum mechanics calculations further argue that changes in experimental observations are also due to a covalent interaction in the protein-phenolic adduct, which according to the best predicted binding pose involves the side chain of lysine 47. Copyright © 2018. Published by Elsevier Ltd.

  1. Quantum chemical study of the mechanism of action of vitamin K epoxide reductase (VKOR)

    NASA Astrophysics Data System (ADS)

    Deerfield, David, II; Davis, Charles H.; Wymore, Troy; Stafford, Darrel W.; Pedersen, Lee G.

    Possible model, but simplistic, mechanisms for the action of vitamin K epoxide reductase (VKOR) are investigated with quantum mechanical methods (B3LYP/6-311G**). The geometries of proposed model intermediates in the mechanisms are energy optimized. Finally, the energetics of the proposed (pseudo-enzymatic) pathways are compared. We find that the several pathways are all energetically feasible. These results will be useful for designing quantum mechanical/molecular mechanical method (QM/MM) studies of the enzymatic pathway once three-dimensional structural data are determined and available for VKOR.

  2. Investigation of the CH{sub 3}Cl + CN{sup −} reaction in water: Multilevel quantum mechanics/molecular mechanics study

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

    Xu, Yulong; College of Physics and Electronics, Shandong Normal University, Jinan 250014; Zhang, Jingxue

    2015-06-28

    The CH{sub 3}Cl + CN{sup −} reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack S{sub N}2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show thatmore » the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.« less

  3. Undergraduate quantum mechanics: lost opportunities for engaging motivated students?

    NASA Astrophysics Data System (ADS)

    Johansson, Anders

    2018-03-01

    Quantum mechanics is widely recognised as an important and difficult subject, and many studies have been published focusing on students’ conceptual difficulties. However, the sociocultural aspects of studying such an emblematic subject have not been researched to any large extent. This study explores students’ experiences of undergraduate quantum mechanics using qualitative analysis of semi-structured interview data. The results inform discussions about the teaching of quantum mechanics by adding a sociocultural dimension. Students pictured quantum mechanics as an intriguing subject that inspired them to study physics. The study environment they encountered when taking their first quantum mechanics course was however not always as inspiring as expected. Quantum mechanics instruction has commonly focused on the mathematical framework of quantum mechanics, and this kind of teaching was also what the interviewees had experienced. Two ways of handling the encounter with a traditional quantum mechanics course were identified in the interviews; either students accept the practice of studying quantum mechanics in a mathematical, exercise-centred way or they distance themselves from these practices and the subject. The students who responded by distancing themselves experienced a crisis and disappointment, where their experiences did not match the way they imagined themselves engaging with quantum mechanics. The implications of these findings are discussed in relation to efforts to reform the teaching of undergraduate quantum mechanics.

  4. Quantum Mechanics predicts evolutionary biology.

    PubMed

    Torday, J S

    2018-07-01

    Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Quantum mechanics as classical statistical mechanics with an ontic extension and an epistemic restriction.

    PubMed

    Budiyono, Agung; Rohrlich, Daniel

    2017-11-03

    Where does quantum mechanics part ways with classical mechanics? How does quantum randomness differ fundamentally from classical randomness? We cannot fully explain how the theories differ until we can derive them within a single axiomatic framework, allowing an unambiguous account of how one theory is the limit of the other. Here we derive non-relativistic quantum mechanics and classical statistical mechanics within a common framework. The common axioms include conservation of average energy and conservation of probability current. But two axioms distinguish quantum mechanics from classical statistical mechanics: an "ontic extension" defines a nonseparable (global) random variable that generates physical correlations, and an "epistemic restriction" constrains allowed phase space distributions. The ontic extension and epistemic restriction, with strength on the order of Planck's constant, imply quantum entanglement and uncertainty relations. This framework suggests that the wave function is epistemic, yet it does not provide an ontic dynamics for individual systems.

  6. Quantum Mechanical Study of Atoms and Molecules

    NASA Technical Reports Server (NTRS)

    Sahni, R. C.

    1961-01-01

    This paper, following a brief introduction, is divided into five parts. Part I outlines the theory of the molecular orbital method for the ground, ionized and excited states of molecules. Part II gives a brief summary of the interaction integrals and their tabulation. Part III outlines an automatic program designed for the computation of various states of molecules. Part IV gives examples of the study of ground, ionized and excited states of CO, BH and N2 where the program of automatic computation and molecular integrals have been utilized. Part V enlists some special problems of Molecular Quantum Mechanics are being tackled at New York University.

  7. Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube.

    PubMed

    Duster, Adam W; Lin, Hai

    2017-09-14

    Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. The results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.

  8. Teaching Quantum Mechanics on an Introductory Level.

    ERIC Educational Resources Information Center

    Muller, Rainer; Wiesner, Hartmut

    2002-01-01

    Presents a new research-based course on quantum mechanics in which the conceptual issues of quantum mechanics are taught at an introductory level. Involves students in the discovery of how quantum phenomena deviate from classical everyday experiences. (Contains 31 references.) (Author/YDS)

  9. Origin of microbial life: Nano- and molecular events, thermodynamics/entropy, quantum mechanisms and genetic instructions.

    PubMed

    Trevors, J T

    2011-03-01

    Currently, there are no agreed upon mechanisms and supporting evidence for the origin of the first microbial cells on the Earth. However, some hypotheses have been proposed with minimal supporting evidence and experimentation/observations. The approach taken in this article is that life originated at the nano- and molecular levels of biological organization, using quantum mechanic principles that became manifested as classical microbial cell(s), allowing the origin of microbial life on the Earth with a core or minimal, organic, genetic code containing the correct instructions for cell(s) for growth and division, in a micron dimension environment, with a local entropy range conducive to life (present about 4 billion years ago), and obeying the laws of thermodynamics. An integrated approach that explores all encompassing factors necessary for the origin of life, may bring forth plausible hypotheses (and mechanisms) with much needed supporting experimentation and observations for an origin of life theory. Copyright © 2010 Elsevier B.V. All rights reserved.

  10. Metabolism of 4-Aminopiperidine Drugs by Cytochrome P450s: Molecular and Quantum Mechanical Insights into Drug Design

    PubMed Central

    2011-01-01

    4-Aminopiperidines are a variety of therapeutic agents that are extensively metabolized by cytochrome P450s with CYP3A4 as a major isoform catalyzing their N-dealkylation reaction. However, its catalytic mechanism has not been fully elucidated in a molecular interaction level. Here, we applied theoretical approaches including the molecular mechanics-based docking to study the binding patterns and quantum mechanics-based reactivity calculations. They were supported by the experimental human liver microsomal clearance and P450 isoform phenotyping data. Our results herein suggested that the molecular interactions between substrates and CYP3A4 active site residues are essential for the N-dealkylation of 4-aminopiperidines. We also found that the serine 119 residue of CYP3A4 may serve as a key hydrogen-bonding partner to interact with the 4-amino groups of the studied drugs. The reactivity of the side chain α-carbon hydrogens drives the direction of catalysis as well. As a result, structure-based drug design approaches look promising to guide drug discovery programs into the optimized drug metabolism space. PMID:21841964

  11. EDITORIAL: Focus on Mechanical Systems at the Quantum Limit FOCUS ON MECHANICAL SYSTEMS AT THE QUANTUM LIMIT

    NASA Astrophysics Data System (ADS)

    Aspelmeyer, Markus; Schwab, Keith

    2008-09-01

    The last five years have witnessed an amazing development in the field of nano- and micromechanics. What was widely considered fantasy ten years ago is about to become an experimental reality: the quantum regime of mechanical systems is within reach of current experiments. Two factors (among many) have contributed significantly to this situation. As part of the widespread effort into nanoscience and nanofabrication, it is now possible to produce high-quality nanomechanical and micromechanical resonators, spanning length scales of millimetres to nanometres, and frequencies from kilohertz to gigahertz. Researchers coupled these mechanical elements to high-sensitivity actuation and readout systems such as single-electron transistors, quantum dots, atomic point contacts, SQUID loops, high-finesse optical or microwave-cavities etc. Some of these ultra-sensitive readout schemes are in principle capable of detection at the quantum limit and a large part of the experimental effort is at present devoted to achieving this. On the other hand, the fact that the groups working in the field come from various different physics backgrounds—the authors of this editorial are a representative sample—has been a constant source of inspiration for helpful theoretical and experimental tools that have been adapted from other fields to the mechanical realm. To name just one example: ideas from quantum optics have led to the recent demonstration (both in theory and experiment) that coupling a mechanical resonator to a high-finesse optical cavity can be fully analogous to the well-known sideband-resolved laser cooling of ions and hence is capable in principle of cooling a mechanical mode into its quantum ground state. There is no doubt that such interdisciplinarity has been a crucial element for the development of the field. It is interesting to note that a very similar sociological phenomenon occurred earlier in the quantum information community, an area which is deeply enriched by the

  12. Quantum inertia stops superposition: Scan Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Gato-Rivera, Beatriz

    2017-08-01

    Scan Quantum Mechanics is a novel interpretation of some aspects of quantum mechanics in which the superposition of states is only an approximate effective concept. Quantum systems scan all possible states in the superposition and switch randomly and very rapidly among them. A crucial property that we postulate is quantum inertia, that increases whenever a constituent is added, or the system is perturbed with all kinds of interactions. Once the quantum inertia Iq reaches a critical value Icr for an observable, the switching among its different eigenvalues stops and the corresponding superposition comes to an end, leaving behind a system with a well defined value of that observable. Consequently, increasing the mass, temperature, gravitational strength, etc. of a quantum system increases its quantum inertia until the superposition of states disappears for all the observables and the system transmutes into a classical one. Moreover, the process could be reversible. Entanglement can only occur between quantum systems because an exact synchronization between the switchings of the systems involved must be established in the first place and classical systems do not have any switchings to start with. Future experiments might determine the critical inertia Icr corresponding to different observables, which translates into a critical mass Mcr for fixed environmental conditions as well as critical temperatures, critical electric and magnetic fields, etc. In addition, this proposal implies a new radiation mechanism from astrophysical objects with strong gravitational fields, giving rise to non-thermal synchrotron emission, that could contribute to neutron star formation. Superconductivity, superfluidity, Bose-Einstein condensates, and any other physical phenomena at very low temperatures must be reanalyzed in the light of this interpretation, as well as mesoscopic systems in general.

  13. Foundations of Quantum Mechanics and Quantum Computation

    NASA Astrophysics Data System (ADS)

    Aspect, Alain; Leggett, Anthony; Preskill, John; Durt, Thomas; Pironio, Stefano

    2013-03-01

    I ask the question: What can we infer about the nature and structure of the physical world (a) from experiments already done to test the predictions of quantum mechanics (b) from the assumption that all future experiments will agree with those predictions? I discuss existing and projected experiments related to the two classic paradoxes of quantum mechanics, named respectively for EPR and Schrödinger's Cat, and show in particular that one natural conclusion from both types of experiment implies the abandonment of the concept of macroscopic counterfactual definiteness.

  14. Probability and Locality: Determinism Versus Indeterminism in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Dickson, William Michael

    1995-01-01

    Quantum mechanics is often taken to be necessarily probabilistic. However, this view of quantum mechanics appears to be more the result of historical accident than of careful analysis. Moreover, quantum mechanics in its usual form faces serious problems. Although the mathematical core of quantum mechanics--quantum probability theory- -does not face conceptual difficulties, the application of quantum probability to the physical world leads to problems. In particular, quantum mechanics seems incapable of describing our everyday macroscopic experience. Therefore, several authors have proposed new interpretations --including (but not limited to) modal interpretations, spontaneous localization interpretations, the consistent histories approach, and the Bohm theory--each of which deals with quantum-mechanical probabilities differently. Each of these interpretations promises to describe our macroscopic experience and, arguably, each succeeds. Is there any way to compare them? Perhaps, if we turn to another troubling aspect of quantum mechanics, non-locality. Non -locality is troubling because prima facie it threatens the compatibility of quantum mechanics with special relativity. This prima facie threat is mitigated by the no-signalling theorems in quantum mechanics, but nonetheless one may find a 'conflict of spirit' between nonlocality in quantum mechanics and special relativity. Do any of these interpretations resolve this conflict of spirit?. There is a strong relation between how an interpretation deals with quantum-mechanical probabilities and how it deals with non-locality. The main argument here is that only a completely deterministic interpretation can be completely local. That is, locality together with the empirical predictions of quantum mechanics (specifically, its strict correlations) entails determinism. But even with this entailment in hand, comparison of the various interpretations requires a look at each, to see how non-locality arises, or in the case of

  15. Entangled states in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Ruža, Jānis

    2010-01-01

    In some circles of quantum physicists, a view is maintained that the nonseparability of quantum systems-i.e., the entanglement-is a characteristic feature of quantum mechanics. According to this view, the entanglement plays a crucial role in the solution of quantum measurement problem, the origin of the “classicality” from the quantum physics, the explanation of the EPR paradox by a nonlocal character of the quantum world. Besides, the entanglement is regarded as a cornerstone of such modern disciplines as quantum computation, quantum cryptography, quantum information, etc. At the same time, entangled states are well known and widely used in various physics areas. In particular, this notion is widely used in nuclear, atomic, molecular, solid state physics, in scattering and decay theories as well as in other disciplines, where one has to deal with many-body quantum systems. One of the methods, how to construct the basis states of a composite many-body quantum system, is the so-called genealogical decomposition method. Genealogical decomposition allows one to construct recurrently by particle number the basis states of a composite quantum system from the basis states of its forming subsystems. These coupled states have a structure typical for entangled states. If a composite system is stable, the internal structure of its forming basis states does not manifest itself in measurements. However, if a composite system is unstable and decays onto its forming subsystems, then the measurables are the quantum numbers, associated with these subsystems. In such a case, the entangled state has a dynamical origin, determined by the Hamiltonian of the corresponding decay process. Possible correlations between the quantum numbers of resulting subsystems are determined by the symmetries-conservation laws of corresponding dynamical variables, and not by the quantum entanglement feature.

  16. Pseudospectra in non-Hermitian quantum mechanics

    NASA Astrophysics Data System (ADS)

    Krejčiřík, D.; Siegl, P.; Tater, M.; Viola, J.

    2015-10-01

    We propose giving the mathematical concept of the pseudospectrum a central role in quantum mechanics with non-Hermitian operators. We relate pseudospectral properties to quasi-Hermiticity, similarity to self-adjoint operators, and basis properties of eigenfunctions. The abstract results are illustrated by unexpected wild properties of operators familiar from PT -symmetric quantum mechanics.

  17. Heisenberg and the Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Camilleri, Kristian

    2011-09-01

    Preface; 1. Introduction; Part I. The Emergence of Quantum Mechanics: 2. Quantum mechanics and the principle of observability; 3. The problem of interpretation; Part II. The Heisenberg-Bohr Dialogue: 4. The wave-particle duality; 5. Indeterminacy and the limits of classical concepts: the turning point in Heisenberg's thought; 6. Heisenberg and Bohr: divergent viewpoints of complementarity; Part III. Heisenberg's Epistemology and Ontology of Quantum Mechanics: 7. The transformation of Kantian philosophy; 8. The linguistic turn in Heisenberg's thought; Conclusion; References; Index.

  18. Heisenberg and the Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Camilleri, Kristian

    2009-02-01

    Preface; 1. Introduction; Part I. The Emergence of Quantum Mechanics: 2. Quantum mechanics and the principle of observability; 3. The problem of interpretation; Part II. The Heisenberg-Bohr Dialogue: 4. The wave-particle duality; 5. Indeterminacy and the limits of classical concepts: the turning point in Heisenberg's thought; 6. Heisenberg and Bohr: divergent viewpoints of complementarity; Part III. Heisenberg's Epistemology and Ontology of Quantum Mechanics: 7. The transformation of Kantian philosophy; 8. The linguistic turn in Heisenberg's thought; Conclusion; References; Index.

  19. Emerging interpretations of quantum mechanics and recent progress in quantum measurement

    NASA Astrophysics Data System (ADS)

    Clarke, M. L.

    2014-01-01

    The focus of this paper is to provide a brief discussion on the quantum measurement process, by reviewing select examples highlighting recent progress towards its understanding. The areas explored include an outline of the measurement problem, the standard interpretation of quantum mechanics, quantum to classical transition, types of measurement (including weak and projective measurements) and newly emerging interpretations of quantum mechanics (decoherence theory, objective reality, quantum Darwinism and quantum Bayesianism).

  20. Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

    PubMed

    Tahan, A; Monajjemi, M

    2011-12-01

    Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

  1. Thermodynamic integration from classical to quantum mechanics.

    PubMed

    Habershon, Scott; Manolopoulos, David E

    2011-12-14

    We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable. © 2011 American Institute of Physics

  2. A Trapped Covalent Intermediate of a Glycoside Hydrolase on the Pathway to Transglycosylation. Insights from Experiments and Quantum Mechanics/Molecular Mechanics Simulations.

    PubMed

    Raich, Lluís; Borodkin, Vladimir; Fang, Wenxia; Castro-López, Jorge; van Aalten, Daan M F; Hurtado-Guerrero, Ramón; Rovira, Carme

    2016-03-16

    The conversion of glycoside hydrolases (GHs) into transglycosylases (TGs), i.e., from enzymes that hydrolyze carbohydrates to enzymes that synthesize them, represents a promising solution for the large-scale synthesis of complex carbohydrates for biotechnological purposes. However, the lack of knowledge about the molecular details of transglycosylation hampers the rational design of TGs. Here we present the first crystallographic structure of a natural glycosyl-enzyme intermediate (GEI) of Saccharomyces cerevisiae Gas2 in complex with an acceptor substrate and demonstrate, by means of quantum mechanics/molecular mechanics metadynamics simulations, that it is tuned for transglycosylation (ΔG(⧧) = 12 kcal/mol). The 2-OH···nucleophile interaction is found to be essential for catalysis: its removal raises the free energy barrier significantly (11 and 16 kcal/mol for glycosylation and transglycosylation, respectively) and alters the conformational itinerary of the substrate (from (4)C1 → [(4)E](⧧) → (1,4)B/(4)E to (4)C1 → [(4)H3](⧧) → (4)C1). Our results suggest that changes in the interactions involving the 2-position could have an impact on the transglycosylation activity of several GHs.

  3. Extracontextuality and extravalence in quantum mechanics.

    PubMed

    Auffèves, Alexia; Grangier, Philippe

    2018-07-13

    We develop the point of view where quantum mechanics results from the interplay between the quantized number of 'modalities' accessible to a quantum system, and the continuum of 'contexts' that are required to define these modalities. We point out the specific roles of 'extracontextuality' and 'extravalence' of modalities, and relate them to the Kochen-Specker and Gleason theorems.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'. © 2018 The Author(s).

  4. Unraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase: a quantum mechanics-molecular mechanics modeling study.

    PubMed

    Bueren-Calabuig, Juan A; Pierdominici-Sottile, Gustavo; Roitberg, Adrian E

    2014-06-05

    Chagas' disease, also known as American trypanosomiasis, is a lethal, chronic disease that currently affects more than 10 million people in Central and South America. The trans-sialidase from Trypanosoma cruzi (T. cruzi, TcTS) is a crucial enzyme for the survival of this parasite: sialic acids from the host are transferred to the cell surface glycoproteins of the trypanosome, thereby evading the host's immune system. On the other hand, the sialidase of T. rangeli (TrSA), which shares 70% sequence identity with TcTS, is a strict hydrolase and shows no trans-sialidase activity. Therefore, TcTS and TrSA represent an excellent framework to understand how different catalytic activities can be achieved with extremely similar structures. By means of combined quantum mechanics-molecular mechanics (QM/MM, SCC-DFTB/Amberff99SB) calculations and umbrella sampling simulations, we investigated the hydrolysis mechanisms of TcTS and TrSA and computed the free energy profiles of these reactions. The results, together with our previous computational investigations, are able to explain the catalytic mechanism of sialidases and describe how subtle differences in the active site make TrSA a strict hydrolase and TcTS a more efficient trans-sialidase.

  5. Non-commutative methods in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Millard, Andrew Clive

    1997-09-01

    Non-commutativity appears in physics almost hand in hand with quantum mechanics. Non-commuting operators corresponding to observables lead to Heisenberg's Uncertainty Principle, which is often used as a prime example of how quantum mechanics transcends 'common sense', while the operators that generate a symmetry group are usually given in terms of their commutation relations. This thesis discusses a number of new developments which go beyond the usual stopping point of non-commuting quantities as matrices with complex elements. Chapter 2 shows how certain generalisations of quantum mechanics, from using complex numbers to using other (often non-commutative) algebras, can still be written as linear systems with symplectic phase flows. Chapter 3 deals with Adler's trace dynamics, a non-linear graded generalisation of Hamiltonian dynamics with supersymmetry applications, where the phase space coordinates are (generally non-commuting) operators, and reports on aspects of a demonstration that the statistical averages of the dynamical variables obey the rules of complex quantum field theory. The last two chapters discuss specific aspects of quaternionic quantum mechanics. Chapter 4 reports a generalised projective representation theory and presents a structure theorem that categorises quaternionic projective representations. Chapter 5 deals with a generalisation of the coherent states formalism and examines how it may be applied to two commonly used groups.

  6. Young’s modulus calculations for cellulose Iß by MM3 and quantum mechanics

    USDA-ARS?s Scientific Manuscript database

    Quantum mechanics (QM) and molecular mechanics (MM) calculations were performed to elucidate Young’s moduli for a series of cellulose Iß models. Computations using the second generation empirical force field MM3 with a disaccharide cellulose model, 1,4'-O-dimethyl-ß-cellobioside (DMCB), and an analo...

  7. Quantum statistical mechanics of dense partially ionized hydrogen

    NASA Technical Reports Server (NTRS)

    Dewitt, H. E.; Rogers, F. J.

    1972-01-01

    The theory of dense hydrogen plasmas beginning with the two component quantum grand partition function is reviewed. It is shown that ionization equilibrium and molecular dissociation equilibrium can be treated in the same manner with proper consideration of all two-body states. A quantum perturbation expansion is used to give an accurate calculation of the equation of state of the gas for any degree of dissociation and ionization. The statistical mechanical calculation of the plasma equation of state is intended for stellar interiors. The general approach is extended to the calculation of the equation of state of the outer layers of large planets.

  8. Chloride Ion Transport by the E. coli CLC Cl-/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study.

    PubMed

    Wang, Chun-Hung; Duster, Adam W; Aydintug, Baris O; Zarecki, MacKenzie G; Lin, Hai

    2018-01-01

    We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl - ion migration through the transmembrane domain of a prototypical E. coli CLC Cl - /H + antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl - . Moving the anion into the external binding site (S ext ) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl - traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl - exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl - along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl - changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl - and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl - ion due

  9. Chloride Ion Transport by the E. coli CLC Cl−/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study

    PubMed Central

    Wang, Chun-Hung; Duster, Adam W.; Aydintug, Baris O.; Zarecki, MacKenzie G.; Lin, Hai

    2018-01-01

    We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl− ion migration through the transmembrane domain of a prototypical E. coli CLC Cl−/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl−. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl− traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl− exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl− along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl− changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl− and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl− ion

  10. Chloride Ion Transport by the E. coli CLC Cl–/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study

    NASA Astrophysics Data System (ADS)

    Wang, Chun-Hung; Duster, Adam W.; Aydintug, Baris O.; Zarecki, MacKenzie G.; Lin, Hai

    2018-03-01

    We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl– ion migration through the transmembrane domain of a prototypical E. coli CLC Cl–/H+ antiporter employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found critical to full access of the channel entrance by Cl–. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl– travelled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl– exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl– along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing pi bonds (e.g. the Tyr445 side chain), while the charges of the H atoms coordinating Cl– changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers ( 10 kcal/mol) than the MM PMF ( 2 kcal/mol). Binding energy calculations indicated that the interactions between Cl– and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing pi bonds, missing the stabilizations of the Cl– ion due to

  11. The Role of Magnesium for Geometry and Charge in GTP Hydrolysis, Revealed by Quantum Mechanics/Molecular Mechanics Simulations

    PubMed Central

    Rudack, Till; Xia, Fei; Schlitter, Jürgen; Kötting, Carsten; Gerwert, Klaus

    2012-01-01

    The coordination of the magnesium ion in proteins by triphosphates plays an important role in catalytic hydrolysis of GTP or ATP, either in signal transduction or energy conversion. For example, in Ras the magnesium ion contributes to the catalysis of GTP hydrolysis. The cleavage of GTP to GDP and Pi in Ras switches off cellular signaling. We analyzed GTP hydrolysis in water, Ras, and Ras·Ras-GTPase-activating protein using quantum mechanics/molecular mechanics simulations. By comparison of the theoretical IR-difference spectra for magnesium ion coordinated triphosphate to experimental ones, the simulations are validated. We elucidated thereby how the magnesium ion contributes to catalysis. It provides a temporary storage for the electrons taken from the triphosphate and it returns them after bond cleavage and Pi release back to the diphosphate. Furthermore, the Ras·Mg2+ complex forces the triphosphate into a stretched conformation in which the β- and γ-phosphates are coordinated in a bidentate manner. In this conformation, the triphosphate elongates the bond, which has to be cleaved during hydrolysis. Furthermore, the γ-phosphate adopts a more planar structure, driving the conformation of the molecule closer to the hydrolysis transition state. GTPase-activating protein enhances these changes in GTP conformation and charge distribution via the intruding arginine finger. PMID:22853907

  12. Quantum mechanical streamlines. I - Square potential barrier

    NASA Technical Reports Server (NTRS)

    Hirschfelder, J. O.; Christoph, A. C.; Palke, W. E.

    1974-01-01

    Exact numerical calculations are made for scattering of quantum mechanical particles hitting a square two-dimensional potential barrier (an exact analog of the Goos-Haenchen optical experiments). Quantum mechanical streamlines are plotted and found to be smooth and continuous, to have continuous first derivatives even through the classical forbidden region, and to form quantized vortices around each of the nodal points. A comparison is made between the present numerical calculations and the stationary wave approximation, and good agreement is found between both the Goos-Haenchen shifts and the reflection coefficients. The time-independent Schroedinger equation for real wavefunctions is reduced to solving a nonlinear first-order partial differential equation, leading to a generalization of the Prager-Hirschfelder perturbation scheme. Implications of the hydrodynamical formulation of quantum mechanics are discussed, and cases are cited where quantum and classical mechanical motions are identical.

  13. A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals

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

    Sinitskiy, Anton V.; Voth, Gregory A., E-mail: gavoth@uchicago.edu

    2015-09-07

    Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman’s imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionistmore » perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.« less

  14. A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals.

    PubMed

    Sinitskiy, Anton V; Voth, Gregory A

    2015-09-07

    Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman's imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionist perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.

  15. Are quantum-mechanical-like models possible, or necessary, outside quantum physics?

    NASA Astrophysics Data System (ADS)

    Plotnitsky, Arkady

    2014-12-01

    This article examines some experimental conditions that invite and possibly require recourse to quantum-mechanical-like mathematical models (QMLMs), models based on the key mathematical features of quantum mechanics, in scientific fields outside physics, such as biology, cognitive psychology, or economics. In particular, I consider whether the following two correlative features of quantum phenomena that were decisive for establishing the mathematical formalism of quantum mechanics play similarly important roles in QMLMs elsewhere. The first is the individuality and discreteness of quantum phenomena, and the second is the irreducibly probabilistic nature of our predictions concerning them, coupled to the particular character of the probabilities involved, as different from the character of probabilities found in classical physics. I also argue that these features could be interpreted in terms of a particular form of epistemology that suspends and even precludes a causal and, in the first place, realist description of quantum objects and processes. This epistemology limits the descriptive capacity of quantum theory to the description, classical in nature, of the observed quantum phenomena manifested in measuring instruments. Quantum mechanics itself only provides descriptions, probabilistic in nature, concerning numerical data pertaining to such phenomena, without offering a physical description of quantum objects and processes. While QMLMs share their use of the quantum-mechanical or analogous mathematical formalism, they may differ by the roles, if any, the two features in question play in them and by different ways of interpreting the phenomena they considered and this formalism itself. This article will address those differences as well.

  16. Elucidating reaction mechanisms on quantum computers.

    PubMed

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M; Wecker, Dave; Troyer, Matthias

    2017-07-18

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  17. Elucidating reaction mechanisms on quantum computers

    PubMed Central

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-01-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources. PMID:28674011

  18. Elucidating reaction mechanisms on quantum computers

    NASA Astrophysics Data System (ADS)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-07-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  19. Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

    PubMed

    Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

    2015-04-14

    We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

  20. Lectures on Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Weinberg, Steven

    2015-09-01

    Preface; Notation; 1. Historical introduction; 2. Particle states in a central potential; 3. General principles of quantum mechanics; 4. Spin; 5. Approximations for energy eigenstates; 6. Approximations for time-dependent problems; 7. Potential scattering; 8. General scattering theory; 9. The canonical formalism; 10. Charged particles in electromagnetic fields; 11. The quantum theory of radiation; 12. Entanglement; Author index; Subject index.

  1. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    PubMed

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  2. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

    PubMed

    Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

    2014-09-16

    Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine

  3. Quantum mechanical light harvesting mechanisms in photosynthesis

    NASA Astrophysics Data System (ADS)

    Scholes, Gregory

    2012-02-01

    More than 10 million billion photons of light strike a leaf each second. Incredibly, almost every red-coloured photon is captured by chlorophyll pigments and initiates steps to plant growth. Last year we reported that marine algae use quantum mechanics in order to optimize photosynthesis [1], a process essential to its survival. These and other insights from the natural world promise to revolutionize our ability to harness the power of the sun. In a recent review [2] we described the principles learned from studies of various natural antenna complexes and suggested how to utilize that knowledge to shape future technologies. We forecast the need to develop ways to direct and regulate excitation energy flow using molecular organizations that facilitate feedback and control--not easy given that the energy is only stored for a billionth of a second. In this presentation I will describe new results that explain the observation and meaning of quantum-coherent energy transfer. [4pt] [1] Elisabetta Collini, Cathy Y. Wong, Krystyna E. Wilk, Paul M. G. Curmi, Paul Brumer, and Gregory D. Scholes, ``Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature'' Nature 463, 644-648 (2010).[0pt] [2] Gregory D. Scholes, Graham R. Fleming, Alexandra Olaya-Castro and Rienk van Grondelle, ``Lessons from nature about solar light harvesting'' Nature Chem. 3, 763-774 (2011).

  4. Insights into photosystem II from isomorphous difference Fourier maps of femtosecond X-ray diffraction data and quantum mechanics/molecular mechanics structural models

    DOE PAGES

    Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W.; ...

    2017-01-12

    Understanding structure–function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metalmore » centers, and different kinetics of the S-state transition in microcrystals compared to solution. Lastly, we summarize recent advances and outstanding challenges in PSII structure–function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.« less

  5. Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models.

    PubMed

    Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

    2017-02-10

    Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metal centers, and different kinetics of the S-state transition in microcrystals compared to solution. Here, we summarize recent advances and outstanding challenges in PSII structure-function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.

  6. Insights into photosystem II from isomorphous difference Fourier maps of femtosecond X-ray diffraction data and quantum mechanics/molecular mechanics structural models

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

    Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W.

    Understanding structure–function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metalmore » centers, and different kinetics of the S-state transition in microcrystals compared to solution. Lastly, we summarize recent advances and outstanding challenges in PSII structure–function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.« less

  7. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

    PubMed

    Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

    2018-03-13

    Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

  8. Quantum Mechanical Study of Nanoscale MOSFET

    NASA Technical Reports Server (NTRS)

    Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan

    2001-01-01

    The steady state characteristics of MOSFETS that are of practical Interest are the drive current, off-current, dope of drain current versus drain voltage, and threshold voltage. In this section, we show that quantum mechanical simulations yield significantly different results from drift-diffusion based methods. These differences arise because of the following quantum mechanical features: (I) polysilicon gate depletion in a manner opposite to the classical case (II) dependence of the resonant levels in the channel on the gate voltage, (III) tunneling of charge across the gate oxide and from source to drain, (IV) quasi-ballistic flow of electrons. Conclusions dI/dV versus V does not increase in a manner commensurate with the increase in number of subbands. - The increase in dI/dV with bias is much smaller then the increase in the number of subbands - a consequence of bragg reflection. Our calculations show an increase in transmission with length of contact, as seen in experiments. It is desirable for molecular electronics applications to have a small contact area, yet large coupling. In this case, the circumferential dependence of the nanotube wave function dictates: - Transmission in armchair tubes saturates around unity - Transmission in zigzag tubes saturates at two.

  9. Analysis of ice-binding sites in fish type II antifreeze protein by quantum mechanics.

    PubMed

    Cheng, Yuhua; Yang, Zuoyin; Tan, Hongwei; Liu, Ruozhuang; Chen, Guangju; Jia, Zongchao

    2002-10-01

    Many organisms living in cold environments can survive subzero temperatures by producing antifreeze proteins (AFPs) or antifreeze glycoproteins. In this paper we investigate the ice-binding surface of type II AFP by quantum mechanical methods, which, to the best of our knowledge, represents the first time that molecular orbital computational approaches have been applied to AFPs. Molecular mechanical approaches, including molecular docking, energy minimization, and molecular dynamics simulation, were used to obtain optimal systems for subsequent quantum mechanical analysis. We selected 17 surface patches covering the entire surface of the type II AFP and evaluated the interaction energy between each of these patches and two different ice planes using semi-empirical quantum mechanical methods. We have demonstrated the weak orbital overlay phenomenon and the change of bond orders in ice. These results consistently indicate that a surface patch containing 19 residues (K37, L38, Y20, E22, Y21, I19, L57, T56, F53, M127, T128, F129, R17, C7, N6, P5, G10, Q1, and W11) is the most favorable ice-binding site for both a regular ice plane and an ice plane where water O atoms are randomly positioned. Furthermore, for the first time the computation results provide new insights into the weakening of the ice lattice upon AFP binding, which may well be a primary factor leading to AFP-induced ice growth inhibition.

  10. Analysis of ice-binding sites in fish type II antifreeze protein by quantum mechanics.

    PubMed Central

    Cheng, Yuhua; Yang, Zuoyin; Tan, Hongwei; Liu, Ruozhuang; Chen, Guangju; Jia, Zongchao

    2002-01-01

    Many organisms living in cold environments can survive subzero temperatures by producing antifreeze proteins (AFPs) or antifreeze glycoproteins. In this paper we investigate the ice-binding surface of type II AFP by quantum mechanical methods, which, to the best of our knowledge, represents the first time that molecular orbital computational approaches have been applied to AFPs. Molecular mechanical approaches, including molecular docking, energy minimization, and molecular dynamics simulation, were used to obtain optimal systems for subsequent quantum mechanical analysis. We selected 17 surface patches covering the entire surface of the type II AFP and evaluated the interaction energy between each of these patches and two different ice planes using semi-empirical quantum mechanical methods. We have demonstrated the weak orbital overlay phenomenon and the change of bond orders in ice. These results consistently indicate that a surface patch containing 19 residues (K37, L38, Y20, E22, Y21, I19, L57, T56, F53, M127, T128, F129, R17, C7, N6, P5, G10, Q1, and W11) is the most favorable ice-binding site for both a regular ice plane and an ice plane where water O atoms are randomly positioned. Furthermore, for the first time the computation results provide new insights into the weakening of the ice lattice upon AFP binding, which may well be a primary factor leading to AFP-induced ice growth inhibition. PMID:12324437

  11. The transactional interpretation of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Cramer, John G.

    2001-06-01

    The transactional interpretation of quantum mechanics [1] was originally published in 1986 and is now about 14 years old. It is an explicitly nonlocal and Lorentz invariant alternative to the Copenhagen interpretation. It interprets the formalism for a quantum interaction as describing a "handshake" between retarded waves (ψ) and advanced waves (ψ*) for each quantum event or "transaction" in which energy, momentum, angular momentum, and other conserved quantities are transferred. The transactional interpretation offers the advantages that (1) it is actually "visible" in the formalism of quantum mechanics, (2) it is economical, involving fewer independent assumptions than its rivals, (3) it is paradox-free, resolving all of the paradoxes of standard quantum theory including nonlocality and wave function collapse, (4) it does not give a privileged role to observers or measurements, and (5) it permits the visualization of quantum events. We will review the transactional interpretation and some of its applications to "quantum paradoxes."

  12. A multilayered-representation quantum mechanical/molecular mechanics study of the SN2 reaction of CH3Br + OH- in aqueous solution

    NASA Astrophysics Data System (ADS)

    Xu, Yulong; Wang, Tingting; Wang, Dunyou

    2012-11-01

    The bimolecular nucleophilic substitution (SN2) reaction of CH3Br and OH- in aqueous solution was investigated using a multilayered-representation quantum mechanical and molecular mechanics methodology. Reactant complex, transition state, and product complex are identified and characterized in aqueous solution. The potentials of mean force are computed under both the density function theory and coupled-cluster single double (triple) (CCSD(T)) levels of theory for the reaction region. The results show that the aqueous environment has a significant impact on the reaction process. The solvation effect and the polarization effect combined raise the activation barrier height by ˜16.2 kcal/mol and the solvation effect is the dominant contribution to the potential of mean force. The CCSD(T)/MM representation presents a free energy activation barrier height of 22.8 kcal/mol and the rate constant at 298 K of 3.7 × 10-25 cm3 molecule-1 s-1 which agree very well with the experiment values at 23.0 kcal/mol and 2.6 × 10-25 cm3 molecule-1 s-1, respectively.

  13. Explicit polarization: a quantum mechanical framework for developing next generation force fields.

    PubMed

    Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel

    2014-09-16

    Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples

  14. Quantum mechanics in complex systems

    NASA Astrophysics Data System (ADS)

    Hoehn, Ross Douglas

    . These nodes are spaced far enough from each other to minimized the electronic repulsion of the electrons, while still providing adequate enough attraction so as to bind the excess elections into orbitals. We have found that even with relativistic considerations these species are stably bound within the field. It was also found that performing the dimensional scaling calculations for systems within the confines of laser fields to be a much simpler and more cost-effective method than the supporting D=3 SCF method. The dimensional scaling method is general and can be extended to include relativistic corrections to describe the stability of simple molecular systems in super-intense laser fields. Chapter 3, we delineate the model, and aspects therein, of inelastic electron tunneling and map this model to the protein environment. G protein-coupled receptors (GPCRs) constitute a large family of receptors that sense molecules outside of a cell and activate signal transduction pathways inside the cell. Modeling how an agonist activates such a receptor is important for understanding a wide variety of physiological processes and it is of tremendous value for pharmacology and drug design. Inelastic electron tunneling spectroscopy (IETS) has been proposed as the mechanism by which olfactory GPCRs are activated by an encapsulated agonist. In this note we apply this notion to GPCRs within the mammalian nervous system using ab initio quantum chemical modeling. We found that non-endogenous agonists of the serotonin receptor share a singular IET spectral aspect both amongst each other and with the serotonin molecule: a peak that scales in intensity with the known agonist activities. We propose an experiential validation of this model by utilizing lysergic acid dimethylamide (DAM-57), an ergot derivative, and its isotopologues in which hydrogen atoms are replaced by deuterium. If validated our theory may provide new avenues for guided drug design and better in silico prediction of

  15. Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study.

