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Sample records for quantum mechanical-molecular mechanical

  1. Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach.

    PubMed

    Ishiyama, Tatsuya; Takahashi, Hideaki; Morita, Akihiro

    2012-03-28

    A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.

  2. 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.

  3. Quantum mechanics/molecular mechanics restrained electrostatic potential fitting.

    PubMed

    Burger, Steven K; Schofield, Jeremy; Ayers, Paul W

    2013-12-05

    We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory. After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pKa shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin. Compared to the AMBER ff99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK(a) values for almost all of the residues considered.

  4. Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

    NASA Astrophysics Data System (ADS)

    Polyak, Iakov; Benighaus, Tobias; Boulanger, Eliot; Thiel, Walter

    2013-08-01

    The dual Hamiltonian free energy perturbation (DH-FEP) method is designed for accurate and efficient evaluation of the free energy profile of chemical reactions in quantum mechanical/molecular mechanical (QM/MM) calculations. In contrast to existing QM/MM FEP variants, the QM region is not kept frozen during sampling, but all degrees of freedom except for the reaction coordinate are sampled. In the DH-FEP scheme, the sampling is done by semiempirical QM/MM molecular dynamics (MD), while the perturbation energy differences are evaluated from high-level QM/MM single-point calculations at regular intervals, skipping a pre-defined number of MD sampling steps. After validating our method using an analytic model potential with an exactly known solution, we report a QM/MM DH-FEP study of the enzymatic reaction catalyzed by chorismate mutase. We suggest guidelines for QM/MM DH-FEP calculations and default values for the required computational parameters. In the case of chorismate mutase, we apply the DH-FEP approach in combination with a single one-dimensional reaction coordinate and with a two-dimensional collective coordinate (two individual distances), with superior results for the latter choice.

  5. 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.

  6. Combined quantum mechanical/molecular mechanics modeling for large organometallic and metallobiochemical systems

    NASA Astrophysics Data System (ADS)

    Leong, Max Kangchien

    A method of combined quantum mechanics/molecular mechanics has been developed to model larger organometallic and metallobiochemical systems where neither quantum mechanics nor molecular mechanics, applied separately, can solve the problem. An electronically transparent interface, which allows charge transfers between the quantum and classical fragments, is devised and realized by employing a special iterative procedure of double (intrafragment and interfragment) self-consistent calculations. The combined QM/MM scheme was successfully applied to model iron picket-fence porphyrin, vitamin B12, aquocobalamin, and vitamin B12 coenzyme molecules.

  7. 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 SN1-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.

  8. A quantum mechanical/molecular mechanical approach to the investigation of particle-molecule interactions

    NASA Astrophysics Data System (ADS)

    Sloth, Marianne; Bilde, Merete; Mikkelsen, Kurt V.

    2003-06-01

    A quantum mechanical/molecular mechanical aerosol model is developed to describe the interaction between gas phase molecules and atmospheric particles. The model enables the calculation of interaction energies and time-dependent properties. We use the model to investigate how a succinic acid molecule interacts with an aqueous particle. We show how the interaction energies and linear response properties (excitation energies, transition moments, and polarizabilities) depend on the distance between aerosol particle and molecule and on their relative orientation. The results are compared with those obtained previously using a dielectric continuum model [Sloth et al., J. Phys. Chem. (submitted)].

  9. 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.

  10. 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.

  11. Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction.

    PubMed

    Polyak, Iakov; Reetz, Manfred T; Thiel, Walter

    2012-02-08

    We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.

  12. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology.

    PubMed

    van der Kamp, Marc W; Mulholland, Adrian J

    2013-04-23

    Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.

  13. Inactivation mechanism of glycerol dehydration by diol dehydratase from combined quantum mechanical/molecular mechanical calculations.

    PubMed

    Doitomi, Kazuki; Kamachi, Takashi; Toraya, Tetsuo; Yoshizawa, Kazunari

    2012-11-13

    Inactivation of diol dehydratase during the glycerol dehydration reaction is studied on the basis of quantum mechanical/molecular mechanical calculations. Glycerol is not a chiral compound but contains a prochiral carbon atom. Once it is bound to the active site, the enzyme adopts two binding conformations. One is predominantly responsible for the product-forming reaction (G(R) conformation), and the other primarily contributes to inactivation (G(S) conformation). Reactant radical is converted into a product and byproduct in the product-forming reaction and inactivation, respectively. The OH group migrates from C2 to C1 in the product-forming reaction, whereas the transfer of a hydrogen from the 3-OH group of glycerol to C1 takes place during the inactivation. The activation barrier of the hydrogen transfer does not depend on the substrate-binding conformation. On the other hand, the activation barrier of OH group migration is sensitive to conformation and is 4.5 kcal/mol lower in the G(R) conformation than in the G(S) conformation. In the OH group migration, Glu170 plays a critical role in stabilizing the reactant radical in the G(S) conformation. Moreover, the hydrogen bonding interaction between Ser301 and the 3-OH group of glycerol lowers the activation barrier in G(R)-TS2. As a result, the difference in energy between the hydrogen transfer and the OH group migration is reduced in the G(S) conformation, which shows that the inactivation is favored in the G(S) conformation.

  14. 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.

  15. 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.

  16. 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.

  17. Quantum mechanics/molecular mechanics study of oxygen binding in hemocyanin.

    PubMed

    Saito, Toru; Thiel, Walter

    2014-05-15

    We report a combined quantum mechanics/molecular mechanics (QM/MM) study on the mechanism of reversible dioxygen binding in the active site of hemocyanin (Hc). The QM region is treated by broken-symmetry density functional theory (DFT) with spin projection corrections. The X-ray structures of deoxygenated (deoxyHc) and oxygenated (oxyHc) hemocyanin are well reproduced by QM/MM geometry optimizations. The computed relative energies strongly depend on the chosen density functional. They are consistent with the available thermodynamic data for oxygen binding in hemocyanin and in synthetic model complexes when the BH&HLYP hybrid functional with 50% Hartree-Fock exchange is used. According to the QM(BH&HLYP)/MM results, the reaction proceeds stepwise with two sequential electron transfer (ET) processes in the triplet state followed by an intersystem crossing to the singlet product. The first ET step leads to a nonbridged superoxo CuB(II)-O2(•-) intermediate via a low-barrier transition state. The second ET step is even more facile and yields a side-on oxyHc complex with the characteristic Cu2O2 butterfly core, accompanied by triplet-singlet intersystem crossing. The computed barriers are very small so that the two ET processes are expected to very rapid and nearly simultaneous.

  18. 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

    active site can be optimized to improve the transition state analogues (TSA) and to enhance the catalytic activity, even improve the active site to favor a desired direction of some promiscuous enzymes. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. Current computational tools to assist experimentalists for the design and engineering of proteins with desired catalytic properties are described. The interplay between enzyme design, molecular simulations, and experiments will be presented to emphasize the interdisciplinary nature of this research field. This text highlights the recent advances and examples selected from our laboratory are shown, of how the applications of these tools are a first attempt to de novo design of protein active sites. Identification of neutral/advantageous/deleterious mutation platforms can be exploited to penetrate some of Nature's closely guarded secrets of chemical reactivity. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. The first part describes briefly how the molecular modeling is carried out. Then, we discuss the requirements of hybrid quantum mechanical/molecular mechanics molecular dynamics (QM/MM MD) simulations, analyzing what are the basis of these theoretical methodologies, how we can use them with a view to its application in the study of enzyme catalysis, and what are the best methodologies for assessing its catalytic potential. In the second part, we focus on some selected examples, taking as a common guide the chorismate to prephenate rearrangement, studying the corresponding molecular mechanism in vacuo, in solution and in an enzyme environment. In addition, examples involving catalytic antibodies (CAs) and promiscuous enzymes will be presented. Finally, a special emphasis is made to provide some hints about the logical evolution that can be anticipated in this research

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. 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.

  6. Gauge-origin independent magnetizabilities from hybrid quantum mechanics/molecular mechanics models: Theory and applications to liquid water

    NASA Astrophysics Data System (ADS)

    Aidas, Kestutis; Kongsted, Jacob; Nielsen, Christian B.; Mikkelsen, Kurt V.; Christiansen, Ove; Ruud, Kenneth

    2007-07-01

    The theory of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach for gauge-origin independent calculations of the molecular magnetizability using Hartree-Fock or Density Functional Theory is presented. The method is applied to liquid water using configurations generated from classical Molecular Dynamics simulation to calculate the statistical averaged magnetizability. Based on a comparison with experimental data, treating only one water molecule quantum mechanically appears to be insufficient, while a quantum mechanical treatment of also the first solvation shell leads to good agreement between theory and experiment. This indicates that the gas-to-liquid phase shift for the molecular magnetizability is to a large extent of non-electrostatic nature.

  7. First quantum mechanics/molecular mechanics studies of the inhibition mechanism of cruzain by peptidyl halomethyl ketones.

    PubMed

    Arafet, Kemel; Ferrer, Silvia; Moliner, Vicent

    2015-06-02

    Cruzain is a primary cysteine protease expressed by the protozoan parasite Trypanosoma cruzi during Chagas disease infection, and thus, the development of inhibitors of this protein is a promising target for designing an effective therapy against the disease. In this paper, the mechanism of inhibition of cruzain by two different irreversible peptidyl halomethyl ketones (PHK) inhibitors has been studied by means of hybrid quantum mechanics/molecular mechanics-molecular dynamics (MD) simulations to obtain a complete representation of the possible free energy reaction paths. These have been traced on free energy surfaces in terms of the potential of mean force computed at AM1d/MM and DFT/MM levels of theory. An analysis of the possible reaction mechanisms of the inhibition process has been performed showing that the nucleophilic attack of an active site cysteine, Cys25, on a carbon atom of the inhibitor and the cleavage of the halogen-carbon bond take place in a single step. PClK appears to be much more favorable than PFK from a kinetic point of view. This result would be in agreement with experimental studies in other papain-like enzymes. A deeper analysis of the results suggests that the origin of the differences between PClK and PFK can be the different stabilizing interactions established between the inhibitors and the residues of the active site of the protein. Any attempt to explore the viability of the inhibition process through a stepwise mechanism involving the formation of a thiohemiketal intermediate and a three-membered sulfonium intermediate has been unsuccessful. Nevertheless, a mechanism through a protonated thiohemiketal, with participation of His159 as a proton donor, appears to be feasible despite showing higher free energy barriers. Our results suggest that PClK can be used as a starting point to develop a proper inhibitor of cruzain.

  8. Mixed ab initio quantum mechanics/molecular mechanics methods using frozen orbitals with applications to peptides and proteins

    NASA Astrophysics Data System (ADS)

    Philipp, Dean Michael

    Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.

  9. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

    PubMed

    Li, Hongzhi; Fajer, Mikolai; Yang, Wei

    2007-01-14

    A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.

  10. Insights into the Thiamine Diphosphate Enzyme Activation Mechanism: Computational Model for Transketolase Using a Quantum Mechanical/Molecular Mechanical Method.

    PubMed

    Nauton, Lionel; Hélaine, Virgil; Théry, Vincent; Hecquet, Laurence

    2016-04-12

    We propose the first computational model for transketolase (TK), a thiamine diphosphate (ThDP)-dependent enzyme, using a quantum mechanical/molecular mechanical method on the basis of crystallographic TK structures from yeast and Escherichia coli, together with experimental kinetic data reported in the literature with wild-type and mutant TK. This model allowed us to define a new route for ThDP activation in the enzyme environment. We evidenced a strong interaction between ThDP and Glu418B of the TK active site, itself stabilized by Glu162A. The crucial point highlighted here is that deprotonation of ThDP C2 is not performed by ThDP N4' as reported in the literature, but by His481B, involving a HOH688A molecule bridge. Thus, ThDP N4' is converted from an amino form to an iminium form, ensuring the stabilization of the C2 carbanion or carbene. Finally, ThDP activation proceeds via an intermolecular process and not by an intramolecular one as reported in the literature. More generally, this proposed ThDP activation mechanism can be applied to some other ThDP-dependent enzymes and used to define the entire TK mechanism with donor and acceptor substrates more accurately.

  11. A dissociative quantum mechanical/molecular mechanical molecular dynamics simulation and infrared experiments reveal characteristics of the strongly hydrolytic arsenic(III).

    PubMed

    Canaval, Lorenz R; Lutz, Oliver M D; Weiss, Alexander K H; Huck, Christian W; Hofer, Thomas S

    2014-11-17

    This work presents a hybrid ab initio quantum mechanical/molecular mechanical simulation at the RI-MP2 level of theory investigating the hydrolysis process of arsenic(III), ultimately leading to arsenous acid (H3AsO3). A newly implemented dissociative water model has been applied to treat the interactions in the classical region, which is capable of describing non-neutral water species such as hydroxide and oxonium ions. Three stages of hydrolysis have been observed during the simulation and besides profound dynamical considerations, detailed insights into structural changes and atomic partial charge shifts are presented. In particular, the geometrical properties of H-bonds involved in each of the three proton transfer events and subsequent proton hopping reactions are discussed. A Laguerre tessellation analysis has been employed to estimate the molecular volume of H3AsO3. Estimations of pKa values of the arsenic(III)-aquo-complexes have been obtained at the G4 and CBS-Q//B3 levels of theory using a thermodynamic cycle, whereas rate constants for the final hydrolysis step have been determined via reaction path optimization and transition state theory. Newly recorded Fourier transform infrared (FT-IR) spectroscopy measurements have been compared to power spectra obtained from the simulation data, confirming its quality. The simulation findings, as well as results from computational spectroscopic calculations utilizing the PT2-VSCF methodology, proved valuable for the interpretation of the experimental FT-IR data, elucidating the particularities of the strongly observed IR Raman noncoincidence effect.

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

    SciTech Connect

    Valiev, Marat; Yang, Jie; Adams, Joseph; Taylor, Susan S.; Weare, John H.

    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 transfer of the γ-phosphoryl group in the protein environment is an exothermic reaction with the reaction barrier of 15 kcal/mol.

  13. Insights into the phosphatase and the synthase activities of human bisphosphoglycerate mutase: a quantum mechanics/molecular mechanics simulation.

    PubMed

    Chu, Wen-Ting; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2014-03-07

    Bisphosphoglycerate mutase (BPGM) is a multi-activity enzyme. Its main function is to synthesize the 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. This enzyme can also catalyze the 2,3-bisphosphoglycerate to the 3-phosphoglycerate. In this study, the reaction mechanisms of both the phosphatase and the synthase activities of human bisphosphoglycerate mutase were theoretically calculated by using the quantum mechanics/molecular mechanics method based on the metadynamics and umbrella sampling simulations. The simulation results not only show the free energy curve of the phosphatase and the synthase reactions, but also reveal the important role of some residues in the active site. Additionally, the energy barriers of the two reactions indicate that the activity of the synthase in human bisphosphoglycerate mutase is much higher than that of the phosphatase. The estimated reaction barriers are consistent with the experimental data. Therefore, our work can give important information to understand the catalytic mechanism of the bisphosphoglycerate mutase family.

  14. Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme

    PubMed Central

    Ortega-Carrasco, Elisabeth; Lledós, Agustí; Maréchal, Jean-Didier

    2014-01-01

    In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy. PMID:24829279

  15. 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.

  16. Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme.

    PubMed

    Ortega-Carrasco, Elisabeth; Lledós, Agustí; Maréchal, Jean-Didier

    2014-07-06

    In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy.

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

    SciTech Connect

    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. YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model.

    PubMed

    Shao, Yihan; Kong, Jing

    2007-05-10

    A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.

  19. Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method.

    PubMed

    Cui, Ganglong; Yang, Weitao

    2011-05-28

    The significance of conical intersections in photophysics, photochemistry, and photodissociation of polyatomic molecules in gas phase has been demonstrated by numerous experimental and theoretical studies. Optimization of conical intersections of small- and medium-size molecules in gas phase has currently become a routine optimization process, as it has been implemented in many electronic structure packages. However, optimization of conical intersections of small- and medium-size molecules in solution or macromolecules remains inefficient, even poorly defined, due to large number of degrees of freedom and costly evaluations of gradient difference and nonadiabatic coupling vectors. In this work, based on the sequential quantum mechanics and molecular mechanics (QM/MM) and QM/MM-minimum free energy path methods, we have designed two conical intersection optimization methods for small- and medium-size molecules in solution or macromolecules. The first one is sequential QM conical intersection optimization and MM minimization for potential energy surfaces; the second one is sequential QM conical intersection optimization and MM sampling for potential of mean force surfaces, i.e., free energy surfaces. In such methods, the region where electronic structures change remarkably is placed into the QM subsystem, while the rest of the system is placed into the MM subsystem; thus, dimensionalities of gradient difference and nonadiabatic coupling vectors are decreased due to the relatively small QM subsystem. Furthermore, in comparison with the concurrent optimization scheme, sequential QM conical intersection optimization and MM minimization or sampling reduce the number of evaluations of gradient difference and nonadiabatic coupling vectors because these vectors need to be calculated only when the QM subsystem moves, independent of the MM minimization or sampling. Taken together, costly evaluations of gradient difference and nonadiabatic coupling vectors in solution or

  20. An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

    NASA Astrophysics Data System (ADS)

    Woods, Christopher J.; Manby, Frederick R.; Mulholland, Adrian J.

    2008-01-01

    The combination of quantum mechanics (QM) with molecular mechanics (MM) offers a route to improved accuracy in the study of biological systems, and there is now significant research effort being spent to develop QM/MM methods that can be applied to the calculation of relative free energies. Currently, the computational expense of the QM part of the calculation means that there is no single method that achieves both efficiency and rigor; either the QM/MM free energy method is rigorous and computationally expensive, or the method introduces efficiency-led assumptions that can lead to errors in the result, or a lack of generality of application. In this paper we demonstrate a combined approach to form a single, efficient, and, in principle, exact QM/MM free energy method. We demonstrate the application of this method by using it to explore the difference in hydration of water and methane. We demonstrate that it is possible to calculate highly converged QM/MM relative free energies at the MP2/aug-cc-pVDZ/OPLS level within just two days of computation, using commodity processors, and show how the method allows consistent, high-quality sampling of complex solvent configurational change, both when perturbing hydrophilic water into hydrophobic methane, and also when moving from a MM Hamiltonian to a QM/MM Hamiltonian. The results demonstrate the validity and power of this methodology, and raise important questions regarding the compatibility of MM and QM/MM forcefields, and offer a potential route to improved compatibility.

  1. 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.

  2. Aeromonas proteolytica aminopeptidase: an investigation of the mode of action using a quantum mechanical/molecular mechanical approach.

    PubMed

    Schürer, Gudrun; Lanig, Harald; Clark, Timothy

    2004-05-11

    The aminopeptidase of Aeromonas proteolytica (AAP) belongs to the group of metallo-hydrolases that require two divalent cations for full activity. Such binuclear metal centers are found in several aminopeptidases, raising the question whether a common mechanism, at least partly, is likely. We have used a quantum mechanical/molecular mechanical (QM/MM) approach to investigate the reaction mechanism of AAP. Among several possibilities, one reaction path was found to be clearly the most favorable. Beside the chemical transformation steps, effects of the enzyme environment and the influence of the solvent on the catalytic reaction were included in the study. The results are in good agreement with experimental studies and correspond to a high degree to our previous QM/MM calculations on the reaction mechanism of the related binuclear bovine lens leucine aminopeptidase (blLAP), which, although related to the AAP, has different Zn(2+)-coordination spheres and a different catalytic residue. The mechanisms of the two enzymes as suggested in the literature differ on the mode of coordination of the nucleophile and the identity of the general base. However, the results of this and our previous work on blLAP allow us to identify a common mechanism for the two enzymes. This mechanism is probably quite general for binuclear zinc enzymes.

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

    SciTech Connect

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

    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 completely 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.

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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 R2 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 R2 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    SciTech Connect

    Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

    2009-04-28

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  16. Density functional theory and quantum mechanics/molecular mechanics study of cysteine protease inhibition by nitrile-based inhibitors.

    NASA Astrophysics Data System (ADS)

    De Visser, Sam; Quesne, Matthew; Ward, Richard

    2013-12-01

    Cysteine protease enzymes are important for human physiology and catalyze key protein degradation pathways. These enzymes react via a nucleophilic reaction mechanism that involves a cysteine residue and the proton of a proximal histidine. Particularly efficient inhibitors of these enzymes are nitrile-based, however, the details of the catalytic reaction mechanism currently are poorly understood. To gain further insight into the inhibition of these molecules, we have performed a combined density functional theory and quantum mechanics/molecular mechanics study on the reaction of a nitrile-based inhibitor with the enzyme active site amino acids. We show here that small perturbations to the inhibitor structure can have dramatic effects on the catalysis and inhibition processes. Thus, we investigated a range of inhibitor templates and show that specific structural changes reduce the inhibitory efficiency by several orders of magnitude. Moreover, as the reaction takes place on a polar surface, we find strong differences between the DFT and QM/MM calculated energetics. In particular, the DFT model led to dramatic distortions from the starting structure and the convergence to a structure that would not fit the enzyme active site. In the subsequent QM/MM study we investigated the use of mechanical versus electronic embedding on the kinetics, thermodynamics and geometries along the reaction mechanism. We find minor effects on the kinetics of the reaction but large geometric and thermodynamics differences as a result of inclusion of electronic embedding corrections. The work here highlights the importance of model choice in the investigation of this biochemical reaction mechanism.

  17. Nuclear magnetic shielding constants of liquid water: Insights from hybrid quantum mechanics/molecular mechanics models

    NASA Astrophysics Data System (ADS)

    Kongsted, Jacob; Nielsen, Christian B.; Mikkelsen, Kurt V.; Christiansen, Ove; Ruud, Kenneth

    2007-01-01

    We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the O17 and H1 isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4ppm for the O17 shielding and 1ppm for the H1 shielding.