    PubMed

    Dong, Minghui; Liu, Haiyan

    2008-08-21

    The Escherichia coli peptide deformylase (PDF) and Bacillus thermoproteolyticus thermolysin (TLN) are two representative metal-requiring peptidases having remarkably similar active centers but distinctively different metal preferences. Zinc is a competent catalytic cofactor for TLN but not for PDF. Reaction pathways and the associated energetics for both enzymes were determined using combined semiempirical and ab initio quantum mechanical/molecular mechanical modeling, without presuming reaction coordinates. The results confirmed that both enzymes catalyze via the same chemical steps, and reproduced their different preferences for zinc or iron as competent cofactors. Further analyses indicated that different feasibility of the nucleophilic attack step leads to different metal preferences of the two enzymes. In TLN, the substrate is strongly activated and can serve as the fifth coordination ligand of zinc prior to the chemical steps. In PDF, the substrate carbonyl is activated by the chemical step itself, and becomes the fifth coordination partner of zinc only in a later stage of the nucleophilic attack. These leads to a much more difficult nucleophilic attack in PDF than in TLN. Different from some earlier suggestions, zinc has no difficulty in accepting an activated substrate as the fifth ligand to switch from tetra- to penta-coordination in either PDF or TLN. When iron replaces zinc, its stronger interaction with the hydroxide ligand may lead to higher activation barrier in TLN. In PDF, the stronger interactions of iron with ligands allow iron-substrate coordination to take place either before or at a very early stage of the chemical step, leading to effective catalysis. Our calculations also show combined semiempirical and ab initio quantum mechanical modeling can be efficient approaches to explore complicated reaction pathways in enzyme systems.

  16. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

    PubMed

    Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

    2016-07-14

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

  17. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface

    NASA Astrophysics Data System (ADS)

    Löytynoja, T.; Li, X.; Jänkälä, K.; Rinkevicius, Z.; Ågren, H.

    2016-07-01

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

  18. On the hypothesis that quantum mechanism manifests classical mechanics: Numerical approach to the correspondence in search of quantum chaos

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

    Lee, Sang-Bong

    1993-09-01

    Quantum manifestation of classical chaos has been one of the extensively studied subjects for more than a decade. Yet clear understanding of its nature still remains to be an open question partly due to the lack of a canonical definition of quantum chaos. The classical definition seems to be unsuitable in quantum mechanics partly because of the Heisenberg quantum uncertainty. In this regard, quantum chaos is somewhat misleading and needs to be clarified at the very fundamental level of physics. Since it is well known that quantum mechanics is more fundamental than classical mechanics, the quantum description of classically chaoticmore » nature should be attainable in the limit of large quantum numbers. The focus of my research, therefore, lies on the correspondence principle for classically chaotic systems. The chaotic damped driven pendulum is mainly studied numerically using the split operator method that solves the time-dependent Schroedinger equation. For classically dissipative chaotic systems in which (multi)fractal strange attractors often emerge, several quantum dissipative mechanisms are also considered. For instance, Hoover`s and Kubo-Fox-Keizer`s approaches are studied with some computational analyses. But the notion of complex energy with non-Hermiticity is extensively applied. Moreover, the Wigner and Husimi distribution functions are examined with an equivalent classical distribution in phase-space, and dynamical properties of the wave packet in configuration and momentum spaces are also explored. The results indicate that quantum dynamics embraces classical dynamics although the classicalquantum correspondence fails to be observed in the classically chaotic regime. Even in the semi-classical limits, classically chaotic phenomena would eventually be suppressed by the quantum uncertainty.« less

  19. Symmetry aspects in emergent quantum mechanics

    NASA Astrophysics Data System (ADS)

    Elze, Hans-Thomas

    2009-06-01

    We discuss an explicit realization of the dissipative dynamics anticipated in the proof of 't Hooft's existence theorem, which states that 'For any quantum system there exists at least one deterministic model that reproduces all its dynamics after prequantization'. - There is an energy-parity symmetry hidden in the Liouville equation, which mimics the Kaplan-Sundrum protective symmetry for the cosmological constant. This symmetry may be broken by the coarse-graining inherent in physics at scales much larger than the Planck length. We correspondingly modify classical ensemble theory by incorporating dissipative fluctuations (information loss) - which are caused by discrete spacetime continually 'measuring' matter. In this way, aspects of quantum mechanics, such as the von Neumann equation, including a Lindblad term, arise dynamically and expectations of observables agree with the Born rule. However, the resulting quantum coherence is accompanied by an intrinsic decoherence and continuous localization mechanism. Our proposal leads towards a theory that is linear and local at the quantum mechanical level, but the relation to the underlying classical degrees of freedom is nonlocal.

  20. On the geometrization of quantum mechanics

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

    Tavernelli, Ivano, E-mail: ita@zurich.ibm.com

    Nonrelativistic quantum mechanics is commonly formulated in terms of wavefunctions (probability amplitudes) obeying the static and the time-dependent Schrödinger equations (SE). Despite the success of this representation of the quantum world a wave–particle duality concept is required to reconcile the theory with observations (experimental measurements). A first solution to this dichotomy was introduced in the de Broglie–Bohm theory according to which a pilot-wave (solution of the SE) is guiding the evolution of particle trajectories. Here, I propose a geometrization of quantum mechanics that describes the time evolution of particles as geodesic lines in a curved space, whose curvature is inducedmore » by the quantum potential. This formulation allows therefore the incorporation of all quantum effects into the geometry of space–time, as it is the case for gravitation in the general relativity.« less

  1. Evolution from S3 to S4 States of the Oxygen-Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics.

    PubMed

    Narzi, Daniele; Capone, Matteo; Bovi, Daniele; Guidoni, Leonardo

    2018-04-16

    Water oxidation in the early steps of natural photosynthesis is fulfilled by photosystem II, which is a protein complex embedded in the thylakoid membrane inside chloroplasts. The water oxidation reaction occurs in the catalytic core of photosystem II, which consists of a Mn4Ca metal cluster, at which, after the accumulation of four oxidising equivalents through five steps (S0-S4) of the Kok-Joliot cycle, two water molecules are split into electrons, protons, and molecular oxygen. In recent years, by combining experimental and theoretical approaches, new insights have been achieved into the structural and electronic properties of different steps of the catalytic cycle. Nevertheless, the exact catalytic mechanism, especially concerning the final stages of the cycle, remains elusive and greatly debated. Herein, by means of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, from the structural, electronic, and magnetic points of view, the S 3 state before and upon oxidation has been characterised. In contrast with the S 2 state, the oxidation of the S 3 state is not followed by a spontaneous proton-coupled electron-transfer event. Nevertheless, upon modelling the reduction of the tyrosine residue in photosystem II (Tyr Z ) and the protonation of Asp61, spontaneous proton transfer occurs, leading to the deprotonation of an oxygen atom bound to Mn1; thus making it available for O-O bond formation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations.

    PubMed

    Dyekjaer, Jane Dannow; Jónsdóttir, Svava Osk

    2004-01-22

    Quantitative Structure-Property Relationships (QSPR) have been developed for a series of monosaccharides, including the physical properties of partial molar heat capacity, heat of solution, melting point, heat of fusion, glass-transition temperature, and solid state density. The models were based on molecular descriptors obtained from molecular mechanics and quantum chemical calculations, combined with other types of descriptors. Saccharides exhibit a large degree of conformational flexibility, therefore a methodology for selecting the energetically most favorable conformers has been developed, and was used for the development of the QSPR models. In most cases good correlations were obtained for monosaccharides. For five of the properties predictions were made for disaccharides, and the predicted values for the partial molar heat capacities were in excellent agreement with experimental values.

  3. A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution.

    PubMed

    Lv, Jing; Zhang, Jingxue; Wang, Dunyou

    2016-02-17

    We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).

  4. A quantum protective mechanism in photosynthesis

    NASA Astrophysics Data System (ADS)

    Marais, Adriana; Sinayskiy, Ilya; Petruccione, Francesco; van Grondelle, Rienk

    2015-03-01

    Since the emergence of oxygenic photosynthesis, living systems have developed protective mechanisms against reactive oxygen species. During charge separation in photosynthetic reaction centres, triplet states can react with molecular oxygen generating destructive singlet oxygen. The triplet product yield in bacteria is observed to be reduced by weak magnetic fields. Reaction centres from plants' photosystem II share many features with bacterial reaction centres, including a high-spin iron whose function has remained obscure. To explain observations that the magnetic field effect is reduced by the iron, we propose that its fast-relaxing spin plays a protective role in photosynthesis by generating an effective magnetic field. We consider a simple model of the system, derive an analytical expression for the effective magnetic field and analyse the resulting triplet yield reduction. The protective mechanism is robust for realistic parameter ranges, constituting a clear example of a quantum effect playing a macroscopic role vital for life.

  5. A quantum protective mechanism in photosynthesis.

    PubMed

    Marais, Adriana; Sinayskiy, Ilya; Petruccione, Francesco; van Grondelle, Rienk

    2015-03-03

    Since the emergence of oxygenic photosynthesis, living systems have developed protective mechanisms against reactive oxygen species. During charge separation in photosynthetic reaction centres, triplet states can react with molecular oxygen generating destructive singlet oxygen. The triplet product yield in bacteria is observed to be reduced by weak magnetic fields. Reaction centres from plants' photosystem II share many features with bacterial reaction centres, including a high-spin iron whose function has remained obscure. To explain observations that the magnetic field effect is reduced by the iron, we propose that its fast-relaxing spin plays a protective role in photosynthesis by generating an effective magnetic field. We consider a simple model of the system, derive an analytical expression for the effective magnetic field and analyse the resulting triplet yield reduction. The protective mechanism is robust for realistic parameter ranges, constituting a clear example of a quantum effect playing a macroscopic role vital for life.

  6. Quantum mechanics and hidden superconformal symmetry

    NASA Astrophysics Data System (ADS)

    Bonezzi, R.; Corradini, O.; Latini, E.; Waldron, A.

    2017-12-01

    Solvability of the ubiquitous quantum harmonic oscillator relies on a spectrum generating osp (1 |2 ) superconformal symmetry. We study the problem of constructing all quantum mechanical models with a hidden osp (1 |2 ) symmetry on a given space of states. This problem stems from interacting higher spin models coupled to gravity. In one dimension, we show that the solution to this problem is the Vasiliev-Plyushchay family of quantum mechanical models with hidden superconformal symmetry obtained by viewing the harmonic oscillator as a one dimensional Dirac system, so that Grassmann parity equals wave function parity. These models—both oscillator and particlelike—realize all possible unitary irreducible representations of osp (1 |2 ).

  7. Fritz London and the scale of quantum mechanisms

    NASA Astrophysics Data System (ADS)

    Monaldi, Daniela

    2017-11-01

    Fritz London's seminal idea of ;quantum mechanisms of macroscopic scale;, first articulated in 1946, was the unanticipated result of two decades of research, during which London pursued quantum-mechanical explanations of various kinds of systems of particles at different scales. He started at the microphysical scale with the hydrogen molecule, generalized his approach to chemical bonds and intermolecular forces, then turned to macrophysical systems like superconductors and superfluid helium. Along this path, he formulated a set of concepts-the quantum mechanism of exchange, the rigidity of the wave function, the role of quantum statistics in multi-particle systems, the possibility of order in momentum space-that eventually coalesced into a new conception of systems of equal particles. In particular, it was London's clarification of Bose-Einstein condensation that enabled him to formulate the notion of superfluids, and led him to the recognition that quantum mechanics was not, as it was commonly assumed, relevant exclusively as a micromechanics.

  8. Variational and perturbative formulations of quantum mechanical/molecular mechanical free energy with mean-field embedding and its analytical gradients.

    PubMed

    Yamamoto, Takeshi

    2008-12-28

    Conventional quantum chemical solvation theories are based on the mean-field embedding approximation. That is, the electronic wavefunction is calculated in the presence of the mean field of the environment. In this paper a direct quantum mechanical/molecular mechanical (QM/MM) analog of such a mean-field theory is formulated based on variational and perturbative frameworks. In the variational framework, an appropriate QM/MM free energy functional is defined and is minimized in terms of the trial wavefunction that best approximates the true QM wavefunction in a statistically averaged sense. Analytical free energy gradient is obtained, which takes the form of the gradient of effective QM energy calculated in the averaged MM potential. In the perturbative framework, the above variational procedure is shown to be equivalent to the first-order expansion of the QM energy (in the exact free energy expression) about the self-consistent reference field. This helps understand the relation between the variational procedure and the exact QM/MM free energy as well as existing QM/MM theories. Based on this, several ways are discussed for evaluating non-mean-field effects (i.e., statistical fluctuations of the QM wavefunction) that are neglected in the mean-field calculation. As an illustration, the method is applied to an S(N)2 Menshutkin reaction in water, NH(3)+CH(3)Cl-->NH(3)CH(3) (+)+Cl(-), for which free energy profiles are obtained at the Hartree-Fock, MP2, B3LYP, and BHHLYP levels by integrating the free energy gradient. Non-mean-field effects are evaluated to be <0.5 kcal/mol using a Gaussian fluctuation model for the environment, which suggests that those effects are rather small for the present reaction in water.

  9. Einstein's equivalence principle in quantum mechanics revisited

    NASA Astrophysics Data System (ADS)

    Nauenberg, Michael

    2016-11-01

    The gravitational equivalence principle in quantum mechanics is of considerable importance, but it is generally not included in physics textbooks. In this note, we present a precise quantum formulation of this principle and comment on its verification in a neutron diffraction experiment. The solution of the time dependent Schrödinger equation for this problem also gives the wave function for the motion of a charged particle in a homogeneous electric field, which is also usually ignored in textbooks on quantum mechanics.

  10. Quantum mechanics and reality: An interpretation of Everett's theory

    NASA Astrophysics Data System (ADS)

    Lehner, Christoph Albert

    The central part of Everett's formulation of quantum mechanics is a quantum mechanical model of memory and of observation as the recording of information in a memory. To use this model as an answer to the measurement problem, Everett has to assume that a conscious observer can be in a superposition of such memory states and be unaware of it. This assumption has puzzled generations of readers. The fundamental aim of this dissertation is to find a set of simpler assumptions which are sufficient to show that Everett's model is empirically adequate. I argue that Everett's model needs three assumptions to account for the process of observation: an assumption of decoherence of observers as quantum mechanical systems; an assumption of supervenience of mental states (qualities) over quantum mechanical properties; and an assumption about the interpretation of quantum mechanical states in general: quantum mechanical states describe ensembles of states of affairs coexisting in the same system. I argue that the only plausible understanding of such ensembles is as ensembles of possibilities, and that all standard no-collapse interpretations agree in this reading of quantum mechanical states. Their differences can be understood as different theories about what marks the real state within this ensemble, and Everett's theory as the claim that no additional 'mark of reality' is necessary. Using the three assumptions, I argue that introspection cannot determine the objective quantum mechanical state of an observer. Rather, the introspective qualities of a quantum mechanical state can be represented by a (classical) statistical ensemble of subjective states. An analysis of these subjective states and their dynamics leads to the conclusion that they suffice to give empirically correct predictions. The argument for the empirical adequacy of the subjective state entails that knowledge of the objective quantum mechanical state is impossible in principle. Empirical reality for a conscious

  11. Generalized Weyl-Wigner map and Vey quantum mechanics

    NASA Astrophysics Data System (ADS)

    Dias, Nuno Costa; Prata, João Nuno

    2001-12-01

    The Weyl-Wigner map yields the entire structure of Moyal quantum mechanics directly from the standard operator formulation. The covariant generalization of Moyal theory, also known as Vey quantum mechanics, was presented in the literature many years ago. However, a derivation of the formalism directly from standard operator quantum mechanics, clarifying the relation between the two formulations, is still missing. In this article we present a covariant generalization of the Weyl order prescription and of the Weyl-Wigner map and use them to derive Vey quantum mechanics directly from the standard operator formulation. The procedure displays some interesting features: it yields all the key ingredients and provides a more straightforward interpretation of the Vey theory including a direct implementation of unitary operator transformations as phase space coordinate transformations in the Vey idiom. These features are illustrated through a simple example.

  12. Estimation of the Young’s modulus of cellulose Iß by MM3 and quantum mechanics

    USDA-ARS?s Scientific Manuscript database

    Young’s modulus provides a measure of the resistance to deformation of an elastic material. In this study, modulus estimations for models of cellulose Iß relied on calculations performed with molecular mechanics (MM) and quantum mechanics (QM) programs. MM computations used the second generation emp...

  13. Many-Body Localization and Thermalization in Quantum Statistical Mechanics

    NASA Astrophysics Data System (ADS)

    Nandkishore, Rahul; Huse, David A.

    2015-03-01

    We review some recent developments in the statistical mechanics of isolated quantum systems. We provide a brief introduction to quantum thermalization, paying particular attention to the eigenstate thermalization hypothesis (ETH) and the resulting single-eigenstate statistical mechanics. We then focus on a class of systems that fail to quantum thermalize and whose eigenstates violate the ETH: These are the many-body Anderson-localized systems; their long-time properties are not captured by the conventional ensembles of quantum statistical mechanics. These systems can forever locally remember information about their local initial conditions and are thus of interest for possibilities of storing quantum information. We discuss key features of many-body localization (MBL) and review a phenomenology of the MBL phase. Single-eigenstate statistical mechanics within the MBL phase reveal dynamically stable ordered phases, and phase transitions among them, that are invisible to equilibrium statistical mechanics and can occur at high energy and low spatial dimensionality, where equilibrium ordering is forbidden.

  14. Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface.

    PubMed

    Li, Hongzhi; Yang, Wei

    2007-03-21

    An approach is developed in the replica exchange framework to enhance conformational sampling for the quantum mechanical (QM) potential based molecular dynamics simulations. Importantly, with our enhanced sampling treatment, a decent convergence for electronic structure self-consistent-field calculation is robustly guaranteed, which is made possible in our replica exchange design by avoiding direct structure exchanges between the QM-related replicas and the activated (scaled by low scaling parameters or treated with high "effective temperatures") molecular mechanical (MM) replicas. Although the present approach represents one of the early efforts in the enhanced sampling developments specifically for quantum mechanical potentials, the QM-based simulations treated with the present technique can possess the similar sampling efficiency to the MM based simulations treated with the Hamiltonian replica exchange method (HREM). In the present paper, by combining this sampling method with one of our recent developments (the dual-topology alchemical HREM approach), we also introduce a method for the sampling enhanced QM-based free energy calculations.

  15. Faithful conversion of propagating quantum information to mechanical motion

    NASA Astrophysics Data System (ADS)

    Reed, A. P.; Mayer, K. H.; Teufel, J. D.; Burkhart, L. D.; Pfaff, W.; Reagor, M.; Sletten, L.; Ma, X.; Schoelkopf, R. J.; Knill, E.; Lehnert, K. W.

    2017-12-01

    The motion of micrometre-sized mechanical resonators can now be controlled and measured at the fundamental limits imposed by quantum mechanics. These resonators have been prepared in their motional ground state or in squeezed states, measured with quantum-limited precision, and even entangled with microwave fields. Such advances make it possible to process quantum information using the motion of a macroscopic object. In particular, recent experiments have combined mechanical resonators with superconducting quantum circuits to frequency-convert, store and amplify propagating microwave fields. But these systems have not been used to manipulate states that encode quantum bits (qubits), which are required for quantum communication and modular quantum computation. Here we demonstrate the conversion of propagating qubits encoded as superpositions of zero and one photons to the motion of a micromechanical resonator with a fidelity in excess of the classical bound. This ability is necessary for mechanical resonators to convert quantum information between the microwave and optical domains or to act as storage elements in a modular quantum information processor. Additionally, these results are an important step towards testing speculative notions that quantum theory may not be valid for sufficiently massive systems.

  16. Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn4CaO5 cluster in photosystem II.

    PubMed

    Nakamura, Shin; Noguchi, Takumi

    2016-10-11

    During photosynthesis, the light-driven oxidation of water performed by photosystem II (PSII) provides electrons necessary to fix CO 2 , in turn supporting life on Earth by liberating molecular oxygen. Recent high-resolution X-ray images of PSII show that the water-oxidizing center (WOC) is composed of an Mn 4 CaO 5 cluster with six carboxylate, one imidazole, and four water ligands. FTIR difference spectroscopy has shown significant structural changes of the WOC during the S-state cycle of water oxidation, especially within carboxylate groups. However, the roles that these carboxylate groups play in water oxidation as well as how they should be properly assigned in spectra are unresolved. In this study, we performed a normal mode analysis of the WOC using the quantum mechanics/molecular mechanics (QM/MM) method to simulate FTIR difference spectra on the S 1 to S 2 transition in the carboxylate stretching region. By evaluating WOC models with different oxidation and protonation states, we determined that models of high-oxidation states, Mn(III) 2 Mn(IV) 2 , satisfactorily reproduced experimental spectra from intact and Ca-depleted PSII compared with low-oxidation models. It is further suggested that the carboxylate groups bridging Ca and Mn ions within this center tune the reactivity of water ligands bound to Ca by shifting charge via their π conjugation.

  17. Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

    PubMed Central

    Náray-Szabó, Gábor; Oláh, Julianna; Krámos, Balázs

    2013-01-01

    Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods. PMID:24970187

  18. [Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

    PubMed

    Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

    2013-01-01

    To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

  19. Individuation in Quantum Mechanics and Space-Time

    NASA Astrophysics Data System (ADS)

    Jaeger, Gregg

    2010-10-01

    Two physical approaches—as distinct, under the classification of Mittelstaedt, from formal approaches—to the problem of individuation of quantum objects are considered, one formulated in spatiotemporal terms and one in quantum mechanical terms. The spatiotemporal approach itself has two forms: one attributed to Einstein and based on the ontology of space-time points, and the other proposed by Howard and based on intersections of world lines. The quantum mechanical approach is also provided here in two forms, one based on interference and another based on a new Quantum Principle of Individuation (QPI). It is argued that the space-time approach to individuation fails and that the quantum approach offers several advantages over it, including consistency with Leibniz’s Principle of Identity of Indiscernibles.

  20. Quantum mechanics of black holes.

    PubMed

    Witten, Edward

    2012-08-03

    The popular conception of black holes reflects the behavior of the massive black holes found by astronomers and described by classical general relativity. These objects swallow up whatever comes near and emit nothing. Physicists who have tried to understand the behavior of black holes from a quantum mechanical point of view, however, have arrived at quite a different picture. The difference is analogous to the difference between thermodynamics and statistical mechanics. The thermodynamic description is a good approximation for a macroscopic system, but statistical mechanics describes what one will see if one looks more closely.

  1. Understanding molecular structure from molecular mechanics.

    PubMed

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  2. Hybrid quantum and molecular mechanics embedded cluster models for chemistry on silicon and silicon carbide surfaces

    NASA Astrophysics Data System (ADS)

    Shoemaker, James Richard

    Fabrication of silicon carbide (SiC) semiconductor devices are of interest for aerospace applications because of their high-temperature tolerance. Growth of an insulating SiO2 layer on SiC by oxidation is a poorly understood process, and sometimes produces interface defects that degrade device performance. Accurate theoretical models of surface chemistry, using quantum mechanics (QM), do not exist because of the huge computational cost of solving Schrodinger's equation for a molecular cluster large enough to represent a surface. Molecular mechanics (MM), which describes a molecule as a collection of atoms interacting through classical potentials, is a fast computational method, good at predicting molecular structure, but cannot accurately model chemical reactions. A new hybrid QM/MM computational method for surface chemistry was developed and applied to silicon and SiC surfaces. The addition of MM steric constraints was shown to have a large effect on the energetics of O atom adsorption on SiC. Adsorption of O atoms on Si-terminated SiC(111) favors above surface sites, in contrast to Si(111), but favors subsurface adsorption sites on C- terminated SiC(111). This difference, and the energetics of C atom etching via CO2 desorption, can explain the observed poor performance of SiC devices in which insulating layers were grown on C-terminated surfaces.

  3. Quantum-mechanical transport equation for atomic systems.

    NASA Technical Reports Server (NTRS)

    Berman, P. R.

    1972-01-01

    A quantum-mechanical transport equation (QMTE) is derived which should be applicable to a wide range of problems involving the interaction of radiation with atoms or molecules which are also subject to collisions with perturber atoms. The equation follows the time evolution of the macroscopic atomic density matrix elements of atoms located at classical position R and moving with classical velocity v. It is quantum mechanical in the sense that all collision kernels or rates which appear have been obtained from a quantum-mechanical theory and, as such, properly take into account the energy-level variations and velocity changes of the active (emitting or absorbing) atom produced in collisions with perturber atoms. The present formulation is better suited to problems involving high-intensity external fields, such as those encountered in laser physics.

  4. On the quantum mechanics of consciousness, with application to anomalous phenomena

    NASA Astrophysics Data System (ADS)

    Jahn, Robert G.; Dunne, Brenda J.

    1986-08-01

    Theoretical explication of a growing body of empirical data on consciousness-related anomalous phenomena is unlikely to be achieved in terms of known physical processes. Rather, it will first be necessary to formulate the basic role of consciousness in the definition of reality before such anomalous experience can adequately be represented. This paper takes the position that reality is constituted only in the interaction of consciousness with its environment, and therefore that any scheme of conceptual organization developed to represent that reality must reflect the processes of consciousness as well as those of its environment. In this spirit, the concepts and formalisms of elementary quantum mechanics, as originally proposed to explain anomalous atomic-scale physical phenomena, are appropriated via metaphor to represent the general characteristics of consciousness interacting with any environment. More specifically, if consciousness is represented by a quantum mechanical wave function, and its environment by an appropriate potential profile, Schrödinger wave mechanics defines eigenfunctions and eigenvalues that can be associated with the cognitive and emotional experiences of that consciousness in that environment. To articulate this metaphor it is necessary to associate certain aspects of the formalism, such as the coordinate system, the quantum numbers, and even the metric itself, with various impressionistic descriptors of consciousness, such as its intensity, perspective, approach/avoidance attitude, balance between cognitive and emotional activity, and receptive/assertive disposition. With these established, a number of the generic features of quantum mechanics, such as the wave/particle duality, and the uncertainty, indistinguishability, and exclusion principles, display metaphoric relevance to familiar individual and collective experiences. Similarly, such traditional quantum theoretic exercises as the central force field and atomic structure, covalent

  5. Nilpotent Quantum Mechanics: Analogues and Applications

    NASA Astrophysics Data System (ADS)

    Marcer, Peter; Rowlands, Peter

    2017-07-01

    The most significant characteristic of nilpotent quantum mechanics is that the quantum system (fermion state) and its environment (vacuum) are, in mathematical terms, mirror images of each other. So a change in one automatically leads to corresponding changes in the other. We have used this characteristic as a model for self-organization, which has applications well beyond quantum physics. The nilpotent structure has also been identified as being constructed from two commutative vector spaces. This construction has a number of identifiable characteristics which we can expect to find in systems where self-organization is dominant, and a case presented after the publication of a paper by us on ‘The ‘Logic’ of Self-Organizing Systems’,1 in the organization of the neurons in the visual cortex. We expect to find many more complex systems where our general principles, based, by analogy, on nilpotent quantum mechanics, will apply.

  6. Conceptual Foundations of Quantum Mechanics:. the Role of Evidence Theory, Quantum Sets, and Modal Logic

    NASA Astrophysics Data System (ADS)

    Resconi, Germano; Klir, George J.; Pessa, Eliano

    Recognizing that syntactic and semantic structures of classical logic are not sufficient to understand the meaning of quantum phenomena, we propose in this paper a new interpretation of quantum mechanics based on evidence theory. The connection between these two theories is obtained through a new language, quantum set theory, built on a suggestion by J. Bell. Further, we give a modal logic interpretation of quantum mechanics and quantum set theory by using Kripke's semantics of modal logic based on the concept of possible worlds. This is grounded on previous work of a number of researchers (Resconi, Klir, Harmanec) who showed how to represent evidence theory and other uncertainty theories in terms of modal logic. Moreover, we also propose a reformulation of the many-worlds interpretation of quantum mechanics in terms of Kripke's semantics. We thus show how three different theories — quantum mechanics, evidence theory, and modal logic — are interrelated. This opens, on one hand, the way to new applications of quantum mechanics within domains different from the traditional ones, and, on the other hand, the possibility of building new generalizations of quantum mechanics itself.

  7. Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

    NASA Astrophysics Data System (ADS)

    Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

    2012-01-01

    Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

  8. Amino acid analogues bind to carbon nanotube via π-π interactions: comparison of molecular mechanical and quantum mechanical calculations.

    PubMed

    Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

    2012-01-14

    Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

  9. What is Quantum Mechanics? A Minimal Formulation

    NASA Astrophysics Data System (ADS)

    Friedberg, R.; Hohenberg, P. C.

    2018-03-01

    This paper presents a minimal formulation of nonrelativistic quantum mechanics, by which is meant a formulation which describes the theory in a succinct, self-contained, clear, unambiguous and of course correct manner. The bulk of the presentation is the so-called "microscopic theory", applicable to any closed system S of arbitrary size N, using concepts referring to S alone, without resort to external apparatus or external agents. An example of a similar minimal microscopic theory is the standard formulation of classical mechanics, which serves as the template for a minimal quantum theory. The only substantive assumption required is the replacement of the classical Euclidean phase space by Hilbert space in the quantum case, with the attendant all-important phenomenon of quantum incompatibility. Two fundamental theorems of Hilbert space, the Kochen-Specker-Bell theorem and Gleason's theorem, then lead inevitably to the well-known Born probability rule. For both classical and quantum mechanics, questions of physical implementation and experimental verification of the predictions of the theories are the domain of the macroscopic theory, which is argued to be a special case or application of the more general microscopic theory.

  10. Effective equations for the quantum pendulum from momentous quantum mechanics

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

    Hernandez, Hector H.; Chacon-Acosta, Guillermo; Departamento de Matematicas Aplicadas y Sistemas, Universidad Autonoma Metropolitana-Cuajimalpa, Artificios 40, Mexico D. F. 01120

    In this work we study the quantum pendulum within the framework of momentous quantum mechanics. This description replaces the Schroedinger equation for the quantum evolution of the system with an infinite set of classical equations for expectation values of configuration variables, and quantum dispersions. We solve numerically the effective equations up to the second order, and describe its evolution.

  11. Decoherence in quantum mechanics and quantum cosmology

    NASA Technical Reports Server (NTRS)

    Hartle, James B.

    1992-01-01

    A sketch of the quantum mechanics for closed systems adequate for cosmology is presented. This framework is an extension and clarification of that of Everett and builds on several aspects of the post-Everett development. It especially builds on the work of Zeh, Zurek, Joos and Zeh, and others on the interactions of quantum systems with the larger universe and on the ideas of Griffiths, Omnes, and others on the requirements for consistent probabilities of histories.

  12. Quantum Information Biology: From Information Interpretation of Quantum Mechanics to Applications in Molecular Biology and Cognitive Psychology

    NASA Astrophysics Data System (ADS)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    2015-10-01

    We discuss foundational issues of quantum information biology (QIB)—one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from "traditional quantum biophysics". The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the information interpretation of quantum mechanics (its various forms were elaborated by Zeilinger and Brukner, Fuchs and Mermin, and D' Ariano) is the most natural interpretation of QIB. Biologically QIB is based on two principles: (a) adaptivity; (b) openness (bio-systems are fundamentally open). These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems.

  13. Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation.

    PubMed

    Matubayasi, Nobuyuki; Takahashi, Hideaki

    2012-01-28

    The relationship is investigated for QM/MM (quantum-mechanical/molecular-mechanical) systems between the fluctuations of the electronic state of the QM subsystem and of the solvation effect due to the QM-MM interaction. The free-energy change due to the electron-density fluctuation around its average is highlighted, and is evaluated through an approximate functional formulated in terms of distribution functions of the many-body coupling (pairwise non-additive) part of the QM-MM interaction energy. A set of QM/MM simulations are conducted in MM water solvent for QM water solute in ambient and supercritical conditions and for QM glycine solute in the neutral and zwitterionic forms. The variation of the electronic distortion energy of the QM solute in the course of QM/MM simulation is then shown to be compensated by the corresponding variation of the free energy of solvation. The solvation free energy conditioned by the electronic distortion energy is further analyzed with its components. It is found that the many-body contribution is essentially equal between the free energy and the average sum of solute-solvent interaction energy. © 2012 American Institute of Physics

  14. Exploring the boundaries of quantum mechanics: advances in satellite quantum communications.

    PubMed

    Agnesi, Costantino; Vedovato, Francesco; Schiavon, Matteo; Dequal, Daniele; Calderaro, Luca; Tomasin, Marco; Marangon, Davide G; Stanco, Andrea; Luceri, Vincenza; Bianco, Giuseppe; Vallone, Giuseppe; Villoresi, Paolo

    2018-07-13

    Recent interest in quantum communications has stimulated great technological progress in satellite quantum technologies. These advances have rendered the aforesaid technologies mature enough to support the realization of experiments that test the foundations of quantum theory at unprecedented scales and in the unexplored space environment. Such experiments, in fact, could explore the boundaries of quantum theory and may provide new insights to investigate phenomena where gravity affects quantum objects. Here, we review recent results in satellite quantum communications and discuss possible phenomena that could be observable with current technologies. Furthermore, stressing the fact that space represents an incredible resource to realize new experiments aimed at highlighting some physical effects, we challenge the community to propose new experiments that unveil the interplay between quantum mechanics and gravity that could be realizable in the near future.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'. © 2018 The Author(s).

  15. Possible Peroxo State of the Dicopper Site of Particulate Methane Monooxygenase from Combined Quantum Mechanics and Molecular Mechanics Calculations.

    PubMed

    Itoyama, Shuhei; Doitomi, Kazuki; Kamachi, Takashi; Shiota, Yoshihito; Yoshizawa, Kazunari

    2016-03-21

    Enzymatic methane hydroxylation is proposed to efficiently occur at the dinuclear copper site of particulate methane monooxygenase (pMMO), which is an integral membrane metalloenzyme in methanotrophic bacteria. The resting state and a possible peroxo state of the dicopper active site of pMMO are discussed by using combined quantum mechanics and molecular mechanics calculations on the basis of reported X-ray crystal structures of the resting state of pMMO by Rosenzweig and co-workers. The dicopper site has a unique structure, in which one copper is coordinated by two histidine imidazoles and another is chelated by a histidine imidazole and primary amine of an N-terminal histidine. The resting state of the dicopper site is assignable to the mixed-valent Cu(I)Cu(II) state from a computed Cu-Cu distance of 2.62 Å from calculations at the B3LYP-D/TZVP level of theory. A μ-η(2):η(2)-peroxo-Cu(II)2 structure similar to those of hemocyanin and tyrosinase is reasonably obtained by using the resting state structure and dioxygen. Computed Cu-Cu and O-O distances are 3.63 and 1.46 Å, respectively, in the open-shell singlet state. Structural features of the dicopper peroxo species of pMMO are compared with those of hemocyanin and tyrosinase and synthetic dicopper model compounds. Optical features of the μ-η(2):η(2)-peroxo-Cu(II)2 state are calculated and analyzed with TD-DFT calculations.

  16. The actual content of quantum theoretical kinematics and mechanics

    NASA Technical Reports Server (NTRS)

    Heisenberg, W.

    1983-01-01

    First, exact definitions are supplied for the terms: position, velocity, energy, etc. (of the electron, for instance), such that they are valid also in quantum mechanics. Canonically conjugated variables are determined simultaneously only with a characteristic uncertainty. This uncertainty is the intrinsic reason for the occurrence of statistical relations in quantum mechanics. Mathematical formulation is made possible by the Dirac-Jordan theory. Beginning from the basic principles thus obtained, macroscopic processes are understood from the viewpoint of quantum mechanics. Several imaginary experiments are discussed to elucidate the theory.

  17. More on homological supersymmetric quantum mechanics

    NASA Astrophysics Data System (ADS)

    Behtash, Alireza

    2018-03-01

    In this work, we first solve complex Morse flow equations for the simplest case of a bosonic harmonic oscillator to discuss localization in the context of Picard-Lefschetz theory. We briefly touch on the exact non-BPS solutions of the bosonized supersymmetric quantum mechanics on algebraic geometric grounds and report that their complex phases can be accessed through the cohomology of WKB 1-form of the underlying singular spectral curve subject to necessary cohomological corrections for nonzero genus. Motivated by Picard-Lefschetz theory, we write down a general formula for the index of N =4 quantum mechanics with background R -symmetry gauge fields. We conjecture that certain symmetries of the refined Witten index and singularities of the moduli space may be used to determine the correct intersection coefficients. A few examples, where this conjecture holds, are shown in both linear and closed quivers with rank-one quiver gauge groups. The R -anomaly removal along the "Morsified" relative homology cycles also called "Lefschetz thimbles" is shown to lead to the appearance of Stokes lines. We show that the Fayet-Iliopoulos parameters appear in the intersection coefficients for the relative homology of the quiver quantum mechanics resulting from dimensional reduction of 2 d N =(2 ,2 ) gauge theory on a circle and explicitly calculate integrals along the Lefschetz thimbles in N =4 C Pk -1 model. The Stokes jumping of coefficients and its relation to wall crossing phenomena is briefly discussed. We also find that the notion of "on-the-wall" index is related to the invariant Lefschetz thimbles under Stokes phenomena. An implication of the Lefschetz thimbles in constructing knots from quiver quantum mechanics is indicated.

  18. Quantum mechanics and the psyche

    NASA Astrophysics Data System (ADS)

    Galli Carminati, G.; Martin, F.

    2008-07-01

    In this paper we apply the last developments of the theory of measurement in quantum mechanics to the phenomenon of consciousness and especially to the awareness of unconscious components. Various models of measurement in quantum mechanics can be distinguished by the fact that there is, or there is not, a collapse of the wave function. The passive aspect of consciousness seems to agree better with models in which there is no collapse of the wave function, whereas in the active aspect of consciousness—i.e., that which goes together with an act or a choice—there seems to be a collapse of the wave function. As an example of the second possibility we study in detail the photon delayed-choice experiment and its consequences for subjective or psychological time. We apply this as an attempt to explain synchronicity phenomena. As a model of application of the awareness of unconscious components we study the mourning process. We apply also the quantum paradigm to the phenomenon of correlation at a distance between minds, as well as to group correlations that appear during group therapies or group training. Quantum entanglement leads to the formation of group unconscious or collective unconscious. Finally we propose to test the existence of such correlations during sessions of group training.

  19. quantum mechanics

    PubMed Central

    Bender, Carl M; DeKieviet, Maarten; Klevansky, S. P.