  18. Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme

    PubMed Central

    2015-01-01

    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 Mg2+ 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 Mg2+ 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 Mg2+ 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. PMID:24383543

  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. Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Re, Suyong; Sugita, Yuji; Ten-no, Seiichiro

    2013-01-01

    The nudged elastic band (NEB) and string methods are widely used to obtain the reaction path of chemical reactions and phase transitions. In these methods, however, it is difficult to define an accurate Lagrangian to generate the conservative forces. On the other hand, the constrained optimization with locally updated planes (CO-LUP) scheme defines target function properly and suitable for micro-iteration optimizations in quantum mechanical/molecular mechanical (QM/MM) systems, which uses the efficient second order QM optimization. However, the method does have problems of inaccurate estimation of reactions and inappropriate accumulation of images around the energy minimum. We introduce three modifications into the CO-LUP scheme to overcome these problems: (1) An improved tangent estimation of the reaction path, which is used in the NEB method, (2) redistribution of images using an energy-weighted interpolation before updating local tangents, and (3) reduction of the number of constraints, in particular translation/rotation constraints, for improved convergence. First, we test the method on the isomerization of alanine dipeptide without QM/MM calculation, showing that the method is comparable to the string method both in accuracy and efficiency. Next, we apply the method for defining the reaction paths of the rearrangement reaction catalyzed by chorismate mutase (CM) and of the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA) using generalized hybrid orbital QM/MM calculations. The reaction energy barrier of CM is in high agreement with the experimental value. The path of PKA reveals that the enzyme reaction is associative and there is a late transfer of the substrate proton to Asp 166, which is in agreement with the recently published result using the NEB method.

  1. Hybrid Quantum Mechanics/Molecular Mechanics-Based Molecular Dynamics Simulation of Acid-Catalyzed Dehydration of Polyols in Liquid Water

    SciTech Connect

    Caratzoulas, Stavros; Courtney, Timothy; Vlachos, Dionisios G.

    2011-01-01

    We use the conversion of protonated glycerol to acrolein for a case study of the mechanism of acid-catalyzed dehydration of polyols in aqueous environments. We employ hybrid Quamtum Mechanics/Molecular Mechanics Molecular Dynamics (QM/MM MD) simulations with biased sampling and perform free energy calculations for the elementary steps of the reaction. We investigate the effects of solvent dynamics and in particular the role of quantum mechanical water in the dehydration mechanism. We present results supporting a mechanism that proceeds via water-mediated proton transfers and thus through an enol intermediate. We find that the first dehydration may take place by two, low-energy pathways requiring, respectively, 20.9 and 18.8 kcal/mol of activation free energy. The second dehydration requires 19.9 kcal/mol of activation free energy while for the overall reaction we compute a free energy change of -8 kcal/mol.

  2. Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations.

    PubMed

    Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra

    2015-09-24

    Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant.

  3. 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.

  4. Quantum mechanical/molecular mechanical study of catalytic mechanism and role of key residues in methylation reactions catalyzed by dimethylxanthine methyltransferase in caffeine biosynthesis.

    PubMed

    Yue, Yufei; Guo, Hong

    2014-02-24

    The caffeine biosynthetic pathway is of considerable importance for the beverage and pharmaceutical industries which produces two blockbuster products: theobromine and caffeine. The major biochemistry in caffeine biosynthesis starts from the initial substrate of xanthosine and ends with the final product caffeine, with theobromine serving as an intermediate. The key enzyme, S-adenosyl-l-methionine (SAM) dependent 3,7-dimethyl-xanthine methyltransferase (DXMT), catalyzes two important methyl transfer steps in caffeine biosynthesis: (1) methylation of N3 of 7-methylxanthine (7mX) to form theobromine (Tb); (2) methylation of N1 of theobromine to form caffeine (Cf). Although DXMT has been structurally characterized recently, our understanding of the detailed catalytic mechanism and role of key catalytic residues is still lacking. In this work, the quantum mechanical/molecular mechanical (QM/MM) MD and free energy simulations are performed to elucidate the catalytic mechanism of the enzyme-catalyzed reactions and to explain experimental observations concerning the activity of this enzyme. The roles of certain active-site residues are studied, and the results of computer simulation seem to suggest that a histidine residue (His160) at the active site of DXMT may act as a general base/acid catalyst during the methyl transfer process.

  5. 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.

  6. 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.

  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.

  8. A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity.

    PubMed

    Alzate-Morales, Jans H; Contreras, Renato; Soriano, Alejandro; Tuñon, Iñaki; Silla, Estanislao

    2007-01-15

    We report a combined quantum mechanics/molecular mechanics (QM/MM) study to determine the protein-ligand interaction energy between CDK2 (cyclin-dependent kinase 2) and five inhibitors with the N(2)-substituted 6-cyclohexyl-methoxy-purine scaffold. The computational results in this work show that the QM/MM interaction energy is strongly correlated to the biological activity and can be used as a predictor, at least within a family of substrates. A detailed analysis of the protein-ligand structures obtained from molecular dynamics simulations shows specific interactions within the active site that, in some cases, have not been reported before to our knowledge. The computed interaction energy gauges the strength of protein-ligand interactions. Finally, energy decomposition and multiple regression analyses were performed to check the contribution of the electrostatic and van der Waals energies to the total interaction energy and to show the capabilities of the computational model to identify new potent inhibitors.

  9. Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyanin.

    PubMed

    Mroginski, Maria Andrea; Mark, Franz; Thiel, Walter; Hildebrandt, Peter

    2007-09-15

    We have established a quantum mechanics (QM)/molecular mechanics (MM) hybrid method for calculating the Raman spectra of protein-bound cofactors using the alpha-subunit of C-phycocyanin containing a phycocyanobilin (PCB) chromophore as a test case. The PCB cofactor was described with density functional theory, whereas the protein matrix was treated with the CHARMM force field. The Hessian matrix of the QM region was built by taking into account bonded and nonbonded interactions with the protein environment and projected onto the internal coordinate space. Force constants were scaled with a global set of scaling factors, and the Raman intensities were computed using a finite-field method combined with a fourth-order differentiation algorithm for the calculation of the polarizability derivatives. In general, the QM/MM results provided a substantially improved description of the experimental resonance Raman (RR) spectra of the protein-bound cofactor compared to QM calculations of isolated PCB models in vacuo. The results allow the assessment of the effect of the protein-cofactor interactions on the RR spectra and reveal the potential and limitations of QM calculations on isolated tetrapyrroles for determining the chromophore structures in the various species and states of phytochromes for which three-dimensional structures are not available.

  10. 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

  11. First half-reaction mechanism of nitric oxide synthase: the role of proton and oxygen coupled electron transfer in the reaction by quantum mechanics/molecular mechanics.

    PubMed

    Cho, Kyung-Bin; Carvajal, Maria Angels; Shaik, Sason

    2009-01-08

    The first half-reaction of nitric oxide synthase (NOS) is investigated by means of quantum mechanical/molecular mechanical (QM/MM) calculations. An energetically feasible arginine hydroxylation path was found only when the iron-oxy complex accepted one proton from an external source. The so formed species has not been considered in heme chemistry; it is described as Por(+*)Fe(III)-OOH and is characterized by the same molecular constituency as the more known ferric-hydroperoxide species, compound 0, but has a cation-radical porphyrin moiety. The reaction itself is found to involve proton coupled electron transfer (PCET) and oxygen coupled electron transfer (OCET) steps en route to the formation of compound I and the ultimate monooxygenation of arginine. The cofactor H(4)B turns out to be a key player in the mechanism acting alternatively as an electron donor (when neutral) and an electron sink (when in its radical-cation state) and, thereby, providing the electron transfer component in the various coupled proton and oxygen transfer steps (see Scheme 4 ). The various pieces of this mechanism account for many of the experimental observations, such as the following: (a) the origins of the second proton supplied to the heme, (b) the elusiveness of compound I, (c) the inactivity of peroxide-shunt pathways in NOS first half-reaction, (d) the inhibition of the H(4)B analogue 4-amino-H(4)B due to protonation at the N3 position, (e) the roles of Trp188 (iNOS numbering) and the crystal water at the active site (W115), and so on. Alternative mechanistic hypotheses are tested and excluded, and a new mechanism for the NOS second half-reaction is proposed.

  12. 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.

  13. 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.

  14. Amine oxidation mediated by lysine-specific demethylase 1: quantum mechanics/molecular mechanics insights into mechanism and role of lysine 661.

    PubMed

    Karasulu, Bora; Patil, Mahendra; Thiel, Walter

    2013-09-11

    We report classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the catalytic mechanism of the rate-determining amine oxidation step in the lysine-specific demethylase 1 (LSD1)-catalyzed demethylation of the histone tail lysine (H3K4), with flavin adenine dinucleotide (FAD) acting as cofactor. The oxidation of substrate lysine (sLys) involves the cleavage of an α-CH bond accompanied by the transfer of a hydride ion equivalent to FAD, leading to an imine intermediate. This hydride transfer pathway is shown to be clearly favored for sLys oxidation over other proposed mechanisms, including the radical (or single-electron transfer) route as well as carbanion and polar-nucleophilic mechanisms. MD simulations on six NVT ensembles (covering different protonation states of sLys and K661 as well as the K661M mutant) identify two possible orientations of the reacting sLys and FAD subunits (called "downward" and "upward"). Calculations at the QM(B3LYP-D/6-31G*)/CHARMM22 level provide molecular-level insights into the mechanism, helping to understand how LSD1 achieves the activation of the rather inert methyl-CH bond in a metal-free environment. Factors such as proper alignment of sLys (downward orientation), transition-state stabilization (due to the protein environment and favorable orbital interactions), and product stabilization via adduct formation are found to be crucial for facilitating the oxidative α-CH bond cleavage. The current study also sheds light on the role of important active-site residues (Y761, K661, and W695) and of the conserved water-bridge motif. The steric influence of Y761 helps to position the reaction partners properly, K661 is predicted to get deprotonated prior to substrate binding and to act as an active-site base that accepts a proton from sLys to enable the subsequent amine oxidation, and the water bridge that is stabilized by K661 and W695 mediates this proton

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. A Quantum Mechanic/Molecular Mechanic Study of the Wild-Type and N155S Mutant HIV-1 Integrase Complexed with Diketo Acid

    PubMed Central

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

    2008-01-01

    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 Mg2+ 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 Mg2+ 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. PMID:17981909

  20. 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.

  1. Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra.