    2013-01-01

    -symmetric quantum mechanics (PTQM) has become a hot area of research and investigation. Since its beginnings in 1998, there have been over 1000 published papers and more than 15 international conferences entirely devoted to this research topic. Originally, PTQM was studied at a highly mathematical level and the techniques of complex variables, asymptotics, differential equations and perturbation theory were used to understand the subtleties associated with the analytic continuation of eigenvalue problems. However, as experiments on -symmetric physical systems have been performed, a simple and beautiful physical picture has emerged, and a -symmetric system can be understood as one that has a balanced loss and gain. Furthermore, the phase transition can now be understood intuitively without resorting to sophisticated mathe- matics. Research on PTQM is following two different paths: at a fundamental level, physicists are attempting to understand the underlying mathematical structure of these theories with the long-range objective of applying the techniques of PTQM to understanding some of the outstanding problems in physics today, such as the nature of the Higgs particle, the properties of dark matter, the matter–antimatter asymmetry in the universe, neutrino oscillations and the cosmological constant; at an applied level, new kinds of -synthetic materials are being developed, and the phase transition is being observed in many physical contexts, such as lasers, optical wave guides, microwave cavities, superconducting wires and electronic circuits. The purpose of this Theme Issue is to acquaint the reader with the latest developments in PTQM. The articles in this volume are written in the style of mini-reviews and address diverse areas of the emerging and exciting new area of -symmetric quantum mechanics. PMID:23509390

  20. Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study

    NASA Astrophysics Data System (ADS)

    Lee, Vannajan Sanghiran; Kodchakorn, Kanchanok; Jitonnom, Jitrayut; Nimmanpipug, Piyarat; Kongtawelert, Prachya; Premanode, Bhusana

    2010-10-01

    The reaction mechanism of creatinine-creatininase binding to form creatine as a final product has been investigated by using a combined ab initio quantum mechanical/molecular mechanical approach and classical molecular dynamics (MD) simulations. In MD simulations, an X-ray crystal structure of the creatininase/creatinine was modified for creatininase/creatinine complexes and the MD simulations were run for free creatininase and creatinine in water. MD results reveal that two X-ray water molecules can be retained in the active site as catalytic water. The binding free energy from Molecular Mechanics Poisson-Boltzmann Surface Area calculation predicted the strong binding of creatinine with Zn2+, Asp45 and Glu183. Two step mechanisms via Mn2+/Zn2+ (as in X-ray structure) and Zn2+/Zn2+ were proposed for water adding step and ring opening step with two catalytic waters. The pathway using synchronous transit methods with local density approximations with PWC functional for the fragment in the active region were obtained. Preferable pathway Zn2+/Zn2+ was observed due to lower activation energy in water adding step. The calculated energy in the second step for both systems were comparable with the barrier of 26.03 and 24.44 kcal/mol for Mn2+/Zn2+ and Zn2+/Zn2+, respectively.

  1. Calendar effects in quantum mechanics in view of interactive holography

    NASA Astrophysics Data System (ADS)

    Berkovich, Simon

    2013-04-01

    Quantum mechanics in terms of interactive holography appears as `normal' science [1]. With the holography quantum behavior is determined by the interplay of material formations and their conjugate images. To begin with, this effortlessly elucidates the nonlocality in quantum entanglements. Then, it has been shown that Schr"odinger's dynamics for a single particle arises from Bi-Fragmental random walks of the particle itself and its holographic image. For many particles this picture blurs with fragments merging as bosons or fermions. In biomolecules, swapping of particles and their holographic placeholders leads to self-replication of the living matter. Because of broad interpretations of quantum formalism direct experiments attributing it to holography may not be very compelling. The holographic mechanism better reveals as an absolute frame of reference. A number of physical and biological events exhibit annual variations when Earth orbital position changes with respect to the universal holographic mechanism. The well established calendar variations of heart attacks can be regarded as a positive outcome of a generalization of the Michelson experiment, where holography is interferometry and ailing hearts are detectors of pathologically replicated proteins. Also, there have been already observed calendar changes in radioactive decay rates. The same could be expected for various fine quantum experiences, like, e.g., Josephson tunneling. In other words, Quantum Mechanics (February) Quantum Mechanics (August). [1] S. Berkovich, ``A comprehensive explanation of quantum mechanics,'' www.cs.gwu.edu/research/technical-report/170 .

  2. Bridging the Gap Between Stationary Homogeneous Isotropic Turbulence and Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Sohrab, Siavash

    A statistical theory of stationary isotropic turbulence is presented with eddies possessing Gaussian velocity distribution, Maxwell-Boltzmann speed distribution in harmony with perceptions of Heisenberg, and Planck energy distribution in harmony with perceptions of Chandrasekhar and in agreement with experimental observations of Van Atta and Chen. Defining the action S = - mΦ in terms of velocity potential of atomic motion, scale-invariant Schrödinger equation is derivedfrom invariant Bernoulli equation. Thus, the gap between the problems of turbulence and quantum mechanics is closed through connections between Cauchy-Euler-Bernoulli equations of hydrodynamics, Hamilton-Jacobi equation of classical mechanics, and finally Schrödinger equation of quantum mechanics. Transitions of particle (molecular cluster cji) from a small rapidly-oscillating eddy ej (high-energy level-j) to a large slowly-oscillating eddy ei (low energy-level-i) leads to emission of a sub-particle (molecule mji) that carries away the excess energy ɛji = h (νj -νi) in harmony with Bohr theory of atomic spectra. ∖ ∖ NASA Grant No. NAG3-1863.

  3. Cognitive Issues in Learning Advanced Physics: An Example from Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Singh, Chandralekha; Zhu, Guangtian

    2009-11-01

    We are investigating cognitive issues in learning quantum mechanics in order to develop effective teaching and learning tools. The analysis of cognitive issues is particularly important for bridging the gap between the quantitative and conceptual aspects of quantum mechanics and for ensuring that the learning tools help students build a robust knowledge structure. We discuss the cognitive aspects of quantum mechanics that are similar or different from those of introductory physics and their implications for developing strategies to help students develop a good grasp of quantum mechanics.

  4. Bridging quantum mechanics and structure-based drug design.

    PubMed

    De Vivo, Marco

    2011-01-01

    The last decade has seen great advances in the use of quantum mechanics (QM) to solve biological problems of pharmaceutical relevance. For instance, enzymatic catalysis is often investigated by means of the so-called QM/MM approach, which uses QM and molecular mechanics (MM) methods to determine the (free) energy landscape of the enzymatic reaction mechanism. Here, I will discuss a few representative examples of QM and QM/MM studies of important metalloenzymes of pharmaceutical interest (i.e. metallophosphatases and metallo-beta-lactamases). This review article aims to show how QM-based methods can be used to elucidate ligand-receptor interactions. The challenge is then to exploit this knowledge for the structure-based design of new and potent inhibitors, such as transition state (TS) analogues that resemble the structure and physicochemical properties of the enzymatic TS. Given the results and potential expressed to date by QM-based methods in studying biological problems, the application of QM in structure-based drug design will likely increase, making of these once-prohibitive computations a routinely used tool for drug design.

  5. Molecular mechanism of lytic polysaccharide monooxygenases.

    PubMed

    Hedegård, Erik Donovan; Ryde, Ulf

    2018-04-21

    The lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism and hence boost generation of biofuel from e.g. cellulose. By employing density functional theory in a combination of quantum mechanics and molecular mechanics (QM/MM), we report a complete description of the molecular mechanism of LPMOs. The QM/MM scheme allows us to describe all reaction steps with a detailed protein environment and we show that this is necessary. Several active species capable of abstracting a hydrogen from the substrate have been proposed previously and starting from recent crystallographic work on a substrate-LPMO complex, we investigate previously suggested paths as well as new ones. We describe the generation of the reactive intermediates, the abstraction of a hydrogen atom from the polysaccharide substrate, as well as the final recombination step in which OH is transferred back to the substrate. We show that a superoxo [CuO 2 ] + complex can be protonated by a nearby histidine residue (suggested by recent mutagenesis studies and crystallographic work) and, provided an electron source is available, leads to formation of an oxyl-complex after cleavage of the O-O bond and dissociation of water. The oxyl complex either reacts with the substrate or is further protonated to a hydroxyl complex. Both the oxyl and hydroxyl complexes are also readily generated from a reaction with H 2 O 2 , which was recently suggested to be the true co-substrate, rather than O 2 . The C-H abstraction by the oxyl and hydroxy complexes is overall favorable with activation barriers of 69 and 94 kJ mol -1 , compared to the much higher barrier (156 kJ mol -1 ) obtained for the copper-superoxo species. We obtain good structural agreement for intermediates for which structural data are available and the estimated reaction energies agree with experimental rate constants. Thus, our suggested mechanism is the most complete

  6. Spin Glass a Bridge Between Quantum Computation and Statistical Mechanics

    NASA Astrophysics Data System (ADS)

    Ohzeki, Masayuki

    2013-09-01

    In this chapter, we show two fascinating topics lying between quantum information processing and statistical mechanics. First, we introduce an elaborated technique, the surface code, to prepare the particular quantum state with robustness against decoherence. Interestingly, the theoretical limitation of the surface code, accuracy threshold, to restore the quantum state has a close connection with the problem on the phase transition in a special model known as spin glasses, which is one of the most active researches in statistical mechanics. The phase transition in spin glasses is an intractable problem, since we must strive many-body system with complicated interactions with change of their signs depending on the distance between spins. Fortunately, recent progress in spin-glass theory enables us to predict the precise location of the critical point, at which the phase transition occurs. It means that statistical mechanics is available for revealing one of the most interesting parts in quantum information processing. We show how to import the special tool in statistical mechanics into the problem on the accuracy threshold in quantum computation. Second, we show another interesting technique to employ quantum nature, quantum annealing. The purpose of quantum annealing is to search for the most favored solution of a multivariable function, namely optimization problem. The most typical instance is the traveling salesman problem to find the minimum tour while visiting all the cities. In quantum annealing, we introduce quantum fluctuation to drive a particular system with the artificial Hamiltonian, in which the ground state represents the optimal solution of the specific problem we desire to solve. Induction of the quantum fluctuation gives rise to the quantum tunneling effect, which allows nontrivial hopping from state to state. We then sketch a strategy to control the quantum fluctuation efficiently reaching the ground state. Such a generic framework is called

  7. Mathematical sense-making in quantum mechanics: An initial peek

    NASA Astrophysics Data System (ADS)

    Dreyfus, Benjamin W.; Elby, Andrew; Gupta, Ayush; Sohr, Erin Ronayne

    2017-12-01

    Mathematical sense-making—looking for coherence between the structure of the mathematical formalism and causal or functional relations in the world—is a core component of physics expertise. Some physics education research studies have explored what mathematical sense-making looks like at the introductory physics level, while some historians and "science studies" have explored how expert physicists engage in it. What is largely missing, with a few exceptions, is theoretical and empirical work at the intermediate level—upper division physics students—especially when they are learning difficult new mathematical formalism. In this paper, we present analysis of a segment of video-recorded discussion between two students grappling with a quantum mechanics question to illustrate what mathematical sense-making can look like in quantum mechanics. We claim that mathematical sense-making is possible and productive for learning and problem solving in quantum mechanics. Mathematical sense-making in quantum mechanics is continuous in many ways with mathematical sense-making in introductory physics. However, in the context of quantum mechanics, the connections between formalism, intuitive conceptual schema, and the physical world become more compound (nested) and indirect. We illustrate these similarities and differences in part by proposing a new symbolic form, eigenvector eigenvalue, which is composed of multiple primitive symbolic forms.

  8. Framework for understanding the patterns of student difficulties in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Marshman, Emily; Singh, Chandralekha

    2015-12-01

    [This paper is part of the Focused Collection on Upper Division Physics Courses.] Compared with introductory physics, relatively little is known about the development of expertise in advanced physics courses, especially in the case of quantum mechanics. Here, we describe a framework for understanding the patterns of student reasoning difficulties and how students develop expertise in quantum mechanics. The framework posits that the challenges many students face in developing expertise in quantum mechanics are analogous to the challenges introductory students face in developing expertise in introductory classical mechanics. This framework incorporates both the effects of diversity in upper-level students' prior preparation, goals, and motivation in general (i.e., the facts that even in upper-level courses, students may be inadequately prepared, have unclear goals, and have insufficient motivation to excel) as well as the "paradigm shift" from classical mechanics to quantum mechanics. The framework is based on empirical investigations demonstrating that the patterns of reasoning, problem-solving, and self-monitoring difficulties in quantum mechanics bear a striking resemblance to those found in introductory classical mechanics. Examples from research in quantum mechanics and introductory classical mechanics are discussed to illustrate how the patterns of difficulties are analogous as students learn to unpack the respective principles and grasp the formalism in each knowledge domain during the development of expertise. Embracing such a framework and contemplating the parallels between the difficulties in these two knowledge domains can enable researchers to leverage the extensive literature for introductory physics education research to guide the design of teaching and learning tools for helping students develop expertise in quantum mechanics.

  9. Insights into Teaching Quantum Mechanics in Secondary and Lower Undergraduate Education

    ERIC Educational Resources Information Center

    Krijtenburg-Lewerissa, K.; Pol, H. J.; Brinkman, A.; van Joolingen, W. R.

    2017-01-01

    This study presents a review of the current state of research on teaching quantum mechanics in secondary and lower undergraduate education. A conceptual approach to quantum mechanics is being implemented in more and more introductory physics courses around the world. Because of the differences between the conceptual nature of quantum mechanics and…

  10. Theoretical description of quantum mechanical permeation of graphene membranes by charged hydrogen isotopes

    NASA Astrophysics Data System (ADS)

    Mazzuca, James W.; Haut, Nathaniel K.

    2018-06-01

    It has been recently shown that in the presence of an applied voltage, hydrogen and deuterium nuclei can be separated from one another using graphene membranes as a nuclear sieve, resulting in a 10-fold enhancement in the concentration of the lighter isotope. While previous studies, both experimental and theoretical, have attributed this effect mostly to differences in vibrational zero point energy (ZPE) of the various isotopes near the membrane surface, we propose that multi-dimensional quantum mechanical tunneling of nuclei through the graphene membrane influences this proton permeation process in a fundamental way. We perform ring polymer molecular dynamics calculations in which we include both ZPE and tunneling effects of various hydrogen isotopes as they permeate the graphene membrane and compute rate constants across a range of temperatures near 300 K. While capturing the experimentally observed separation factor, our calculations indicate that the transverse motion of the various isotopes across the surface of the graphene membrane is an essential part of this sieving mechanism. An understanding of the multi-dimensional quantum mechanical nature of this process could serve to guide the design of other such isotopic enrichment processes for a variety of atomic and molecular species of interest.

  11. Theoretical description of quantum mechanical permeation of graphene membranes by charged hydrogen isotopes.

    PubMed

    Mazzuca, James W; Haut, Nathaniel K

    2018-06-14

    It has been recently shown that in the presence of an applied voltage, hydrogen and deuterium nuclei can be separated from one another using graphene membranes as a nuclear sieve, resulting in a 10-fold enhancement in the concentration of the lighter isotope. While previous studies, both experimental and theoretical, have attributed this effect mostly to differences in vibrational zero point energy (ZPE) of the various isotopes near the membrane surface, we propose that multi-dimensional quantum mechanical tunneling of nuclei through the graphene membrane influences this proton permeation process in a fundamental way. We perform ring polymer molecular dynamics calculations in which we include both ZPE and tunneling effects of various hydrogen isotopes as they permeate the graphene membrane and compute rate constants across a range of temperatures near 300 K. While capturing the experimentally observed separation factor, our calculations indicate that the transverse motion of the various isotopes across the surface of the graphene membrane is an essential part of this sieving mechanism. An understanding of the multi-dimensional quantum mechanical nature of this process could serve to guide the design of other such isotopic enrichment processes for a variety of atomic and molecular species of interest.

  12. Insights into teaching quantum mechanics in secondary and lower undergraduate education

    NASA Astrophysics Data System (ADS)

    Krijtenburg-Lewerissa, K.; Pol, H. J.; Brinkman, A.; van Joolingen, W. R.

    2017-06-01

    This study presents a review of the current state of research on teaching quantum mechanics in secondary and lower undergraduate education. A conceptual approach to quantum mechanics is being implemented in more and more introductory physics courses around the world. Because of the differences between the conceptual nature of quantum mechanics and classical physics, research on misconceptions, testing, and teaching strategies for introductory quantum mechanics is needed. For this review, 74 articles were selected and analyzed for the misconceptions, research tools, teaching strategies, and multimedia applications investigated. Outcomes were categorized according to their contribution to the various subtopics of quantum mechanics. Analysis shows that students have difficulty relating quantum physics to physical reality. It also shows that the teaching of complex quantum behavior, such as time dependence, superposition, and the measurement problem, has barely been investigated for the secondary and lower undergraduate level. At the secondary school level, this article shows a need to investigate student difficulties concerning wave functions and potential wells. Investigation of research tools shows the necessity for the development of assessment tools for secondary and lower undergraduate education, which cover all major topics and are suitable for statistical analysis. Furthermore, this article shows the existence of very diverse ideas concerning teaching strategies for quantum mechanics and a lack of research into which strategies promote understanding. This article underlines the need for more empirical research into student difficulties, teaching strategies, activities, and research tools intended for a conceptual approach for quantum mechanics.

  13. Challenges in large scale quantum mechanical calculations: Challenges in large scale quantum mechanical calculations

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

    Ratcliff, Laura E.; Mohr, Stephan; Huhs, Georg

    2016-11-07

    During the past decades, quantum mechanical methods have undergone an amazing transition from pioneering investigations of experts into a wide range of practical applications, made by a vast community of researchers. First principles calculations of systems containing up to a few hundred atoms have become a standard in many branches of science. The sizes of the systems which can be simulated have increased even further during recent years, and quantum-mechanical calculations of systems up to many thousands of atoms are nowadays possible. This opens up new appealing possibilities, in particular for interdisciplinary work, bridging together communities of different needs andmore » sensibilities. In this review we will present the current status of this topic, and will also give an outlook on the vast multitude of applications, challenges and opportunities stimulated by electronic structure calculations, making this field an important working tool and bringing together researchers of many different domains.« less

  14. Uncertainty in quantum mechanics: faith or fantasy?

    PubMed

    Penrose, Roger

    2011-12-13

    The word 'uncertainty', in the context of quantum mechanics, usually evokes an impression of an essential unknowability of what might actually be going on at the quantum level of activity, as is made explicit in Heisenberg's uncertainty principle, and in the fact that the theory normally provides only probabilities for the results of quantum measurement. These issues limit our ultimate understanding of the behaviour of things, if we take quantum mechanics to represent an absolute truth. But they do not cause us to put that very 'truth' into question. This article addresses the issue of quantum 'uncertainty' from a different perspective, raising the question of whether this term might be applied to the theory itself, despite its unrefuted huge success over an enormously diverse range of observed phenomena. There are, indeed, seeming internal contradictions in the theory that lead us to infer that a total faith in it at all levels of scale leads us to almost fantastical implications.

  15. Quantum mechanics over sets

    NASA Astrophysics Data System (ADS)

    Ellerman, David

    2014-03-01

    In models of QM over finite fields (e.g., Schumacher's ``modal quantum theory'' MQT), one finite field stands out, Z2, since Z2 vectors represent sets. QM (finite-dimensional) mathematics can be transported to sets resulting in quantum mechanics over sets or QM/sets. This gives a full probability calculus (unlike MQT with only zero-one modalities) that leads to a fulsome theory of QM/sets including ``logical'' models of the double-slit experiment, Bell's Theorem, QIT, and QC. In QC over Z2 (where gates are non-singular matrices as in MQT), a simple quantum algorithm (one gate plus one function evaluation) solves the Parity SAT problem (finding the parity of the sum of all values of an n-ary Boolean function). Classically, the Parity SAT problem requires 2n function evaluations in contrast to the one function evaluation required in the quantum algorithm. This is quantum speedup but with all the calculations over Z2 just like classical computing. This shows definitively that the source of quantum speedup is not in the greater power of computing over the complex numbers, and confirms the idea that the source is in superposition.

  16. Coherent Dynamics of a Hybrid Quantum Spin-Mechanical Oscillator System

    NASA Astrophysics Data System (ADS)

    Lee, Kenneth William, III

    A fully functional quantum computer must contain at least two important components: a quantum memory for storing and manipulating quantum information and a quantum data bus to securely transfer information between quantum memories. Typically, a quantum memory is composed of a matter system, such as an atom or an electron spin, due to their prolonged quantum coherence. Alternatively, a quantum data bus is typically composed of some propagating degree of freedom, such as a photon, which can retain quantum information over long distances. Therefore, a quantum computer will likely be a hybrid quantum device, consisting of two or more disparate quantum systems. However, there must be a reliable and controllable quantum interface between the memory and bus in order to faithfully interconvert quantum information. The current engineering challenge for quantum computers is scaling the device to large numbers of controllable quantum systems, which will ultimately depend on the choice of the quantum elements and interfaces utilized in the device. In this thesis, we present and characterize a hybrid quantum device comprised of single nitrogen-vacancy (NV) centers embedded in a high quality factor diamond mechanical oscillator. The electron spin of the NV center is a leading candidate for the realization of a quantum memory due to its exceptional quantum coherence times. On the other hand, mechanical oscillators are highly sensitive to a wide variety of external forces, and have the potential to serve as a long-range quantum bus between quantum systems of disparate energy scales. These two elements are interfaced through crystal strain generated by vibrations of the mechanical oscillator. Importantly, a strain interface allows for a scalable architecture, and furthermore, opens the door to integration into a larger quantum network through coupling to an optical interface. There are a few important engineering challenges associated with this device. First, there have been no

  17. In Defense of a Heuristic Interpretation of Quantum Mechanics

    ERIC Educational Resources Information Center

    Healy, Eamonn F.

    2010-01-01

    Although the presentation of quantum mechanics found in traditional textbooks is intellectually well founded, it suffers from a number of deficiencies. Specifically introducing quantum mechanics as a solution to the arcane dilemma, the ultraviolet catastrophe, does little to impress a nonscientific audience of the tremendous paradigmatic shift…

  18. Measurements and mathematical formalism of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Slavnov, D. A.

    2007-03-01

    A scheme for constructing quantum mechanics is given that does not have Hilbert space and linear operators as its basic elements. Instead, a version of algebraic approach is considered. Elements of a noncommutative algebra (observables) and functionals on this algebra (elementary states) associated with results of single measurements are used as primary components of the scheme. On the one hand, it is possible to use within the scheme the formalism of the standard (Kolmogorov) probability theory, and, on the other hand, it is possible to reproduce the mathematical formalism of standard quantum mechanics, and to study the limits of its applicability. A short outline is given of the necessary material from the theory of algebras and probability theory. It is described how the mathematical scheme of the paper agrees with the theory of quantum measurements, and avoids quantum paradoxes.

  19. Geometrical Phases in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Christian, Joy Julius

    In quantum mechanics, the path-dependent geometrical phase associated with a physical system, over and above the familiar dynamical phase, was initially discovered in the context of adiabatically changing environments. Subsequently, Aharonov and Anandan liberated this phase from the original formulation of Berry, which used Hamiltonians, dependent on curves in a classical parameter space, to represent the cyclic variations of the environments. Their purely quantum mechanical treatment, independent of Hamiltonians, instead used the non-trivial topological structure of the projective space of one-dimensional subspaces of an appropriate Hilbert space. The geometrical phase, in their treatment, results from a parallel transport of the time-dependent pure quantum states along a curve in this space, which is endowed with an abelian connection. Unlike Berry, they were able to achieve this without resort to an adiabatic approximation or to a time-independent eigenvalue equation. Prima facie, these two approaches are conceptually quite different. After a review of both approaches, an exposition bridging this apparent conceptual gap is given; by rigorously analyzing a model composite system, it is shown that, in an appropriate correspondence limit, the Berry phase can be recovered as a special case from the Aharonov-Anandan phase. Moreover, the model composite system is used to show that Berry's correction to the traditional Born-Oppenheimer energy spectra indeed brings the spectra closer to the exact results. Then, an experimental arrangement to measure geometrical phases associated with cyclic and non-cyclic variations of quantum states of an entangled composite system is proposed, utilizing the fundamental ideas of the recently opened field of two-particle interferometry. This arrangement not only resolves the controversy regarding the true nature of the phases associated with photon states, but also unequivocally predicts experimentally accessible geometrical phases in a

  20. Characterization of the Sr(2+)- and Cd(2+)-Substituted Oxygen-Evolving Complex of Photosystem II by Quantum Mechanics/Molecular Mechanics Calculations.

    PubMed

    Pitari, Fabio; Bovi, Daniele; Narzi, Daniele; Guidoni, Leonardo

    2015-09-29

    The Mn4CaO5 cluster in the oxygen-evolving complex is the catalytic core of the Photosystem II (PSII) enzyme, responsible for the water splitting reaction in oxygenic photosynthesis. The role of the redox-inactive ion in the cluster has not yet been fully clarified, although several experimental data are available on Ca2+-depleted and Ca2+-substituted PSII complexes, indicating Sr2+-substituted PSII as the only modification that preserves oxygen evolution. In this work, we investigated the structural and electronic properties of the PSII catalytic core with Ca2+ replaced with Sr2+ and Cd2+ in the S2 state of the Kok−Joliot cycle by means of density functional theory and ab initio molecular dynamics based on a quantum mechanics/ molecular mechanics approach. Our calculations do not reveal significant differences between the substituted and wild-type systems in terms of geometries, thermodynamics, and kinetics of two previously identified intermediate states along the S2 to S3 transition, namely, the open cubane S2 A and closed cubane S2 B conformers. Conversely, our calculations show different pKa values for the water molecule bound to the three investigated heterocations. Specifically, for Cd-substituted PSII, the pKa value is 5.3 units smaller than the respective value in wild type Ca-PSII. On the basis of our results, we conclude that, assuming all the cations sharing the same binding site, the induced difference in the acidity of the binding pocket might influence the hydrogen bonding network and the redox levels to prevent the further evolution of the cycle toward the S3 state.

  1. Quantum-coherent coupling of a mechanical oscillator to an optical cavity mode.

    PubMed

    Verhagen, E; Deléglise, S; Weis, S; Schliesser, A; Kippenberg, T J

    2012-02-01

    Optical laser fields have been widely used to achieve quantum control over the motional and internal degrees of freedom of atoms and ions, molecules and atomic gases. A route to controlling the quantum states of macroscopic mechanical oscillators in a similar fashion is to exploit the parametric coupling between optical and mechanical degrees of freedom through radiation pressure in suitably engineered optical cavities. If the optomechanical coupling is 'quantum coherent'--that is, if the coherent coupling rate exceeds both the optical and the mechanical decoherence rate--quantum states are transferred from the optical field to the mechanical oscillator and vice versa. This transfer allows control of the mechanical oscillator state using the wide range of available quantum optical techniques. So far, however, quantum-coherent coupling of micromechanical oscillators has only been achieved using microwave fields at millikelvin temperatures. Optical experiments have not attained this regime owing to the large mechanical decoherence rates and the difficulty of overcoming optical dissipation. Here we achieve quantum-coherent coupling between optical photons and a micromechanical oscillator. Simultaneously, coupling to the cold photon bath cools the mechanical oscillator to an average occupancy of 1.7 ± 0.1 motional quanta. Excitation with weak classical light pulses reveals the exchange of energy between the optical light field and the micromechanical oscillator in the time domain at the level of less than one quantum on average. This optomechanical system establishes an efficient quantum interface between mechanical oscillators and optical photons, which can provide decoherence-free transport of quantum states through optical fibres. Our results offer a route towards the use of mechanical oscillators as quantum transducers or in microwave-to-optical quantum links.

  2. Categorization of Quantum Mechanics Problems by Professors and Students

    ERIC Educational Resources Information Center

    Lin, Shih-Yin; Singh, Chandralekha

    2010-01-01

    We discuss the categorization of 20 quantum mechanics problems by physics professors and undergraduate students from two honours-level quantum mechanics courses. Professors and students were asked to categorize the problems based upon similarity of solution. We also had individual discussions with professors who categorized the problems. Faculty…

  3. Developing and Evaluating Animations for Teaching Quantum Mechanics Concepts

    ERIC Educational Resources Information Center

    Kohnle, Antje; Douglass, Margaret; Edwards, Tom J.; Gillies, Alastair D.; Hooley, Christopher A.; Sinclair, Bruce D.

    2010-01-01

    In this paper, we describe animations and animated visualizations for introductory and intermediate-level quantum mechanics instruction developed at the University of St Andrews. The animations aim to help students build mental representations of quantum mechanics concepts. They focus on known areas of student difficulty and misconceptions by…

  4. Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex.

    PubMed

    Dohn, A O; Jónsson, E Ö; Levi, G; Mortensen, J J; Lopez-Acevedo, O; Thygesen, K S; Jacobsen, K W; Ulstrup, J; Henriksen, N E; Møller, K B; Jónsson, H

    2017-12-12

    A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H 2 O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt 2 (P 2 O 5 H 2 ) 4 ] 4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

  5. Prediction and Repetition in Quantum Mechanics: The EPR Experiment and Quantum Probability

    NASA Astrophysics Data System (ADS)

    Plotnitsky, Arkady

    2007-02-01

    The article considers the implications of the experiment of A. Einstein, B. Podolsky, and N. Rosen (EPR), and of the exchange (concerning this experiment) between EPR and Bohr concerning the incompleteness, or else nonlocality, of quantum mechanics for our understanding of quantum phenomena and quantum probability. The article specifically argues that in the case of quantum phenomena, including those involved in the experiments of the EPR type, the probabilistic considerations are important even when the predictions concerned can be made with certainty, due to the impossibility, in general, to repeat any given quantum experiment with the same outcome. The article argue that this fact, not properly considered or taken into account by EPR, makes it difficult and ultimately impossible to sustain their argument, which it is consistent with Bohr's counterargument to EPR and with his view of quantum phenomena and quantum mechanics.

  6. Anharmonic quantum mechanical systems do not feature phase space trajectories

    NASA Astrophysics Data System (ADS)

    Oliva, Maxime; Kakofengitis, Dimitris; Steuernagel, Ole

    2018-07-01

    Phase space dynamics in classical mechanics is described by transport along trajectories. Anharmonic quantum mechanical systems do not allow for a trajectory-based description of their phase space dynamics. This invalidates some approaches to quantum phase space studies. We first demonstrate the absence of trajectories in general terms. We then give an explicit proof for all quantum phase space distributions with negative values: we show that the generation of coherences in anharmonic quantum mechanical systems is responsible for the occurrence of singularities in their phase space velocity fields, and vice versa. This explains numerical problems repeatedly reported in the literature, and provides deeper insight into the nature of quantum phase space dynamics.

  7. Tampering detection system using quantum-mechanical systems

    DOEpatents

    Humble, Travis S [Knoxville, TN; Bennink, Ryan S [Knoxville, TN; Grice, Warren P [Oak Ridge, TN

    2011-12-13

    The use of quantum-mechanically entangled photons for monitoring the integrity of a physical border or a communication link is described. The no-cloning principle of quantum information science is used as protection against an intruder's ability to spoof a sensor receiver using a `classical` intercept-resend attack. Correlated measurement outcomes from polarization-entangled photons are used to protect against quantum intercept-resend attacks, i.e., attacks using quantum teleportation.

  8. Students' Conceptual Difficulties in Quantum Mechanics: Potential Well Problems

    ERIC Educational Resources Information Center

    Ozcan, Ozgur; Didis, Nilufer; Tasar, Mehmet Fatih

    2009-01-01

    In this study, students' conceptual difficulties about some basic concepts in quantum mechanics like one-dimensional potential well problems and probability density of tunneling particles were identified. For this aim, a multiple choice instrument named Quantum Mechanics Conceptual Test has been developed by one of the researchers of this study…

  9. Students' Epistemological Framing in Quantum Mechanics Problem Solving

    ERIC Educational Resources Information Center

    Modir, Bahar; Thompson, John D.; Sayre, Eleanor C.

    2017-01-01

    Students' difficulties in quantum mechanics may be the result of unproductive framing and not a fundamental inability to solve the problems or misconceptions about physics content. We observed groups of students solving quantum mechanics problems in an upper-division physics course. Using the lens of epistemological framing, we investigated four…

  10. Hermeneutics, Underdetermination and Quantum Mechanics.

    ERIC Educational Resources Information Center

    Cushing, James T.

    1995-01-01

    States that the existence of an essential underdetermination in the interpretation of the formalism of quantum mechanics, in spite of the widespread belief that logic and empirical considerations alone demand an indeterministic world view in physics, legitimizes the analysis of hermeneutics in science education. (LZ)

  11. Reality, Causality, and Probability, from Quantum Mechanics to Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Plotnitsky, Arkady

    2015-10-01

    These three lectures consider the questions of reality, causality, and probability in quantum theory, from quantum mechanics to quantum field theory. They do so in part by exploring the ideas of the key founding figures of the theory, such N. Bohr, W. Heisenberg, E. Schrödinger, or P. A. M. Dirac. However, while my discussion of these figures aims to be faithful to their thinking and writings, and while these lectures are motivated by my belief in the helpfulness of their thinking for understanding and advancing quantum theory, this project is not driven by loyalty to their ideas. In part for that reason, these lectures also present different and even conflicting ways of thinking in quantum theory, such as that of Bohr or Heisenberg vs. that of Schrödinger. The lectures, most especially the third one, also consider new physical, mathematical, and philosophical complexities brought in by quantum field theory vis-à-vis quantum mechanics. I close by briefly addressing some of the implications of the argument presented here for the current state of fundamental physics.

  12. Quantum mechanics: why complex Hilbert space?

    NASA Astrophysics Data System (ADS)

    Cassinelli, G.; Lahti, P.

    2017-10-01

    We outline a programme for an axiomatic reconstruction of quantum mechanics based on the statistical duality of states and effects that combines the use of a theorem of Solér with the idea of symmetry. We also discuss arguments favouring the choice of the complex field. This article is part of the themed issue `Second quantum revolution: foundational questions'.

  13. A Framework for Understanding the Patterns of Student Difficulties in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Singh, Chandralekha

    2015-04-01

    Compared with introductory physics, relatively little is known about the development of expertise in advanced physics courses, especially in the case of quantum mechanics. We describe a theoretical framework for understanding the patterns of student reasoning difficulties and how students develop expertise in quantum mechanics. The framework posits that the challenges many students face in developing expertise in quantum mechanics are analogous to the challenges introductory students face in developing expertise in introductory classical mechanics. This framework incorporates the effects of diversity in students' prior preparation, goals and motivation for taking upper-level physics courses in general as well as the ``paradigm shift'' from classical mechanics to quantum mechanics. The framework is based on empirical investigations demonstrating that the patterns of reasoning, problem-solving, and self-monitoring difficulties in quantum mechanics bear a striking resemblance to those found in introductory classical mechanics. Examples from research in quantum mechanics and introductory classical mechanics will be discussed to illustrate how the patterns of difficulties are analogous as students learn to unpack the respective principles and grasp the formalism in each knowledge domain during the development of expertise. Embracing such a theoretical framework and contemplating the parallels between the difficulties in these two knowledge domains can enable researchers to leverage the extensive literature for introductory physics education research to guide the design of teaching and learning tools for helping students develop expertise in quantum mechanics. Support from the National Science Foundation is gratefully acknowledged.

  14. Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations.

    PubMed

    Shi, Qicun; Meroueh, Samy O; Fisher, Jed F; Mobashery, Shahriar

    2008-07-23

    Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2

  15. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    PubMed

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  16. CARBON-RICH MOLECULAR CHAINS IN PROTOPLANETARY AND PLANETARY ATMOSPHERES: QUANTUM MECHANISMS AND ELECTRON ATTACHMENT RATES FOR ANION FORMATION

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

    Carelli, F.; Grassi, T.; Gianturco, F. A.

    The elementary mechanisms through which molecular polyynes could form stable negative ions after interacting with free electrons in planetary atmospheres (e.g., Titan's) are analyzed using quantum scattering calculations and quantum structure methods. The case of radical species and of nonpolar partners are analyzed via specific examples for both the C{sub n}H and HC{sub n}H series, with n values from 4 to 12. We show that attachment processes to polar radicals are dominating the anionic production and that the mediating role of dipolar scattering states is crucial to their formation. The corresponding attachment rates are presented as calculated upper limits tomore » their likely values and are obtained down to the low temperatures of interest. The effects of the computed rates, when used in simple evolutionary models, are also investigated and presented in detail.« less

  17. Design and Validation of the Quantum Mechanics Conceptual Survey

    ERIC Educational Resources Information Center

    McKagan, S. B.; Perkins, K. K.; Wieman, C. E.

    2010-01-01

    The Quantum Mechanics Conceptual Survey (QMCS) is a 12-question survey of students' conceptual understanding of quantum mechanics. It is intended to be used to measure the relative effectiveness of different instructional methods in modern physics courses. In this paper, we describe the design and validation of the survey, a process that included…

  18. Measurements in Quantum Mechanics and von NEUMANN's Model

    NASA Astrophysics Data System (ADS)

    Mello, Pier A.; Johansen, Lars M.

    2010-12-01

    Many textbooks on Quantum Mechanics are not very precise as to the meaning of making a measurement: as a consequence, they frequently make assertions which are not based on a dynamical description of the measurement process. A model proposed by von Neumann allows a dynamical description of measurement in Quantum Mechanics, including the measuring instrument in the formalism. In this article we apply von Neumann's model to illustrate the measurement of an observable by means of a measuring instrument and show how various results, which are sometimens postulated without a dynamical basis, actually emerge. We also investigate the more complex, intriguing and fundamental problem of two successive measurements in Quantum Mechanics, extending von Neumann's model to two measuring instruments. We present a description which allows obtaining, in a unified way, various results that have been given in the literature.

  19. Quantum Mechanics - Fundamentals and Applications to Technology

    NASA Astrophysics Data System (ADS)

    Singh, Jasprit

    1996-10-01

    Explore the relationship between quantum mechanics and information-age applications This volume takes an altogether unique approach to quantum mechanics. Providing an in-depth exposition of quantum mechanics fundamentals, it shows how these concepts are applied to most of today's information technologies, whether they are electronic devices or materials. No other text makes this critical, essential leap from theory to real-world applications. The book's lively discussion of the mathematics involved fits right in with contemporary multidisciplinary trends in education: Once the basic formulation has been derived in a given chapter, the connection to important technological problems is summarily described. The many helpful features include * Twenty-eight application-oriented sections that focus on lasers, transistors, magnetic memories, superconductors, nuclear magnetic resonance (NMR), and other important technology-driving materials and devices * One hundred solved examples, with an emphasis on numerical results and the connection between the physics and its applications * End-of-chapter problems that ground the student in both fundamental and applied concepts * Numerous figures and tables to clarify the various topics and provide a global view of the problems under discussion * Over two hundred illustrations to highlight problems and text A book for the information age, Quantum Mechanics: Fundamentals and Applications to Technology promises to become a standard in departments of electrical engineering, applied physics, and materials science, as well as physics. It is an excellent text for senior undergraduate and graduate students, and a helpful reference for practicing scientists, engineers, and chemists in the semiconductor and electronic industries.

  20. Superconducting Qubits as Mechanical Quantum Engines

    NASA Astrophysics Data System (ADS)

    Sachtleben, Kewin; Mazon, Kahio T.; Rego, Luis G. C.

    2017-09-01

    We propose the equivalence of superconducting qubits with a pistonlike mechanical quantum engine. The work reports a study on the nature of the nonequilibrium work exchanged with the quantum-nonadiabatic working medium, which is modeled as a multilevel coupled quantum well system subject to an external control parameter. The quantum dynamics is solved for arbitrary control protocols. It is shown that the work output has two components: one that depends instantaneously on the level populations and another that is due to the quantum coherences built in the system. The nonadiabatic coherent dynamics of the quantum engine gives rise to a resistance (friction) force that decreases the work output. We consider the functional equivalence of such a device and a rf-SQUID flux qubit.

  1. Quantum mechanics: why complex Hilbert space?

    PubMed

    Cassinelli, G; Lahti, P

    2017-11-13

    We outline a programme for an axiomatic reconstruction of quantum mechanics based on the statistical duality of states and effects that combines the use of a theorem of Solér with the idea of symmetry. We also discuss arguments favouring the choice of the complex field.This article is part of the themed issue 'Second quantum revolution: foundational questions'. © 2017 The Author(s).