    PubMed

    Goyal, Puja; Ghosh, Nilanjan; Phatak, Prasad; Clemens, Maike; Gaus, Michael; Elstner, Marcus; Cui, Qiang

    2011-09-28

    Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as the PRG would require the protein to raise the pK(a) of a hydronium by almost 11 pK(a) units, which is difficult considering known cases of pK(a) shifts in proteins. Our recent quantum mechanics/molecular mechanics (QM/MM) simulations suggested an alternative "intermolecular proton bond" model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pK(a) values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting X-ray structure, and nuclear quantum effects, the "intermolecular proton bond" model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the "intermolecular proton bond" model is likely applicable to the PRG in biomolecular proton pumps in general.

  2. 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.

  3. Integral Equation Theory of Molecular Solvation Coupled with Quantum Mechanical/Molecular Mechanics Method in NWChem Package

    SciTech Connect

    Chuev, Gennady N.; Valiev, Marat; Fedotova, Marina V.

    2012-04-10

    We have developed a hybrid approach based on a combination of integral equation theory of molecular liquids and QM/MM methodology in NorthWest computational Chemistry (NWChem) software package. We have split the evaluations into conse- quent QM/MM and statistical mechanics calculations based on the one-dimensional reference interaction site model, which allows us to reduce signicantly the time of computation. The method complements QM/MM capabilities existing in the NWChem package. The accuracy of the presented method was tested through com- putation of water structure around several organic solutes and their hydration free energies. We have also evaluated the solvent effect on the conformational equilibria. The applicability and limitations of the developed approach are discussed.

  4. 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.

  5. 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 CO2, 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 Mn4CaO5 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 S1 to S2 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)2Mn(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.

  6. 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.

  7. 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.

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

    PubMed Central

    2017-01-01

    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. PMID:28217747

  9. Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method: applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution.

    PubMed

    Higashi, Masahiro; Hayashi, Shigehiko; Kato, Shigeki

    2007-04-14

    The authors present a method based on a linear response theory that allows one to optimize the geometries of quantum mechanical/molecular mechanical (QM/MM) systems on the free energy surfaces. Two different forms of linear response free energy functionals are introduced, and electronic wave functions of the QM region, as well as the responses of electrostatic and Lennard-Jones potentials between QM and MM regions, are self-consistently determined. The covariant matrix relating the QM charge distribution to the MM response is evaluated by molecular dynamics (MD) simulation of the MM system. The free energy gradients with respect to the QM atomic coordinates are also calculated using the MD trajectory results. They apply the present method to calculate the free energy profiles of Menshutkin-type reaction of NH3 with CH3Cl and Claisen rearrangement of allyl vinyl ether in aqueous solution. For the Menshutkin reaction, the free energy profile calculated with the modified linear response free energy functional is in good agreement with that by the free energy perturbation calculations. They examine the nonequilibrium solvation effect on the transmission coefficient and the kinetic isotope effect for the Claisen rearrangement.

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

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takeshi

    2008-12-01

    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 SN2 Menshutkin reaction in water, NH3+CH3Cl→NH3CH3++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.

  11. 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

  12. The first step of the dioxygenation reaction carried out by tryptophan dioxygenase and indoleamine 2,3-dioxygenase as revealed by quantum mechanical/molecular mechanical studies

    PubMed Central

    Capece, Luciana; Lewis-Ballester, Ariel; Batabyal, Dipanwita; Di Russo, Natali; Estrin, Dario A.

    2015-01-01

    Tryptophan dioxygenase (TDO) and indole-amine 2,3-dioxygenase (IDO) are two heme-containing enzymes which catalyze the conversion of L-tryptophan to N-formylkynurenine (NFK). In mammals, TDO is mostly expressed in liver and is involved in controlling homeostatic serum tryptophan concentrations, whereas IDO is ubiquitous and is involved in modulating immune responses. Previous studies suggested that the first step of the dioxygenase reaction involves the deprotonation of the indoleamine group of the substrate by an evolutionarily conserved distal histidine residue in TDO and the heme-bound dioxygen in IDO. Here, we used classical molecular dynamics and hybrid quantum mechanical/molecular mechanical methods to evaluate the base-catalyzed mechanism. Our data suggest that the deprotonation of the indoleamine group of the substrate by either histidine in TDO or heme-bound dioxygen in IDO is not energetically favorable. Instead, the dioxygenase reaction can be initiated by a direct attack of heme-bound dioxygen on the C2=C3 bond of the indole ring, leading to a protein-stabilized 2,3-alkylperoxide transition state and a ferryl epoxide intermediate, which subsequently recombine to generate NFK. The novel sequential two-step oxygen addition mechanism is fully supported by our recent resonance Raman data that allowed identification of the ferryl intermediate (Lewis-Ballester et al. in Proc Natl Acad Sci USA 106:17371–17376, 2009). The results reveal the subtle differences between the TDO and IDO reactions and highlight the importance of protein matrix in modulating stereoelectronic factors for oxygen activation and the stabilization of both transition and intermediate states. PMID:20361220

  13. A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution.

    PubMed

    Aidas, Kęstutis; Ågren, Hans; Kongsted, Jacob; Laaksonen, Aatto; Mocci, Francesca

    2013-02-07

    The (23)Na quadrupolar coupling constant of the Na(+) ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na(+) ions in solution are found to differ significantly.

  14. Why does the G117H mutation considerably improve the activity of human butyrylcholinesterase against sarin? Insights from quantum mechanical/molecular mechanical free energy calculations.

    PubMed

    Yao, Yuan; Liu, Junjun; Zhan, Chang-Guo

    2012-11-06

    Human butyrylcholinesterase (BChE) is recognized as the most promising bioscavenger for organophosphorus (OP) warfare nerve agents. The G117H mutant of human BChE has been identified as a potential catalytic bioscavenger with a remarkably improved activity against OP nerve agents such as sarin, but it still does not satisfy the clinical use. For further design of the higher-activity mutants against OP nerve agents, it is essential to understand how the G117H mutation improves the activity. The reaction mechanisms and the free energy profiles for spontaneous reactivation of wild-type BChE and its G117H mutant phosphorylated by sarin have been explored, in this study, by performing first-principles quantum mechanical/molecular mechanical free energy calculations, and the remarkable role of the G117H mutation on the activity has been elucidated. For both the wild-type and G117H mutant enzymes, H438 acts as a general base to initiate the spontaneous reactivation that consists of two reaction steps: the nucleophilic attack at the phosphorus by a water molecule and decomposition of the pentacoordinated phosphorus intermediate. The calculated overall free energy barriers, i.e., 30.2 and 23.9 kcal/mol for the wild type and G117H mutant, respectively, are in good agreement with available experimental kinetic data. On the basis of the calculated results, the mutated residue (H117 in the G117H mutant) cannot initiate the spontaneous reactivation as a general base. Instead, it skews the oxyanion hole and makes the phosphorus more open to the nucleophilic water molecule, resulting in a remarkable change in the rate-determining step and significantly improved catalytic activity of human BChE.

  15. 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.

  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. Solvatochromic shift of phenol blue in water from a combined Car-Parrinello molecular dynamics hybrid quantum mechanics-molecular mechanics and ZINDO approach

    NASA Astrophysics Data System (ADS)

    Murugan, N. Arul; Jha, Prakash Chandra; Rinkevicius, Z.; Ruud, Kenneth; Ågren, Hans

    2010-06-01

    The present work addresses the solvatochromic shift of phenol blue (PB) dye. For this purpose the results of Car-Parrinello molecular dynamics (CPMD) simulations for PB in gas phase are compared with results obtained for PB in water from CPMD hybrid quantum mechanics-molecular mechanics (CPMD-QM/MM) calculations. The absorption spectra were obtained using the intermediate neglect of differential overlap/spectroscopic-configuration interaction (INDO/CIS) method and were calculated for a multitude of configurations of the trajectory. The calculated λmax for PB in gas phase was found to be about 535 nm, which is considerably lower than the λmax reported for PB in nonpolar solvents. Different solvation shells for PB in water have been defined based on the solute-all-atoms and solvent center of mass radial distribution function (g(rX-O)). The electronic excitation energies for PB computed in the presence of solvent molecules in an increasing number of solvation shells were calculated in a systematic way to evaluate their contributions to the solvatochrmic shift. The inclusion of solvent molecules in the hydration shell yields a λmax of 640 nm, which contributes to almost 78% of the solvatochromic shift. The inclusion of solvent molecules up to 10 Å in the g(rX-O) rdf yields a λmax of 670 nm which is in good agreement with the experimentally reported value of 654-684 nm. Overall, the present study suggests that the combined CPMD-QM/MM and INDO-CIS approach can be used successfully to model solvatochromic shifts of organic dye molecules.

  18. Solvatochromic shift of phenol blue in water from a combined Car-Parrinello molecular dynamics hybrid quantum mechanics-molecular mechanics and ZINDO approach.

    PubMed

    Murugan, N Arul; Jha, Prakash Chandra; Rinkevicius, Z; Ruud, Kenneth; Agren, Hans

    2010-06-21

    The present work addresses the solvatochromic shift of phenol blue (PB) dye. For this purpose the results of Car-Parrinello molecular dynamics (CPMD) simulations for PB in gas phase are compared with results obtained for PB in water from CPMD hybrid quantum mechanics-molecular mechanics (CPMD-QM/MM) calculations. The absorption spectra were obtained using the intermediate neglect of differential overlap/spectroscopic-configuration interaction (INDO/CIS) method and were calculated for a multitude of configurations of the trajectory. The calculated lambda(max) for PB in gas phase was found to be about 535 nm, which is considerably lower than the lambda(max) reported for PB in nonpolar solvents. Different solvation shells for PB in water have been defined based on the solute-all-atoms and solvent center of mass radial distribution function (g(r(X-O))). The electronic excitation energies for PB computed in the presence of solvent molecules in an increasing number of solvation shells were calculated in a systematic way to evaluate their contributions to the solvatochrmic shift. The inclusion of solvent molecules in the hydration shell yields a lambda(max) of 640 nm, which contributes to almost 78% of the solvatochromic shift. The inclusion of solvent molecules up to 10 A in the g(r(X-O)) rdf yields a lambda(max) of 670 nm which is in good agreement with the experimentally reported value of 654-684 nm. Overall, the present study suggests that the combined CPMD-QM/MM and INDO-CIS approach can be used successfully to model solvatochromic shifts of organic dye molecules.

  19. Importance of polarization in quantum mechanics/molecular mechanics descriptions of electronic excited states: NaI(H2O)n photodissociation dynamics as a case study.