  2. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  3. Elucidating Reaction Mechanisms on Quantum Computers

    NASA Astrophysics Data System (ADS)

    Wiebe, Nathan; Reiher, Markus; Svore, Krysta; Wecker, Dave; Troyer, Matthias

    We show how a quantum computer can be employed to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical-computer simulations for such problems, to significantly increase their accuracy and enable hitherto intractable simulations. Detailed resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. This demonstrates that quantum computers will realistically be able to tackle important problems in chemistry that are both scientifically and economically significant.

  4. Hunting for Snarks in Quantum Mechanics

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

    Hestenes, David

    2009-12-08

    A long-standing debate over the interpretation of quantum mechanics has centered on the meaning of Schroedinger's wave function {psi} for an electron. Broadly speaking, there are two major opposing schools. On the one side, the Copenhagen school(led by Bohr, Heisenberg and Pauli) holds that {psi} provides a complete description of a single electron state; hence the probability interpretation of {psi}{psi}* expresses an irreducible uncertainty in electron behavior that is intrinsic in nature. On the other side, the realist school(led by Einstein, de Broglie, Bohm and Jaynes) holds that {psi} represents a statistical ensemble of possible electron states; hence it ismore » an incomplete description of a single electron state. I contend that the debaters have overlooked crucial facts about the electron revealed by Dirac theory. In particular, analysis of electron zitterbewegung(first noticed by Schroedinger) opens a window to particle substructure in quantum mechanics that explains the physical significance of the complex phase factor in {psi}. This led to a testable model for particle substructure with surprising support by recent experimental evidence. If the explanation is upheld by further research, it will resolve the debate in favor of the realist school. I give details. The perils of research on the foundations of quantum mechanics have been foreseen by Lewis Carroll in The Hunting of the Snark{exclamation_point}.« less

  5. 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

  6. Quantum mechanics: The Bayesian theory generalized to the space of Hermitian matrices

    NASA Astrophysics Data System (ADS)

    Benavoli, Alessio; Facchini, Alessandro; Zaffalon, Marco

    2016-10-01

    We consider the problem of gambling on a quantum experiment and enforce rational behavior by a few rules. These rules yield, in the classical case, the Bayesian theory of probability via duality theorems. In our quantum setting, they yield the Bayesian theory generalized to the space of Hermitian matrices. This very theory is quantum mechanics: in fact, we derive all its four postulates from the generalized Bayesian theory. This implies that quantum mechanics is self-consistent. It also leads us to reinterpret the main operations in quantum mechanics as probability rules: Bayes' rule (measurement), marginalization (partial tracing), independence (tensor product). To say it with a slogan, we obtain that quantum mechanics is the Bayesian theory in the complex numbers.

  7. Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

    PubMed

    Li, Pengfei; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2018-02-28

    The proton-coupled electron transfer (PCET) reaction catalyzed by soybean lipoxygenase has served as a prototype for understanding hydrogen tunneling in enzymes. Herein this PCET reaction is studied with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The free energy surfaces are computed as functions of the proton donor-acceptor (C-O) distance and the proton coordinate, and the potential of mean force is computed as a function of the C-O distance, inherently including anharmonicity. The simulation results are used to calculate the kinetic isotope effects for the wild-type enzyme (WT) and the L546A/L754A double mutant (DM), which have been measured experimentally to be ∼80 and ∼700, respectively. The PCET reaction is found to be exoergic for WT and slightly endoergic for the DM, and the equilibrium C-O distance for the reactant is found to be ∼0.2 Å greater for the DM than for WT. The larger equilibrium distance for the DM, which is due mainly to less optimal substrate binding in the expanded binding cavity, is primarily responsible for its higher kinetic isotope effect. The calculated potentials of mean force are anharmonic and relatively soft at shorter C-O distances, allowing efficient thermal sampling of the shorter distances required for effective hydrogen tunneling. The primarily local electrostatic field at the transferring hydrogen is ∼100 MV/cm in the direction to facilitate proton transfer and increases dramatically as the C-O distance decreases. These simulations suggest that the overall protein environment is important for conformational sampling of active substrate configurations aligned for proton transfer, but the PCET reaction is influenced primarily by local electrostatic effects that facilitate conformational sampling of shorter proton donor-acceptor distances required for effective hydrogen tunneling.

  8. Principles of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Landé, Alfred

    2013-10-01

    ödinger's equation for non-conservative systems; 46. Pertubation theory; 47. Orthogonality, normalization and Hermitian conjugacy; 48. General matrix elements; Part IV. The Principle of Correspondence: 49. Contact transformations in classical mechanics; 50. Point transformations; 51. Contact transformations in quantum mechanics; 52. Constants of motion and angular co-ordinates; 53. Periodic orbits; 54. De Broglie and Schrödinger function; correspondence to classical mechanics; 55. Packets of probability; 56. Correspondence to hydrodynamics; 57. Motion and scattering of wave packets; 58. Formal correspondence between classical and quantum mechanics; Part V. Mathematical Appendix: Principle of Invariance: 59. The general theorem of transformation; 60. Operator calculus; 61. Exchange relations; three criteria for conjugacy; 62. First method of canonical transformation; 63. Second method of canonical transformation; 64. Proof of the transformation theorem; 65. Invariance of the matrix elements against unitary transformations; 66. Matrix mechanics; Index of literature; Index of names and subjects.

  9. Molecular Mechanics: Illustrations of Its Application.

    ERIC Educational Resources Information Center

    Cox, Philip J.

    1982-01-01

    The application of molecular mechanics (a nonquantum mechanical method for solving problems concerning molecular geometries) to calculate force fields for n-butane and cyclohexane is discussed. Implications regarding the stable conformations of the example molecules are also discussed. (Author/SK)

  10. Mechanical equivalent of quantum heat engines.

    PubMed

    Arnaud, Jacques; Chusseau, Laurent; Philippe, Fabrice

    2008-06-01

    Quantum heat engines employ as working agents multilevel systems instead of classical gases. We show that under some conditions quantum heat engines are equivalent to a series of reservoirs at different altitudes containing balls of various weights. A cycle consists of picking up at random a ball from one reservoir and carrying it to the next, thereby performing or absorbing some work. In particular, quantum heat engines, employing two-level atoms as working agents, are modeled by reservoirs containing balls of weight 0 or 1. The mechanical model helps us prove that the maximum efficiency of quantum heat engines is the Carnot efficiency. Heat pumps and negative temperatures are considered.

  11. Quantum mechanical/molecular mechanical and docking study of the novel analogues based on hybridization of common pharmacophores as potential anti-breast cancer agents

    PubMed Central

    Asadi, Parvin; Khodarahmi, Ghadamali; Farrokhpour, Hossein; Hassanzadeh, Farshid; Saghaei, Lotfollah

    2017-01-01

    In an attempt to identify some new potential leads as anti-breast cancer agents, novel hybrid compounds were designed by molecular hybridization approach. These derivatives were structurally derived from hybrid benzofuran–imidazole and quinazolinone derivatives, which had shown good cytotoxicity against the breast cancer cell line (MCF-7). Since aromatase enzyme (CYP19) is highly expressed in the MCF-7 cell line, the binding of these novel hybrid compounds to aromatase was investigated using the docking method. In this study, due to the positive charge on the imidazole ring of the designed ligands and also, the presence of heme iron in the active site of the enzyme, it was decided to optimize the ligand inside the protein to obtain more realistic atomic charges for it. Quantum mechanical/molecular mechanical (QM/MM) method was used to obtain more accurate atomic charges of ligand for docking calculations by considering the polarization effects of CYP19 on ligands. It was observed that the refitted charge improved the binding energy of the docked compounds. Also, the results showed that these novel hybrid compounds were adopted properly within the aromatase binding site, thereby suggesting that they could be potential inhibitors of aromatase. The main binding modes in these complexes were through hydrophobic and H bond interactions showing agreement with the basic physicochemical features of known anti aromatase compounds. Finally, the complex structures obtained from the docking study were used for single point QM/MM calculations to obtain more accurate electronic interaction energy, considering the electronic polarization of the ligand by its protein environment. PMID:28626481

  12. An Overview of the Transactional Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Cramer, John G.

    1988-02-01

    The transactional interpretation of quantum mechanics (TI) is summarized and various points concerning the TI and its relation to the Copenhagen interpretation (CI) are considered. Questions concerning mapping the TI onto the CI, of advanced waves as solutions to proper wave equations, of collapse and the QM formalism, and of the relation of quantum mechanical interpretations to experimental tests and results are discussed.

  13. An overview of the transactional interpretation of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Cramer, J. G.

    We summarize the transactional interpretation (TI) of quantum mechanics (QM) and consider various points concerning the TI and its relation to the Copenhagen interpretation (CI). Questions concerning mapping the TI onto the CI, of advanced waves as solutions to proper wave equations, of collapse and the QM formalism, and of the relation of quantum mechanical interpretations to experimental tests and results are discussed.

  14. Lyapounov variable: Entropy and measurement in quantum mechanics

    PubMed Central

    Misra, B.; Prigogine, I.; Courbage, M.

    1979-01-01

    We discuss the question of the dynamical meaning of the second law of thermodynamics in the framework of quantum mechanics. Previous discussion of the problem in the framework of classical dynamics has shown that the second law can be given a dynamical meaning in terms of the existence of so-called Lyapounov variables—i.e., dynamical variables varying monotonically in time without becoming contradictory. It has been found that such variables can exist in an extended framework of classical dynamics, provided that the dynamical motion is suitably unstable. In this paper we begin to extend these results to quantum mechanics. It is found that no dynamical variable with the characteristic properties of nonequilibrium entropy can be defined in the standard formulation of quantum mechanics. However, if the Hamiltonian has certain well-defined spectral properties, such variables can be defined but only as a nonfactorizable superoperator. Necessary nonfactorizability of such entropy operators M has the consequence that they cannot preserve the class of pure states. Physically, this means that the distinguishability between pure states and corresponding mixtures must be lost in the case of a quantal system for which the algebra of observables can be extended to include a new dynamical variable representing nonequilibrium entropy. We discuss how this result leads to a solution of the quantum measurement problem. It is also found that the question of existence of entropy of superoperators M is closely linked to the problem of defining an operator of time in quantum mechanics. PMID:16578757

  15. Quantum Mechanics for Everyone: Hands-On Activities Integrated with Technology.

    ERIC Educational Resources Information Center

    Zollman, Dean A.; Rebello, N. Sanjay; Hogg, Kirsten

    2002-01-01

    Explains a hands-on approach to teaching quantum mechanics that challenges the belief shared by many physics instructors that quantum mechanics is a very abstract subject that cannot be understood until students have learned much of the classical physics. (Contains 23 references.) (Author/YDS)

  16. Quantum approach to classical statistical mechanics.

    PubMed

    Somma, R D; Batista, C D; Ortiz, G

    2007-07-20

    We present a new approach to study the thermodynamic properties of d-dimensional classical systems by reducing the problem to the computation of ground state properties of a d-dimensional quantum model. This classical-to-quantum mapping allows us to extend the scope of standard optimization methods by unifying them under a general framework. The quantum annealing method is naturally extended to simulate classical systems at finite temperatures. We derive the rates to assure convergence to the optimal thermodynamic state using the adiabatic theorem of quantum mechanics. For simulated and quantum annealing, we obtain the asymptotic rates of T(t) approximately (pN)/(k(B)logt) and gamma(t) approximately (Nt)(-c/N), for the temperature and magnetic field, respectively. Other annealing strategies are also discussed.

  17. A theoretical study of the molecular mechanism of the GAPDH Trypanosoma cruzi enzyme involving iodoacetate inhibitor

    NASA Astrophysics Data System (ADS)

    Carneiro, Agnaldo Silva; Lameira, Jerônimo; Alves, Cláudio Nahum

    2011-10-01

    The glyceraldehyde-3-phosphate dehydrogenase enzyme (GAPDH) is an important biological target for the development of new chemotherapeutic agents against Chagas disease. In this Letter, the inhibition mechanism of GAPDH involving iodoacetate (IAA) inhibitor was studied using the hybrid quantum mechanical/molecular mechanical (QM/MM) approach and molecular dynamic simulations. Analysis of the potential energy surface and potential of mean force show that the covalent attachment of IAA inhibitor to the active site of the enzyme occurs as a concerted process. In addition, the energy terms decomposition shows that NAD+ plays an important role in stabilization of the reagents and transition state.

  18. Student Understanding of Time Dependence in Quantum Mechanics

    ERIC Educational Resources Information Center

    Emigh, Paul J.; Passante, Gina; Shaffer, Peter S.

    2015-01-01

    The time evolution of quantum states is arguably one of the more difficult ideas in quantum mechanics. In this article, we report on results from an investigation of student understanding of this topic after lecture instruction. We demonstrate specific problems that students have in applying time dependence to quantum systems and in recognizing…

  19. From classical to quantum mechanics: ``How to translate physical ideas into mathematical language''

    NASA Astrophysics Data System (ADS)

    Bergeron, H.

    2001-09-01

    Following previous works by E. Prugovečki [Physica A 91A, 202 (1978) and Stochastic Quantum Mechanics and Quantum Space-time (Reidel, Dordrecht, 1986)] on common features of classical and quantum mechanics, we develop a unified mathematical framework for classical and quantum mechanics (based on L2-spaces over classical phase space), in order to investigate to what extent quantum mechanics can be obtained as a simple modification of classical mechanics (on both logical and analytical levels). To obtain this unified framework, we split quantum theory in two parts: (i) general quantum axiomatics (a system is described by a state in a Hilbert space, observables are self-adjoints operators, and so on) and (ii) quantum mechanics proper that specifies the Hilbert space as L2(Rn); the Heisenberg rule [pi,qj]=-iℏδij with p=-iℏ∇, the free Hamiltonian H=-ℏ2Δ/2m and so on. We show that general quantum axiomatics (up to a supplementary "axiom of classicity") can be used as a nonstandard mathematical ground to formulate physical ideas and equations of ordinary classical statistical mechanics. So, the question of a "true quantization" with "ℏ" must be seen as an independent physical problem not directly related with quantum formalism. At this stage, we show that this nonstandard formulation of classical mechanics exhibits a new kind of operation that has no classical counterpart: this operation is related to the "quantization process," and we show why quantization physically depends on group theory (the Galilei group). This analytical procedure of quantization replaces the "correspondence principle" (or canonical quantization) and allows us to map classical mechanics into quantum mechanics, giving all operators of quantum dynamics and the Schrödinger equation. The great advantage of this point of view is that quantization is based on concrete physical arguments and not derived from some "pure algebraic rule" (we exhibit also some limit of the correspondence

  20. Reply to "Comment on 'Fractional quantum mechanics' and 'Fractional Schrödinger equation' ".

    PubMed

    Laskin, Nick

    2016-06-01

    The fractional uncertainty relation is a mathematical formulation of Heisenberg's uncertainty principle in the framework of fractional quantum mechanics. Two mistaken statements presented in the Comment have been revealed. The origin of each mistaken statement has been clarified and corrected statements have been made. A map between standard quantum mechanics and fractional quantum mechanics has been presented to emphasize the features of fractional quantum mechanics and to avoid misinterpretations of the fractional uncertainty relation. It has been shown that the fractional probability current equation is correct in the area of its applicability. Further studies have to be done to find meaningful quantum physics problems with involvement of the fractional probability current density vector and the extra term emerging in the framework of fractional quantum mechanics.

  1. Fundamental Quantum Mechanics--A Graphic Presentation

    ERIC Educational Resources Information Center

    Wise, M. N.; Kelley, T. G.

    1977-01-01

    Describes a presentation of basic quantum mechanics for nonscience majors that relies on a computer-generated graphic display to circumvent the usual mathematical difficulties. It allows a detailed treatment of free-particle motion in a wave picture. (MLH)

  2. A Concise Introduction to Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Swanson, Mark S.

    2018-02-01

    Assuming a background in basic classical physics, multivariable calculus, and differential equations, A Concise Introduction to Quantum Mechanics provides a self-contained presentation of the mathematics and physics of quantum mechanics. The relevant aspects of classical mechanics and electrodynamics are reviewed, and the basic concepts of wave-particle duality are developed as a logical outgrowth of experiments involving blackbody radiation, the photoelectric effect, and electron diffraction. The Copenhagen interpretation of the wave function and its relation to the particle probability density is presented in conjunction with Fourier analysis and its generalization to function spaces. These concepts are combined to analyze the system consisting of a particle confined to a box, developing the probabilistic interpretation of observations and their associated expectation values. The Schrödinger equation is then derived by using these results and demanding both Galilean invariance of the probability density and Newtonian energy-momentum relations. The general properties of the Schrödinger equation and its solutions are analyzed, and the theory of observables is developed along with the associated Heisenberg uncertainty principle. Basic applications of wave mechanics are made to free wave packet spreading, barrier penetration, the simple harmonic oscillator, the Hydrogen atom, and an electric charge in a uniform magnetic field. In addition, Dirac notation, elements of Hilbert space theory, operator techniques, and matrix algebra are presented and used to analyze coherent states, the linear potential, two state oscillations, and electron diffraction. Applications are made to photon and electron spin and the addition of angular momentum, and direct product multiparticle states are used to formulate both the Pauli exclusion principle and quantum decoherence. The book concludes with an introduction to the rotation group and the general properties of angular momentum.

  3. Two Mechanisms Determine Quantum Dot Blinking.

    PubMed

    Yuan, Gangcheng; Gómez, Daniel E; Kirkwood, Nicholas; Boldt, Klaus; Mulvaney, Paul

    2018-04-24

    Many potential applications of quantum dots (QDs) can only be realized once the luminescence from single nanocrystals (NCs) is understood. These applications include the development of quantum logic devices, single-photon sources, long-life LEDs, and single-molecule biolabels. At the single-nanocrystal level, random fluctuations in the QD photoluminescence occur, a phenomenon termed blinking. There are two competing models to explain this blinking: Auger recombination and surface trap induced recombination. Here we use lifetime scaling on core-shell chalcogenide NCs to demonstrate that both types of blinking occur in the same QDs. We prove that Auger-blinking can yield single-exponential on/off times in contrast to earlier work. The surface passivation strategy determines which blinking mechanism dominates. This study summarizes earlier studies on blinking mechanisms and provides some clues that stable single QDs can be engineered for optoelectronic applications.

  4. The Misapplication of Probability Theory in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Racicot, Ronald

    2014-03-01

    This article is a revision of two papers submitted to the APS in the past two and a half years. In these papers, arguments and proofs are summarized for the following: (1) The wrong conclusion by EPR that Quantum Mechanics is incomplete, perhaps requiring the addition of ``hidden variables'' for completion. Theorems that assume such ``hidden variables,'' such as Bell's theorem, are also wrong. (2) Quantum entanglement is not a realizable physical phenomenon and is based entirely on assuming a probability superposition model for quantum spin. Such a model directly violates conservation of angular momentum. (3) Simultaneous multiple-paths followed by a quantum particle traveling through space also cannot possibly exist. Besides violating Noether's theorem, the multiple-paths theory is based solely on probability calculations. Probability calculations by themselves cannot possibly represent simultaneous physically real events. None of the reviews of the submitted papers actually refuted the arguments and evidence that was presented. These analyses should therefore be carefully evaluated since the conclusions reached have such important impact in quantum mechanics and quantum information theory.

  5. Teaching Quantum Mechanics with qCraft: Outreach and Video Games

    NASA Astrophysics Data System (ADS)

    Kubica, Aleksander; Chatwin-Davies, Aidan; Michalakis, Spyridon

    Why is quantum mechanics considered a hard and inaccessible subject? Part of the difficulty is due to the nature of the subject itself. However, no small part of the difficulty is its pedagogy, which often relies on out-of-date historical motivation and experimental evidence that is disconnected from day-to-day experiences. In this first talk, we explore ways in which video games are well-suited to teaching quantum mechanics, in particular with regards to building intuition, as well as some of their limitations. We then illustrate these considerations through qCraft, an extension for Minecraft that incorporates aspects of quantum mechanics into the game.

  6. Interactive Simulations to Support Quantum Mechanics Instruction for Chemistry Students

    ERIC Educational Resources Information Center

    Kohnle, Antje; Benfield, Cory; Hahner, Georg; Paetkau, Mark

    2017-01-01

    The QuVis Quantum Mechanics Visualization Project provides freely available research-based interactive simulations with accompanying activities for the teaching and learning of quantum mechanics across a wide range of topics and levels. This article gives an overview of some of the simulations and describes their use in an introductory physical…

  7. Nine formulations of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Styer, Daniel F.; Balkin, Miranda S.; Becker, Kathryn M.; Burns, Matthew R.; Dudley, Christopher E.; Forth, Scott T.; Gaumer, Jeremy S.; Kramer, Mark A.; Oertel, David C.; Park, Leonard H.; Rinkoski, Marie T.; Smith, Clait T.; Wotherspoon, Timothy D.

    2002-03-01

    Nine formulations of nonrelativistic quantum mechanics are reviewed. These are the wavefunction, matrix, path integral, phase space, density matrix, second quantization, variational, pilot wave, and Hamilton-Jacobi formulations. Also mentioned are the many-worlds and transactional interpretations. The various formulations differ dramatically in mathematical and conceptual overview, yet each one makes identical predictions for all experimental results.

  8. The emergent Copenhagen interpretation of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Hollowood, Timothy J.

    2014-05-01

    We introduce a new and conceptually simple interpretation of quantum mechanics based on reduced density matrices of sub-systems from which the standard Copenhagen interpretation emerges as an effective description of macroscopically large systems. This interpretation describes a world in which definite measurement results are obtained with probabilities that reproduce the Born rule. Wave function collapse is seen to be a useful but fundamentally unnecessary piece of prudent book keeping which is only valid for macro-systems. The new interpretation lies in a class of modal interpretations in that it applies to quantum systems that interact with a much larger environment. However, we show that it does not suffer from the problems that have plagued similar modal interpretations like macroscopic superpositions and rapid flipping between macroscopically distinct states. We describe how the interpretation fits neatly together with fully quantum formulations of statistical mechanics and that a measurement process can be viewed as a process of ergodicity breaking analogous to a phase transition. The key feature of the new interpretation is that joint probabilities for the ergodic subsets of states of disjoint macro-systems only arise as emergent quantities. Finally we give an account of the EPR-Bohm thought experiment and show that the interpretation implies the violation of the Bell inequality characteristic of quantum mechanics but in a way that is rather novel. The final conclusion is that the Copenhagen interpretation gives a completely satisfactory phenomenology of macro-systems interacting with micro-systems.

  9. Virtual Learning Environment for Interactive Engagement with Advanced Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Pedersen, Mads Kock; Skyum, Birk; Heck, Robert; Müller, Romain; Bason, Mark; Lieberoth, Andreas; Sherson, Jacob F.

    2016-06-01

    A virtual learning environment can engage university students in the learning process in ways that the traditional lectures and lab formats cannot. We present our virtual learning environment StudentResearcher, which incorporates simulations, multiple-choice quizzes, video lectures, and gamification into a learning path for quantum mechanics at the advanced university level. StudentResearcher is built upon the experiences gathered from workshops with the citizen science game Quantum Moves at the high-school and university level, where the games were used extensively to illustrate the basic concepts of quantum mechanics. The first test of this new virtual learning environment was a 2014 course in advanced quantum mechanics at Aarhus University with 47 enrolled students. We found increased learning for the students who were more active on the platform independent of their previous performances.

  10. Plasmonic resonances of nanoparticles from large-scale quantum mechanical simulations

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; Xiang, Hongping; Zhang, Mingliang; Lu, Gang

    2017-09-01

    Plasmonic resonance of metallic nanoparticles results from coherent motion of its conduction electrons, driven by incident light. For the nanoparticles less than 10 nm in diameter, localized surface plasmonic resonances become sensitive to the quantum nature of the conduction electrons. Unfortunately, quantum mechanical simulations based on time-dependent Kohn-Sham density functional theory are computationally too expensive to tackle metal particles larger than 2 nm. Herein, we introduce the recently developed time-dependent orbital-free density functional theory (TD-OFDFT) approach which enables large-scale quantum mechanical simulations of plasmonic responses of metallic nanostructures. Using TD-OFDFT, we have performed quantum mechanical simulations to understand size-dependent plasmonic response of Na nanoparticles and plasmonic responses in Na nanoparticle dimers and trimers. An outlook of future development of the TD-OFDFT method is also presented.

  11. BOOK REVIEWS: Quantum Mechanics: Fundamentals

    NASA Astrophysics Data System (ADS)

    Whitaker, A.

    2004-02-01

    This review is of three books, all published by Springer, all on quantum theory at a level above introductory, but very different in content, style and intended audience. That of Gottfried and Yan is of exceptional interest, historical and otherwise. It is a second edition of Gottfried’s well-known book published by Benjamin in 1966. This was written as a text for a graduate quantum mechanics course, and has become one of the most used and respected accounts of quantum theory, at a level mathematically respectable but not rigorous. Quantum mechanics was already solidly established by 1966, but this second edition gives an indication of progress made and changes in perspective over the last thirty-five years, and also recognises the very substantial increase in knowledge of quantum theory obtained at the undergraduate level. Topics absent from the first edition but included in the second include the Feynman path integral, seen in 1966 as an imaginative but not very useful formulation of quantum theory. Feynman methods were given only a cursory mention by Gottfried. Their practical importance has now been fully recognised, and a substantial account of them is provided in the new book. Other new topics include semiclassical quantum mechanics, motion in a magnetic field, the S matrix and inelastic collisions, radiation and scattering of light, identical particle systems and the Dirac equation. A topic that was all but totally neglected in 1966, but which has flourished increasingly since, is that of the foundations of quantum theory. John Bell’s work of the mid-1960s has led to genuine theoretical and experimental achievement, which has facilitated the development of quantum optics and quantum information theory. Gottfried’s 1966 book played a modest part in this development. When Bell became increasingly irritated with the standard theoretical approach to quantum measurement, Viki Weisskopf repeatedly directed him to Gottfried’s book. Gottfried had devoted a

  12. Probability in the Many-Worlds Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Vaidman, Lev

    It is argued that, although in the Many-Worlds Interpretation of quantum mechanics there is no "probability" for an outcome of a quantum experiment in the usual sense, we can understand why we have an illusion of probability. The explanation involves: (a) A "sleeping pill" gedanken experiment which makes correspondence between an illegitimate question: "What is the probability of an outcome of a quantum measurement?" with a legitimate question: "What is the probability that `I' am in the world corresponding to that outcome?"; (b) A gedanken experiment which splits the world into several worlds which are identical according to some symmetry condition; and (c) Relativistic causality, which together with (b) explain the Born rule of standard quantum mechanics. The Quantum Sleeping Beauty controversy and "caring measure" replacing probability measure are discussed.

  13. The molecular mechanics of eukaryotic translation.

    PubMed

    Kapp, Lee D; Lorsch, Jon R

    2004-01-01

    Great advances have been made in the past three decades in understanding the molecular mechanics underlying protein synthesis in bacteria, but our understanding of the corresponding events in eukaryotic organisms is only beginning to catch up. In this review we describe the current state of our knowledge and ignorance of the molecular mechanics underlying eukaryotic translation. We discuss the mechanisms conserved across the three kingdoms of life as well as the important divergences that have taken place in the pathway.

  14. PT quantum mechanics.

    PubMed

    Bender, Carl M; DeKieviet, Maarten; Klevansky, S P

    2013-04-28

    PT-symmetric quantum mechanics (PTQM) has become a hot area of research and investigation. Since its beginnings in 1998, there have been over 1000 published papers and more than 15 international conferences entirely devoted to this research topic. Originally, PTQM was studied at a highly mathematical level and the techniques of complex variables, asymptotics, differential equations and perturbation theory were used to understand the subtleties associated with the analytic continuation of eigenvalue problems. However, as experiments on PT-symmetric physical systems have been performed, a simple and beautiful physical picture has emerged, and a PT-symmetric system can be understood as one that has a balanced loss and gain. Furthermore, the PT phase transition can now be understood intuitively without resorting to sophisticated mathematics. Research on PTQM is following two different paths: at a fundamental level, physicists are attempting to understand the underlying mathematical structure of these theories with the long-range objective of applying the techniques of PTQM to understanding some of the outstanding problems in physics today, such as the nature of the Higgs particle, the properties of dark matter, the matter-antimatter asymmetry in the universe, neutrino oscillations and the cosmological constant; at an applied level, new kinds of PT-synthetic materials are being developed, and the PT phase transition is being observed in many physical contexts, such as lasers, optical wave guides, microwave cavities, superconducting wires and electronic circuits. The purpose of this Theme Issue is to acquaint the reader with the latest developments in PTQM. The articles in this volume are written in the style of mini-reviews and address diverse areas of the emerging and exciting new area of PT-symmetric quantum mechanics.

  15. Student understanding of time dependence in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Emigh, Paul J.; Passante, Gina; Shaffer, Peter S.

    2015-12-01

    [This paper is part of the Focused Collection on Upper Division Physics Courses.] The time evolution of quantum states is arguably one of the more difficult ideas in quantum mechanics. In this article, we report on results from an investigation of student understanding of this topic after lecture instruction. We demonstrate specific problems that students have in applying time dependence to quantum systems and in recognizing the key role of the energy eigenbasis in determining the time dependence of wave functions. Through analysis of student responses to a set of four interrelated tasks, we categorize some of the difficulties that underlie common errors. The conceptual and reasoning difficulties that have been identified are illustrated through student responses to four sets of questions administered at different points in a junior-level course on quantum mechanics. Evidence is also given that the problems persist throughout undergraduate instruction and into the graduate level.

  16. Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

    PubMed Central

    Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo

    2013-01-01

    Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489

  17. Investigating and Improving Student Understanding of Key Ideas in Quantum Mechanics throughout Instruction

    NASA Astrophysics Data System (ADS)

    Emigh, Paul Jeffrey

    This dissertation describes research on student understanding of quantum mechanics across multiple levels of instruction. The primary focus has been to identify patterns in student reasoning related to key concepts in quantum mechanics. The specific topics include quantum measurements, time dependence, vector spaces, and angular momentum. The research has spanned a variety of different quantum courses intended for introductory physics students, upper-division physics majors, and graduate students in physics. The results of this research have been used to develop a set of curriculum, Tutorials in Physics: Quantum Mechanics, for addressing the most persistent student difficulties. We document both the development of this curriculum and how it has impacted and improved student understanding of quantum mechanics.

  18. Strange Bedfellows: Quantum Mechanics and Data Mining

    NASA Astrophysics Data System (ADS)

    Weinstein, Marvin

    2010-02-01

    Last year, in 2008, I gave a talk titled Quantum Calisthenics. This year I am going to tell you about how the work I described then has spun off into a most unlikely direction. What I am going to talk about is how one maps the problem of finding clusters in a given data set into a problem in quantum mechanics. I will then use the tricks I described to let quantum evolution lets the clusters come together on their own.

  19. Machine Learning and Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Chapline, George

    The author has previously pointed out some similarities between selforganizing neural networks and quantum mechanics. These types of neural networks were originally conceived of as away of emulating the cognitive capabilities of the human brain. Recently extensions of these networks, collectively referred to as deep learning networks, have strengthened the connection between self-organizing neural networks and human cognitive capabilities. In this note we consider whether hardware quantum devices might be useful for emulating neural networks with human-like cognitive capabilities, or alternatively whether implementations of deep learning neural networks using conventional computers might lead to better algorithms for solving the many body Schrodinger equation.

  20. 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).

  1. Relativity, Symmetry, and the Structure of Quantum Theory, Volume 2; Point form relativistic quantum mechanics

    NASA Astrophysics Data System (ADS)

    Klink, William H.; Schweiger, Wolfgang

    2018-03-01

    This book covers relativistic quantum theory from the point of view of a particle theory, based on the irreducible representations of the Poincaré group, the group that expresses the symmetry of Einstein relativity. There are several ways of formulating such a theory; this book develops what is called relativistic point form quantum mechanics, which, unlike quantum field theory, deals with a fixed number of particles in a relativistically invariant way. A chapter is devoted to applications of point form quantum mechanics to nuclear physics.

  2. Investigating Learners' Epistemological Framings of Quantum Mechanics

    ERIC Educational Resources Information Center

    Dini, Vesal

    2017-01-01

    Classical mechanics challenges students to use their intuitions and experiences as a basis for understanding, in effect to approach learning as "a refinement of everyday thinking'' (Einstein, 1936). Moving on to quantum mechanics (QM), students, like physicists, need to adjust this approach, in particular with respect to the roles that…

  3. Links between fluid mechanics and quantum mechanics: a model for information in economics?

    PubMed

    Haven, Emmanuel

    2016-05-28

    This paper tallies the links between fluid mechanics and quantum mechanics, and attempts to show whether those links can aid in beginning to build a formal template which is usable in economics models where time is (a)symmetric and memory is absent or present. An objective of this paper is to contemplate whether those formalisms can allow us to model information in economics in a novel way. © 2016 The Author(s).

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

    PubMed

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

    2012-06-07

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

  5. QuVis interactive simulations: tools to support quantum mechanics instruction

    NASA Astrophysics Data System (ADS)

    Kohnle, Antje

    2015-04-01

    Quantum mechanics holds a fascination for many students, but its mathematical complexity and counterintuitive results can present major barriers. The QuVis Quantum Mechanics Visualization Project (www.st-andrews.ac.uk/physics/quvis) aims to overcome these issues through the development and evaluation of interactive simulations with accompanying activities for the learning and teaching of quantum mechanics. Over 90 simulations are now available on the QuVis website. One collection of simulations is embedded in the Institute of Physics Quantum Physics website (quantumphysics.iop.org), which consists of freely available resources for an introductory course in quantum mechanics starting from two-level systems. Simulations support model-building by reducing complexity, focusing on fundamental ideas and making the invisible visible. They promote engaged exploration, sense-making and linking of multiple representations, and include high levels of interactivity and direct feedback. Simulations are research-based and evaluation with students informs all stages of the development process. Simulations are iteratively refined using student feedback in individual observation sessions and in-class trials. Evaluation has shown that the simulations can help students learn quantum mechanics concepts at both the introductory and advanced undergraduate level and that students perceive simulations to be beneficial to their learning. Recent activity includes the launch of a new collection of HTML5 simulations that run on both desktop and tablet-based devices and the introduction of a goal and reward structure in simulations through the inclusion of challenges. This presentation will give an overview of the QuVis resources, highlight recent work and outline future plans. QuVis is supported by the UK Institute of Physics, the UK Higher Education Academy and the University of St Andrews.

  6. Preface: Special Topic: From Quantum Mechanics to Force Fields.

    PubMed

    Piquemal, Jean-Philip; Jordan, Kenneth D

    2017-10-28

    This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

  7. Preface: Special Topic: From Quantum Mechanics to Force Fields

    NASA Astrophysics Data System (ADS)

    Piquemal, Jean-Philip; Jordan, Kenneth D.

    2017-10-01

    This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

  8. Nonrelativistic Quantum Mechanics with Fundamental Environment

    NASA Astrophysics Data System (ADS)

    Gevorkyan, Ashot S.

    2011-03-01

    Spontaneous transitions between bound states of an atomic system, "Lamb Shift" of energy levels and many other phenomena in real nonrelativistic quantum systems are connected within the influence of the quantum vacuum fluctuations ( fundamental environment (FE)) which are impossible to consider in the limits of standard quantum-mechanical approaches. The joint system "quantum system (QS) + FE" is described in the framework of the stochastic differential equation (SDE) of Langevin-Schrödinger (L-Sch) type, and is defined on the extended space R 3 ⊗ R { ξ}, where R 3 and R { ξ} are the Euclidean and functional spaces, respectively. The density matrix for single QS in FE is defined. The entropy of QS entangled with FE is defined and investigated in detail. It is proved that as a result of interaction of QS with environment there arise structures of various topologies which are a new quantum property of the system.

  9. Developing and assessing research-based tools for teaching quantum mechanics and thermodynamics

    NASA Astrophysics Data System (ADS)

    Brown, Benjamin R.

    Research-based tools to educate college students in physics courses from introductory level to graduate level are essential for helping students with a diverse set of goals and backgrounds learn physics. This thesis explores issues related to student common difficulties with some topics in undergraduate quantum mechanics and thermodynamics courses. Student difficulties in learning quantum mechanics and thermodynamics are investigated by administering written tests and surveys to many classes and conducting individual interviews with a subset of students outside the class to unpack the cognitive mechanisms of the difficulties. The quantum mechanics research also focuses on using the research on student difficulties for the development and evaluation of a Quantum Interactive Learning Tutorial (QuILT) to help students learn about the time-dependence of expectation values using the context of Larmor precession of spin and evaluating the role of asking students to self-diagnose their mistakes on midterm examination on their performance on subsequent problem solving. The QuILT on Larmor precession of spin has both paper-pencil activities and a simulation component to help students learn these foundational issues in quantum mechanics. Preliminary evaluations suggest that the QuILT, which strives to help students build a robust knowledge structure of time-dependence of expectation values in quantum mechanics using a guided approach, is successful in helping students learn these topics in the junior-senior level quantum mechanics courses. The technique to help upper-level students in quantum mechanics courses effectively engage in the process of learning from their mistakes is also found to be effective. In particular, research shows that the self-diagnosis activity in upper-level quantum mechanics significantly helps students who are struggling and this activity can reduce the gap between the high and low achieving students on subsequent problem solving. Finally, a survey

  10. Computer simulations of local anesthetic mechanisms: Quantum chemical investigation of procaine

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

    Smith, Jeremy C; Bondar, A.N.; Suhai, Sandor

    2007-02-01

    A description at the atomic level of detail of the interaction between local anesthetics, lipid membranes and membrane proteins, is essential for understanding the mechanism of local anesthesia. The importance of performing computer simulations to decipher the mechanism of local anesthesia is discussed here in the context of the current status of understanding of the local anesthetics action. As a first step towards accurate simulations of the interaction between local anesthetics, proteins, lipid and water molecules, here we use quantum mechanical methods to assess the charge distribution and structural properties of procaine in the presence and in the absence ofmore » water molecules. The calculations indicate that, in the absence of hydrogen-bonding water molecules, protonated procaine strongly prefers a compact structure enabled by intramolecular hydrogen bonding. In the presence of water molecules the torsional energy pro?le of procaine is modified, and hydrogen bonding to water molecules is favored relative to intra-molecular hydrogen bonding.« less

  11. Is quantum theory a form of statistical mechanics?

    NASA Astrophysics Data System (ADS)

    Adler, S. L.

    2007-05-01

    We give a review of the basic themes of my recent book: Adler S L 2004 Quantum Theory as an Emergent Phenomenon (Cambridge: Cambridge University Press). We first give motivations for considering the possibility that quantum mechanics is not exact, but is instead an accurate asymptotic approximation to a deeper level theory. For this deeper level, we propose a non-commutative generalization of classical mechanics, that we call "trace dynamics", and we give a brief survey of how it works, considering for simplicity only the bosonic case. We then discuss the statistical mechanics of trace dynamics and give our argument that with suitable approximations, the Ward identities for trace dynamics imply that ensemble averages in the canonical ensemble correspond to Wightman functions in quantum field theory. Thus, quantum theory emerges as the statistical thermodynamics of trace dynamics. Finally, we argue that Brownian motion corrections to this thermodynamics lead to stochastic corrections to the Schrödinger equation, of the type that have been much studied in the "continuous spontaneous localization" model of objective state vector reduction. In appendices to the talk, we give details of the existence of a conserved operator in trace dynamics that encodes the structure of the canonical algebra, of the derivation of the Ward identities, and of the proof that the stochastically-modified Schrödinger equation leads to state vector reduction with Born rule probabilities.