    PubMed

    Koch, Denise M; Peslherbe, Gilles H

    2008-01-17

    Sodium iodide has long been a paradigm for ionic and covalent curve crossing and ultrafast nonadiabatic dynamics, and our interest lies in the influence of solvation on this process. The NaI(H2O)n photodissociation dynamics are simulated with the molecular dynamics with quantum transitions method. A quantum mechanics/molecular mechanics (QM/MM) description is adopted for the NaI(H2O)n electronic states, in which a semiempirical valence bond approach is used to describe the NaI electronic structure, and a polarizable optimized potential for cluster simulations model is used to describe solute-solvent and solvent-solvent interactions. In contrast to previous work with a nonpolarizable MM model [Koch et al., J. Phys. Chem. A, 2006, 110, 1438], this approach predicts that the NaI ionic ground- to covalent first-excited-state Franck-Condon energy gaps reach a plateau by cluster size 16, in relatively good agreement with experiment and electronic structure calculations; this allows us to safely extend our previous simulations to larger cluster sizes, i.e., n > 4. The simulations suggest that the disappearance of the two-photon ionization probe signals observed in femtosecond pump-probe experiments of NaI(H2O)n, n >/= 4, is due to the shift of the NaI curve-crossing region toward larger NaI internuclear separations because of solvent stabilization of the NaI ionic state. Further, the latter causes the adiabatic ground and excited states to acquire pure ionic and covalent character, respectively, by cluster 8, resulting in NaI ionic ground-state recombination or dissociation. To make a connection with electron transfer in solution, free energy curves have been generated as a function of a solvent coordinate similar to that of solution theory. Inspection of the free energy curves together with the results of excited-state simulations reveal that the electron-transfer process in clusters is not governed by the collective motion of the solvent molecules, as in solution, but

  20. Fluorescence of tryptophan in designed hairpin and Trp-cage miniproteins: measurements of fluorescence yields and calculations by quantum mechanical molecular dynamics simulations.

    PubMed

    McMillan, Andrew W; Kier, Brandon L; Shu, Irene; Byrne, Aimee; Andersen, Niels H; Parson, William W

    2013-02-14

    The quantum yield of tryptophan (Trp) fluorescence was measured in 30 designed miniproteins (17 β-hairpins and 13 Trp-cage peptides), each containing a single Trp residue. Measurements were made in D(2)O and H(2)O to distinguish between fluorescence quenching mechanisms involving electron and proton transfer in the hairpin peptides, and at two temperatures to check for effects of partial unfolding of the Trp-cage peptides. The extent of folding of all the peptides also was measured by NMR. The fluorescence yields ranged from 0.01 in some of the Trp-cage peptides to 0.27 in some hairpins. Fluorescence quenching was found to occur by electron transfer from the excited indole ring of the Trp to a backbone amide group or the protonated side chain of a nearby histidine, glutamate, aspartate, tyrosine, or cysteine residue. Ionized tyrosine side chains quenched strongly by resonance energy transfer or electron transfer to the excited indole ring. Hybrid classical/quantum mechanical molecular dynamics simulations were performed by a method that optimized induced electric dipoles separately for the ground and excited states in multiple π-π* and charge-transfer (CT) excitations. Twenty 0.5 ns trajectories in the tryptophan's lowest excited singlet π-π* state were run for each peptide, beginning by projections from trajectories in the ground state. Fluorescence quenching was correlated with the availability of a CT or exciton state that was strongly coupled to the π-π* state and that matched or fell below the π-π* state in energy. The fluorescence yields predicted by summing the calculated rates of charge and energy transfer are in good accord with the measured yields.

  1. Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: study of the optical and magnetic properties of diazines in water.

    PubMed

    Manzoni, Vinícius; Lyra, Marcelo L; Coutinho, Kaline; Canuto, Sylvio

    2011-10-14

    A combination of the polarizable continuum model (PCM) and the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology, PCM-MM/QM, is used to include the solute electronic polarization and then study the solvent effects on the low-lying n→π(∗) excitation energy and the (15)N nuclear magnetic shielding of pyrazine and pyridazine in aqueous environment. The results obtained with PCM-MM/QM are compared with two other procedures, i.e., the conventional PCM and the iterative and sequential QM/MM (I-QM/MM). The QM calculations are made using density functional theory in the three procedures. For the excitation energies, the time-dependent B3LYP/6-311+G(d) model is used. For the magnetic shielding, the B3LYP/aug-pcS2(N)/pcS2(C,O,H) is used with the gauge-including atomic orbitals. In both cases, i.e., PCM-MM/QM and I-QM/MM, that use a discrete model of the solvent, the solute is surrounded by a first shell of explicit water molecules embedded by an electrostatic field of point charges for the outer shells. The best results are obtained including 28 explicit water molecules for the spectral calculations and 9 explicit water molecules for the magnetic shielding. Using the PCM-MM/QM methodology the results for the n→π(∗) excitation energies of pyridazine and pyrazine are 32,070 ± 80 cm(-1) and 32,675 ± 60 cm(-1), respectively, in good agreement with the corresponding I-MM/QM results of 32,540 ± 80 cm(-1) and 32,710 ± 60 cm(-1) and the experimental results of 33,450-33,580 cm(-1) and 32,700-33,300 cm(-1). For the (15)N magnetic shielding, the corresponding numbers for the gas-water shifts obtained with PCM-MM/QM are 47.4 ± 1.3 ppm for pyridazine and 19.7 ± 1.1 ppm for pyrazine, compared with the I-QM/MM values of 53.4 ± 1.3 ppm and 19.5 ± 1.2 ppm and the experimental results of 42-54 ppm and 17-22 ppm, respectively. The agreement between the two procedures is found to be very good and both are in agreement with the experimental values. PCM

  2. Photoabsorption of acridine yellow and proflavin bound to human serum albumin studied by means of quantum mechanics/molecular dynamics.

    PubMed

    Aidas, Kęstutis; Olsen, Jógvan Magnus H; Kongsted, Jacob; Ågren, Hans

    2013-02-21

    Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site 1 nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

  3. Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase

    NASA Astrophysics Data System (ADS)

    Ishida, Toyokazu

    2008-09-01

    In this study, we investigated the electronic character of protein environment in enzymatic processes by performing all-electron QM calculations based on the fragment molecular orbital (FMO) method. By introducing a new computational strategy combining all-electron QM analysis with ab initio QM/MM modeling, we investigated the details of molecular interaction energy between a reactive substrate and amino acid residues at a catalytic site. For a practical application, we selected the chorismate mutase catalyzed reaction as an example. Because the computational time required to perform all-electron QM reaction path searches was very large, we employed the ab initio QM/MM modeling technique to construct reliable reaction profiles and performed all-electron FMO calculations for the selected geometries. The main focus of the paper is to analyze the details of electrostatic stabilization, which is considered to be the major feature of enzymatic catalyses, and to clarify how the electronic structure of proteins is polarized in response to the change in electron distribution of the substrate. By performing interaction energy decomposition analysis from a quantum chemical viewpoint, we clarified the relationship between the location of amino acid residues on the protein domain and the degree of electronic polarization of each residue. In particular, in the enzymatic transition state, Arg7, Glu78, and Arg90 are highly polarized in response to the delocalized electronic character of the substrate, and as a result, a large amount of electrostatic stabilization energy is stored in the molecular interaction between the enzyme and the substrate and supplied for transition state stabilization.

  4. Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase.

    PubMed

    Ishida, Toyokazu

    2008-09-28

    In this study, we investigated the electronic character of protein environment in enzymatic processes by performing all-electron QM calculations based on the fragment molecular orbital (FMO) method. By introducing a new computational strategy combining all-electron QM analysis with ab initio QM/MM modeling, we investigated the details of molecular interaction energy between a reactive substrate and amino acid residues at a catalytic site. For a practical application, we selected the chorismate mutase catalyzed reaction as an example. Because the computational time required to perform all-electron QM reaction path searches was very large, we employed the ab initio QM/MM modeling technique to construct reliable reaction profiles and performed all-electron FMO calculations for the selected geometries. The main focus of the paper is to analyze the details of electrostatic stabilization, which is considered to be the major feature of enzymatic catalyses, and to clarify how the electronic structure of proteins is polarized in response to the change in electron distribution of the substrate. By performing interaction energy decomposition analysis from a quantum chemical viewpoint, we clarified the relationship between the location of amino acid residues on the protein domain and the degree of electronic polarization of each residue. In particular, in the enzymatic transition state, Arg7, Glu78, and Arg90 are highly polarized in response to the delocalized electronic character of the substrate, and as a result, a large amount of electrostatic stabilization energy is stored in the molecular interaction between the enzyme and the substrate and supplied for transition state stabilization.

  5. 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.

  6. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations.

    PubMed

    Ardèvol, Albert; Rovira, Carme

    2015-06-24

    Carbohydrate-active enzymes such as glycoside hydrolases (GHs) and glycosyltransferases (GTs) are of growing importance as drug targets. The development of efficient competitive inhibitors and chaperones to treat diseases related to these enzymes requires a detailed knowledge of their mechanisms of action. In recent years, sophisticated first-principles modeling approaches have significantly advanced in our understanding of the catalytic mechanisms of GHs and GTs, not only the molecular details of chemical reactions but also the significant implications that just the conformational dynamics of a sugar ring can have on these mechanisms. Here we provide an overview of the progress that has been made in the past decade, combining molecular dynamics simulations with density functional theory to solve these sweet mysteries of nature.

  7. 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.

  8. 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.

  9. Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations.

    PubMed

    Giese, Timothy J; York, Darrin M

    2007-11-21

    This work explores a new charge-dependent energy model consisting of van der Waals and polarization interactions between the quantum mechanical (QM) and molecular mechanical (MM) regions in a combined QMMM calculation. van der Waals interactions are commonly treated using empirical Lennard-Jones potentials, whose parameters are often chosen based on the QM atom type (e.g., based on hybridization or specific covalent bonding environment). This strategy for determination of QMMM nonbonding interactions becomes tedious to parametrize and lacks robust transferability. Problems occur in the study of chemical reactions where the "atom type" is a complex function of the reaction coordinate. This is particularly problematic for reactions, where atoms or localized functional groups undergo changes in charge state and hybridization. In the present work we propose a new model for nonelectrostatic nonbonded interactions in QMMM calculations that overcomes many of these problems. The model is based on a scaled overlap model for repulsive exchange and attractive dispersion interactions that is a function of atomic charge. The model is chemically significant since it properly correlates atomic size, softness, polarizability, and dispersion terms with minimal one-body parameters that are functions of the atomic charge. Tests of the model are examined for rare-gas interactions with neutral and charged atoms in order to demonstrate improved transferability. The present work provides a new framework for modeling QMMM interactions with improved accuracy and transferability.

  10. Molybdenum carbide nanocatalysts at work in the in situ environment: a density functional tight-binding and quantum mechanical/molecular mechanical study.

    PubMed

    Liu, Xingchen; Salahub, Dennis R

    2015-04-01

    Heterogeneous reactions catalyzed by transition-metal-containing nanoparticles represent a crucial type of reaction in chemical industry. Because of the existing gap in understanding heterogeneous catalysis between a cluster of a few atoms and a bulk model of periodic slabs, reactions catalyzed by transition-metal-containing nanoparticles are still not well understood. Herein, we provide a multiscale modeling approach to study the benzene hydrogenation reactions on molybdenum carbide nanoparticles (MCNPs) in the process of in situ heavy oil upgrading. By coupling the quantum mechanical (QM) density functional tight-binding (DFTB) method with a molecular mechanical (MM) force field, a QM/MM model was built to describe the reactants, the nanoparticles and the surroundings. Umbrella sampling (US) was used to calculate the free energy profiles of the benzene hydrogenation reactions in a model aromatic solvent in the in situ heavy oil upgrading conditions. By comparing with the traditional method in computational heterogeneous catalysis, the results reveal new features of the metallic MCNPs. Rather than being rigid, they are very flexible under working condition due to the entropic contributions of the MCNPs and the solvent, which greatly affect the free energy profiles of these nanoscale heterogeneous reactions.