  12. Axioms for quantum mechanics: relativistic causality, retrocausality, and the existence of a classical limit

    NASA Astrophysics Data System (ADS)

    Rohrlich, Daniel

    Y. Aharonov and A. Shimony both conjectured that two axioms - relativistic causality (``no superluminal signalling'') and nonlocality - so nearly contradict each other that only quantum mechanics reconciles them. Can we indeed derive quantum mechanics, at least in part, from these two axioms? No: ``PR-box'' correlations show that quantum correlations are not the most nonlocal correlations consistent with relativistic causality. Here we replace ``nonlocality'' with ``retrocausality'' and supplement the axioms of relativistic causality and retrocausality with a natural and minimal third axiom: the existence of a classical limit, in which macroscopic observables commute. That is, just as quantum mechanics has a classical limit, so must any generalization of quantum mechanics. In this limit, PR-box correlations violaterelativistic causality. Generalized to all stronger-than-quantum bipartite correlations, this result is a derivation of Tsirelson's bound (a theorem of quantum mechanics) from the three axioms of relativistic causality, retrocausality and the existence of a classical limit. Although the derivation does not assume quantum mechanics, it points to the Hilbert space structure that underlies quantum correlations. I thank the John Templeton Foundation (Project ID 43297) and the Israel Science Foundation (Grant No. 1190/13) for support.

  13. Horizon Quantum Mechanics: Spherically Symmetric and Rotating Sources

    NASA Astrophysics Data System (ADS)

    Casadio, Roberto; Giugno, Andrea; Giusti, Andrea; Micu, Octavian

    2018-04-01

    The Horizon Quantum Mechanics is an approach that allows one to analyse the gravitational radius of spherically symmetric systems and compute the probability that a given quantum state is a black hole. We first review the (global) formalism and show how it reproduces a gravitationally inspired GUP relation. This results leads to unacceptably large fluctuations in the horizon size of astrophysical black holes if one insists in describing them as (smeared) central singularities. On the other hand, if they are extended systems, like in the corpuscular models, no such issue arises and one can in fact extend the formalism to include asymptotic mass and angular momentum with the harmonic model of rotating corpuscular black holes. The Horizon Quantum Mechanics then shows that, in simple configurations, the appearance of the inner horizon is suppressed and extremal (macroscopic) geometries seem disfavoured.

  14. Framework for Understanding the Patterns of Student Difficulties in Quantum Mechanics

    ERIC Educational Resources Information Center

    Marshman, Emily; Singh, Chandralekha

    2015-01-01

    Compared with introductory physics, relatively little is known about the development of expertise in advanced physics courses, especially in the case of quantum mechanics. Here, we describe a framework for understanding the patterns of student reasoning difficulties and how students develop expertise in quantum mechanics. The framework posits that…

  15. Exactly and quasi-exactly solvable 'discrete' quantum mechanics.

    PubMed

    Sasaki, Ryu

    2011-03-28

    A brief introduction to discrete quantum mechanics is given together with the main results on various exactly solvable systems. Namely, the intertwining relations, shape invariance, Heisenberg operator solutions, annihilation/creation operators and dynamical symmetry algebras, including the q-oscillator algebra and the Askey-Wilson algebra. A simple recipe to construct exactly and quasi-exactly solvable (QES) Hamiltonians in one-dimensional 'discrete' quantum mechanics is presented. It reproduces all the known Hamiltonians whose eigenfunctions consist of the Askey scheme of hypergeometric orthogonal polynomials of a continuous or a discrete variable. Several new exactly and QES Hamiltonians are constructed. The sinusoidal coordinate plays an essential role.

  16. PREFACE: EmQM13: Emergent Quantum Mechanics 2013

    NASA Astrophysics Data System (ADS)

    2014-04-01

    These proceedings comprise the invited lectures of the second international symposium on Emergent Quantum Mechanics (EmQM13), which was held at the premises of the Austrian Academy of Sciences in Vienna, Austria, 3-6 October 2013. The symposium was held at the ''Theatersaal'' of the Academy of Sciences, and was devoted to the open exploration of emergent quantum mechanics, a possible ''deeper level theory'' that interconnects three fields of knowledge: emergence, the quantum, and information. Could there appear a revised image of physical reality from recognizing new links between emergence, the quantum, and information? Could a novel synthesis pave the way towards a 21st century, ''superclassical'' physics? The symposium provided a forum for discussing (i) important obstacles which need to be overcome as well as (ii) promising developments and research opportunities on the way towards emergent quantum mechanics. Contributions were invited that presented current advances in both standard as well as unconventional approaches to quantum mechanics. The EmQM13 symposium was co-organized by Gerhard Grössing (Austrian Institute for Nonlinear Studies (AINS), Vienna), and by Jan Walleczek (Fetzer Franklin Fund, USA, and Phenoscience Laboratories, Berlin). After a very successful first conference on the same topic in 2011, the new partnership between AINS and the Fetzer Franklin Fund in producing the EmQM13 symposium was able to further expand interest in the promise of emergent quantum mechanics. The symposium consisted of two parts, an opening evening addressing the general public, and the scientific program of the conference proper. The opening evening took place at the Great Ceremonial Hall (Grosser Festsaal) of the Austrian Academy of Sciences, and it presented talks and a panel discussion on ''The Future of Quantum Mechanics'' with three distinguished speakers: Stephen Adler (Princeton), Gerard 't Hooft (Utrecht) and Masanao Ozawa (Nagoya). The articles contained in

  17. The pursuit of locality in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Hodkin, Malcolm

    The rampant success of quantum theory is the result of applications of the 'new' quantum mechanics of Schrodinger and Heisenberg (1926-7), the Feynman-Schwinger-Tomonaga Quantum Electro-dynamics (1946-51), the electro-weak theory of Salaam, Weinberg, and Glashow (1967-9), and Quantum Chromodynamics (1973-); in fact, this success of 'the' quantum theory has depended on a continuous stream of brilliant and quite disparate mathematical formulations. In this carefully concealed ferment there lie plenty of unresolved difficulties, simply because in churning out fabulously accurate calculational tools there has been no sensible explanation of all that is going on. It is even argued that such an understanding is nothing to do with physics. A long-standing and famous illustration of this is the paradoxical thought-experiment of Einstein, Podolsky and Rosen (1935). Fundamental to all quantum theories, and also their paradoxes, is the location of sub-microscopic objects; or, rather, that the specification of such a location is fraught with mathematical inconsistency. This project encompasses a detailed, critical survey of the tangled history of Position within quantum theories. The first step is to show that, contrary to appearances, canonical quantum mechanics has only a vague notion of locality. After analysing a number of previous attempts at a 'relativistic quantum mechanics', two lines of thought are considered in detail. The first is the work of Wan and students, which is shown to be no real improvement on the iisu.al 'nonrelativistic' theory. The second is based on an idea of Dirac's - using backwards-in-time light-cones as the hypersurface in space-time. There remain considerable difficulties in the way of producing a consistent scheme here. To keep things nicely stirred up, the author then proposes his own approach - an adaptation of Feynman's QED propagators. This new approach is distinguished from Feynman's since the propagator or Green's function is not obtained

  18. Musical Example to Visualize Abstract Quantum Mechanical Ideas

    ERIC Educational Resources Information Center

    Eagle, Forrest W.; Seaney, Kyser D.; Grubb, Michael P.

    2017-01-01

    Quantum mechanics is a notoriously difficult subject to learn, due to a lack of real-world analogies that might help provide an intuitive grasp of the underlying ideas. Discrete energy levels and absorption and emission wavelengths in atoms are sometimes described as uniquely quantum phenomena, but are actually general to spatially confined waves…

  19. Transfer of non-Gaussian quantum states of mechanical oscillator to light

    NASA Astrophysics Data System (ADS)

    Filip, Radim; Rakhubovsky, Andrey A.

    2015-11-01

    Non-Gaussian quantum states are key resources for quantum optics with continuous-variable oscillators. The non-Gaussian states can be deterministically prepared by a continuous evolution of the mechanical oscillator isolated in a nonlinear potential. We propose feasible and deterministic transfer of non-Gaussian quantum states of mechanical oscillators to a traveling light beam, using purely all-optical methods. The method relies on only basic feasible and high-quality elements of quantum optics: squeezed states of light, linear optics, homodyne detection, and electro-optical feedforward control of light. By this method, a wide range of novel non-Gaussian states of light can be produced in the future from the mechanical states of levitating particles in optical tweezers, including states necessary for the implementation of an important cubic phase gate.

  20. Quantum Interactive Learning Tutorial on the Double-Slit Experiment to Improve Student Understanding of Quantum Mechanics

    ERIC Educational Resources Information Center

    Sayer, Ryan; Maries, Alexandru; Singh, Chandralekha

    2017-01-01

    Learning quantum mechanics is challenging, even for upper-level undergraduate and graduate students. Research-validated interactive tutorials that build on students' prior knowledge can be useful tools to enhance student learning. We have been investigating student difficulties with quantum mechanics pertaining to the double-slit experiment in…

  1. Quantum mechanical reality according to Copenhagen 2.0

    NASA Astrophysics Data System (ADS)

    Din, Allan M.

    2016-05-01

    The long-standing conceptual controversies concerning the interpretation of nonrelativistic quantum mechanics are argued, on one hand, to be due to its incompleteness, as affirmed by Einstein. But on the other hand, it appears to be possible to complete it at least partially, as Bohr might have appreciated it, in the framework of its standard mathematical formalism with observables as appropriately defined self-adjoint operators. This completion of quantum mechanics is based on the requirement on laboratory physics to be effectively confined to a bounded space region and on the application of the von Neumann deficiency theorem to properly define a set of self-adjoint extensions of standard observables, e.g. the momenta and the Hamiltonian, in terms of certain isometries on the region boundary. This is formalized mathematically in the setting of a boundary ontology for the so-called Qbox in which the wave function acquires a supplementary dependence on a set of Additional Boundary Variables (ABV). It is argued that a certain geometric subset of the ABV parametrizing Quasi-Periodic Translational Isometries (QPTI) has a particular physical importance by allowing for the definition of an ontic wave function, which has the property of epitomizing the spatial wave function “collapse.” Concomitantly the standard wave function in an unbounded geometry is interpreted as an epistemic wave function, which together with the ontic QPTI wave function gives rise to the notion of two-wave duality, replacing the standard concept of wave-particle duality. More generally, this approach to quantum physics in a bounded geometry provides a novel analytical basis for a better understanding of several conceptual notions of quantum mechanics, including reality, nonlocality, entanglement and Heisenberg’s uncertainty relation. The scope of this analysis may be seen as a foundational update of the multiple versions 1.x of the Copenhagen interpretation of quantum mechanics, which is

  2. A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments.

    PubMed

    Sellers, Benjamin D; James, Natalie C; Gobbi, Alberto

    2017-06-26

    Reducing internal strain energy in small molecules is critical for designing potent drugs. Quantum mechanical (QM) and molecular mechanical (MM) methods are often used to estimate these energies. In an effort to determine which methods offer an optimal balance in accuracy and performance, we have carried out torsion scan analyses on 62 fragments. We compared nine QM and four MM methods to reference energies calculated at a higher level of theory: CCSD(T)/CBS single point energies (coupled cluster with single, double, and perturbative triple excitations at the complete basis set limit) calculated on optimized geometries using MP2/6-311+G**. The results show that both the more recent MP2.X perturbation method as well as MP2/CBS perform quite well. In addition, combining a Hartree-Fock geometry optimization with a MP2/CBS single point energy calculation offers a fast and accurate compromise when dispersion is not a key energy component. Among MM methods, the OPLS3 force field accurately reproduces CCSD(T)/CBS torsion energies on more test cases than the MMFF94s or Amber12:EHT force fields, which struggle with aryl-amide and aryl-aryl torsions. Using experimental conformations from the Cambridge Structural Database, we highlight three example structures for which OPLS3 significantly overestimates the strain. The energies and conformations presented should enable scientists to estimate the expected error for the methods described and we hope will spur further research into QM and MM methods.

  3. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions.

    PubMed

    Acevedo, Orlando; Jorgensen, William L

    2010-01-19

    Application of combined quantum and molecular mechanical (QM/MM) methods focuses on predicting activation barriers and the structures of stationary points for organic and enzymatic reactions. Characterization of the factors that stabilize transition structures in solution and in enzyme active sites provides a basis for design and optimization of catalysts. Continued technological advances allowed for expansion from prototypical cases to mechanistic studies featuring detailed enzyme and condensed-phase environments with full integration of the QM calculations and configurational sampling. This required improved algorithms featuring fast QM methods, advances in computing changes in free energies including free-energy perturbation (FEP) calculations, and enhanced configurational sampling. In particular, the present Account highlights development of the PDDG/PM3 semi-empirical QM method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo (MC) simulations, and a polynomial quadrature method for efficient modeling of proton-transfer reactions. The utility of this QM/MM/MC/FEP methodology is illustrated for a variety of organic reactions including substitution, decarboxylation, elimination, and pericyclic reactions. A comparison to experimental kinetic results on medium effects has verified the accuracy of the QM/MM approach in the full range of solvents from hydrocarbons to water to ionic liquids. Corresponding results from ab initio and density functional theory (DFT) methods with continuum-based treatments of solvation reveal deficiencies, particularly for protic solvents. Also summarized in this Account are three specific QM/MM applications to biomolecular systems: (1) a recent study that clarified the mechanism for the reaction of 2-pyrone derivatives catalyzed by macrophomate synthase as a tandem Michael-aldol sequence rather than a Diels-Alder reaction, (2) elucidation of the mechanism of action of fatty

  4. Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics.

    PubMed

    Darkhovskii, M B; Pletnev, I V; Tchougréeff, A L

    2003-11-15

    A computational method targeted to Werner-type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie-Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d-shell. The quantum mechanical EHCF part is limited to the metal ion d-shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration. Copyright 2003 Wiley Periodicals, Inc.

  5. Quantum mechanics without the projection postulate and its realistic interpretation

    NASA Astrophysics Data System (ADS)

    Dieks, D.

    1989-11-01

    It is widely held that quantum mechanics is the first scientific theory to present scientifically internal, fundamental difficulties for a realistic interpretation (in the philosophical sense). The standard (Copenhagen) interpretation of the quantum theory is often described as the inevitable instrumentalistic response. It is the purpose of the present article to argue that quantum theory does not present fundamental new problems to a realistic interpretation. The formalism of quantum theory has the same states—it will be argued—as the formalisms of older physical theories and is capable of the same kinds of philosophical interpretation. This result is reached via an analysis of what it means to give a realistic interpretation to a theory. The main point of difference between quantum mechanics and other theories—as far as the possibilities of interpretation are concerned—is the special treatment given to measurement by the “projection postulate.” But it is possible to do without this postulate. Moreover, rejection of the projection postulate does not, in spite of what is often maintained in the literature, automatically lead to the many-worlds interpretation of quantum mechanics. A realistic interpretation is possible in which only the reality of one (our) world is recognized. It is argued that the Copenhagen interpretation as expounded by Bohr is not in conflict with the here proposed realistic interpretation of quantum theory.

  6. Time and the foundations of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Pashby, Thomas

    Quantum mechanics has provided philosophers of science with many counterintuitive insights and interpretive puzzles, but little has been written about the role that time plays in the theory. One reason for this is the celebrated argument of Wolfgang Pauli against the inclusion of time as an observable of the theory, which has been seen as a demonstration that time may only enter the theory as a classical parameter. Against this orthodoxy I argue that there are good reasons to expect certain kinds of `time observables' to find a representation within quantum theory, including clock operators (which provide the means to measure the passage of time) and event time operators, which provide predictions for the time at which a particular event occurs, such as the appearance of a dot on a luminescent screen. I contend that these time operators deserve full status as observables of the theory, and on re ection provide a uniquely compelling reason to expand the set of observables allowed by the standard formalism of quantum mechanics. In addition, I provide a novel association of event time operators with conditional probabilities, and propose a temporally extended form of quantum theory to better accommodate the time of an event as an observable quantity. This leads to a proposal to interpret quantum theory within an event ontology, inspired by Bertrand Russell's Analysis of Matter. On this basis I mount a defense of Russell's relational theory of time against a recent attack.

  7. 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.

  8. Discrete Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Williams, H. Thomas

    2015-12-01

    After a quarter century of discoveries that rattled the foundations of classical mechanics and electrodynamics, the year 1926 saw the publication of two works intended to provide a theoretical structure to support new quantum explanations of the subatomic world. Heisenberg's matrix mechanics and Schrödinger's wave mechanics provided compatible but mathematically disparate ways of unifying the discoveries of Planck, Einstein, Bohr and many others. Efforts began immediately to prove the equivalence of these two structures, culminated successfully by John von Neumann's 1932 volume Mathematical Foundations of Quantum Mechanics. This forms the springboard for the current effort. We begin with a presentation of a minimal set of von Neumann postulates while introducing language and notation to facilitate subsequent discussion of quantum calculations based in finite dimensional Hilbert spaces. Chapters that follow address two-state quantum systems (with spin one-half as the primary example), entanglement of multiple two-state systems, quantum angular momentum theory and quantum approaches to statistical mechanics. A concluding chapter gives an overview of issues associated with quantum mechanics in continuous infinite-dimensional Hilbert spaces. [Planck1900] Planck M 1900 Zur Teorie des Gesetzes der Energieverteilung in Normalspektrum Verhandlung der Deutscher Physikalischen Gesellschaft 2 237 [Heisenberg1925] Heisenberg W 1925

  9. Identifying the receptor subtype selectivity of retinoid X and retinoic acid receptors via quantum mechanics.

    PubMed

    Tsuji, Motonori; Shudo, Koichi; Kagechika, Hiroyuki

    2017-03-01

    Understanding and identifying the receptor subtype selectivity of a ligand is an important issue in the field of drug discovery. Using a combination of classical molecular mechanics and quantum mechanical calculations, this report assesses the receptor subtype selectivity for the human retinoid X receptor (hRXR) and retinoic acid receptor (hRAR) ligand-binding domains (LBDs) complexed with retinoid ligands. The calculated energies show good correlation with the experimentally reported binding affinities. The technique proposed here is a promising method as it reveals the origin of the receptor subtype selectivity of selective ligands.

  10. On total noncommutativity in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Lahti, Pekka J.; Ylinen, Kari

    1987-11-01

    It is shown within the Hilbert space formulation of quantum mechanics that the total noncommutativity of any two physical quantities is necessary for their satisfying the uncertainty relation or for their being complementary. The importance of these results is illustrated with the canonically conjugate position and momentum of a free particle and of a particle closed in a box.

  11. Quantum enhanced feedback cooling of a mechanical oscillator using nonclassical light.

    PubMed

    Schäfermeier, Clemens; Kerdoncuff, Hugo; Hoff, Ulrich B; Fu, Hao; Huck, Alexander; Bilek, Jan; Harris, Glen I; Bowen, Warwick P; Gehring, Tobias; Andersen, Ulrik L

    2016-11-29

    Laser cooling is a fundamental technique used in primary atomic frequency standards, quantum computers, quantum condensed matter physics and tests of fundamental physics, among other areas. It has been known since the early 1990s that laser cooling can, in principle, be improved by using squeezed light as an electromagnetic reservoir; while quantum feedback control using a squeezed light probe is also predicted to allow improved cooling. Here we show the implementation of quantum feedback control of a micro-mechanical oscillator using squeezed probe light. This allows quantum-enhanced feedback cooling with a measurement rate greater than it is possible with classical light, and a consequent reduction in the final oscillator temperature. Our results have significance for future applications in areas ranging from quantum information networks, to quantum-enhanced force and displacement measurements and fundamental tests of macroscopic quantum mechanics.

  12. Particles, Waves, and the Interpretation of Quantum Mechanics

    ERIC Educational Resources Information Center

    Christoudouleas, N. D.

    1975-01-01

    Presents an explanation, without mathematical equations, of the basic principles of quantum mechanics. Includes wave-particle duality, the probability character of the wavefunction, and the uncertainty relations. (MLH)

  13. Quantum Mechanics, Pattern Recognition, and the Mammalian Brain

    NASA Astrophysics Data System (ADS)

    Chapline, George

    2008-10-01

    Although the usual way of representing Markov processes is time asymmetric, there is a way of describing Markov processes, due to Schrodinger, which is time symmetric. This observation provides a link between quantum mechanics and the layered Bayesian networks that are often used in automated pattern recognition systems. In particular, there is a striking formal similarity between quantum mechanics and a particular type of Bayesian network, the Helmholtz machine, which provides a plausible model for how the mammalian brain recognizes important environmental situations. One interesting aspect of this relationship is that the "wake-sleep" algorithm for training a Helmholtz machine is very similar to the problem of finding the potential for the multi-channel Schrodinger equation. As a practical application of this insight it may be possible to use inverse scattering techniques to study the relationship between human brain wave patterns, pattern recognition, and learning. We also comment on whether there is a relationship between quantum measurements and consciousness.

  14. What's the Matter with Waves?; An introduction to techniques and applications of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Parkinson, William

    2017-12-01

    Like rocket science or brain surgery, quantum mechanics is pigeonholed as a daunting and inaccessible topic, which is best left to an elite or peculiar few. This classification was not earned without some degree of merit. Depending on perspective; quantum mechanics is a discipline or philosophy, a convention or conundrum, an answer or question. Authors have run the gamut from hand waving to heavy handed in the hope to dispel the common beliefs about quantum mechanics, but perhaps they continue to promulgate the stigma. The focus of this particular effort is to give the reader an introduction, if not at least an appreciation, of the role that linear algebra techniques play in the practical application of quantum mechanical methods. It interlaces aspects of the classical and quantum picture, including a number of both worked and parallel applications. Students with no prior experience in quantum mechanics, motivated graduate students, or researchers in other areas attempting to gain some introduction to quantum theory will find particular interest in this book. Part of Series on wave phenomena in the physical sciences

  15. Can Quantum-Mechanical Description of Physical Reality Be Considered Correct?

    NASA Astrophysics Data System (ADS)

    Brassard, Gilles; Méthot, André Allan

    2010-04-01

    In an earlier paper written in loving memory of Asher Peres, we gave a critical analysis of the celebrated 1935 paper in which Einstein, Podolsky and Rosen (EPR) challenged the completeness of quantum mechanics. There, we had pointed out logical shortcomings in the EPR paper. Now, we raise additional questions concerning their suggested program to find a theory that would “provide a complete description of the physical reality”. In particular, we investigate the extent to which the EPR argumentation could have lead to the more dramatic conclusion that quantum mechanics is in fact incorrect. With this in mind, we propose a speculation, made necessary by a logical shortcoming in the EPR paper caused by the lack of a necessary condition for “elements of reality”, and surmise that an eventually complete theory would either be inconsistent with quantum mechanics, or would at least violate Heisenberg’s Uncertainty Principle.

  16. Quantum-mechanical treatment of an electron undergoing synchrotron radiation.

    NASA Technical Reports Server (NTRS)

    White, D.

    1972-01-01

    The problem of an electron moving perpendicular to an intense magnetic field is approached from the framework of quantum mechanics. A numerical solution to the related rate equations describing the probabilities of occupation of the electron's energy states is put forth along with the expected errors involved. The quantum-mechanical approach is found to predict a significant amount of energy broadening with time for an initially monoenergetic electron beam entering a region of an intense magnetic field as long as the product of initial energy and magnetic field is of order 50 MG BeV or larger.

  17. A modified Lax-Phillips scattering theory for quantum mechanics

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

    Strauss, Y., E-mail: ystrauss@cs.bgu.ac.il

    The Lax-Phillips scattering theory is an appealing abstract framework for the analysis of scattering resonances. Quantum mechanical adaptations of the theory have been proposed. However, since these quantum adaptations essentially retain the original structure of the theory, assuming the existence of incoming and outgoing subspaces for the evolution and requiring the spectrum of the generator of evolution to be unbounded from below, their range of applications is rather limited. In this paper, it is shown that if we replace the assumption regarding the existence of incoming and outgoing subspaces by the assumption of the existence of Lyapunov operators for themore » quantum evolution (the existence of which has been proved for certain classes of quantum mechanical scattering problems), then it is possible to construct a structure analogous to the Lax-Phillips structure for scattering problems for which the spectrum of the generator of evolution is bounded from below.« less

  18. Estimates on Functional Integrals of Quantum Mechanics and Non-relativistic Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Bley, Gonzalo A.; Thomas, Lawrence E.

    2017-01-01

    We provide a unified method for obtaining upper bounds for certain functional integrals appearing in quantum mechanics and non-relativistic quantum field theory, functionals of the form {E[{exp}(A_T)]} , the (effective) action {A_T} being a function of particle trajectories up to time T. The estimates in turn yield rigorous lower bounds for ground state energies, via the Feynman-Kac formula. The upper bounds are obtained by writing the action for these functional integrals in terms of stochastic integrals. The method is illustrated in familiar quantum mechanical settings: for the hydrogen atom, for a Schrödinger operator with {1/|x|^2} potential with small coupling, and, with a modest adaptation of the method, for the harmonic oscillator. We then present our principal applications of the method, in the settings of non-relativistic quantum field theories for particles moving in a quantized Bose field, including the optical polaron and Nelson models.

  19. Formation mechanism and mechanics of dip-pen nanolithography using molecular dynamics.

    PubMed

    Wu, Cheng-Da; Fang, Te-Hua; Lin, Jen-Fin

    2010-03-02

    Molecular dynamics simulations are used to investigate the mechanisms of molecular transference, pattern formation, and mechanical behavior in the dip-pen nanolithography (DPN) process. The effects of deposition temperature were studied using molecular trajectories, the meniscus characteristic, surface absorbed energy, and pattern formation analysis. At the first transferred stage (at the initial indentation depth), the conformation of SAM molecules lies almost on the substrate surface. The molecules start to stand on the substrate due to the pull and drag forces at the second transferred stage (after the tip is pulled up). According to the absorbed energy behavior, the second transferred stage has larger transferred amounts and the transfer rate is strongly related to temperature. When molecules were deposited at low temperature (e.g., room temperature), the pattern shape was more highly concentrated. The pattern shape at high temperatures expanded and the area increased because of good molecular diffusion.

  20. Confinement control mechanism for two-electron Hulthen quantum dots in plasmas

    NASA Astrophysics Data System (ADS)

    Bahar, M. K.; Soylu, A.

    2018-05-01

    In this study, for the first time, the energies of two-electron Hulthen quantum dots (TEHQdots) embedded in Debye and quantum plasmas modeled by the more general exponential cosine screened Coulomb (MGECSC) potential under the combined influence of electric and magnetic fields are investigated by numerically solving the Schrödinger equation using the asymptotic iteration method. To do this, the four different forms of the MGECSC potential, which set through the different cases of the potential parameters, are taken into consideration. We propose that plasma environments form considerable quantum mechanical effects for quantum dots and other atomic systems and that plasmas are important experimental arguments. In this study, by considering the quantum dot parameters, the external field parameters, and the plasma screening parameters, a control mechanism of the confinement on energies of TEHQdots and the frequency of the radiation emitted by TEHQdots as a result of any excitation is discussed. In this mechanism, the behaviors, similarities, the functionalities of the control parameters, and the influences of plasmas on these quantities are explored.

  1. Equivalence principle and quantum mechanics: quantum simulation with entangled photons.

    PubMed

    Longhi, S

    2018-01-15

    Einstein's equivalence principle (EP) states the complete physical equivalence of a gravitational field and corresponding inertial field in an accelerated reference frame. However, to what extent the EP remains valid in non-relativistic quantum mechanics is a controversial issue. To avoid violation of the EP, Bargmann's superselection rule forbids a coherent superposition of states with different masses. Here we suggest a quantum simulation of non-relativistic Schrödinger particle dynamics in non-inertial reference frames, which is based on the propagation of polarization-entangled photon pairs in curved and birefringent optical waveguides and Hong-Ou-Mandel quantum interference measurement. The photonic simulator can emulate superposition of mass states, which would lead to violation of the EP.

  2. Modelling the molecular mechanisms of aging

    PubMed Central

    Mc Auley, Mark T.; Guimera, Alvaro Martinez; Hodgson, David; Mcdonald, Neil; Mooney, Kathleen M.; Morgan, Amy E.

    2017-01-01

    The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field. PMID:28096317

  3. BOOK REVIEW: Mind, Matter and Quantum Mechanics (2nd edition)

    NASA Astrophysics Data System (ADS)

    Mahler, G.

    2004-07-01

    Quantum mechanics is usually defined in terms of some loosely connected axioms and rules. Such a foundation is far from the beauty of, e.g., the `principles' underlying classical mechanics. Motivated, in addition, by notorious interpretation problems, there have been numerous attempts to modify or `complete' quantum mechanics. A first attempt was based on so-called hidden variables; its proponents essentially tried to expel the non-classical nature of quantum mechanics. More recent proposals intend to complete quantum mechanics not within mechanics proper but on a `higher (synthetic) level'; by means of a combination with gravitation theory (R Penrose), with quantum information theory (C M Caves, C A Fuchs) or with psychology and brain science (H P Stapp). I think it is fair to say that in each case the combination is with a subject that, per se, suffers from a very limited understanding that is even more severe than that of quantum mechanics. This was acceptable, though, if it could convincingly be argued that scientific progress desperately needs to join forces. Quantum mechanics of a closed system was a beautiful and well understood theory with its respective state being presented as a point on a deterministic trajectory in Liouville space---not unlike the motion of a classical N-particle system in its 6N-dimensional phase-space. Unfortunately, we need an inside and an outside view, we need an external reference frame, we need an observer. This unavoidable partition is the origin of most of the troubles we have with quantum mechanics. A pragmatic solution is introduced in the form of so-called measurement postulates: one of the various incompatible properties of the system under consideration is supposed to be realized (i.e. to become a fact, to be defined without fundamental dispersion) based on `instantaneous' projections within some externally selected measurement basis. As a result, the theory becomes essentially statistical rather than deterministic

  4. Uncertain for a century: quantum mechanics and the dilemma of interpretation.

    PubMed

    Frank, Adam

    2015-12-01

    Quantum mechanics, the physical theory describing the microworld, is one of science's greatest triumphs. Remarkably, however, after more than 100 years it is still unclear what quantum mechanics means in terms of basic philosophical questions about the nature of reality. While there are many interpretations of the mathematical machinery of quantum physics, there remain no experimental means to distinguish between most of them. In this contribution, I wish to consider the ways in which the enduring lack of an agreed-upon interpretation of quantum physics influences a number of critical philosophical debates about physics and reality. I briefly review two problems affected by quantum interpretations: the meaning of the term universe and the nature of consciousness. © 2015 New York Academy of Sciences.

  5. Investigation of spin-zero bosons in q-deformed relativistic quantum mechanics

    NASA Astrophysics Data System (ADS)

    Sobhani, H.; Chung, W. S.; Hassanabadi, H.

    2018-04-01

    In this article, Scattering states of Klein-Gordon equation for three scatter potentials of single and double Dirac delta and a potential well in the q-deformed formalism of relativistic quantum mechanics have been derived. At first, we discussed how q-deformed formalism can be constructed and used. Postulates of this q-deformed quantum mechanics are noted. Then scattering problems for spin-zero bosons are studied.

  6. Molecular Mechanics

    PubMed Central

    Vanommeslaeghe, Kenno; Guvench, Olgun; MacKerell, Alexander D.

    2014-01-01

    Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The section ends with a brief overview of common force fields in CSBDD. PMID:23947650

  7. Quantum Mechanics of the Einstein-Hopf Model.

    ERIC Educational Resources Information Center

    Milonni, P. W.

    1981-01-01

    The Einstein-Hopf model for the thermodynamic equilibrium between the electromagnetic field and dipole oscillators is considered within the framework of quantum mechanics. Both the wave and particle aspects of the Einstein fluctuation formula are interpreted in terms of the fundamental absorption and emission processes. (Author/SK)

  8. Comparison of Classical and Quantum Mechanical Uncertainties.

    ERIC Educational Resources Information Center

    Peslak, John, Jr.

    1979-01-01

    Comparisons are made for the particle-in-a-box, the harmonic oscillator, and the one-electron atom. A classical uncertainty principle is derived and compared with its quantum-mechanical counterpart. The results are discussed in terms of the statistical interpretation of the uncertainty principle. (Author/BB)

  9. Jarzynski equality in PT-symmetric quantum mechanics

    DOE PAGES

    Deffner, Sebastian; Saxena, Avadh

    2015-04-13

    We show that the quantum Jarzynski equality generalizes to PT -symmetric quantum mechanics with unbroken PT -symmetry. In the regime of broken PT -symmetry the Jarzynski equality does not hold as also the CPT -norm is not preserved during the dynamics. These findings are illustrated for an experimentally relevant system – two coupled optical waveguides. It turns out that for these systems the phase transition between the regimes of unbroken and broken PT -symmetry is thermodynamically inhibited as the irreversible work diverges at the critical point.

  10. The measurement problem in quantum mechanics: A phenomenological investigation

    NASA Astrophysics Data System (ADS)

    Hunter, Joel Brooks

    2008-10-01

    This dissertation is a phenomenological investigation of the measurement problem in quantum mechanics. The primary subject matter for description and analysis is scientific instruments and their use in experiments which elicit the measurement problem. A methodological critique is mounted against the ontological commitments taken for granted in the canonical interpretations of quantum theory and the scientific activity of measurement as the necessary interface between theoretical interest and perceptual results. I argue that an aesthetic dimension of reality functions as aproto-scientific establishment of sense-making that constantly operates to set integratively all other cognitively neat determinations, including scientifically rendered objects that are intrinsically non-visualizable. The way in which data "key in" to the original and originative register of the sensible in observation is clarified by examining prostheses, measuring apparatuses and instruments that are sense-conveying and -integrative with the human sensorium. Experiments, technology and instrumentation are examined in order to understand how knowing and that which is known is bonded by praxis-aisthesis. Quantum measurement is a praxic-dynamie activity and homologically structured and structur ing functional engagement in terms of instantiation, quantifiability, and spatiotemporal differentiation. The distinctions between a beauty-aesthetic and praxis-aisthesis are delineated. It is argued that a beauty-aesthetic is a construal of the economic dimension of scientific objects and work, and is not the primary manner in which the aesthetic dimension is disclosed. The economic dimension of abstractions reduces to an austere aesthetic of calculative economy. Nature itself, however, is not stingy; it is intrinsically capacious, extravagant, full of surprise, nuance, ambiguity and allusiveness. The capaciousness of Nature and the way in which we are integratively set within Nature in a materiality

  11. Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules.

    PubMed

    Andrijchenko, Natalya N; Ermilov, Alexander Yu; Khriachtchev, Leonid; Räsänen, Markku; Nemukhin, Alexander V

    2015-03-19

    The present study illustrates the steps toward understanding molecular mechanism of xenon anesthesia by focusing on a link to the structures and spectra of intermolecular complexes of xenon with small aromatic molecules. A primary cause of xenon anesthesia is attributed to inhibition of N-methyl-D-aspartate (NMDA) receptors by an unknown mechanism. Following the results of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) calculations we report plausible xenon action sites in the ligand binding domain of the NMDA receptor, which are due to interaction of xenon atoms with aromatic amino-acid residues. We rely in these calculations on computational protocols adjusted in combined experimental and theoretical studies of intermolecular complexes of xenon with phenol. Successful reproduction of vibrational shifts in molecular species upon complexation with xenon measured in low-temperature matrices allowed us to select a proper functional form in density functional theory (DFT) approach for use in QM subsystems, as well as to calibrate force field parameters for MD simulations. The results of molecular modeling show that xenon atoms can compete with agonists for a place in the corresponding protein cavity, thus indicating their active role in anesthetic action.

  12. Wigner functions for noncommutative quantum mechanics: A group representation based construction

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

    Chowdhury, S. Hasibul Hassan, E-mail: shhchowdhury@gmail.com; Department of Mathematics and Statistics, Concordia University, Montréal, Québec H3G 1M8; Ali, S. Twareque, E-mail: twareque.ali@concordia.ca

    This paper is devoted to the construction and analysis of the Wigner functions for noncommutative quantum mechanics, their marginal distributions, and star-products, following a technique developed earlier, viz, using the unitary irreducible representations of the group G{sub NC}, which is the three fold central extension of the Abelian group of ℝ{sup 4}. These representations have been exhaustively studied in earlier papers. The group G{sub NC} is identified with the kinematical symmetry group of noncommutative quantum mechanics of a system with two degrees of freedom. The Wigner functions studied here reflect different levels of non-commutativity—both the operators of position and thosemore » of momentum not commuting, the position operators not commuting and finally, the case of standard quantum mechanics, obeying the canonical commutation relations only.« less

  13. The molecular mechanism of plant gravitropism.

    PubMed

    Wu, Di; Huang, Lin-zhou; Gao, Jin; Wang, Yong-hong

    2016-07-20

    Gravity is an important environmental factor that regulates plant growth and morphogenesis. In response to gravity stimulus, plants can set the optimum angle between the organs and the gravity vector. Plant gravitropism is divided into four sequential steps, including gravity perception, signal transduction, asymmetrical distribution of auxin, and organ curvature. In recent years, large numbers of mutants with defective gravitropism have been identified and genes involved in the regulation of gravitropism have been functionally characterized. In particular, progress has been achieved on elucidating the molecular mechanisms of gravity perception and asymmetrical distribution of auxin. As one of the most important strategies for plant to adapt environmental changes, gravitropism is also involved in the regulation of rice plant architecture and grain yield through modulating rice tiller angle. Therefore, the investigation of plant gravitropism not only contributes to decipher the regulatory mechanisms of plant growth and development, but also helps to guide the genetic improvement of crop architecture. However, the molecular mechanisms and regulatory network of gravitropism remain to be elusive. In this review, we focus on recent progress on elucidating molecular mechanisms underlying gravitropism and its involvement in regulating rice tiller angle, which is an important agronomic trait that determines rice plant architecture and thus grain yields.

  14. Understanding the adsorptive interactions of arsenate-iron nanoparticles with curved fullerene-like sheets in activated carbon using a quantum mechanics/molecular mechanics computational approach.

    PubMed

    Ha, Nguyen Ngoc; Cam, Le Minh; Ha, Nguyen Thi Thu; Goh, Bee-Min; Saunders, Martin; Jiang, Zhong-Tao; Altarawneh, Mohammednoor; Dlugogorski, Bogdan Z; El-Harbawi, Mohanad; Yin, Chun-Yang

    2017-06-07

    The prevalence of global arsenic groundwater contamination has driven widespread research on developing effective treatment systems including adsorption using various sorbents. The uptake of arsenic-based contaminants onto established sorbents such as activated carbon (AC) can be effectively enhanced via immobilization/impregnation of iron-based elements on the porous AC surface. Recent suggestions that AC pores structurally consist of an eclectic mix of curved fullerene-like sheets may affect the arsenic adsorption dynamics within the AC pores and is further complicated by the presence of nano-sized iron-based elements. We have therefore, attempted to shed light on the adsorptive interactions of arsenate-iron nanoparticles with curved fullerene-like sheets by using hybridized quantum mechanics/molecular mechanics (QMMM) calculations and microscopy characterization. It is found that, subsequent to optimization, chemisorption between HAsO 4 2- and the AC carbon sheet (endothermic process) is virtually non-existent - this observation is supported by experimental results. Conversely, the incorporation of iron nanoparticles (FeNPs) into the AC carbon sheet greatly facilitates chemisorption of HAsO 4 2- . Our calculation implies that iron carbide is formed at the junction between the iron and the AC interface and this tightly chemosorbed layer prevents detachment of the FeNPs on the AC surface. Other aspects including electronic structure/properties, carbon arrangement defects and rate of adsorptive interaction, which are determined using the Climbing-Image NEB method, are also discussed.