  11. Role of a Water Network around the Mn4CaO5 Cluster in Photosynthetic Water Oxidation: A Fourier Transform Infrared Spectroscopy and Quantum Mechanics/Molecular Mechanics Calculation Study.

    PubMed

    Nakamura, Shin; Ota, Kai; Shibuya, Yuichi; Noguchi, Takumi

    2016-01-26

    Photosynthetic water oxidation takes place at the Mn4CaO5 cluster in photosystem II. Around the Mn4CaO5 cluster, a hydrogen bond network is formed by several water molecules, including four water ligands. To clarify the role of this water network in the mechanism of water oxidation, we investigated the effects of the removal of Ca(2+) and substitution with metal ions on the vibrations of water molecules coupled to the Mn4CaO5 cluster by means of Fourier transform infrared (FTIR) difference spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. The OH stretching vibrations of nine water molecules forming a network between D1-D61 and YZ were calculated using the QM/MM method. On the the calculated normal modes, a broad positive feature at 3200-2500 cm(-1) in an S2-minus-S1 FTIR spectrum was attributed to the vibrations of strongly hydrogen-bonded OH bonds of water involving the vibrations of water ligands to a Mn ion and the in-phase coupled vibration of a water network connected to YZ, while bands in the 3700-3500 cm(-1) region were assigned to the coupled vibrations of weakly hydrogen-bonded OH bonds of water. All the water bands were lost upon Ca(2+) depletion and Ba(2+) substitution, which inhibit the S2 → S3 transition, indicating that a solid water network was broken by these treatments. By contrast, Sr(2+) substitution slightly altered the water bands around 3600 cm(-1), reflecting minor modification in water interactions, consistent with the retention of water oxidation activity with a decreased efficiency. These results suggest that the water network around the Mn4CaO5 cluster plays an essential role in the water oxidation mechanism particularly in a concerted process of proton transfer and water insertion during the S2 → S3 transition.

  12. X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs

    PubMed Central

    2015-01-01

    Mercuric reductase, MerA, is a key enzyme in bacterial mercury resistance. This homodimeric enzyme captures and reduces toxic Hg2+ to Hg0, which is relatively unreactive and can exit the cell passively. Prior to reduction, the Hg2+ 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 Hg2+ complex of the C136A/C141A double mutant of the Tn501 MerA catalytic 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, Hg2+ 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 Hg2+ transfer, C141 is negatively charged. As Hg2+ 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 Hg2+ with a competition between the Hg2+ and protons for the thiolates. PMID:25343681

  13. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

    NASA Astrophysics Data System (ADS)

    Hu, Hao; Lu, Zhenyu; Parks, Jerry M.; Burger, Steven K.; Yang, Weitao

    2008-01-01

    To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the

  14. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

    SciTech Connect

    Hu Hao; Lu Zhenyu; Parks, Jerry M.; Burger, Steven K.; Yang Weitao

    2008-01-21

    To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the

  15. Novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: Free energy calculation for the Beckmann rearrangement promoted by proton transfers in the supercritical water

    NASA Astrophysics Data System (ADS)

    Takahashi, Hideaki; Tanabe, Kohsuke; Aketa, Masataka; Kishi, Ryohei; Furukawa, Shin-ichi; Nakano, Masayoshi

    2007-02-01

    The Beckmann rearrangement of acetone oxime promoted by proton transfers in the supercritical water has been investigated by means of the hybrid quantum mechanical/molecular mechanical approach combined with the theory of energy representation (QM/MM-ER) recently developed. The transition state (TS) structures have been explored by ab initio calculations for the reaction of hydrated acetone oxime on the assumption that the reaction is catalyzed by proton transfers along the hydrogen bonds connecting the solute and the solvent water molecules. Up to two water molecules have been considered as reactants that take part in the proton transfers. As a result of the density functional theory calculations with B3LYP functional and aug-cc-pVDZ basis set, it has been found that participation of two water molecules in the reaction reduces the activation free energy by -12.3kcal/mol. Furthermore, the QM/MM-ER simulations have revealed that the TS is more stabilized than the reactant state in the supercritical water by 2.7kcal/mol when two water molecules are involved in the reaction. Solvation free energies of the reactant and the TS have been decomposed into terms due to the electronic polarization of the solute, electron density fluctuation, and others to elucidate the origin of the stabilization of the TS as compared with the reactant. It has been revealed that the promotion of the chemical reaction due to the hydration mainly originates from the interaction between the nonpolarized solute and the solvent water molecules at the supercritical state.

  16. Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

    PubMed

    Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

    2016-08-05

    The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc.

  17. The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.

    PubMed

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

    2017-01-17

    Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn4O5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S1 state. However, the atom positions in this crystal

  18. Solvatochromic shifts of polar and non-polar molecules in ambient and supercritical water: a sequential quantum mechanics/molecular mechanics study including solute-solvent electron exchange-correlation.

    PubMed

    Ma, Haibo; Ma, Yingjin

    2012-12-07

    Polar and non-polar solutes (acetone and benzene) dissolved in ambient water and supercritical water are investigated theoretically using a sequential quantum mechanics (QM)/molecular mechanics (MM) method which combines classical molecular dynamics simulations and QM/MM calculations. From the detailed analysis of the dependence of the QM region size and point charge background region size as well as the different functionals, it is found that the inclusion of the solvent molecules within the first solvation shell into the QM region to account for the exchange-correlation between a solute and neighboring solvent molecules is important for the highly accurate spectral shift calculations, especially vital for the non-polar solutes whose interactions with the solvents are dominated by the quantum dispersions. At the same time, sufficiently large surrounding partial charge region (r(cutoff) ≥15 Å) as well as the functional corrections to describe the long-range dispersion-corrections are also essential for the study of the electronic excited states in condensed phase. Our calculated solvatochromic shift values and their density dependencies at ambient and high temperature conditions are found to be in good agreements with experimental observations. This indicates that sound theoretical studies of solvatochromic shift can be achieved provided that a reasonable computational scheme with sufficiently large N(water) (QM) and r(cutoff) values is implemented. We also find both of aqueous acetone and aqueous benzene under high temperatures present three distinctive regions: low-density gas-like region, supercritical region, and high-density liquid-like region. The plateau behavior of solvatochromic shift in the supercritical region can be ascribed to the solvent clustering around the solute, which is a fundamental phenomenon of supercritical fluids (SCFs). The density dependence of our calculated coordination number of the first solvation shell nicely reproduces the trend

  19. Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Commins, Eugene D.

    2014-10-01

    Preface; 1. Introduction; 2. Mathematical preliminaries; 3. The rules of quantum mechanics; 4. The connection between the fundamental rules and wave mechanics; 5. Further illustrations of the rules of quantum mechanics; 6. Further developments in one-dimensional wave mechanics; 7. The theory of angular momentum; 8. Wave mechanics in three dimensions: hydrogenic atoms; 9. Time-independent approximations for bound state problems; 10. Applications of static perturbation theory; 11. Identical particles; 12. Atomic structure; 13. Molecules; 14. The stability of matter; 15. Photons; 16. Interaction of non-relativistic charged particles and radiation; 17. Further topics in perturbation theory; 18. Scattering; 19. Special relativity and quantum mechanics: the Klein-Gordon equation; 20. The Dirac equation; 21. Interaction of a relativistic spin 1/2 particle with an external electromagnetic field; 22. The Dirac field; 23. Interaction between relativistic electrons, positrons, and photons; 24. The quantum mechanics of weak interactions; 25. The quantum measurement problem; Appendix A: useful inequalities for quantum mechanics; Appendix B: Bell's inequality; Appendix C: spin of the photon: vector spherical waves; Works cited; Bibliography; Index.

  20. Emergence of Function in P450-Proteins: A Combined Quantum Mechanical/Molecular Mechanical and Molecular Dynamics Study of the Reactive Species in the H2O2-Dependent Cytochrome P450SPα and Its Regio- and Enantioselective Hydroxylation of Fatty Acids.

    PubMed

    Ramanan, Rajeev; Dubey, Kshatresh Dutta; Wang, Binju; Mandal, Debasish; Shaik, Sason

    2016-06-01

    This work uses combined quantum mechanical/molecular mechanical and molecular dynamics simulations to investigate the mechanism and selectivity of H2O2-dependent hydroxylation of fatty acids by the P450SPα class of enzymes. H2O2 is found to serve as the surrogate oxidant for generating the principal oxidant, Compound I (Cpd I), in a mechanism that involves homolytic O-O bond cleavage followed by H-abstraction from the Fe-OH moiety. Our results rule out a substrate-assisted heterolytic cleavage of H2O2 en route to Cpd I. We show, however, that substrate binding stabilizes the resultant Fe-H2O2 complex, which is crucial for the formation of Cpd I in the homolytic pathway. A network of hydrogen bonds locks the HO· radical, formed by the O-O homolysis, thus directing it to exclusively abstract the hydrogen atom from Fe-OH, thereby forming Cpd I, while preventing the autoxoidative reaction, with the porphyrin ligand, and the substrate oxidation. The so formed Cpd I subsequently hydroxylates fatty acids at their α-position with S-enantioselectivity. These selectivity patterns are controlled by the active site: substrate's binding by Arg241 determines the α-regioselectivity, while the Pro242 residue locks the prochiral α-CH2, thereby leading to hydroxylation of the pro-S C-H bond. Our study of the mutant Pro242Ala sheds light on potential modifications of the enzyme's active site in order to modify reaction selectivity. Comparisons of P450SPα to P450BM3 and to P450BSβ reveal that function has evolved in these related metalloenzymes by strategically placing very few residues in the active site.

  1. Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2000-11-01

    A development of quantum theory that was initiated in the 1920s by Werner Heisenberg (1901-76) and Erwin Schrödinger (1887-1961). The theory drew on a proposal made in 1925 Prince Louis de Broglie (1892-1987), that particles have wavelike properties (the wave-particle duality) and that an electron, for example, could in some respects be regarded as a wave with a wavelength that depended on its mo...

  2. 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.

  3. Is quantum mechanics exact?

    SciTech Connect

    Kapustin, Anton

    2013-06-15

    We formulate physically motivated axioms for a physical theory which for systems with a finite number of degrees of freedom uniquely lead to quantum mechanics as the only nontrivial consistent theory. Complex numbers and the existence of the Planck constant common to all systems arise naturally in this approach. The axioms are divided into two groups covering kinematics and basic measurement theory, respectively. We show that even if the second group of axioms is dropped, there are no deformations of quantum mechanics which preserve the kinematic axioms. Thus, any theory going beyond quantum mechanics must represent a radical departure from the usual a priori assumptions about the laws of nature.