  15. Analytic structure of the S-matrix for singular quantum mechanics

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

    Camblong, Horacio E.; Epele, Luis N.; Fanchiotti, Huner

    2015-06-15

    The analytic structure of the S-matrix of singular quantum mechanics is examined within a multichannel framework, with primary focus on its dependence with respect to a parameter (Ω) that determines the boundary conditions. Specifically, a characterization is given in terms of salient mathematical and physical properties governing its behavior. These properties involve unitarity and associated current-conserving Wronskian relations, time-reversal invariance, and Blaschke factorization. The approach leads to an interpretation of effective nonunitary solutions in singular quantum mechanics and their determination from the unitary family.

  16. The application of quantum mechanics in structure-based drug design.

    PubMed

    Mucs, Daniel; Bryce, Richard A

    2013-03-01

    Computational chemistry has become an established and valuable component in structure-based drug design. However the chemical complexity of many ligands and active sites challenges the accuracy of the empirical potentials commonly used to describe these systems. Consequently, there is a growing interest in utilizing electronic structure methods for addressing problems in protein-ligand recognition. In this review, the authors discuss recent progress in the development and application of quantum chemical approaches to modeling protein-ligand interactions. The authors specifically consider the development of quantum mechanics (QM) approaches for studying large molecular systems pertinent to biology, focusing on protein-ligand docking, protein-ligand binding affinities and ligand strain on binding. Although computation of binding energies remains a challenging and evolving area, current QM methods can underpin improved docking approaches and offer detailed insights into ligand strain and into the nature and relative strengths of complex active site interactions. The authors envisage that QM will become an increasingly routine and valued tool of the computational medicinal chemist.

  17. Sachdev–Ye–Kitaev model as Liouville quantum mechanics

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

    Bagrets, Dmitry; Altland, Alexander; Kamenev, Alex

    2016-08-08

    Here, we show that the proper inclusion of soft reparameterization modes in the Sachdev–Ye–Kitaev model of N randomly interacting Majorana fermions reduces its long-time behavior to that of Liouville quantum mechanics.

  18. Ocular diseases: immunological and molecular mechanisms.

    PubMed

    Song, Jing; Huang, Yi-Fei; Zhang, Wen-Jing; Chen, Xiao-Fei; Guo, Yu-Mian

    2016-01-01

    Many factors, such as environmental, microbial and endogenous stress, antigen localization, can trigger the immunological events that affect the ending of the diverse spectrum of ocular disorders. Significant advances in understanding of immunological and molecular mechanisms have been researched to improve the diagnosis and therapy for patients with ocular inflammatory diseases. Some kinds of ocular diseases are inadequately responsive to current medications; therefore, immunotherapy may be a potential choice as an alternative or adjunctive treatment, even in the prophylactic setting. This article first provides an overview of the immunological and molecular mechanisms concerning several typical and common ocular diseases; second, the functions of immunological roles in some of systemic autoimmunity will be discussed; third, we will provide a summary of the mechanisms that dictate immune cell trafficking to ocular local microenvironment in response to inflammation.

  19. Mechanism of fast lattice diffusion of hydrogen in palladium: Interplay of quantum fluctuations and lattice strain

    NASA Astrophysics Data System (ADS)

    Kimizuka, Hajime; Ogata, Shigenobu; Shiga, Motoyuki

    2018-01-01

    Understanding the underlying mechanism of the nanostructure-mediated high diffusivity of H in Pd is of recent scientific interest and also crucial for industrial applications. Here, we present a decisive scenario explaining the emergence of the fast lattice-diffusion mode of interstitial H in face-centered cubic Pd, based on the quantum mechanical natures of both electrons and nuclei under finite strains. Ab initio path-integral molecular dynamics was applied to predict the temperature- and strain-dependent free energy profiles for H migration in Pd over a temperature range of 150-600 K and under hydrostatic tensile strains of 0.0%-2.4%; such strain conditions are likely to occur in real systems, especially around the elastic fields induced by nanostructured defects. The simulated results revealed that, for preferential H location at octahedral sites, as in unstrained Pd, the activation barrier for H migration (Q ) was drastically increased with decreasing temperature owing to nuclear quantum effects. In contrast, as tetrahedral sites increased in stability with lattice expansion, nuclear quantum effects became less prominent and ceased impeding H migration. This implies that the nature of the diffusion mechanism gradually changes from quantum- to classical-like as the strain is increased. For H atoms in Pd at the hydrostatic strain of ˜2.4 % , we determined that the mechanism promoted fast lattice diffusion (Q =0.11 eV) of approximately 20 times the rate of conventional H diffusion (Q =0.23 eV) in unstrained Pd at a room temperature of 300 K.

  20. "A dedicated missionary". Charles Galton Darwin and the new quantum mechanics in Britain

    NASA Astrophysics Data System (ADS)

    Navarro, Jaume

    In this paper I discuss the work on quantum physics and wave mechanics by Charles Galton Darwin, a Cambridge wrangler of the last generation, as a case study to better understand the early reception of quantum physics in Britain. I argue that his proposal in the early 1920s to abandon the strict conservation of energy, as well as his enthusiastic embracement of wave mechanics at the end of the decade, can be easily understood by tracing his ontological and epistemological commitments to his early training in the Cambridge Mathematical Tripos. I also suggest that Darwin's work cannot be neglected in a study of quantum physics in Britain, since he was one of very few fellows of the Royal Society able to judge and explain quantum physics and quantum mechanics.

  1. Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

    PubMed

    Wang, Meiting; Li, Pengfei; Jia, Xiangyu; Liu, Wei; Shao, Yihan; Hu, Wenxin; Zheng, Jun; Brooks, Bernard R; Mei, Ye

    2017-10-23

    The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum mechanics (QM) can provide more reliable predictions. In this work, the partition coefficients of the side chain analogs of some amino acids between water and chloroform were computed. The QM solvation free energies were calculated indirectly via a series of MM states using the multistate Bennett acceptance ratio (MBAR) and the MM-to-QM corrections were applied at the two endpoints using thermodynamic perturbation (TP). Previously, it has been shown (Jia et al. J. Chem. Theory Comput. 2016, 12, 499-511) that this method provides the minimal variance in the results without running QM simulations. However, if there is insufficient overlap in phase space between the MM and QM Hamiltonians, this method fails. In this work, we propose, for the first time, a quantity termed the reweighting entropy that serves as a metric for the reliability of the TP calculations. If the reweighting entropy is below a certain threshold (0.65 for the solvation free energy calculations in this work), this MM-to-QM correction should be avoided and two alternative methods can be employed by either introducing a semiempirical state or conducting nonequilibrium simulations. However, the results show that the QM methods are not guaranteed to yield better results than the MM methods. Further improvement of the QM methods are imperative, especially the treatment of the van der Waals and the electrostatic interactions between the QM region and the MM region in the first shell. We also propose a scheme for the calculation of the van der Waals parameters for the solute molecules in nonaqueous solvent, which improves the quality of the

  2. Quantum mechanical models for the Fermi shuttle

    NASA Astrophysics Data System (ADS)

    Sternberg, James; Ovchinnikov, S. Yu.; Macek, J. H.

    2009-05-01

    Although the Fermi shuttle was originally proposed as an explanation for highly energetic cosmic rays, it is also a mechanism for the production of high energy electrons in atomic collisions [1]. The Fermi shuttle is usually thought of as a classical effect and most models of this process rely on classical or semi-classical approximations. In this work we explore several quantum mechanical models for ion-atom collisions and examine the evidence for the Fermi shuttle in these models. [4pt] [1] B. Sulik, Cs. Koncz, K. Tok'esi, A. Orb'an, and D. Ber'enyi, Phys Rev. Lett. 88 073201 (2002)

  3. 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.

  4. Ocular diseases: immunological and molecular mechanisms

    PubMed Central

    Song, Jing; Huang, Yi-Fei; Zhang, Wen-Jing; Chen, Xiao-Fei; Guo, Yu-Mian

    2016-01-01

    Many factors, such as environmental, microbial and endogenous stress, antigen localization, can trigger the immunological events that affect the ending of the diverse spectrum of ocular disorders. Significant advances in understanding of immunological and molecular mechanisms have been researched to improve the diagnosis and therapy for patients with ocular inflammatory diseases. Some kinds of ocular diseases are inadequately responsive to current medications; therefore, immunotherapy may be a potential choice as an alternative or adjunctive treatment, even in the prophylactic setting. This article first provides an overview of the immunological and molecular mechanisms concerning several typical and common ocular diseases; second, the functions of immunological roles in some of systemic autoimmunity will be discussed; third, we will provide a summary of the mechanisms that dictate immune cell trafficking to ocular local microenvironment in response to inflammation. PMID:27275439

  5. Diffeomorphism groups and nonlinear quantum mechanics

    NASA Astrophysics Data System (ADS)

    Goldin, Gerald A.

    2012-02-01

    This talk is dedicated to my friend and collaborator, Prof. Dr. Heinz-Dietrich Doebner, on the occasion of his 80th birthday. I shall review some highlights of the approach we have taken in deriving and interpreting an interesting class of nonlinear time-evolution equations for quantum-mechanical wave functions, with few equations; more detail may be found in the references. Then I shall comment on the corresponding hydrodynamical description.

  6. Molecular Mechanics: The Method and Its Underlying Philosophy.

    ERIC Educational Resources Information Center

    Boyd, Donald B.; Lipkowitz, Kenny B.

    1982-01-01

    Molecular mechanics is a nonquantum mechanical method for solving problems concerning molecular geometries and energy. Methodology based on: the principle of combining potential energy functions of all structural features of a particular molecule into a total force field; derivation of basic equations; and use of available computer programs is…

  7. A simple quantum mechanical treatment of scattering in nanoscale transistors

    NASA Astrophysics Data System (ADS)

    Venugopal, R.; Paulsson, M.; Goasguen, S.; Datta, S.; Lundstrom, M. S.

    2003-05-01

    We present a computationally efficient, two-dimensional quantum mechanical simulation scheme for modeling dissipative electron transport in thin body, fully depleted, n-channel, silicon-on-insulator transistors. The simulation scheme, which solves the nonequilibrium Green's function equations self consistently with Poisson's equation, treats the effect of scattering using a simple approximation inspired by the "Büttiker probes," often used in mesoscopic physics. It is based on an expansion of the active device Hamiltonian in decoupled mode space. Simulation results are used to highlight quantum effects, discuss the physics of scattering and to relate the quantum mechanical quantities used in our model to experimentally measured low field mobilities. Additionally, quantum boundary conditions are rigorously derived and the effects of strong off-equilibrium transport are examined. This paper shows that our approximate treatment of scattering, is an efficient and useful simulation method for modeling electron transport in nanoscale, silicon-on-insulator transistors.

  8. The criterion for time symmetry of probabilistic theories and the reversibility of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Holster, A. T.

    2003-10-01

    Physicists routinely claim that the fundamental laws of physics are 'time symmetric' or 'time reversal invariant' or 'reversible'. In particular, it is claimed that the theory of quantum mechanics is time symmetric. But it is shown in this paper that the orthodox analysis suffers from a fatal conceptual error, because the logical criterion for judging the time symmetry of probabilistic theories has been incorrectly formulated. The correct criterion requires symmetry between future-directed laws and past-directed laws. This criterion is formulated and proved in detail. The orthodox claim that quantum mechanics is reversible is re-evaluated. The property demonstrated in the orthodox analysis is shown to be quite distinct from time reversal invariance. The view of Satosi Watanabe that quantum mechanics is time asymmetric is verified, as well as his view that this feature does not merely show a de facto or 'contingent' asymmetry, as commonly supposed, but implies a genuine failure of time reversal invariance of the laws of quantum mechanics. The laws of quantum mechanics would be incompatible with a time-reversed version of our universe.

  9. Quantum Mechanics for Everyone: Can it be done with Technology?

    NASA Astrophysics Data System (ADS)

    Zollman, Dean

    2004-10-01

    The Visual Quantum Mechanics project has created a series of teaching/learning units to introduce quantum physics to a variety of audiences ranging from high school students who normally would not study these topics to undergraduate physics majors. Most recently we have been developing materials relating modern medical procedures and contemporary physics. In all of these materials interactive computer visualizations are coupled with hands-on experiences to create a series of activities which help students learn about some aspects of quantum mechanics. Our goal is to enable students to obtain a qualitative and, where appropriate, a quantitative understanding of contemporary ideas in physics. Included in the instructional materials are student-centered activities that address a variety of concepts in quantum physics and applications to devices such as the light emitting diode, the electron microscope, an inexpensive infrared detection card, and the Star Trek Transporter. Whenever possible the students begin the study of a new concept with an experiment using inexpensive equipment. They, then, build models of the physical phenomenon using interactive computer visualization and conclude by applying those models to new situations. For physics students these visualizations are usually followed by a mathematical approach. For others the visualizations provide a framework for understanding the concepts. Thus, Visual Quantum Mechanics allows a wide range of students to begin to understand the basic concepts, implications and interpretations of quantum physics. At present we are building on this foundation to create materials which show the connection between contemporary physics and modern medical diagnosis. Additional information is available at http://web.phys.ksu.edu/.

  10. Novel symmetries in N=2 supersymmetric quantum mechanical models

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

    Malik, R.P., E-mail: malik@bhu.ac.in; DST-CIMS, Faculty of Science, BHU-Varanasi-221 005; Khare, Avinash, E-mail: khare@iiserpune.ac.in

    We demonstrate the existence of a novel set of discrete symmetries in the context of the N=2 supersymmetric (SUSY) quantum mechanical model with a potential function f(x) that is a generalization of the potential of the 1D SUSY harmonic oscillator. We perform the same exercise for the motion of a charged particle in the X–Y plane under the influence of a magnetic field in the Z-direction. We derive the underlying algebra of the existing continuous symmetry transformations (and corresponding conserved charges) and establish its relevance to the algebraic structures of the de Rham cohomological operators of differential geometry. We showmore » that the discrete symmetry transformations of our present general theories correspond to the Hodge duality operation. Ultimately, we conjecture that any arbitrary N=2 SUSY quantum mechanical system can be shown to be a tractable model for the Hodge theory. -- Highlights: •Discrete symmetries of two completely different kinds of N=2 supersymmetric quantum mechanical models have been discussed. •The discrete symmetries provide physical realizations of Hodge duality. •The continuous symmetries provide the physical realizations of de Rham cohomological operators. •Our work sheds a new light on the meaning of the above abstract operators.« less

  11. Quantum vs Classical Mechanics for a 'Simple' Dissociation Reaction. Should They Give the Same Results?

    NASA Astrophysics Data System (ADS)

    Holloway, Stephen

    1997-03-01

    When performing molecular dynamical simulations on light systems at low energies, there is always the risk of producing data that bear no similarity to experiment. Indeed, John Barker himself was particularly anxious about treating Ar scattering from surfaces using classical mechanics where it had been shown experimentally in his own lab that diffraction occurs. In such cases, the correct procedure is probably to play the trump card "... well of course, quantum effects will modify this so that....." and retire gracefully. For our particular interests, the tables are turned in that we are interested in gas-surface dynamical studies for highly quantized systems, but would be interested to know when it is possible to use classical mechanics in order that a greater dimensionality might be treated. For molecular dissociation and scattering, it has been oft quoted that the greater the number of degrees of freedom, the more appropriate is classical mechanics, primarily because of the mass averaging over the quantized dimensions. Is this true? We have been investigating the dissociation of hydrogen molecules at surfaces and in this talk I will present quantum results for dissociation and scattering, along with a novel method for their interpretation based upon adiabatic potential energy surfaces. Comparison with classical calculations will be made and conclusions drawn. a novel method for their interpretation based upon adiabatic potential energy surfaces

  12. Resonant electronic excitation energy transfer by Dexter mechanism in the quantum dot system

    NASA Astrophysics Data System (ADS)

    Samosvat, D. M.; Chikalova-Luzina, O. P.; Vyatkin, V. M.; Zegrya, G. G.

    2016-11-01

    In present work the energy transfer between quantum dots by the exchange (Dexter) mechanism is analysed. The interdot Coulomb interaction is taken into consideration. It is assumed that the quantum dot-donor and the quantum dot-acceptor are made from the same compound A3B5 and embedded in the matrix of other material creating potential barriers for electron and holes. The dependences of the energy transfer rate on the quantum-dot system parameters are found using the Kane model that provides the most adequate description spectra of semiconductors A3B5. Numerical calculations show that the rate of the energy transfer by Dexter mechanism is comparable to the rate of the energy transfer by electrostatic mechanism at the distances approaching to the contact ones.

  13. Highlighting the Mechanism of the Quantum Speedup by Time-Symmetric and Relational Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Castagnoli, Giuseppe

    2016-03-01

    Bob hides a ball in one of four drawers. Alice is to locate it. Classically she has to open up to three drawers, quantally just one. The fundamental reason for this quantum speedup is not known. The usual representation of the quantum algorithm is limited to the process of solving the problem. We extend it to the process of setting the problem. The number of the drawer with the ball becomes a unitary transformation of the random outcome of the preparation measurement. This extended, time-symmetric, representation brings in relational quantum mechanics. It is with respect to Bob and any external observer and cannot be with respect to Alice. It would tell her the number of the drawer with the ball before she opens any drawer. To Alice, the projection of the quantum state due to the preparation measurement should be retarded at the end of her search; in the input state of the search, the drawer number is determined to Bob and undetermined to Alice. We show that, mathematically, one can ascribe any part of the selection of the random outcome of the preparation measurement to the final Alice's measurement. Ascribing half of it explains the speedup of the present algorithm. This leaves the input state to Bob unaltered and projects that to Alice on a state of lower entropy where she knows half of the number of the drawer with the ball in advance. The quantum algorithm turns out to be a sum over histories in each of which Alice knows in advance that the ball is in a pair of drawers and locates it by opening one of the two. In the sample of quantum algorithms examined, the part of the random outcome of the initial measurement selected by the final measurement is one half or slightly above it. Conversely, given an oracle problem, the assumption it is one half always corresponds to an existing quantum algorithm and gives the order of magnitude of the number of oracle queries required by the optimal one.

  14. A cellular automaton for the signed particle formulation of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Sellier, J. M.; Kapanova, K. G.; Dimov, I.

    2017-02-01

    Recently, a new formulation of quantum mechanics, based on the concept of signed particles, has been suggested. In this paper, we introduce a cellular automaton which mimics the dynamics of quantum objects in the phase-space in a time-dependent fashion. This is twofold: it provides a simplified and accessible language to non-physicists who wants to simulate quantum mechanical systems, at the same time it enables a different way to explore the laws of Physics. Moreover, it opens the way towards hybrid simulations of quantum systems by combining full quantum models with cellular automata when the former fail. In order to show the validity of the suggested cellular automaton and its combination with the signed particle formalism, several numerical experiments are performed, showing very promising results. Being this article a preliminary study on quantum simulations in phase-space by means of cellular automata, some conclusions are drawn about the encouraging results obtained so far and the possible future developments.

  15. Differentiability of correlations in realistic quantum mechanics

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

    Cabrera, Alejandro; Faria, Edson de; Pujals, Enrique

    2015-09-15

    We prove a version of Bell’s theorem in which the locality assumption is weakened. We start by assuming theoretical quantum mechanics and weak forms of relativistic causality and of realism (essentially the fact that observable values are well defined independently of whether or not they are measured). Under these hypotheses, we show that only one of the correlation functions that can be formulated in the framework of the usual Bell theorem is unknown. We prove that this unknown function must be differentiable at certain angular configuration points that include the origin. We also prove that, if this correlation is assumedmore » to be twice differentiable at the origin, then we arrive at a version of Bell’s theorem. On the one hand, we are showing that any realistic theory of quantum mechanics which incorporates the kinematic aspects of relativity must lead to this type of rough correlation function that is once but not twice differentiable. On the other hand, this study brings us a single degree of differentiability away from a relativistic von Neumann no hidden variables theorem.« less

  16. Periodic Toda lattice in quantum mechanics

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

    Matsuyama, A.

    The quantum mechanical periodic Toda lattice is studied by the direct diagonalization of the Hamiltonian. The eigenstates are classified according to the irreducible representations of the dihedral group D[sub N]. It is shown that Gutzwiller's quantization conditions are satisfied and they have a one-to-one correspondence to the irreducible representation of the D[sub N] group. The authors have also carried out the semiclassical quantization of the periodic Toda lattice by the EBK formulation. The eigenvalues of the semiclassical quantization have a one-to-one correspondence to the integer quantum numbers, and those quantum numbers also have a close relationship to the symmetry ofmore » the state. Numerical calculations have been done for N = 3, 4, 5, and 6 particle periodic Toda lattices. The distributions of the eigenvalues are systematic and distinguished by the symmetry of the state. As illustrative examples, amplitudes of the wave functions and density distributions are shown. 14 refs., 8 figs., 11 tabs.« less

  17. Conformal quantum mechanics and holography in noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Gupta, Kumar S.; Harikumar, E.; Zuhair, N. S.

    2017-09-01

    We analyze the effects of noncommutativity in conformal quantum mechanics (CQM) using the κ-deformed space-time as a prototype. Up to the first order in the deformation parameter, the symmetry structure of the CQM algebra is preserved but the coupling in a canonical model of the CQM gets deformed. We show that the boundary conditions that ensure a unitary time evolution in the noncommutative CQM can break the scale invariance, leading to a quantum mechanical scaling anomaly. We calculate the scaling dimensions of the two and three point functions in the noncommutative CQM which are shown to be deformed. The AdS2 / CFT1 duality for the CQM suggests that the corresponding correlation functions in the holographic duals are modified. In addition, the Breitenlohner-Freedman bound also picks up a noncommutative correction. The strongly attractive regime of a canonical model of the CQM exhibit quantum instability. We show that the noncommutativity softens this singular behaviour and its implications for the corresponding holographic duals are discussed.

  18. On the Conformable Fractional Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Mozaffari, F. S.; Hassanabadi, H.; Sobhani, H.; Chung, W. S.

    2018-05-01

    In this paper, a conformable fractional quantum mechanic has been introduced using three postulates. Then in such a formalism, Schr¨odinger equation, probability density, probability flux and continuity equation have been derived. As an application of considered formalism, a fractional-radial harmonic oscillator has been considered. After obtaining its wave function and energy spectrum, effects of the conformable fractional parameter on some quantities have been investigated and plotted for different excited states.

  19. What are the mechanics of quantum cognition?

    PubMed

    Navarro, Daniel Joseph; Fuss, Ian

    2013-06-01

    Pothos & Busemeyer (P&B) argue that quantum probability (QP) provides a descriptive model of behavior and can also provide a rational analysis of a task. We discuss QP models using Marr's levels of analysis, arguing that they make most sense as algorithmic level theories. We also highlight the importance of having clear interpretations for basic mechanisms such as interference.

  20. Quantum mechanics in noninertial reference frames: Violations of the nonrelativistic equivalence principle

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

    Klink, W.H.; Wickramasekara, S., E-mail: wickrama@grinnell.edu; Department of Physics, Grinnell College, Grinnell, IA 50112

    2014-01-15

    In previous work we have developed a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group that includes transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as is the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. A special feature of these previously constructed representations is that they all respect the non-relativistic equivalence principle, wherein the fictitious forces associated with linear acceleration canmore » equivalently be described by gravitational forces. In this paper we exhibit a large class of cocycle representations of the Galilean line group that violate the equivalence principle. Nevertheless the classical mechanics analogue of these cocycle representations all respect the equivalence principle. -- Highlights: •A formulation of Galilean quantum mechanics in non-inertial reference frames is given. •The key concept is the Galilean line group, an infinite dimensional group. •A large class of general cocycle representations of the Galilean line group is constructed. •These representations show violations of the equivalence principle at the quantum level. •At the classical limit, no violations of the equivalence principle are detected.« less

  1. Strong quantum squeezing of mechanical resonator via parametric amplification and coherent feedback

    NASA Astrophysics Data System (ADS)

    You, Xiang; Li, Zongyang; Li, Yongmin

    2017-12-01

    A scheme to achieve strong quantum squeezing of a mechanical resonator in a membrane-in-the-middle optomechanical system is developed. To this end, simultaneous linear and nonlinear coupling between the mechanical resonator and the cavity modes is applied. A two-tone driving light field, comprising unequal red-detuned and blue-detuned sidebands, helps in generating a coherent feedback force through the linear coupling with the membrane resonator. Another driving light field with its amplitude modulated at twice the mechanical frequency drives the mechanical parametric amplification through a second-order coupling with the resonator. The combined effect produces strong quantum squeezing of the mechanical state. The proposed scheme is quite robust to excess second-order coupling observed in coherent feedback operations and can suppress the fluctuations in the mechanical quadrature to far below the zero point and achieve strong squeezing (greater than 10 dB) for realistic parameters.

  2. Non Locality Proofs in Quantum Mechanics Analyzed by Ordinary Mathematical Logic

    NASA Astrophysics Data System (ADS)

    Nisticò, Giuseppe

    2014-10-01

    The so-called non-locality theorems aim to show that Quantum Mechanics is not consistent with the Locality Principle. Their proofs require, besides the standard postulates of Quantum Theory, further conditions, as for instance the Criterion of Reality, which cannot be formulated in the language of Standard Quantum Theory; this difficulty makes the proofs not verifiable according to usual logico-mathematical methods, and therefore it is a source of the controversial debate about the real implications of these theorems. The present work addresses this difficulty for Bell-type and Stapp's arguments of non-locality. We supplement the formalism of Quantum Mechanics with formal statements inferred from the further conditions in the two different cases. Then an analysis of the two arguments is performed according to ordinary mathematical logic.

  3. Quantum Mechanics for Everybody: An autonomous MOOC on EdX for nonscientists

    NASA Astrophysics Data System (ADS)

    Freericks, James; Cutler, Dylan; Vieira-Barbosa, Lucas

    2017-01-01

    We have launched a MOOC for nonscientists that teaches quantum mechanics using the Feynman methodology as outlined in his QED book and in a similar book by Daniel Styer. Using a combination of videos, voice-over powerpoint animations, computer simulations and interactive tutorials, we teach the fundamentals of quantum mechanics employing a minimum of math (high school algebra, square roots, and a little trigonometry) but going into detail on a number of complex quantum ideas. We begin with the Stern-Gerlach experiment, including delayed choice and Bell's inequality variants. Then we focus on light developing the quantum theory for partial reflection and diffraction. At this point we demonstrate the complexity of quantum physics by showing how watched and unwatched two-slit experiments behave differently and how quantum particles interfere. The four week course ends with advanced topics in light where we cover the idea of an interaction free measurement, the quantum Zeno effect and indistinguishable particles via the Hong-Ou-Mandel experiment. We hope this MOOC will reach thousands of students interesting in learning quantum mechanics without any dumbing down or the need to learn complex math. It can also be used with undergraduates to help with conceptual understanding. Funded by the National Science Foundation under grants numbered PHY-1620555 and PHY-1314295 and by Georgetown University.

  4. Quantum Mechanics: Myths and Facts

    NASA Astrophysics Data System (ADS)

    Nikolić, Hrvoje

    2007-11-01

    A common understanding of quantum mechanics (QM) among students and practical users is often plagued by a number of “myths”, that is, widely accepted claims on which there is not really a general consensus among experts in foundations of QM. These myths include wave-particle duality, time-energy uncertainty relation, fundamental randomness, the absence of measurement-independent reality, locality of QM, nonlocality of QM, the existence of well-defined relativistic QM, the claims that quantum field theory (QFT) solves the problems of relativistic QM or that QFT is a theory of particles, as well as myths on black-hole entropy. The fact is that the existence of various theoretical and interpretational ambiguities underlying these myths does not yet allow us to accept them as proven facts. I review the main arguments and counterarguments lying behind these myths and conclude that QM is still a not-yet-completely-understood theory open to further fundamental research.

  5. Multidimensional supersymmetric quantum mechanics: spurious states for the tensor sector two Hamiltonian.

    PubMed

    Chou, Chia-Chun; Kouri, Donald J

    2013-04-25

    We show that there exist spurious states for the sector two tensor Hamiltonian in multidimensional supersymmetric quantum mechanics. For one-dimensional supersymmetric quantum mechanics on an infinite domain, the sector one and two Hamiltonians have identical spectra with the exception of the ground state of the sector one. For tensorial multidimensional supersymmetric quantum mechanics, there exist normalizable spurious states for the sector two Hamiltonian with energy equal to the ground state energy of the sector one. These spurious states are annihilated by the adjoint charge operator, and hence, they do not correspond to physical states for the original Hamiltonian. The Hermitian property of the sector two Hamiltonian implies the orthogonality between spurious and physical states. In addition, we develop a method for construction of a specific form of the spurious states for any quantum system and also generate several spurious states for a two-dimensional anharmonic oscillator system and for the hydrogen atom.

  6. Efficient hybrid-symbolic methods for quantum mechanical calculations

    NASA Astrophysics Data System (ADS)

    Scott, T. C.; Zhang, Wenxing

    2015-06-01

    We present hybrid symbolic-numerical tools to generate optimized numerical code for rapid prototyping and fast numerical computation starting from a computer algebra system (CAS) and tailored to any given quantum mechanical problem. Although a major focus concerns the quantum chemistry methods of H. Nakatsuji which has yielded successful and very accurate eigensolutions for small atoms and molecules, the tools are general and may be applied to any basis set calculation with a variational principle applied to its linear and non-linear parameters.

  7. Optimization of metabolite detection by quantum mechanics simulations in magnetic resonance spectroscopy.

    PubMed

    Gambarota, Giulio

    2017-07-15

    Magnetic resonance spectroscopy (MRS) is a well established modality for investigating tissue metabolism in vivo. In recent years, many efforts by the scientific community have been directed towards the improvement of metabolite detection and quantitation. Quantum mechanics simulations allow for investigations of the MR signal behaviour of metabolites; thus, they provide an essential tool in the optimization of metabolite detection. In this review, we will examine quantum mechanics simulations based on the density matrix formalism. The density matrix was introduced by von Neumann in 1927 to take into account statistical effects within the theory of quantum mechanics. We will discuss the main steps of the density matrix simulation of an arbitrary spin system and show some examples for the strongly coupled two spin system. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Quantum Dot Platform for Single-Cell Molecular Profiling

    NASA Astrophysics Data System (ADS)

    Zrazhevskiy, Pavel S.

    In-depth understanding of the nature of cell physiology and ability to diagnose and control the progression of pathological processes heavily rely on untangling the complexity of intracellular molecular mechanisms and pathways. Therefore, comprehensive molecular profiling of individual cells within the context of their natural tissue or cell culture microenvironment is essential. In principle, this goal can be achieved by tagging each molecular target with a unique reporter probe and detecting its localization with high sensitivity at sub-cellular resolution, primarily via microscopy-based imaging. Yet, neither widely used conventional methods nor more advanced nanoparticle-based techniques have been able to address this task up to date. High multiplexing potential of fluorescent probes is heavily restrained by the inability to uniquely match probes with corresponding molecular targets. This issue is especially relevant for quantum dot probes---while simultaneous spectral imaging of up to 10 different probes is possible, only few can be used concurrently for staining with existing methods. To fully utilize multiplexing potential of quantum dots, it is necessary to design a new staining platform featuring unique assignment of each target to a corresponding quantum dot probe. This dissertation presents two complementary versatile approaches towards achieving comprehensive single-cell molecular profiling and describes engineering of quantum dot probes specifically tailored for each staining method. Analysis of expanded molecular profiles is achieved through augmenting parallel multiplexing capacity with performing several staining cycles on the same specimen in sequential manner. In contrast to other methods utilizing quantum dots or other nanoparticles, which often involve sophisticated probe synthesis, the platform technology presented here takes advantage of simple covalent bioconjugation and non-covalent self-assembly mechanisms for straightforward probe

  9. Quantum localization of classical mechanics

    NASA Astrophysics Data System (ADS)

    Batalin, Igor A.; Lavrov, Peter M.

    2016-07-01

    Quantum localization of classical mechanics within the BRST-BFV and BV (or field-antifield) quantization methods are studied. It is shown that a special choice of gauge fixing functions (or BRST-BFV charge) together with the unitary limit leads to Hamiltonian localization in the path integral of the BRST-BFV formalism. In turn, we find that a special choice of gauge fixing functions being proportional to extremals of an initial non-degenerate classical action together with a very special solution of the classical master equation result in Lagrangian localization in the partition function of the BV formalism.

  10. Does boundary quantum mechanics imply quantum mechanics in the bulk?

    NASA Astrophysics Data System (ADS)

    Kabat, Daniel; Lifschytz, Gilad

    2018-03-01

    Perturbative bulk reconstruction in AdS/CFT starts by representing a free bulk field ϕ (0) as a smeared operator in the CFT. A series of 1 /N corrections must be added to ϕ (0) to represent an interacting bulk field ϕ. These corrections have been determined in the literature from several points of view. Here we develop a new perspective. We show that correlation functions involving ϕ (0) suffer from ambiguities due to analytic continuation. As a result ϕ (0) fails to be a well-defined linear operator in the CFT. This means bulk reconstruction can be understood as a procedure for building up well-defined operators in the CFT which thereby singles out the interacting field ϕ. We further propose that the difficulty with defining ϕ (0) as a linear operator can be re-interpreted as a breakdown of associativity. Presumably ϕ (0) can only be corrected to become an associative operator in perturbation theory. This suggests that quantum mechanics in the bulk is only valid in perturbation theory around a semiclassical bulk geometry.

  11. Modeling molecular mechanisms in the axon

    NASA Astrophysics Data System (ADS)

    de Rooij, R.; Miller, K. E.; Kuhl, E.

    2017-03-01

    Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that interprets cellular-level characteristics as emergent properties from molecular-level events. We create an axon model of discrete microtubules, which are connected to neighboring microtubules via discrete crosslinking mechanisms that obey a set of simple rules. We explore two types of mechanisms: passive and active crosslinking. Our passive and active simulations suggest that the stiffness and viscosity of the axon increase linearly with the crosslink density, and that both are highly sensitive to the crosslink detachment and reattachment times. Our model explains how active crosslinking with dynein motors generates internal stresses and actively drives axon elongation. We anticipate that our model will allow us to probe a wide variety of molecular phenomena—both in isolation and in interaction—to explore emergent cellular-level features under physiological and pathological conditions.

  12. Student Ability to Distinguish between Superposition States and Mixed States in Quantum Mechanics

    ERIC Educational Resources Information Center

    Passante, Gina; Emigh, Paul J.; Shaffer, Peter S.

    2015-01-01

    Superposition gives rise to the probabilistic nature of quantum mechanics and is therefore one of the concepts at the heart of quantum mechanics. Although we have found that many students can successfully use the idea of superposition to calculate the probabilities of different measurement outcomes, they are often unable to identify the…

  13. Frequency-domain multiscale quantum mechanics/electromagnetics simulation method

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

    Meng, Lingyi; Yin, Zhenyu; Yam, ChiYung, E-mail: yamcy@yangtze.hku.hk, E-mail: ghc@everest.hku.hk

    A frequency-domain quantum mechanics and electromagnetics (QM/EM) method is developed. Compared with the time-domain QM/EM method [Meng et al., J. Chem. Theory Comput. 8, 1190–1199 (2012)], the newly developed frequency-domain QM/EM method could effectively capture the dynamic properties of electronic devices over a broader range of operating frequencies. The system is divided into QM and EM regions and solved in a self-consistent manner via updating the boundary conditions at the QM and EM interface. The calculated potential distributions and current densities at the interface are taken as the boundary conditions for the QM and EM calculations, respectively, which facilitate themore » information exchange between the QM and EM calculations and ensure that the potential, charge, and current distributions are continuous across the QM/EM interface. Via Fourier transformation, the dynamic admittance calculated from the time-domain and frequency-domain QM/EM methods is compared for a carbon nanotube based molecular device.« less

  14. [Neonatal hyperbilirubinemia and molecular mechanisms of jaundice].

    PubMed

    Jirsa, M; Sticová, E

    2013-07-01

    The introductory summarises the classical path of heme degradation and classification of jaundice. Subsequently, a description of neonatal types of jaundice is given, known as Crigler Najjar, Gilberts, DubinJohnson and Rotor syndromes, emphasising the explanation of the molecular mechanisms of these metabolic disorders. Special attention is given to a recently discovered molecular mechanism of the Rotor syndrome. The mechanism is based on the inability of the liver to retrospectively uptake the conjugated bilirubin fraction primarily excreted into the blood, not bile. A reduced ability of the liver to uptake the conjugated bilirubin contributes to the development of hyperbilirubinemia in common disorders of the liver and bile ducts and to the toxicity of xenobiotics and drugs using transport proteins for conjugated bilirubin.

  15. Equilibration, thermalisation, and the emergence of statistical mechanics in closed quantum systems

    NASA Astrophysics Data System (ADS)

    Gogolin, Christian; Eisert, Jens

    2016-05-01

    We review selected advances in the theoretical understanding of complex quantum many-body systems with regard to emergent notions of quantum statistical mechanics. We cover topics such as equilibration and thermalisation in pure state statistical mechanics, the eigenstate thermalisation hypothesis, the equivalence of ensembles, non-equilibration dynamics following global and local quenches as well as ramps. We also address initial state independence, absence of thermalisation, and many-body localisation. We elucidate the role played by key concepts for these phenomena, such as Lieb-Robinson bounds, entanglement growth, typicality arguments, quantum maximum entropy principles and the generalised Gibbs ensembles, and quantum (non-)integrability. We put emphasis on rigorous approaches and present the most important results in a unified language.

  16. Equilibration, thermalisation, and the emergence of statistical mechanics in closed quantum systems.

    PubMed

    Gogolin, Christian; Eisert, Jens

    2016-05-01

    We review selected advances in the theoretical understanding of complex quantum many-body systems with regard to emergent notions of quantum statistical mechanics. We cover topics such as equilibration and thermalisation in pure state statistical mechanics, the eigenstate thermalisation hypothesis, the equivalence of ensembles, non-equilibration dynamics following global and local quenches as well as ramps. We also address initial state independence, absence of thermalisation, and many-body localisation. We elucidate the role played by key concepts for these phenomena, such as Lieb-Robinson bounds, entanglement growth, typicality arguments, quantum maximum entropy principles and the generalised Gibbs ensembles, and quantum (non-)integrability. We put emphasis on rigorous approaches and present the most important results in a unified language.

  17. Unitary cocycle representations of the Galilean line group: Quantum mechanical principle of equivalence

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

    MacGregor, B.R.; McCoy, A.E.; Wickramasekara, S., E-mail: wickrama@grinnell.edu

    2012-09-15

    We present a formalism of Galilean quantum mechanics in non-inertial reference frames and discuss its implications for the equivalence principle. This extension of quantum mechanics rests on the Galilean line group, the semidirect product of the real line and the group of analytic functions from the real line to the Euclidean group in three dimensions. This group provides transformations between all inertial and non-inertial reference frames and contains the Galilei group as a subgroup. We construct a certain class of unitary representations of the Galilean line group and show that these representations determine the structure of quantum mechanics in non-inertialmore » reference frames. Our representations of the Galilean line group contain the usual unitary projective representations of the Galilei group, but have a more intricate cocycle structure. The transformation formula for the Hamiltonian under the Galilean line group shows that in a non-inertial reference frame it acquires a fictitious potential energy term that is proportional to the inertial mass, suggesting the equivalence of inertial mass and gravitational mass in quantum mechanics. - Highlights: Black-Right-Pointing-Pointer A formulation of Galilean quantum mechanics in non-inertial reference frames is given. Black-Right-Pointing-Pointer The key concept is the Galilean line group, an infinite dimensional group. Black-Right-Pointing-Pointer Unitary, cocycle representations of the Galilean line group are constructed. Black-Right-Pointing-Pointer A non-central extension of the group underlies these representations. Black-Right-Pointing-Pointer Quantum equivalence principle and gravity emerge from these representations.« less

  18. Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl

    NASA Astrophysics Data System (ADS)

    Kuechler, Erich R.; York, Darrin M.

    2014-02-01

    The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

  19. Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

    PubMed

    Kuechler, Erich R; York, Darrin M

    2014-02-07

    The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

  20. The Quantum and Fluid Mechanics of Global Warming

    NASA Astrophysics Data System (ADS)

    Marston, Brad

    2008-03-01

    Quantum physics and fluid mechanics are the foundation of any understanding of the Earth's climate. In this talk I invoke three well-known aspects of quantum mechanics to explore what will happen as the concentrations of greenhouse gases such as carbon dioxide continue to increase. Fluid dynamical models of the Earth's atmosphere, demonstrated here in live simulations, yield further insight into past, present, and future climates. Statistics of geophysical flows can, however, be ascertained directly without recourse to numerical simulation, using concepts borrowed from nonequilibrium statistical mechanicsootnotetextJ. B. Marston, E. Conover, and Tapio Schneider, ``Statistics of an Unstable Barotropic Jet from a Cumulant Expansion,'' arXiv:0705.0011, J. Atmos. Sci. (in press).. I discuss several other ways that theoretical physics may be able to contribute to a deeper understanding of climate changeootnotetextJ. Carlson, J. Harte, G. Falkovich, J. B. Marston, and R. Pierrehumbert, ``Physics of Climate Change'' 2008 Program of the Kavli Institute for Theoretical Physics..

  1. New Potentials for Old: The Darboux Transformation in Quantum Mechanics

    ERIC Educational Resources Information Center

    Williams, Brian Wesley; Celius, Tevye C.

    2008-01-01

    The Darboux transformation in quantum mechanics is reviewed at a basic level. Examples of how this transformation leads to exactly solvable potentials related to the "particle in a box" and the harmonic oscillator are shown in detail. The connection between the Darboux transformation and some modern operator based approaches to quantum mechanics…

  2. Cellular and molecular mechanisms for the bone response to mechanical loading

    NASA Technical Reports Server (NTRS)

    Bloomfield, S. A.

    2001-01-01

    To define the cellular and molecular mechanisms for the osteogenic response of bone to increased loading, several key steps must be defined: sensing of the mechanical signal by cells in bone, transduction of the mechanical signal to a biochemical one, and transmission of that biochemical signal to effector cells. Osteocytes are likely to serve as sensors of loading, probably via interstitial fluid flow produced during loading. Evidence is presented for the role of integrins, the cell's actin cytoskeleton, G proteins, and various intracellular signaling pathways in transducing that mechanical signal to a biochemical one. Nitric oxide, prostaglandins, and insulin-like growth factors all play important roles in these pathways. There is growing evidence for modulation of these mechanotransduction steps by endocrine factors, particularly parathyroid hormone and estrogen. The efficiency of this process is also impaired in the aged animal, yet what remains undefined is at what step mechanotransduction is affected.

  3. Quantum Mechanical Study of γ-Fe2O3 Nanoparticle as a Nanocarrier for Anticancer Drug Delivery

    NASA Astrophysics Data System (ADS)

    Lari, Hadi; Morsali, Ali; Heravi, Mohammad Momen

    2018-05-01

    Using density functional theory (DFT), noncovalent interactions and four mechanisms of covalent functionalization of melphalan anticancer drug onto γ-Fe2O3 nanoparticles have been studied. Quantum molecular descriptors of noncovalent configurations were investigated. It was specified that binding of melphalan onto γ-Fe2O3 nanoparticles is thermodynamically suitable. Hardness and the gap of energy between LUMO and HOMO of melphalan are higher than the noncovalent configurations, showing the reactivity of drug increases in the presence of γ-Fe2O3 nanoparticles. Melphalan can bond to γ-Fe2O3 nanoparticles through NH2 (k1 mechanism), OH (k2 mechanism), C=O (k3 mechanism) and Cl (k4 mechanism) groups. The activation energies, the activation enthalpies and the activation Gibbs free energies of these reactions were calculated. Thermodynamic data indicate that k3 mechanism is exothermic and spontaneous and can take place at room temperature. These results could be generalized to other similar drugs.

  4. Material Phase Causality or a Dynamics-Statistical Interpretation of Quantum Mechanics

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

    Koprinkov, I. G.

    2010-11-25

    The internal phase dynamics of a quantum system interacting with an electromagnetic field is revealed in details. Theoretical and experimental evidences of a causal relation of the phase of the wave function to the dynamics of the quantum system are presented sistematically for the first time. A dynamics-statistical interpretation of the quantum mechanics is introduced.

  5. From correspondence to complementarity: The emergence of Bohr's Copenhagen interpretation of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Tanona, Scott Daniel

    I develop a new analysis of Niels Bohr's Copenhagen interpretation of quantum mechanics by examining the development of his views from his earlier use of the correspondence principle in the so-called 'old quantum theory' to his articulation of the idea of complementarity in the context of the novel mathematical formalism of quantum mechanics. I argue that Bohr was motivated not by controversial and perhaps dispensable epistemological ideas---positivism or neo-Kantianism, for example---but by his own unique perspective on the difficulties of creating a new working physics of the internal structure of the atom. Bohr's use of the correspondence principle in the old quantum theory was associated with an empirical methodology that used this principle as an epistemological bridge to connect empirical phenomena with quantum models. The application of the correspondence principle required that one determine the validity of the idealizations and approximations necessary for the judicious use of classical physics within quantum theory. Bohr's interpretation of the new quantum mechanics then focused on the largely unexamined ways in which the developing abstract mathematical formalism is given empirical content by precisely this process of approximation. Significant consistency between his later interpretive framework and his forms of argument with the correspondence principle indicate that complementarity is best understood as a relationship among the various approximations and idealizations that must be made when one connects otherwise meaningless quantum mechanical symbols to empirical situations or 'experimental arrangements' described using concepts from classical physics. We discover that this relationship is unavoidable not through any sort of a priori analysis of the priority of classical concepts, but because quantum mechanics incorporates the correspondence approach in the way in which it represents quantum properties with matrices of transition probabilities, the

  6. Review of the inverse scattering problem at fixed energy in quantum mechanics

    NASA Technical Reports Server (NTRS)

    Sabatier, P. C.

    1972-01-01

    Methods of solution of the inverse scattering problem at fixed energy in quantum mechanics are presented. Scattering experiments of a beam of particles at a nonrelativisitic energy by a target made up of particles are analyzed. The Schroedinger equation is used to develop the quantum mechanical description of the system and one of several functions depending on the relative distance of the particles. The inverse problem is the construction of the potentials from experimental measurements.

  7. Elementary Quantum Mechanics in a High-Energy Process

    ERIC Educational Resources Information Center

    Denville, A.; And Others

    1978-01-01

    Compares two approaches to strong absorption in elementary quantum mechanics; the black sphere and a model based on the continuum theory of nuclear reactions. Examines the application to proton-antiproton interactions at low momenta and concludes that the second model is the appropriate and simplest to use. (Author/GA)

  8. Modal Interpretation of Quantum Mechanics and Classical Physical Theories

    NASA Astrophysics Data System (ADS)

    Ingarden, R. S.

    In 1990, Bas C. van Fraassen defined the modal interpretation of quantum mechanics as the consideration of it as ``a pure theory of the possible, with testable, empirical implications for what actually happens". This is a narrow, traditional understanding of modality, only in the sense of the concept of possibility (usually denoted in logic by the C. I. Lewis's symbol 3) and the concept of necessity 2 defined by means of 3. In modern logic, however, modality is understood in a much wider sense as any intensional functor (i.e. non-extensional or determined not only by the truth value of a sentence). In the recent (independent of van Fraassen) publications of the author (1997), an attempt was made to apply this wider understanding of modality to interpretation of classical and quantum physics. In the present lecture, these problems are discussed on the background of a brief review of the logical approch to quantum mechanics in the recent 7 decades. In this discussion, the new concepts of sub-modality and super-modality of many orders are used.

  9. Molecular deformation mechanisms of the wood cell wall material.

    PubMed

    Jin, Kai; Qin, Zhao; Buehler, Markus J

    2015-02-01

    Wood is a biological material with outstanding mechanical properties resulting from its hierarchical structure across different scales. Although earlier work has shown that the cellular structure of wood is a key factor that renders it excellent mechanical properties at light weight, the mechanical properties of the wood cell wall material itself still needs to be understood comprehensively. The wood cell wall material features a fiber reinforced composite structure, where cellulose fibrils act as stiff fibers, and hemicellulose and lignin molecules act as soft matrix. The angle between the fiber direction and the loading direction has been found to be the key factor controlling the mechanical properties. However, how the interactions between theses constitutive molecules contribute to the overall properties is still unclear, although the shearing between fibers has been proposed as a primary deformation mechanism. Here we report a molecular model of the wood cell wall material with atomistic resolution, used to assess the mechanical behavior under shear loading in order to understand the deformation mechanisms at the molecular level. The model includes an explicit description of cellulose crystals, hemicellulose, as well as lignin molecules arranged in a layered nanocomposite. The results obtained using this model show that the wood cell wall material under shear loading deforms in an elastic and then plastic manner. The plastic regime can be divided into two parts according to the different deformation mechanisms: yielding of the matrix and sliding of matrix along the cellulose surface. Our molecular dynamics study provides insights of the mechanical behavior of wood cell wall material at the molecular level, and paves a way for the multi-scale understanding of the mechanical properties of wood. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Molecular mechanics of tropocollagen-hydroxyapatite biomaterials

    NASA Astrophysics Data System (ADS)

    Dubey, Devendra Kumar

    Hard biomaterials such as bone, dentin, and nacre show remarkable mechanical performance and serve as inspiration for development of next generation of composite materials with high strength and toughness. Such materials have primarily an organic phase (e.g. tropocollagen (TC) or chitin) and a mineral phase (e.g. hydroxyapatite (HAP) or aragonite) arranged in a staggered arrangement at nanoscopic length scales. Interfacial interactions between the organic phases and the mineral phases and structural effects arising due to the staggered and hierarchical arrangements are identified to be the two most important determinants for high mechanical performance of such biomaterials. Effects of these determinants in such biomaterials are further intertwined with factors such as loading configuration, chemical environment, mineral crystal shape, and residue sequences in polymer chains. Atomistic modeling is a desired approach to investigate such sub nanoscale issues as experimental techniques for investigations at such small scale are still in nascent stage. For this purpose, explicit three dimensional (3D) molecular dynamics (MD) and ab initio MD simulations of quasi-static mechanical deformations of idealized Tropocollagen-Hydroxyapatite (TC-HAP) biomaterials with distinct interfacial arrangements and different loading configurations are performed. Focus is on developing insights into the molecular level mechanics of TC-HAP biomaterials at fundamental lengthscale with emphasis on interface phenomenon. Idealized TC-HAP atomistic models are analyzed for their mechanical strength and fracture failure behavior from the viewpoint of interfacial interactions between TC and HAP and associated molecular mechanisms. In particular, study focuses on developing an understanding of factors such as role of interfacial structural arrangement, hierarchical structure design, influence of water, effect of changes in HAP crystal shape, and mutations in TC molecule on the mechanical strength

  11. Analysis of decoherence mechanisms in a single-atom quantum memory

    NASA Astrophysics Data System (ADS)

    Koerber, Matthias; Langenfeld, Stefan; Morin, Olivier; Neuzner, Andreas; Ritter, Stephan; Rempe, Gerhard

    2017-04-01

    While photons are ideal for the transmission of quantum information, they require dedicated memories for long-term storage. The challenge for such a photonic quantum memory is the combination of an efficient light-matter interface with a low-decoherence encoding. To increase the time before the quantum information is lost, a thorough analysis of the relevant decoherence mechanisms is indispensable. Our optical quantum memory consists of a single rubidium atom trapped in a two dimensional optical lattice in a high-finesse Fabry-Perot-type optical resonator. The qubit is initially stored in a superposition of Zeeman states, making magnetic field fluctuations the dominant source of decoherence. The impact to this type of noise is greatly reduced by transferring the qubit into a subspace less susceptible to magnetic field fluctuations. In this configuration, the achievable coherence times are no longer limited by those fluctuations, but decoherence mechanisms induced by the trapping beams pose a new limit. We will discuss the origin and magnitude of the relevant effects and strategies for possible resolutions.

  12. Investigating and improving student understanding of quantum mechanics in the context of single photon interference

    NASA Astrophysics Data System (ADS)

    Marshman, Emily; Singh, Chandralekha

    2017-06-01

    Single photon experiments involving a Mach-Zehnder interferometer can illustrate the fundamental principles of quantum mechanics, e.g., the wave-particle duality of a single photon, single photon interference, and the probabilistic nature of quantum measurement involving single photons. These experiments explicitly make the connection between the abstract quantum theory and concrete laboratory settings and have the potential to help students develop a solid grasp of the foundational issues in quantum mechanics. Here we describe students' conceptual difficulties with these topics in the context of Mach-Zehnder interferometer experiments with single photons and how the difficulties found in written surveys and individual interviews were used as a guide in the development of a Quantum Interactive Learning Tutorial (QuILT). The QuILT uses an inquiry-based approach to learning and takes into account the conceptual difficulties found via research to help upper-level undergraduate and graduate students learn about foundational quantum mechanics concepts using the concrete quantum optics context. It strives to help students learn the basics of quantum mechanics in the context of single photon experiment, develop the ability to apply fundamental quantum principles to experimental situations in quantum optics, and explore the differences between classical and quantum ideas in a concrete context. We discuss the findings from in-class evaluations suggesting that the QuILT was effective in helping students learn these abstract concepts.

  13. The geometric semantics of algebraic quantum mechanics.

    PubMed

    Cruz Morales, John Alexander; Zilber, Boris

    2015-08-06

    In this paper, we will present an ongoing project that aims to use model theory as a suitable mathematical setting for studying the formalism of quantum mechanics. We argue that this approach provides a geometric semantics for such a formalism by means of establishing a (non-commutative) duality between certain algebraic and geometric objects. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  14. Advance of Mechanically Controllable Break Junction for Molecular Electronics.

    PubMed

    Wang, Lu; Wang, Ling; Zhang, Lei; Xiang, Dong

    2017-06-01

    Molecular electronics stands for the ultimate size of functional elements, keeping up with an unstoppable trend over the past few decades. As a vital component of molecular electronics, single molecular junctions have attracted significant attention from research groups all over the world. Due to its pronounced superiority, the mechanically controllable break junctions (MCBJ) technique has been widely applied to characterize the dynamic performance of single molecular junctions. This review presents a system analysis for single-molecule junctions and offers an overview of four test-beds for single-molecule junctions, thus offering more insight into the mechanisms of electron transport. We mainly focus on the development of state-of-the-art mechanically controlled break junctions. The three-terminal gated MCBJ approaches are introduced to manipulate the electron transport of molecules, and MCBJs are combined with characterization techniques. Additionally, applications of MCBJs and remarkable properties of single molecules are addressed. Finally, the challenges and perspective for the mechanically controllable break junctions technique are provided.

  15. Quantum Mechanics Concept Assessment: Development and Validation Study

    ERIC Educational Resources Information Center

    Sadaghiani, Homeyra R.; Pollock, Steven J.

    2015-01-01

    As part of an ongoing investigation of students' learning in first semester upper-division quantum mechanics, we needed a high-quality conceptual assessment instrument for comparing outcomes of different curricular approaches. The process of developing such a tool started with converting a preliminary version of a 14-item open-ended quantum…

  16. MOLECULAR MECHANISMS OF FEAR LEARNING AND MEMORY

    PubMed Central

    Johansen, Joshua P.; Cain, Christopher K.; Ostroff, Linnaea E.; LeDoux, Joseph E.

    2011-01-01

    Pavlovian fear conditioning is a useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Together, this research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals, and potentially for understanding fear related disorders, such as PTSD and phobias. PMID:22036561

  17. Molecular mechanisms of fear learning and memory.

    PubMed

    Johansen, Joshua P; Cain, Christopher K; Ostroff, Linnaea E; LeDoux, Joseph E

    2011-10-28

    Pavlovian fear conditioning is a particularly useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here, we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Collectively, this body of research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals and potentially for understanding fear-related disorders, such as PTSD and phobias. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Hybrid Quantum Mechanical and Molecular Mechanics Study of the SN2 Reaction of CCl4 + OH- in Aqueous Solution: The Potential of Mean Force, Reaction Energetics, and Rate Constants

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

    Wang, Ting; Yin, Hongyun; Wang, Dunyou

    2012-02-16

    The bimolecular nucleophilic substitution reaction of CCl{sub 4} and OH{sup -} in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculatedmore » rate constant coefficient is 8.6 x 10{sup -28} cm{sup 3} molecule{sup -1} s{sup -1} at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH{sub 3}Cl, CH{sub 2}Cl{sub 2}, CHCl{sub 3}, and CCl{sub 4}), CCl{sub 4} has the lowest free energy activation barrier for the reaction with OH{sup -1} in aqueous solution, confirming the trend that substitution of Cl by H in chloromethanes diminishes the reactivity.« less

  19. Molecular mechanics of silk nanostructures under varied mechanical loading.

    PubMed

    Bratzel, Graham; Buehler, Markus J

    2012-06-01

    Spider dragline silk is a self-assembling tunable protein composite fiber that rivals many engineering fibers in tensile strength, extensibility, and toughness, making it one of the most versatile biocompatible materials and most inviting for synthetic mimicry. While experimental studies have shown that the peptide sequence and molecular structure of silk have a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies, in particular, under variations of genetic sequences have been reported. In this study, atomistic-level structures of wildtype as well as modified MaSp1 protein from the Nephila clavipes spider dragline silk sequences, obtained using an in silico approach based on replica exchange molecular dynamics and explicit water molecular dynamics, are subjected to simulated nanomechanical testing using different force-control loading conditions including stretch, pull-out, and peel. The authors have explored the effects of the poly-alanine length of the N. clavipes MaSp1 peptide sequence and identify differences in nanomechanical loading conditions on the behavior of a unit cell of 15 strands with 840-990 total residues used to represent a cross-linking β-sheet crystal node in the network within a fibril of the dragline silk thread. The specific loading condition used, representing concepts derived from the protein network connectivity at larger scales, have a significant effect on the mechanical behavior. Our analysis incorporates stretching, pull-out, and peel testing to connect biochemical features to mechanical behavior. The method used in this study could find broad applications in de novo design of silk-like tunable materials for an array of applications. Copyright © 2011 Wiley Periodicals, Inc.

  20. Teaching the Common Aspects in Mechanical, Electromagnetic and Quantum Waves at Interfaces and Waveguides

    ERIC Educational Resources Information Center

    Rojas, R.; Robles, P.

    2011-01-01

    We discuss common features in mechanical, electromagnetic and quantum systems, supporting identical results for the transmission and reflection coefficients of waves arriving perpendicularly at a plane interface. Also, we briefly discuss the origin of special notions such as refractive index in quantum mechanics, massive photons in wave guides and…

  1. Effects of a scalar scaling field on quantum mechanics

    DOE PAGES

    Benioff, Paul

    2016-04-18

    This paper describes the effects of a complex scalar scaling field on quantum mechanics. The field origin is an extension of the gauge freedom for basis choice in gauge theories to the underlying scalar field. The extension is based on the idea that the value of a number at one space time point does not determine the value at another point. This, combined with the description of mathematical systems as structures of different types, results in the presence of separate number fields and vector spaces as structures, at different space time locations. Complex number structures and vector spaces at eachmore » location are scaled by a complex space time dependent scaling factor. The effect of this scaling factor on several physical and geometric quantities has been described in other work. Here the emphasis is on quantum mechanics of one and two particles, their states and properties. Multiparticle states are also briefly described. The effect shows as a complex, nonunitary, scalar field connection on a fiber bundle description of nonrelativistic quantum mechanics. Here, the lack of physical evidence for the presence of this field so far means that the coupling constant of this field to fermions is very small. It also means that the gradient of the field must be very small in a local region of cosmological space and time. Outside this region, there are no restrictions on the field gradient.« less

  2. Nonlinear Riccati equations as a unifying link between linear quantum mechanics and other fields of physics

    NASA Astrophysics Data System (ADS)

    Schuch, Dieter

    2014-04-01

    Theoretical physics seems to be in a kind of schizophrenic state. Many phenomena in the observable macroscopic world obey nonlinear evolution equations, whereas the microscopic world is governed by quantum mechanics, a fundamental theory that is supposedly linear. In order to combine these two worlds in a common formalism, at least one of them must sacrifice one of its dogmas. I claim that linearity in quantum mechanics is not as essential as it apparently seems since quantum mechanics can be reformulated in terms of nonlinear Riccati equations. In a first step, it will be shown where complex Riccati equations appear in time-dependent quantum mechanics and how they can be treated and compared with similar space-dependent Riccati equations in supersymmetric quantum mechanics. Furthermore, the time-independent Schrödinger equation can also be rewritten as a complex Riccati equation. Finally, it will be shown that (real and complex) Riccati equations also appear in many other fields of physics, like statistical thermodynamics and cosmology.

  3. Quantum mechanics without potential function

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

    Alhaidari, A. D., E-mail: haidari@sctp.org.sa; Ismail, M. E. H.

    2015-07-15

    In the standard formulation of quantum mechanics, one starts by proposing a potential function that models the physical system. The potential is then inserted into the Schrödinger equation, which is solved for the wavefunction, bound states energy spectrum, and/or scattering phase shift. In this work, however, we propose an alternative formulation in which the potential function does not appear. The aim is to obtain a set of analytically realizable systems, which is larger than in the standard formulation and may or may not be associated with any given or previously known potential functions. We start with the wavefunction, which ismore » written as a bounded infinite sum of elements of a complete basis with polynomial coefficients that are orthogonal on an appropriate domain in the energy space. Using the asymptotic properties of these polynomials, we obtain the scattering phase shift, bound states, and resonances. This formulation enables one to handle not only the well-known quantum systems but also previously untreated ones. Illustrative examples are given for two- and three-parameter systems.« less

  4. Using Quantum Mechanics to Facilitate the Introduction of a Broad Range of Chemical Concepts to First-Year Undergraduate Students

    ERIC Educational Resources Information Center

    deSouza, Romualdo T.; Iyengar, Srinivasan S.

    2013-01-01

    A first-year undergraduate course that introduces students to chemistry through a conceptually detailed description of quantum mechanics is outlined. Quantization as arising from the confinement of a particle is presented and these ideas are used to introduce the reasons behind resonance, molecular orbital theory, degeneracy of electronic states,…

  5. Do we really understand quantum mechanics? Strange correlations, paradoxes, and theorems

    NASA Astrophysics Data System (ADS)

    Laloë, F.

    2001-06-01

    This article presents a general discussion of several aspects of our present understanding of quantum mechanics. The emphasis is put on the very special correlations that this theory makes possible: They are forbidden by very general arguments based on realism and local causality. In fact, these correlations are completely impossible in any circumstance, except for very special situations designed by physicists especially to observe these purely quantum effects. Another general point that is emphasized is the necessity for the theory to predict the emergence of a single result in a single realization of an experiment. For this purpose, orthodox quantum mechanics introduces a special postulate: the reduction of the state vector, which comes in addition to the Schrödinger evolution postulate. Nevertheless, the presence in parallel of two evolution processes of the same object (the state vector) may be a potential source for conflicts; various attitudes that are possible to avoid this problem are discussed in this text. After a brief historical introduction, recalling how the very special status of the state vector has emerged in quantum mechanics, various conceptual difficulties are introduced and discussed. The Einstein-Podolsky-Rosen (EPR) theorem is presented with the help of a botanical parable, in a way that emphasizes how deeply the EPR reasoning is rooted into what is often called "scientific method." In another section the Greenberger-Horne-Zeilinger argument, the Hardy impossibilities, as well as the Bell-Kochen-Specker theorem are introduced in simple terms. The final two sections attempt to give a summary of the present situation: One section discusses nonlocality and entanglement as we see it presently, with brief mention of recent experiments; the last section contains a (nonexhaustive) list of various attitudes that are found among physicists, and that are helpful to alleviate the conceptual difficulties of quantum mechanics.

  6. Double-slit experiment with single wave-driven particles and its relation to quantum mechanics.

    PubMed

    Andersen, Anders; Madsen, Jacob; Reichelt, Christian; Rosenlund Ahl, Sonja; Lautrup, Benny; Ellegaard, Clive; Levinsen, Mogens T; Bohr, Tomas

    2015-07-01

    In a thought-provoking paper, Couder and Fort [Phys. Rev. Lett. 97, 154101 (2006)] describe a version of the famous double-slit experiment performed with droplets bouncing on a vertically vibrated fluid surface. In the experiment, an interference pattern in the single-particle statistics is found even though it is possible to determine unambiguously which slit the walking droplet passes. Here we argue, however, that the single-particle statistics in such an experiment will be fundamentally different from the single-particle statistics of quantum mechanics. Quantum mechanical interference takes place between different classical paths with precise amplitude and phase relations. In the double-slit experiment with walking droplets, these relations are lost since one of the paths is singled out by the droplet. To support our conclusions, we have carried out our own double-slit experiment, and our results, in particular the long and variable slit passage times of the droplets, cast strong doubt on the feasibility of the interference claimed by Couder and Fort. To understand theoretically the limitations of wave-driven particle systems as analogs to quantum mechanics, we introduce a Schrödinger equation with a source term originating from a localized particle that generates a wave while being simultaneously guided by it. We show that the ensuing particle-wave dynamics can capture some characteristics of quantum mechanics such as orbital quantization. However, the particle-wave dynamics can not reproduce quantum mechanics in general, and we show that the single-particle statistics for our model in a double-slit experiment with an additional splitter plate differs qualitatively from that of quantum mechanics.

  7. Phase operator problem and macroscopic extension of quantum mechanics

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

    Ozawa, M.

    1997-06-01

    To find the Hermitian phase operator of a single-mode electromagnetic field in quantum mechanics, the Schr{umlt o}dinger representation is extended to a larger Hilbert space augmented by states with infinite excitation by nonstandard analysis. The Hermitian phase operator is shown to exist on the extended Hilbert space. This operator is naturally considered as the controversial limit of the approximate phase operators on finite dimensional spaces proposed by Pegg and Barnett. The spectral measure of this operator is a Naimark extension of the optimal probability operator-valued measure for the phase parameter found by Helstrom. Eventually, the two promising approaches to themore » statistics of the phase in quantum mechanics are synthesized by means of the Hermitian phase operator in the macroscopic extension of the Schr{umlt o}dinger representation. {copyright} 1997 Academic Press, Inc.« less

  8. Some thoughts about consciousness: from a quantum mechanics perspective.

    PubMed

    Gargiulo, Gerald J

    2013-08-01

    The article explores some of the basic findings of quantum physics and information theory and their possible usefulness in offering new vistas for understanding psychoanalysis and the patient-analyst interchange. Technical terms are explained and placed in context, and examples of applying quantum models to clinical experience are offered. Given the complexity of the findings of quantum mechanics and information theory, the article aims only to introduce some of the major concepts from these disciplines. Within this framework the article also briefly addresses the question of mind as well as the problematic of reducing the experience of consciousness to neurological brain functioning.

  9. Numerical simulations in stochastic mechanics

    NASA Astrophysics Data System (ADS)

    McClendon, Marvin; Rabitz, Herschel

    1988-05-01

    The stochastic differential equation of Nelson's stochastic mechanics is integrated numerically for several simple quantum systems. The calculations are performed with use of Helfand and Greenside's method and pseudorandom numbers. The resulting trajectories are analyzed both individually and collectively to yield insight into momentum, uncertainty principles, interference, tunneling, quantum chaos, and common models of diatomic molecules from the stochastic quantization point of view. In addition to confirming Shucker's momentum theorem, these simulations illustrate, within the context of stochastic mechanics, the position-momentum and time-energy uncertainty relations, the two-slit diffraction pattern, exponential decay of an unstable system, and the greater degree of anticorrelation in a valence-bond model as compared with a molecular-orbital model of H2. The attempt to find exponential divergence of initially nearby trajectories, potentially useful as a criterion for quantum chaos, in a periodically forced oscillator is inconclusive. A way of computing excited energies from the ground-state motion is presented. In all of these studies the use of particle trajectories allows a more insightful interpretation of physical phenomena than is possible within traditional wave mechanics.

  10. From First Principles: The Application of Quantum Mechanics to Complex Molecules and Solvated Systems

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

    Freitag, Mark A.

    2001-12-31

    The major title of this dissertation, 'From first principles,' is a phase often heard in the study of thermodynamics and quantum mechanics. These words embody a powerful idea in the physical sciences; namely, that it is possible to distill the complexities of nature into a set of simple, well defined mathematical laws from which specific relations can then be derived . In thermodynamics, these fundamental laws are immediately familiar to the physical scientist by their numerical order: the First, Second and Third Laws. However, the subject of the present volume is quantum mechanics-specifically, non-relativistic quantum mechanics, which is appropriate formore » most systems of chemical interest.« less

  11. Atomistic mechanisms of rapid energy transport in light-harvesting molecules

    NASA Astrophysics Data System (ADS)

    Ohmura, Satoshi; Koga, Shiro; Akai, Ichiro; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2011-03-01

    Synthetic supermolecules such as π-conjugated light-harvesting dendrimers efficiently harvest energy from sunlight, which is of significant importance for the global energy problem. Key to their success is rapid transport of electronic excitation energy from peripheral antennas to photochemical reaction cores, the atomistic mechanisms of which remains elusive. Here, quantum-mechanical molecular dynamics simulation incorporating nonadiabatic electronic transitions reveals the key molecular motion that significantly accelerates the energy transport based on the Dexter mechanism.

  12. A Non-Intuitionist's Approach To The Interpretation Problem Of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Grelland, Hans Herlof

    2005-02-01

    A philosophy of physics called "linguistic empiricism" is presented and applied to the interpretation problem of quantum mechanics. This philosophical position is based on the works of Jacques Derrida. The main propositions are (i) that meaning, included the meaning attached to observations, are language-dependent and (ii) that mathematics in physics should be considered as a proper language, not necessary translatable to a more basic language of intuition and immediate experience. This has fundamental implications for quantum mechanics, which is a mathematically coherent and consistent theory; its interpretation problem is associated with its lack of physical images expressible in ordinary language.

  13. Molecular Mechanisms of Right Ventricular Failure

    PubMed Central

    Reddy, Sushma; Bernstein, Daniel

    2015-01-01

    An abundance of data has provided insight into the mechanisms underlying the development of left ventricular (LV) hypertrophy and its progression to LV failure. In contrast, there is minimal data on the adaptation of the right ventricle (RV) to pressure and volume overload and the transition to RV failure. This is a critical clinical question, as the RV is uniquely at risk in many patients with repaired or palliated congenital heart disease and in those with pulmonary hypertension. Standard heart failure therapies have failed to improve function or survival in these patients, suggesting a divergence in the molecular mechanisms of RV vs. LV failure. Although, on the cellular level, the remodeling responses of the RV and LV to pressure overload are largely similar, there are several key differences: the stressed RV is more susceptible to oxidative stress, has a reduced angiogenic response, and is more likely to activate cell death pathways than the stressed LV. Together, these differences could explain the more rapid progression of the RV to failure vs. the LV. This review will highlight known molecular differences between the RV and LV responses to hemodynamic stress, the unique stressors on the RV associated with congenital heart disease, and the need to better understand these molecular mechanisms if we are to develop RV-specific heart failure therapeutics. PMID:26527692

  14. Improving Student Understanding of Addition of Angular Momentum in Quantum Mechanics

    ERIC Educational Resources Information Center

    Zhu, Guangtian; Singh, Chandralekha

    2013-01-01

    We describe the difficulties advanced undergraduate and graduate students have with concepts related to addition of angular momentum in quantum mechanics. We also describe the development and implementation of a research-based learning tool, Quantum Interactive Learning Tutorial (QuILT), to reduce these difficulties. The preliminary evaluation…

  15. Quantum mechanical modeling the emission pattern and polarization of nanoscale light emitting diodes.

    PubMed

    Wang, Rulin; Zhang, Yu; Bi, Fuzhen; Frauenheim, Thomas; Chen, GuanHua; Yam, ChiYung

    2016-07-21

    Understanding of the electroluminescence (EL) mechanism in optoelectronic devices is imperative for further optimization of their efficiency and effectiveness. Here, a quantum mechanical approach is formulated for modeling the EL processes in nanoscale light emitting diodes (LED). Based on non-equilibrium Green's function quantum transport equations, interactions with the electromagnetic vacuum environment are included to describe electrically driven light emission in the devices. The presented framework is illustrated by numerical simulations of a silicon nanowire LED device. EL spectra of the nanowire device under different bias voltages are obtained and, more importantly, the radiation pattern and polarization of optical emission can be determined using the current approach. This work is an important step forward towards atomistic quantum mechanical modeling of the electrically induced optical response in nanoscale systems.

  16. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations.

    PubMed

    Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad

    2015-02-15

    The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported. © 2014 Wiley Periodicals, Inc.

  17. Quantum interactive learning tutorial on the double-slit experiment to improve student understanding of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Sayer, Ryan; Maries, Alexandru; Singh, Chandralekha

    2017-06-01

    Learning quantum mechanics is challenging, even for upper-level undergraduate and graduate students. Research-validated interactive tutorials that build on students' prior knowledge can be useful tools to enhance student learning. We have been investigating student difficulties with quantum mechanics pertaining to the double-slit experiment in various situations that appear to be counterintuitive and contradict classical notions of particles and waves. For example, if we send single electrons through the slits, they may behave as a "wave" in part of the experiment and as a "particle" in another part of the same experiment. Here we discuss the development and evaluation of a research-validated Quantum Interactive Learning Tutorial (QuILT) which makes use of an interactive simulation to improve student understanding of the double-slit experiment and strives to help students develop a good grasp of foundational issues in quantum mechanics. We discuss common student difficulties identified during the development and evaluation of the QuILT and analyze the data from the pretest and post test administered to the upper-level undergraduate and first-year physics graduate students before and after they worked on the QuILT to assess its effectiveness. These data suggest that on average, the QuILT was effective in helping students develop a more robust understanding of foundational concepts in quantum mechanics that defy classical intuition using the context of the double-slit experiment. Moreover, upper-level undergraduates outperformed physics graduate students on the post test. One possible reason for this difference in performance may be the level of student engagement with the QuILT due to the grade incentive. In the undergraduate course, the post test was graded for correctness while in the graduate course, it was only graded for completeness.

  18. Catalytic mechanism of phenylacetone monooxygenases for non-native linear substrates.

    PubMed

    Carvalho, Alexandra T P; Dourado, Daniel F A R; Skvortsov, Timofey; de Abreu, Miguel; Ferguson, Lyndsey J; Quinn, Derek J; Moody, Thomas S; Huang, Meilan

    2017-10-11

    Phenylacetone monooxygenase (PAMO) is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenase family, and therefore it is an ideal candidate for the synthesis of industrially relevant compounds. However, its limited substrate scope has largely limited its industrial applications. In the present work, we provide, for the first time, the catalytic mechanism of PAMO for the native substrate phenylacetone as well as for a linear non-native substrate 2-octanone, using molecular dynamics simulations, quantum mechanics and quantum mechanics/molecular mechanics calculations. We provide a theoretical basis for the preference of the enzyme for the native aromatic substrate over non-native linear substrates. Our study provides fundamental atomic-level insights that can be employed in the rational engineering of PAMO for wide applications in industrial biocatalysis, in particular, in the biotransformation of long-chain aliphatic oils into potential biodiesels.

  19. Exploring the molecular mechanism of karrikins and strigolactones.

    PubMed

    Scaffidi, Adrian; Waters, Mark T; Bond, Charles S; Dixon, Kingsley W; Smith, Steven M; Ghisalberti, Emilio L; Flematti, Gavin R

    2012-06-01

    Karrikins and strigolactones are novel plant growth regulators that contain similar molecular features, but very little is known about how they elicit responses in plants. A tentative molecular mechanism has previously been proposed involving a Michael-type addition for both compounds. Through structure-activity studies with karrikins, we now propose an alternative mechanism for karrikin and strigolactone mode of action that involves hydrolysis of the butenolide ring. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  20. A full quantum analysis of the Stern-Gerlach experiment using the evolution operator method: analyzing current issues in teaching quantum mechanics

    NASA Astrophysics Data System (ADS)

    Benítez Rodríguez, E.; Arévalo Aguilar, L. M.; Piceno Martínez, E.

    2017-03-01

    To the quantum mechanics specialists community it is a well-known fact that the famous original Stern-Gerlach experiment (SGE) produces entanglement between the external degrees of freedom (position) and the internal degree of freedom (spin) of silver atoms. Despite this fact, almost all textbooks on quantum mechanics explain this experiment using a semiclassical approach, where the external degrees of freedom are considered classical variables, the internal degree is treated as a quantum variable, and Newton's second law is used to describe the dynamics. In the literature there are some works that analyze this experiment in its full quantum mechanical form. However, astonishingly, to the best of our knowledge the original experiment, where the initial states of the spin degree of freedom are randomly oriented coming from the oven, has not been analyzed yet in the available textbooks using the Schrödinger equation (to the best of our knowledge there is only one paper that treats this case: Hsu et al (2011 Phys. Rev. A 83 012109)). Therefore, in this contribution we use the time-evolution operator to give a full quantum mechanics analysis of the SGE when the initial state of the internal degree of freedom is completely random, i.e. when it is a statistical mixture. Additionally, as the SGE and the development of quantum mechanics are heavily intermingled, we analyze some features and drawbacks in the current teaching of quantum mechanics. We focus on textbooks that use the SGE as a starting point, based on the fact that most physicist do not use results from physics education research, and comment on traditional pedagogical attitudes in the physics community.