  4. Relativity and Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Brändas, Erkki J.

    2007-12-01

    The old dilemma of quantum mechanics versus the theory of relativity is reconsidered via a first principles relativistically invariant theory. By analytic extension of quantum mechanics into the complex plane one may (i) include dynamical features such as time- and length-scales and (ii) examine the possibility and flexibility of so-called general Jordan block formations. The present viewpoint asks for a new perspective on the age-old problem of quantum mechanics versus the theory of relativity. To bring these ideas together, we will establish the relation with the Klein-Gordon-Dirac relativistic theory and confirm some dynamical features of both the special and the general relativity theory.

  5. 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)

  6. 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

  7. Grassmann matrix quantum mechanics

    SciTech Connect

    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. In conclusion, we discuss possible holographic interpretations of such matrix models which, by construction, are endowed with a finite dimensional Hilbert space.

  8. Copenhagen quantum mechanics

    NASA Astrophysics Data System (ADS)

    Hollowood, Timothy J.

    2016-07-01

    In our quantum mechanics courses, measurement is usually taught in passing, as an ad-hoc procedure involving the ugly collapse of the wave function. No wonder we search for more satisfying alternatives to the Copenhagen interpretation. But this overlooks the fact that the approach fits very well with modern measurement theory with its notions of the conditioned state and quantum trajectory. In addition, what we know of as the Copenhagen interpretation is a later 1950s development and some of the earlier pioneers like Bohr did not talk of wave function collapse. In fact, if one takes these earlier ideas and mixes them with later insights of decoherence, a much more satisfying version of Copenhagen quantum mechanics emerges, one for which the collapse of the wave function is seen to be a harmless book keeping device. Along the way, we explain why chaotic systems lead to wave functions that spread out quickly on macroscopic scales implying that Schrödinger cat states are the norm rather than curiosities generated in physicists' laboratories. We then describe how the conditioned state of a quantum system depends crucially on how the system is monitored illustrating this with the example of a decaying atom monitored with a time of arrival photon detector, leading to Bohr's quantum jumps. On the other hand, other kinds of detection lead to much smoother behaviour, providing yet another example of complementarity. Finally we explain how classical behaviour emerges, including classical mechanics but also thermodynamics.

  9. A generic basis for some simple light-operated mechanical molecular machines.

    PubMed

    Pérez, Emilio M; Dryden, David T F; Leigh, David A; Teobaldi, Gilberto; Zerbetto, Francesco

    2004-10-06

    A novel type of mechanical switch is described in which light-induced translation of a macrocycle in a [2]rotaxane quenches anthracene fluorescence. Features of the system include the remarkable 200:1 difference in fluorescence intensity between the two positional states of the molecule ( approximately 85:1 between one isomer and the photostationary state). In principle the same concept could be used for mechanically switching virtually any property that can be influenced by functional group proximity effects.

  10. Introduction to Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Griffiths, David J.

    2016-09-01

    Part I. Theory: 1. The wave function; 2. Time-independent Schrödinger equation; 3. Formalism; 4. Quantum mechanics in three dimensions; 5. Identical particles; Part II. Applications: 6. Time-independent perturbation theory; 7. The variational principle; 8. The WKB approximation; 9. Time-dependent perturbation theory; 10. The adiabatic approximation; 11. Scattering; 12. Afterword; Appendix. Linear algebra.

  11. Bohmian quantum mechanics with quantum trajectories

    NASA Astrophysics Data System (ADS)

    Jeong, Yeuncheol

    The quantum trajectory method in the hydrodynamical formulation of Madelung-Bohm-Takabayasi quantum mechanics is an example of showing the cognitive importance of scientific illustrations and metaphors, especially, in this case, in computational quantum chemistry and electrical engineering. The method involves several numerical schemes of solving a set of hydrodynamical equations of motion for probability density fluids, based on the propagation of those probability density trajectories. The quantum trajectory method gives rise to, for example, an authentic quantum electron transport theory of motion to, among others, classically-minded applied scientists who probably have less of a commitment to traditional quantum mechanics. They were not the usual audience of quantum mechanics and simply choose to use a non-Copenhagen type interpretation to their advantage. Thus, the metaphysical issues physicists had a trouble with are not the main concern of the scientists. With the advantages of a visual and illustrative trajectory, the quantum theory of motion by Bohm effectively bridges quantum and classical physics, especially, in the mesoscale domain. Without having an abrupt shift in actions and beliefs from the classical to the quantum world, scientists and engineers are able to enjoy human cognitive capacities extended into the quantum mechanical domain.

  12. Epigenetics: Biology's Quantum Mechanics.

    PubMed

    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.

  13. Quantum mechanics and quantum information theory

    NASA Astrophysics Data System (ADS)

    van Camp, Wesley William

    The principle aim of this dissertation is to investigate the philosophical application of quantum information theory to interpretational issues regarding the theory of quantum mechanics. Recently, quantum information theory has emerged as a potential source for such an interpretation. The main question with which this dissertation will be concerned is whether or not an information-theoretic interpretation can serve as a conceptually acceptable interpretation of quantum mechanics. It will be argued that some of the more obvious approaches -- that quantum information theory shows us that ultimately the world is made of information, and quantum Bayesianism -- fail as philosophical interpretations of quantum mechanics. However, the information-theoretic approach of Clifton, Bub, and Halvorson introduces Einstein's distinction between principle theories and constructive theories, arguing that quantum mechanics is best understood as an information-theoretic principle theory. While I argue that this particular approach fails, it does offer a viable new philosophical role for information theory. Specifically, an investigation of interpretationally successful principle theories such as Newtonian mechanics, special relativity, and general relativity, shows that the particular principles employed are necessary as constitutive elements of a framework which partially defines the basic explanatory concepts of space, time, and motion. Without such constitutive principles as preconditions for empirical meaning, scientific progress is hampered. It is argued that the philosophical issues in quantum mechanics stem from an analogous conceptual crisis. On the basis of this comparison, the best strategy for resolving these problems is to apply a similar sort of conceptual analysis to quantum mechanics so as to provide an appropriate set of constitutive principles clarifying the conceptual issues at stake. It is further argued that quantum information theory is ideally placed as a novel

  14. Quantum Mechanics, Volume 1

    NASA Astrophysics Data System (ADS)

    Cohen-Tannoudji, Claude; Diu, Bernard; Laloe, Frank

    1986-06-01

    Beginning students of quantum mechanics frequently experience difficulties separating essential underlying principles from the specific examples to which these principles have been historically applied. Nobel-Prize-winner Claude Cohen-Tannoudji and his colleagues have written this book to eliminate precisely these difficulties. Fourteen chapters provide a clarity of organization, careful attention to pedagogical details, and a wealth of topics and examples which make this work a textbook as well as a timeless reference, allowing to tailor courses to meet students' specific needs. Each chapter starts with a clear exposition of the problem which is then treated, and logically develops the physical and mathematical concept. These chapters emphasize the underlying principles of the material, undiluted by extensive references to applications and practical examples which are put into complementary sections. The book begins with a qualitative introduction to quantum mechanical ideas using simple optical analogies and continues with a systematic and thorough presentation of the mathematical tools and postulates of quantum mechanics as well as a discussion of their physical content. Applications follow, starting with the simplest ones like e.g. the harmonic oscillator, and becoming gradually more complicated (the hydrogen atom, approximation methods, etc.). The complementary sections each expand this basic knowledge, supplying a wide range of applications and related topics as well as detailed expositions of a large number of special problems and more advanced topics, integrated as an essential portion of the text.

  15. Supersymmetric Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    David, J.; Fernández, C.

    2010-10-01

    Supersymmetric quantum mechanics (SUSY QM) is a powerful tool for generating new potentials with known spectra departing from an initial solvable one. In these lecture notes we will present some general formulae concerning SUSY QM of first second order for one-dimensional arbitrary systems, we will illustrate the method through the trigonometric Pöschl-Teller potentials. Some intrinsically related subjects, as the algebraic structure inherited by the new Hamiltonians and the corresponding coherent states will be analyzed. The technique will be as well implemented for periodic potentials, for which the corresponding spectrum is composed of allowed bands separated by energy gaps.

  16. 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.

  17. Quantum Mechanics and Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Dimock, Jonathan

    2011-02-01

    Introduction; Part I. Non-relativistic: 1. Mathematical prelude; 2. Classical mechanics; 3. Quantum mechanics; 4. Single particle; 5. Many particles; 6. Statistical mechanics; Part II. Relativistic: 7. Relativity; 8. Scalar particles and fields; 9. Electrons and photons; 10. Field theory on a manifold; Part III. Probabilistic Methods: 11. Path integrals; 12. Fields as random variables; 13. A nonlinear field theory; Appendices; References; Index.

  18. 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

  19. Diagrammatic quantum mechanics

    NASA Astrophysics Data System (ADS)

    Kauffman, Louis H.; Lomonaco, Samuel J.

    2015-05-01

    This paper explores how diagrams of quantum processes can be used for modeling and for quantum epistemology. The paper is a continuation of the discussion where we began this formulation. Here we give examples of quantum networks that represent unitary transformations by dint of coherence conditions that constitute a new form of non-locality. Local quantum devices interconnected in space can form a global quantum system when appropriate coherence conditions are maintained.

  20. Klein's programme and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Clemente-Gallardo, Jesús; Marmo, Giuseppe

    2015-04-01

    We review the geometrical formulation of quantum mechanics to identify, according to Klein's programme, the corresponding group of transformations. For closed systems, it is the unitary group. For open quantum systems, the semigroup of Kraus maps contains, as a maximal subgroup, the general linear group. The same group emerges as the exponentiation of the C*-algebra associated with the quantum system, when thought of as a Lie algebra. Thus, open quantum systems seem to identify the general linear group as associated with quantum mechanics and moreover suggest to extend the Klein programme also to groupoids. The usual unitary group emerges as a maximal compact subgroup of the general linear group.

  1. 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.

  2. 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.

  3. 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.

  4. QUANTUM MECHANICS WITHOUT STATISTICAL POSTULATES

    SciTech Connect

    G. GEIGER; ET AL

    2000-11-01

    The Bohmian formulation of quantum mechanics describes the measurement process in an intuitive way without a reduction postulate. Due to the chaotic motion of the hidden classical particle all statistical features of quantum mechanics during a sequence of repeated measurements can be derived in the framework of a deterministic single system theory.

  5. Dissipative Forces and Quantum Mechanics

    ERIC Educational Resources Information Center

    Eck, John S.; Thompson, W. J.