  1. The History of Teaching Quantum Mechanics in Greece

    ERIC Educational Resources Information Center

    Tampakis, Constantin; Skordoulis, Constantin

    2007-01-01

    In this work, our goal is to examine the attitude of the Greek scientific community towards Quantum Mechanics and establish the history of teaching of this theory in Greece. We have examined Physics textbooks written by professors of the University of Athens, as well as records of public speeches, university yearbooks from 1923 to 1970, articles…

  2. Molecular mechanisms for protein-encoded inheritance

    PubMed Central

    Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

    2013-01-01

    Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

  3. Molecular Mechanisms of Root Gravitropism.

    PubMed

    Su, Shih-Heng; Gibbs, Nicole M; Jancewicz, Amy L; Masson, Patrick H

    2017-09-11

    Plant shoots typically grow against the gravity vector to access light, whereas roots grow downward into the soil to take up water and nutrients. These gravitropic responses can be altered by developmental and environmental cues. In this review, we discuss the molecular mechanisms that govern the gravitropism of angiosperm roots, where a physical separation between sites for gravity sensing and curvature response has facilitated discovery. Gravity sensing takes place in the columella cells of the root cap, where sedimentation of starch-filled plastids (amyloplasts) triggers a pathway that results in a relocalization to the lower side of the cell of PIN proteins, which facilitate efflux of the plant hormone auxin efflux. Consequently, auxin accumulates in the lower half of the root, triggering bending of the root tip at the elongation zone. We review our understanding of the molecular mechanisms that control this process in primary roots, and discuss recent insights into the regulation of oblique growth in lateral roots and its impact on root-system architecture and soil exploration. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Constituent quark masses in Poincaré-invariant quantum mechanics

    NASA Astrophysics Data System (ADS)

    Andreev, Viktor; Haurysh, Vadzim

    2017-12-01

    The masses of the quarks in the Poincaré-invariant quantum mechanics are the constituent masses. Even in this framework it is possible to obtain an estimate of the constituent quark masses from the Ward identity for the axial current ant the current quark masses.

  5. Quantum-mechanical analysis of low-gain free-electron laser oscillators

    NASA Astrophysics Data System (ADS)

    Fares, H.; Yamada, M.; Chiadroni, E.; Ferrario, M.

    2018-05-01

    In the previous classical theory of the low-gain free-electron laser (FEL) oscillators, the electron is described as a point-like particle, a delta function in the spatial space. On the other hand, in the previous quantum treatments, the electron is described as a plane wave with a single momentum state, a delta function in the momentum space. In reality, an electron must have statistical uncertainties in the position and momentum domains. Then, the electron is neither a point-like charge nor a plane wave of a single momentum. In this paper, we rephrase the theory of the low-gain FEL where the interacting electron is represented quantum mechanically by a plane wave with a finite spreading length (i.e., a wave packet). Using the concepts of the transformation of reference frames and the statistical quantum mechanics, an expression for the single-pass radiation gain is derived. The spectral broadening of the radiation is expressed in terms of the spreading length of an electron, the relaxation time characterizing the energy spread of electrons, and the interaction time. We introduce a comparison between our results and those obtained in the already known classical analyses where a good agreement between both results is shown. While the correspondence between our results and the classical results are shown, novel insights into the electron dynamics and the interaction mechanism are presented.

  6. Quantum effects of Aharonov-Bohm type and noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Rodriguez R., Miguel E.

    2018-01-01

    Quantum mechanics in noncommutative space modifies the standard result of the Aharonov-Bohm effect for electrons and other recent quantum effects. Here we obtain the phase in noncommutative space for the Spavieri effect, a generalization of Aharonov-Bohm effect which involves a coherent superposition of particles with opposite charges moving along a single open interferometric path. By means of the experimental considerations a limit √{θ }≃(0.13TeV)-1 is achieved, improving by 10 orders of magnitude the results derived by Chaichian et al. [Phys. Lett. B 527, 149 (2002), 10.1016/S0370-2693(02)01176-0] for the Aharonov-Bohm effect. It is also shown that the noncommutative phases of the Aharonov-Casher and He-McKellar-Willkens effects are nullified in the current experimental tests.

  7. Molecular mechanisms of fluoride toxicity.

    PubMed

    Barbier, Olivier; Arreola-Mendoza, Laura; Del Razo, Luz María

    2010-11-05

    Halfway through the twentieth century, fluoride piqued the interest of toxicologists due to its deleterious effects at high concentrations in human populations suffering from fluorosis and in in vivo experimental models. Until the 1990s, the toxicity of fluoride was largely ignored due to its "good reputation" for preventing caries via topical application and in dental toothpastes. However, in the last decade, interest in its undesirable effects has resurfaced due to the awareness that this element interacts with cellular systems even at low doses. In recent years, several investigations demonstrated that fluoride can induce oxidative stress and modulate intracellular redox homeostasis, lipid peroxidation and protein carbonyl content, as well as alter gene expression and cause apoptosis. Genes modulated by fluoride include those related to the stress response, metabolic enzymes, the cell cycle, cell-cell communications and signal transduction. The primary purpose of this review is to examine recent findings from our group and others that focus on the molecular mechanisms of the action of inorganic fluoride in several cellular processes with respect to potential physiological and toxicological implications. This review presents an overview of the current research on the molecular aspects of fluoride exposure with emphasis on biological targets and their possible mechanisms of involvement in fluoride cytotoxicity. The goal of this review is to enhance understanding of the mechanisms by which fluoride affects cells, with an emphasis on tissue-specific events in humans. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  8. Molecular mechanisms of optic axon guidance

    NASA Astrophysics Data System (ADS)

    Inatani, Masaru

    2005-12-01

    Axon guidance is one of the critical processes during vertebrate central nervous system (CNS) development. The optic nerve, which contains the axons of retinal ganglion cells, has been used as a powerful model to elucidate some of the mechanisms underlying axon guidance because it is easily manipulated experimentally, and its function is well understood. Recent molecular biology studies have revealed that numerous guidance molecules control the development of the visual pathway. This review introduces the molecular mechanisms involved in each critical step during optic axon guidance. Axonal projections to the optic disc are thought to depend on adhesion molecules and inhibitory extracellular matrices such as chondroitin sulfate. The formation of the head of the optic nerve and the optic chiasm require ligand-receptor interactions between netrin-1 and the deleted in colorectal cancer receptor, and Slit proteins and Robo receptors, respectively. The gradient distributions of ephrin ligands and Eph receptors are essential for correct ipsilateral projections at the optic chiasm and the topographic mapping of axons in the superior colliculus/optic tectum. The precise gradient is regulated by transcription factors determining the retinal dorso-ventral and nasal-temporal polarities. Moreover, the axon guidance activities by Slit and semaphorin 5A require the existence of heparan sulfate, which binds to numerous guidance molecules. Recent discoveries about the molecular mechanisms underlying optic nerve guidance will facilitate progress in CNS developmental biology and axon-regeneration therapy.

  9. Quantum mechanics from Newton's second law and the canonical commutation relation [X, P] = i

    NASA Astrophysics Data System (ADS)

    Palenik, Mark C.

    2014-07-01

    Despite the fact that it has been known since the time of Heisenberg that quantum operators obey a quantum version of Newton's laws, students are often told that derivations of quantum mechanics must necessarily follow from the Hamiltonian or Lagrangian formulations of mechanics. Here, we first derive the existing Heisenberg equations of motion from Newton's laws and the uncertainty principle using only the equations F=\\frac{dP}{dt}, P=m\\frac{dV}{dt}, and [X, P] = i. Then, a new expression for the propagator is derived that makes a connection between time evolution in quantum mechanics and the motion of a classical particle under Newton's laws. The propagator is solved for three cases where an exact solution is possible: (1) the free particle; (2) the harmonic oscillator; and (3) a constant force, or linear potential in the standard interpretation. We then show that for a general for a general force F(X), by Taylor expanding X(t) in time, we can use this methodology to reproduce the Feynman path integral formula for the propagator. Such a picture may be useful for students as they make the transition from classical to quantum mechanics and help solidify the equivalence of the Hamiltonian, Lagrangian, and Newtonian pictures of physics in their minds.

  10. Preparation and coherent manipulation of pure quantum states of a single molecular ion

    NASA Astrophysics Data System (ADS)

    Chou, Chin-Wen; Kurz, Christoph; Hume, David B.; Plessow, Philipp N.; Leibrandt, David R.; Leibfried, Dietrich

    2017-05-01

    Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH+) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

  11. Preparation and coherent manipulation of pure quantum states of a single molecular ion.

    PubMed

    Chou, Chin-Wen; Kurz, Christoph; Hume, David B; Plessow, Philipp N; Leibrandt, David R; Leibfried, Dietrich

    2017-05-10

    Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH + ) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

  12. Spin and Uncertainty in the Interpretation of Quantum Mechanics.

    ERIC Educational Resources Information Center

    Hestenes, David

    1979-01-01

    Points out that quantum mechanics interpretations, using Heisenberg's Uncertainty Relations for the position and momentum of an electron, have their drawbacks. The interpretations are limited to the Schrodinger theory and fail to take into account either spin or relativity. Shows why spin cannot be ignored. (Author/GA)

  13. [Molecular mechanisms of neurotransmission].

    PubMed

    Nagatsu, T

    2000-12-01

    Neurotransmission is regulated by neurotransmitters at the synapses in the neuronal circuits. Main neurotransmitters are classified into the groups of amino acids, amines, purines, peptides, and nitric oxide. In principle, neurotransmitters except peptides are synthesized in the presynaptic neuroterminals from the precursors by the synthesizing enzymes, stored in the synaptic vesicles, released by exocytosis into the synaptic cleft, combined with the postsynaptic membrane receptors, and induce a series of signal transduction to produce acute, short-term, or long-term physiological effects. Termination of the neurotransmission is carried out either by re-uptake into presynaptic nerve terminals through plasma membrane transporters and storage into synaptic vesicles through vesicular transporters or by degradation through metabolizing enzymes (acetylcholine and peptides). Almost all genes related to neurotransmitters have been cloned and the structures of the genes and the protein products have been characterized. Molecular mechanisms of neurotransmission have been elucidated by mouse molecular genetics such as transgenic or knockout mice. Over-expression of human tyrosine hydroxylase (TH). the rate-limiting enzyme of catecholamine synthesis, in transgenic mice (Kaneda et al, Neuron 6, 583-584, 1991) or conversion of norepinephrine neurons to epinephrine neurons (Kobayashi et al, Proc Natl Acad Sci USA 89, 1631-1635, 1992) does not significantly change the phenotype due to compensatory mechanisms such as receptor down-regulation. In contrast, TH (-/-) mutant mice die at perinatal period due to heart failure caused by norepinephrine deficiency in the sympathetic neurons (Kobayashi et al, J Biol Chem 270, 27235-27243, 1995). TH (+/-) mice show a partial decrease in norepinephrine and a modest memory impairment (Kobayashi et al, J Neurosci 20, 2418-2426, 2000). One problem with adult phenotype in transgenic or knockout mice is that mutations cause the confounding effect

  14. The variational method in quantum mechanics: an elementary introduction

    NASA Astrophysics Data System (ADS)

    Borghi, Riccardo

    2018-05-01

    Variational methods in quantum mechanics are customarily presented as invaluable techniques to find approximate estimates of ground state energies. In the present paper a short catalogue of different celebrated potential distributions (both 1D and 3D), for which an exact and complete (energy and wavefunction) ground state determination can be achieved in an elementary way, is illustrated. No previous knowledge of calculus of variations is required. Rather, in all presented cases the exact energy functional minimization is achieved by using only a couple of simple mathematical tricks: ‘completion of square’ and integration by parts. This makes our approach particularly suitable for undergraduates. Moreover, the key role played by particle localization is emphasized through the entire analysis. This gentle introduction to the variational method could also be potentially attractive for more expert students as a possible elementary route toward a rather advanced topic on quantum mechanics: the factorization method. Such an unexpected connection is outlined in the final part of the paper.

  15. Measurements of entanglement over a kilometric distance to test superluminal models of Quantum Mechanics: preliminary results.

    NASA Astrophysics Data System (ADS)

    Cocciaro, B.; Faetti, S.; Fronzoni, L.

    2017-08-01

    As shown in the EPR paper (Einstein, Podolsky e Rosen, 1935), Quantum Mechanics is a non-local Theory. The Bell theorem and the successive experiments ruled out the possibility of explaining quantum correlations using only local hidden variables models. Some authors suggested that quantum correlations could be due to superluminal communications that propagate isotropically with velocity vt > c in a preferred reference frame. For finite values of vt and in some special cases, Quantum Mechanics and superluminal models lead to different predictions. So far, no deviations from the predictions of Quantum Mechanics have been detected and only lower bounds for the superluminal velocities vt have been established. Here we describe a new experiment that increases the maximum detectable superluminal velocities and we give some preliminary results.

  16. Emergence and mechanism in the fractional quantum Hall effect

    NASA Astrophysics Data System (ADS)

    Bain, Jonathan

    2016-11-01

    For some authors, an adequate notion of emergence must include an account of a mechanism by means of which emergent behavior is realized. This appeal to mechanism is problematic in the case of the fractional quantum Hall effect (FQHE). There is a consensus among physicists that the FQHE exhibits emergent phenomena, but there are at least four alternative explanations of the latter that, arguably, appeal to ontologically distinct mechanisms, both at the microphysics level and at the level of general organizing principles. In light of this underdetermination of mechanism, one is faced with the following options: (I) deny that emergence is present in the FQHE; (II) argue for the priority of one mechanistic explanation over the others; or (III) temper the desire for a mechanism-centric account of emergence. I will argue that there are good reasons to reject (I) and (II) and accept (III). In particular, I will suggest that a law-centric account of emergence does just fine in explaining the emergent phenomena associated with the FQHE.

  17. Molecular mechanisms of peritoneal dissemination in gastric cancer.

    PubMed

    Kanda, Mitsuro; Kodera, Yasuhiro

    2016-08-14

    Peritoneal dissemination represents a devastating form of gastric cancer (GC) progression with a dismal prognosis. There is no effective therapy for this condition. The 5-year survival rate of patients with peritoneal dissemination is 2%, even including patients with only microscopic free cancer cells without macroscopic peritoneal nodules. The mechanism of peritoneal dissemination of GC involves several steps: detachment of cancer cells from the primary tumor, survival in the free abdominal cavity, attachment to the distant peritoneum, invasion into the subperitoneal space and proliferation with angiogenesis. These steps are not mutually exclusive, and combinations of different molecular mechanisms can occur in each process of peritoneal dissemination. A comprehensive understanding of the molecular events involved in peritoneal dissemination is important and should be systematically pursued. It is crucial to identify novel strategies for the prevention of this condition and for identification of markers of prognosis and the development of molecular-targeted therapies. In this review, we provide an overview of recently published articles addressing the molecular mechanisms of peritoneal dissemination of GC to provide an update on what is currently known in this field and to propose novel promising candidates for use in diagnosis and as therapeutic targets.

  18. Quantum mechanical treatment of large spin baths

    NASA Astrophysics Data System (ADS)

    Röhrig, Robin; Schering, Philipp; Gravert, Lars B.; Fauseweh, Benedikt; Uhrig, Götz S.

    2018-04-01

    The electronic spin in quantum dots can be described by central spin models (CSMs) with a very large number Neff≈104 to 106 of bath spins posing a tremendous challenge to theoretical simulations. Here, a fully quantum mechanical theory is developed for the limit Neff→∞ by means of iterated equations of motion (iEoM). We find that the CSM can be mapped to a four-dimensional impurity coupled to a noninteracting bosonic bath in this limit. Remarkably, even for infinite bath the CSM does not become completely classical. The data obtained by the proposed iEoM approach are tested successfully against data from other, established approaches. Thus the iEoM mapping extends the set of theoretical tools that can be used to understand the spin dynamics in large CSMs.

  19. Particle in a box in PT-symmetric quantum mechanics and an electromagnetic analog

    NASA Astrophysics Data System (ADS)

    Dasarathy, Anirudh; Isaacson, Joshua P.; Jones-Smith, Katherine; Tabachnik, Jason; Mathur, Harsh

    2013-06-01

    In PT-symmetric quantum mechanics a fundamental principle of quantum mechanics, that the Hamiltonian must be Hermitian, is replaced by another set of requirements, including notably symmetry under PT, where P denotes parity and T denotes time reversal. Here we study the role of boundary conditions in PT-symmetric quantum mechanics by constructing a simple model that is the PT-symmetric analog of a particle in a box. The model has the usual particle-in-a-box Hamiltonian but boundary conditions that respect PT symmetry rather than Hermiticity. We find that for a broad class of PT-symmetric boundary conditions the model respects the condition of unbroken PT symmetry, namely, that the Hamiltonian and the symmetry operator PT have simultaneous eigenfunctions, implying that the energy eigenvalues are real. We also find that the Hamiltonian is self-adjoint under the PT-symmetric inner product. Thus we obtain a simple soluble model that fulfills all the requirements of PT-symmetric quantum mechanics. In the second part of this paper we formulate a variational principle for PT-symmetric quantum mechanics that is the analog of the textbook Rayleigh-Ritz principle. Finally we consider electromagnetic analogs of the PT-symmetric particle in a box. We show that the isolated particle in a box may be realized as a Fabry-Perot cavity between an absorbing medium and its conjugate gain medium. Coupling the cavity to an external continuum of incoming and outgoing states turns the energy levels of the box into sharp resonances. Remarkably we find that the resonances have a Breit-Wigner line shape in transmission and a Fano line shape in reflection; by contrast, in the corresponding Hermitian case the line shapes always have a Breit-Wigner form in both transmission and reflection.

  20. Quantum mechanics in non-inertial reference frames: Time-dependent rotations and loop prolongations

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

    Klink, W.H., E-mail: william-klink@uiowa.edu; Wickramasekara, S., E-mail: wickrama@grinnell.edu; Department of Physics, Grinnell College, Grinnell, IA 50112

    2013-09-15

    This is the fourth in a series of papers on developing a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group to include transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. In previous work, we have shown that there exist representations of the Galilean line group that uphold the non-relativistic equivalence principle asmore » well as representations that violate the equivalence principle. In these previous studies, the focus was on linear accelerations. In this paper, we undertake an extension of the formulation to include rotational accelerations. We show that the incorporation of rotational accelerations requires a class of loop prolongations of the Galilean line group and their unitary cocycle representations. We recover the centrifugal and Coriolis force effects from these loop representations. Loops are more general than groups in that their multiplication law need not be associative. Hence, our broad theoretical claim is that a Galilean quantum theory that holds in arbitrary non-inertial reference frames requires going beyond groups and group representations, the well-established framework for implementing symmetry transformations in quantum mechanics. -- Highlights: •A formulation of Galilean quantum mechanics in non-inertial reference frames is presented. •The Galilei group is generalized to infinite dimensional Galilean line group. •Loop prolongations of Galilean line group contain central extensions of Galilei group. •Unitary representations of the loops are constructed. •These representations lead to terms in the Hamiltonian corresponding to fictitious forces, including centrifugal and

  1. The molecular mechanism of excitation in visual transduction and bacteriorhodopsin

    PubMed Central

    Lewis, Aaron

    1978-01-01

    An electronic theory of excitation is proposed and described in terms of a three-dimensional excited/ground-state energy surface which elucidates the photochemical and excited-state dynamics of rhodopsins. In this theory the primary action of light is to produce significant electron redistribution in the retinal, thereby generating new interactions that vibrationally excite and perturb the ground-state protein conformation. Thus, light energy causes charge redistribution in the retinal and induces transient charge-density assisted bond rearrangements (such as proton translocation) in the protein structure which is stabilized by subsequent retinal structural alteration. In this theory the isoprenoid chain of the retinal is considered a structurally pliable molecular entity that can generate charge redistributions and can be subsequently achieve intermediate conformations or various isomeric states to minimize the energy of the new protein structure generated by light. Thus, the 11-cis to all trans isomerization of the retinylidene chromophore is not considered a primary mechanism of excitation. An alternate biological role for this molecular process (which is eventually completed in all photoreceptors but not in bacterial rhodopsins) is to provide the irreversibility needed for effective quantum detection on the time scale of a neural response. Finally, it will be demonstrated that this mechanism, which readily accounts for the photophysical and photochemical data, can also be restated in terms of the Monod, Wyman, and Changeux terminology suggesting that aggregates of these pigments may function allosterically. PMID:273216

  2. Mechanisms of two-color laser-induced field-free molecular orientation.

    PubMed

    Spanner, Michael; Patchkovskii, Serguei; Frumker, Eugene; Corkum, Paul

    2012-09-14

    Two mechanisms of two-color (ω+2ω) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While the hyperpolarizability mechanism generates small amounts of orientation at intensities below the ionization threshold, ionization depletion quickly becomes the dominant mechanism as soon as ionizing intensities are reached. Only the ionization mechanism leads to substantial orientation (e.g., on the order of ≳0.1). For intensities typical of laser-induced molecular alignment and orientation experiments, the two mechanisms lead to robust, characteristic timings of the field-free orientation wave-packet revivals relative to the alignment revivals and the revival time. The revival timings can be used to detect the active orientation mechanism experimentally.

  3. Quantum epistemology from subquantum ontology: Quantum mechanics from theory of classical random fields

    NASA Astrophysics Data System (ADS)

    Khrennikov, Andrei

    2017-02-01

    The scientific methodology based on two descriptive levels, ontic (reality as it is) and epistemic (observational), is briefly presented. Following Schrödinger, we point to the possible gap between these two descriptions. Our main aim is to show that, although ontic entities may be unaccessible for observations, they can be useful for clarification of the physical nature of operational epistemic entities. We illustrate this thesis by the concrete example: starting with the concrete ontic model preceding quantum mechanics (the latter is treated as an epistemic model), namely, prequantum classical statistical field theory (PCSFT), we propose the natural physical interpretation for the basic quantum mechanical entity-the quantum state ("wave function"). The correspondence PCSFT ↦ QM is not straightforward, it couples the covariance operators of classical (prequantum) random fields with the quantum density operators. We use this correspondence to clarify the physical meaning of the pure quantum state and the superposition principle-by using the formalism of classical field correlations. In classical mechanics the phase space description can be considered as the ontic description, here states are given by points λ =(x , p) of phase space. The dynamics of the ontic state is given by the system of Hamiltonian equations.We can also consider probability distributions on the phase space (or equivalently random variables valued in it). We call them probabilistic ontic states. Dynamics of probabilistic ontic states is given by the Liouville equation.In classical physics we can (at least in principle) measure both the coordinate and momentum and hence ontic states can be treated as epistemic states as well (or it is better to say that here epistemic states can be treated as ontic states). Probabilistic ontic states represent probabilities for outcomes of joint measurement of position and momentum.However, this was

  4. Quantum mechanics of excitation transport in photosynthetic complexes: a key issues review.

    PubMed

    Levi, Federico; Mostarda, Stefano; Rao, Francesco; Mintert, Florian

    2015-07-01

    For a long time microscopic physical descriptions of biological processes have been based on quantum mechanical concepts and tools, and routinely employed by chemical physicists and quantum chemists. However, the last ten years have witnessed new developments on these studies from a different perspective, rooted in the framework of quantum information theory. The process that more, than others, has been subject of intense research is the transfer of excitation energy in photosynthetic light-harvesting complexes, a consequence of the unexpected experimental discovery of oscillating signals in such highly noisy systems. The fundamental interdisciplinary nature of this research makes it extremely fascinating, but can also constitute an obstacle to its advance. Here in this review our objective is to provide an essential summary of the progress made in the theoretical description of excitation energy dynamics in photosynthetic systems from a quantum mechanical perspective, with the goal of unifying the language employed by the different communities. This is initially realized through a stepwise presentation of the fundamental building blocks used to model excitation transfer, including protein dynamics and the theory of open quantum system. Afterwards, we shall review how these models have evolved as a consequence of experimental discoveries; this will lead us to present the numerical techniques that have been introduced to quantitatively describe photo-absorbed energy dynamics. Finally, we shall discuss which mechanisms have been proposed to explain the unusual coherent nature of excitation transport and what insights have been gathered so far on the potential functional role of such quantum features.

  5. Completeness of the Coulomb Wave Functions in Quantum Mechanics

    ERIC Educational Resources Information Center

    Mukunda, N.

    1978-01-01

    Gives an explicit and elementary proof that the radial energy eigenfunctions for the hydrogen atom in quantum mechanics, bound and scattering states included, form a complete set. The proof uses some properties of the confluent hypergeometric functions and the Cauchy residue theorem from analytic function theory. (Author/GA)

  6. Against the empirical viability of the Deutsch-Wallace-Everett approach to quantum mechanics

    NASA Astrophysics Data System (ADS)

    Dawid, Richard; Thébault, Karim P. Y.

    2014-08-01

    The subjective Everettian approach to quantum mechanics presented by Deutsch and Wallace fails to constitute an empirically viable theory of quantum phenomena. The decision theoretic implementation of the Born rule realized in this approach provides no basis for rejecting Everettian quantum mechanics in the face of empirical data that contradicts the Born rule. The approach of Greaves and Myrvold, which provides a subjective implementation of the Born rule as well but derives it from empirical data rather than decision theoretic arguments, avoids the problem faced by Deutsch and Wallace and is empirically viable. However, there is good reason to cast doubts on its scientific value.

  7. Spekkens’ toy model in all dimensions and its relationship with stabiliser quantum mechanics

    NASA Astrophysics Data System (ADS)

    Catani, Lorenzo; E Browne, Dan

    2017-07-01

    Spekkens’ toy model is a non-contextual hidden variable model with an epistemic restriction, a constraint on what an observer can know about reality. The aim of the model, developed for continuous and discrete prime degrees of freedom, is to advocate the epistemic view of quantum theory, where quantum states are states of incomplete knowledge about a deeper underlying reality. Many aspects of quantum mechanics and protocols from quantum information can be reproduced in the model. In spite of its significance, a number of aspects of Spekkens’ model remained incomplete. Formal rules for the update of states after measurement had not been written down, and the theory had only been constructed for prime-dimensional and infinite dimensional systems. In this work, we remedy this, by deriving measurement update rules and extending the framework to derive models in all dimensions, both prime and non-prime. Stabiliser quantum mechanics (SQM) is a sub-theory of quantum mechanics with restricted states, transformations and measurements. First derived for the purpose of constructing error correcting codes, it now plays a role in many areas of quantum information theory. Previously, it had been shown that Spekkens’ model was operationally equivalent to SQM in the case of odd prime dimensions. Here, exploiting known results on Wigner functions, we extend this to show that Spekkens’ model is equivalent to SQM in all odd dimensions, prime and non-prime. This equivalence provides new technical tools for the study of technically difficult compound-dimensional SQM.

  8. Quantum mechanical wavefunction: visualization at undergraduate level

    NASA Astrophysics Data System (ADS)

    Chhabra, Mahima; Das, Ritwick

    2017-01-01

    Quantum mechanics (QM) forms the most crucial ingredient of modern-era physical science curricula at undergraduate level. The abstract ideas involved in QM related concepts pose a challenge towards appropriate visualization as a consequence of their counter-intuitive nature and lack of experiment-assisted visualization tools. At the heart of the quantum mechanical formulation lies the concept of ‘wavefunction’, which forms the basis for understanding the behavior of physical systems. At undergraduate level, the concept of ‘wavefunction’ is introduced in an abstract framework using mathematical tools and therefore opens up an enormous scope for alternative conceptions and erroneous visualization. The present work is an attempt towards exploring the visualization models constructed by undergraduate students for appreciating the concept of ‘wavefunction’. We present a qualitative analysis of the data obtained from administering a questionnaire containing four visualization based questions on the topic of ‘wavefunction’ to a group of ten undergraduate-level students at an institute in India which excels in teaching and research of basic sciences. Based on the written responses, all ten students were interviewed in detail to unravel the exact areas of difficulty in visualization of ‘wavefunction’. The outcome of present study not only reveals the gray areas in students’ conceptualization, but also provides a plausible route to address the issues at the pedagogical level within the classroom.

  9. Memories of Crisis: Bohr, Kuhn, and the Quantum Mechanical ``Revolution''

    NASA Astrophysics Data System (ADS)

    Seth, Suman

    2013-04-01

    ``The history of science, to my knowledge,'' wrote Thomas Kuhn, describing the years just prior to the development of matrix and wave mechanics, ``offers no equally clear, detailed, and cogent example of the creative functions of normal science and crisis.'' By 1924, most quantum theorists shared a sense that there was much wrong with all extant atomic models. Yet not all shared equally in the sense that the failure was either terribly surprising or particularly demoralizing. Not all agreed, that is, that a crisis for Bohr-like models was a crisis for quantum theory. This paper attempts to answer four questions: two about history, two about memory. First, which sub-groups of the quantum theoretical community saw themselves and their field in a state of crisis in the early 1920s? Second, why did they do so, and how was a sense of crisis related to their theoretical practices in physics? Third, do we regard the years before 1925 as a crisis because they were followed by the quantum mechanical revolution? And fourth, to reverse the last question, were we to call into the question the existence of a crisis (for some at least) does that make a subsequent revolution less revolutionary?

  10. Physiological and molecular biochemical mechanisms of bile formation

    PubMed Central

    Reshetnyak, Vasiliy Ivanovich

    2013-01-01

    This review considers the physiological and molecular biochemical mechanisms of bile formation. The composition of bile and structure of a bile canaliculus, biosynthesis and conjugation of bile acids, bile phospholipids, formation of bile micellar structures, and enterohepatic circulation of bile acids are described. In general, the review focuses on the molecular physiology of the transporting systems of the hepatocyte sinusoidal and apical membranes. Knowledge of physiological and biochemical basis of bile formation has implications for understanding the mechanisms of development of pathological processes, associated with diseases of the liver and biliary tract. PMID:24259965

  11. General Anesthetics and Molecular Mechanisms of Unconsciousness

    PubMed Central

    Forman, Stuart A.; Chin, Victor A.

    2013-01-01

    General anesthetic agents are unique in clinical medicine, because they are the only drugs used to produce unconsciousness as a therapeutic goal. In contrast to older hypotheses that assumed all general anesthetics produce their central nervous system effects through a common mechanism, we outline evidence that general anesthesia represents a number of distinct pharmacological effects that are likely mediated by different neural circuits, and perhaps via different molecular targets. Within the context of this neurobiological framework, we review recent molecular pharmacological and transgenic animal studies. These studies reveal that different groups of general anesthetics, which can be discerned based on their clinical features, produce unconsciousness via distinct molecular targets and therefore via distinct mechanisms. We further postulate that different types of general anesthetics selectively disrupt different critical steps (perhaps in different neuronal circuits) in the processing of sensory information and memory that results in consciousness. PMID:18617817

  12. Condensed Matter Physics: Does Quantum Mechanics Matter?

    NASA Astrophysics Data System (ADS)

    Fisher, Michael E.

    Herman Feshbach, the organizer of this Symposium in honor of Niels Bohr, asked me, in his original invitation, for a review of the present state of condensed matter physics, with emphasis on major unsolved problems and comments on any overlap with Bohr's ideas regarding the fundamentals of quantum mechanics. That is surely a difficult assignment and, indeed, goes well beyond what is attempted here; nevertheless, I will take the liberty of raising one issue of a philosophical or metaphysical flavor.

  13. The metaphysics of quantum mechanics: Modal interpretations

    NASA Astrophysics Data System (ADS)

    Gluck, Stuart Murray

    2004-11-01

    This dissertation begins with the argument that a preferred way of doing metaphysics is through philosophy of physics. An understanding of quantum physics is vital to answering questions such as: What counts as an individual object in physical ontology? Is the universe fundamentally indeterministic? Are indiscernibles identical? This study explores how the various modal interpretations of quantum mechanics answer these sorts of questions; modal accounts are one of the two classes of interpretations along with so-called collapse accounts. This study suggests a new alternative within the class of modal views that yields a more plausible ontology, one in which the Principle of the Identity of Indisceribles is necessarily true. Next, it shows that modal interpretations can consistently deny that the universe must be fundamentally indeterministic so long as they accept certain other metaphysical commitments: either a perfect initial distribution of states in the universe or some form of primitive dispositional properties. Finally, the study sketches out a future research project for modal interpretations based on developing quantified quantum logic.

  14. Hidden algebra method (quasi-exact-solvability in quantum mechanics)

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

    Turbiner, Alexander; Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, Apartado, Postal 70-543, 04510 Mexico, D. F.

    1996-02-20

    A general introduction to quasi-exactly-solvable problems of quantum mechanics is presented. Main attention is given to multidimensional quasi-exactly-solvable and exactly-solvable Schroedinger operators. Exact-solvability of the Calogero and Sutherland N-body problems ass ociated with an existence of the hidden algebra slN is discussed extensively.

  15. Review of Student Difficulties in Upper-Level Quantum Mechanics

    ERIC Educational Resources Information Center

    Singh, Chandralekha; Marshman, Emily

    2015-01-01

    Learning advanced physics, in general, is challenging not only due to the increased mathematical sophistication but also because one must continue to build on all of the prior knowledge acquired at the introductory and intermediate levels. In addition, learning quantum mechanics can be especially challenging because the paradigms of classical…

  16. Systematic and Automated Development of Quantum Mechanically Derived Force Fields: The Challenging Case of Halogenated Hydrocarbons.

    PubMed

    Prampolini, Giacomo; Campetella, Marco; De Mitri, Nicola; Livotto, Paolo Roberto; Cacelli, Ivo

    2016-11-08

    A robust and automated protocol for the derivation of sound force field parameters, suitable for condensed-phase classical simulations, is here tested and validated on several halogenated hydrocarbons, a class of compounds for which standard force fields have often been reported to deliver rather inaccurate performances. The major strength of the proposed protocol is that all of the parameters are derived only from first principles because all of the information required is retrieved from quantum mechanical data, purposely computed for the investigated molecule. This a priori parametrization is carried out separately for the intra- and intermolecular contributions to the force fields, respectively exploiting the Joyce and Picky programs, previously developed in our group. To avoid high computational costs, all quantum mechanical calculations were performed exploiting the density functional theory. Because the choice of the functional is known to be crucial for the description of the intermolecular interactions, a specific procedure is proposed, which allows for a reliable benchmark of different functionals against higher-level data. The intramolecular and intermolecular contribution are eventually joined together, and the resulting quantum mechanically derived force field is thereafter employed in lengthy molecular dynamics simulations to compute several thermodynamic properties that characterize the resulting bulk phase. The accuracy of the proposed parametrization protocol is finally validated by comparing the computed macroscopic observables with the available experimental counterparts. It is found that, on average, the proposed approach is capable of yielding a consistent description of the investigated set, often outperforming the literature standard force fields, or at least delivering results of similar accuracy.

  17. Exponential energy growth due to slow parameter oscillations in quantum mechanical systems.

    PubMed

    Turaev, Dmitry

    2016-05-01

    It is shown that a periodic emergence and destruction of an additional quantum number leads to an exponential growth of energy of a quantum mechanical system subjected to a slow periodic variation of parameters. The main example is given by systems (e.g., quantum billiards and quantum graphs) with periodically divided configuration space. In special cases, the process can also lead to a long period of cooling that precedes the acceleration, and to the desertion of the states with a particular value of the quantum number.

  18. X-ray Structure of a Hg 2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg 2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs

    DOE PAGES

    Lian, Peng; Guo, Hao-Bo; Riccardi, Demian; ...

    2014-10-24

    Here we report that mercuric reductase, MerA, is a key enzyme in bacterial mercury resistance. This homodimeric enzyme captures and reduces toxic Hg 2+ to Hg 0, which is relatively unreactive and can exit the cell passively. Prior to reduction, the Hg 2+ is transferred from a pair of cysteines (C558' and C559' using Tn501 numbering) at the C-terminus of one monomer to another pair of cysteines (C136 and C141) in the catalytic site of the other monomer. Here, we present the X-ray structure of the C-terminal Hg 2+ complex of the C136A/C141A double mutant of the Tn501 MerA catalyticmore » core and explore the molecular mechanism of this Hg transfer with quantum mechanical/molecular mechanical (QM/MM) calculations. The transfer is found to be nearly thermoneutral and to pass through a stable tricoordinated intermediate that is marginally less stable than the two end states. For the overall process, Hg 2+ is always paired with at least two thiolates and thus is present at both the C-terminal and catalytic binding sites as a neutral complex. Prior to Hg 2+ transfer, C141 is negatively charged. As Hg 2+ is transferred into the catalytic site, a proton is transferred from C136 to C559' while C558' becomes negatively charged, resulting in the net transfer of a negative charge over a distance of ~7.5 Å. Thus, the transport of this soft divalent cation is made energetically feasible by pairing a competition between multiple Cys thiols and/or thiolates for Hg 2+ with a competition between the Hg 2+ and protons for the thiolates.« less

  19. Testing Quantum Mechanics and Bell's Inequality with Astronomical Observations

    NASA Astrophysics Data System (ADS)

    Friedman, Andrew S.; Kaiser, David I.; Gallicchio, Jason; Team 1: University of Vienna, InstituteQuantum Optics and Quantum Information; Team 2: UC San Diego Cosmology Group; Team 3: NASA/JPL/Caltech

    2016-06-01

    We report on an in progress "Cosmic Bell" experiment that will leverage cosmology to test quantum mechanics and Bell's inequality using astronomical observations. Different iterations of our experiment will send polarization-entangled photons through the open air to detectors ~1-100 kilometers apart, whose settings would be rapidly chosen using real-time telescopic observations of Milky Way stars, and eventually distant, causally disconnected, cosmological sources - such as pairs of quasars or patches of the cosmic microwave background - all while the entangled pair is still in flight. This would, for the first time, attempt to fully close the so-called "setting independence" or "free will" loophole in experimental tests of Bell's inequality, whereby an alternative theory could mimic the quantum predictions if the experimental settings choices shared even a small correlation with unknown, local, causal influences a mere few milliseconds prior to the experiment. A full Cosmic Bell test would push any such influence all the way back to the hot big bang, since the end of any period of inflation, 13.8 billion years ago, an improvement of 20 orders of magnitude compared to the best previous experiments. Redshift z > 3.65 quasars observed at optical wavelengths are the optimal candidate source pairs using present technology. Our experiment is partially funded by the NSF INSPIRE program, in collaboration with MIT, UC San Diego, Harvey Mudd College, NASA/JPL/Caltech, and the University of Vienna. Such an experiment has implications for our understanding of nature at the deepest level. By testing quantum mechanics in a regime never before explored, we would at the very least extend our confidence in quantum theory, while at the same time severely constraining large classes of alternative theories. If the experiment were to uncover discrepancies from the quantum predictions, there could be crucial implications for early-universe cosmology, the security of quantum encryption

  20. The Radical Pair Mechanism and the Avian Chemical Compass: Quantum Coherence and Entanglement

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

    Zhang, Yiteng; Kais, Sabre; Berman, Gennady Petrovich

    2015-02-02

    We review the spin radical pair mechanism which is a promising explanation of avian navigation. This mechanism is based on the dependence of product yields on 1) the hyperfine interaction involving electron spins and neighboring nuclear spins and 2) the intensity and orientation of the geomagnetic field. One surprising result is that even at ambient conditions quantum entanglement of electron spins can play an important role in avian magnetoreception. This review describes the general scheme of chemical reactions involving radical pairs generated from singlet and triplet precursors; the spin dynamics of the radical pairs; and the magnetic field dependence ofmore » product yields caused by the radical pair mechanism. The main part of the review includes a description of the chemical compass in birds. We review: the general properties of the avian compass; the basic scheme of the radical pair mechanism; the reaction kinetics in cryptochrome; quantum coherence and entanglement in the avian compass; and the effects of noise. We believe that the quantum avian compass can play an important role in avian navigation and can also provide the foundation for a new generation of sensitive and selective magnetic-sensing nano-devices.« less