    1977-01-01

    Shows how to include the dissipative forces of classical mechanics in quantum mechanics by the use of non-Hermetian Hamiltonians. The Ehrenfest theorem for such Hamiltonians is derived, and simple examples which show the classical correspondences are given. (MLH)

  6. Communication: Quantum mechanics without wavefunctions

    SciTech Connect

    Schiff, Jeremy; Poirier, Bill

    2012-01-21

    We present a self-contained formulation of spin-free non-relativistic quantum mechanics that makes no use of wavefunctions or complex amplitudes of any kind. Quantum states are represented as ensembles of real-valued quantum trajectories, obtained by extremizing an action and satisfying energy conservation. The theory applies for arbitrary configuration spaces and system dimensionalities. Various beneficial ramifications--theoretical, computational, and interpretational--are discussed.

  7. Quantum Mechanics in Insulators

    SciTech Connect

    Aeppli, G.

    2009-08-20

    Atomic physics is undergoing a large revival because of the possibility of trapping and cooling ions and atoms both for individual quantum control as well as collective quantum states, such as Bose-Einstein condensates. The present lectures start from the 'atomic' physics of isolated atoms in semiconductors and insulators and proceed to coupling them together to yield magnets undergoing quantum phase transitions as well as displaying novel quantum states with no classical analogs. The lectures are based on: G.-Y. Xu et al., Science 317, 1049-1052 (2007); G. Aeppli, P. Warburton, C. Renner, BT Technology Journal, 24, 163-169 (2006); H. M. Ronnow et al., Science 308, 392-395 (2005) and N. Q. Vinh et al., PNAS 105, 10649-10653 (2008).

  8. Quantum mechanics from invariance principles

    NASA Astrophysics Data System (ADS)

    Moldoveanu, Florin

    2015-07-01

    Quantum mechanics is an extremely successful theory of nature and yet it lacks an intuitive axiomatization. In contrast, the special theory of relativity is well understood and is rooted into natural or experimentally justified postulates. Here we introduce an axiomatization approach to quantum mechanics which is very similar to special theory of relativity derivation. The core idea is that a composed system obeys the same laws of nature as its components. This leads to a Jordan-Lie algebraic formulation of quantum mechanics. The starting assumptions are minimal: the laws of nature are invariant under time evolution, the laws of nature are invariant under tensor composition, the laws of nature are relational, together with the ability to define a physical state (positivity). Quantum mechanics is singled out by a fifth experimentally justified postulate: nature violates Bell's inequalities.

  9. Application of the AM1 and MNDO Semiempirical Quantum Mechanical Molecular Models.

    DTIC Science & Technology

    1986-12-01

    basic role in chemistry, in particular in biochemistry . A knowledge of the proton affinities (PA) of bases, and of the deprotonation enthalpies (DPE) of...moderate cost, AMI should prove useful as an aid in interpretating FIR proton transfer in chemistry and biochemistry . 4.’% -I,. 5...Buttrill, S.E., Jr. Org. Mass Spectrom. 1976, 11, 762. 23(a). Pollack, S. K.; Devlin , J.L., III; Suxnmerhays, K.D.; Taft, R.W.; Hehre, W. J. J. Am. Chem

  10. Non-Hermitian quantum mechanics

    NASA Astrophysics Data System (ADS)

    Jones-Smith, Katherine

    The basic structure of quantum mechanics was delineated in the early days of the theory and has not been modified since. One of the fundamental assumptions used in formulating the theory is that operators are represented by Hermitian matrices. In recent years it has been shown that quantum mechanics can be formulated consistently without making this assumption, using instead a combination of the parity (P) and time-reversal (T) operators and a number of other requirements related to P and T. Only the case of even T has been analyzed in the literature; here we generalize the principles to include odd time-reversal. We use this generalization to construct a non-Hermitian version of the Dirac equation, and in doing so discover a new type of particle not allowed within the (Hermitian) Standard Model. Finally we present a potential application of the ideas of non-Hermitian quantum mechanics to the unsolved problems of quantum magnetism and high temperature superconductivity.

  11. Kowalevski top in quantum mechanics

    SciTech Connect

    Matsuyama, A.

    2013-09-15

    The quantum mechanical Kowalevski top is studied by the direct diagonalization of the Hamiltonian. The spectra show different behaviors depending on the region divided by the bifurcation sets of the classical invariant tori. Some of these spectra are nearly degenerate due to the multiplicity of the invariant tori. The Kowalevski top has several symmetries and symmetry quantum numbers can be assigned to the eigenstates. We have also carried out the semiclassical quantization of the Kowalevski top by the EBK formulation. It is found that the semiclassical spectra are close to the exact values, thus the eigenstates can be also labeled by the integer quantum numbers. The symmetries of the system are shown to have close relations with the semiclassical quantum numbers and the near-degeneracy of the spectra. -- Highlights: •Quantum spectra of the Kowalevski top are calculated. •Semiclassical quantization is carried out by the EBK formulation. •Quantum states are labeled by the semiclassical integer quantum numbers. •Multiplicity of the classical torus makes the spectra nearly degenerate. •Symmetries, quantum numbers and near-degenerate spectra are closely related.

  12. Quantum Mechanics and Narratability

    NASA Astrophysics Data System (ADS)

    Myrvold, Wayne C.

    2016-07-01

    As has been noted by several authors, in a relativistic context, there is an interesting difference between classical and quantum state evolution. For a classical system, a state history of a quantum system given along one foliation uniquely determines, without any consideration of the system's dynamics, a state history along any other foliation. This is not true for quantum state evolution; there are cases in which a state history along one foliation is compatible with multiple distinct state histories along some other, a phenomenon that David Albert has dubbed "non-narratability." In this article, we address the question of whether non-narratability is restricted to the sorts of special states that so far have been used to illustrate it. The results of the investigation suggest that there has been a misplaced emphasis on underdetermination of state histories; though this is generic for the special cases that have up until now been considered, involving bipartite systems in pure entangled states, it fails generically in cases in which more component systems are taken into account, and for bipartite systems that have some entanglement with their environment. For such cases, if we impose relativistic causality constraints on the evolution, then, except for very special states, a state history along one foliation uniquely determines a state history along any other. But this in itself is a marked difference between classical and quantum state evolution, because, in a classical setting, no considerations of dynamics at all are needed to go from a state history along one foliation to a state history along another.

  13. 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…

  14. Energy conservation in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Prentis, Jeffrey J.; Fedak, William A.

    2004-05-01

    In the classical mechanics of conservative systems, the position and momentum evolve deterministically such that the sum of the kinetic energy and potential energy remains constant in time. This canonical trademark of energy conservation is absent in the standard presentations of quantum mechanics based on the Schrödinger picture. We present a purely canonical proof of energy conservation that focuses exclusively on the time-dependent position x(t) and momentum p(t) operators. This treatment of energy conservation serves as an introduction to the Heisenberg picture and illuminates the classical-quantum connection. We derive a quantum-mechanical work-energy theorem and show explicitly how the time dependence of x and p and the noncommutivity of x and p conspire to bring about a perfect temporal balance between the evolving kinetic and potential parts of the total energy operator.

  15. 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.

  16. Intrusion Detection With Quantum Mechanics: A Photonic Quantum Fence

    DTIC Science & Technology

    2008-12-01

    computing and quantum key distribution (QKD). Some of the most remarkable examples include quantum teleportation for the non-local transfer of...1 INTRUSION DETECTION WITH QUANTUM MECHANICS: A PHOTONIC QUANTUM FENCE T. S. Humble*, R. S. Bennink, and W. P. Grice Oak Ridge National...use of quantum -mechanically entangled photons for sensing intrusions across a physical perimeter. Our approach to intrusion detection uses the no

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

    SciTech Connect

    Hernandez, Hector H.; Chacon-Acosta, Guillermo

    2012-08-24

    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.

  18. Improving student understanding of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Singh, Chandralekha

    2015-04-01

    Learning quantum mechanics is challenging for many students. We are investigating the difficulties that upper-level students have in learning quantum mechanics. To help improve student understanding of quantum concepts, we are developing quantum interactive learning tutorials (QuILTs) and tools for peer-instruction. Many of the QuILTs employ computer simulations to help students visualize and develop better intuition about quantum phenomena. We will discuss the common students' difficulties and research-based tools we are developing to bridge the gap between quantitative and conceptual aspects of quantum mechanics and help students develop a solid grasp of quantum concepts. Support from the National Science Foundation is gratefully acknowledged.

  19. 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.

  20. 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.

  1. Quantum communication between remote mechanical resonators

    NASA Astrophysics Data System (ADS)

    Felicetti, S.; Fedortchenko, S.; Rossi, R.; Ducci, S.; Favero, I.; Coudreau, T.; Milman, P.

    2017-02-01

    Mechanical resonators represent one of the most promising candidates to mediate the interaction between different quantum technologies, bridging the gap between efficient quantum computation and long-distance quantum communication. Here, we introduce an interferometric scheme where the interaction of a mechanical resonator with input-output quantum pulses is controlled by an independent classical drive. We design protocols for state teleportation and direct quantum state transfer, between distant mechanical resonators. The proposed device, feasible with state-of-the-art technology, can serve as a building block for the implementation of long-distance quantum networks of mechanical resonators.

  2. 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

  3. Facets of contextual realism in quantum mechanics

    SciTech Connect

    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.

  4. Treating time travel quantum mechanically

    NASA Astrophysics Data System (ADS)

    Allen, John-Mark A.

    2014-10-01

    The fact that closed timelike curves (CTCs) are permitted by general relativity raises the question as to how quantum systems behave when time travel to the past occurs. Research into answering this question by utilizing the quantum circuit formalism has given rise to two theories: Deutschian-CTCs (D-CTCs) and "postselected" CTCs (P-CTCs). In this paper the quantum circuit approach is thoroughly reviewed, and the strengths and shortcomings of D-CTCs and P-CTCs are presented in view of their nonlinearity and time-travel paradoxes. In particular, the "equivalent circuit model"—which aims to make equivalent predictions to D-CTCs, while avoiding some of the difficulties of the original theory—is shown to contain errors. The discussion of D-CTCs and P-CTCs is used to motivate an analysis of the features one might require of a theory of quantum time travel, following which two overlapping classes of alternate theories are identified. One such theory, the theory of "transition probability" CTCs (T-CTCs), is fully developed. The theory of T-CTCs is shown not to have certain undesirable features—such as time-travel paradoxes, the ability to distinguish nonorthogonal states with certainty, and the ability to clone or delete arbitrary pure states—that are present with D-CTCs and P-CTCs. The problems with nonlinear extensions to quantum mechanics are discussed in relation to the interpretation of these theories, and the physical motivations of all three theories are discussed and compared.

  5. 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)

  6. Deformation of noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Jiang, Jian-Jian; Chowdhury, S. Hasibul Hassan

    2016-09-01

    In this paper, the Lie group GNC α , β , γ , of which the kinematical symmetry group GNC of noncommutative quantum mechanics (NCQM) is a special case due to fixed nonzero α, β, and γ, is three-parameter deformation quantized using the method suggested by Ballesteros and Musso [J. Phys. A: Math. Theor. 46, 195203 (2013)]. A certain family of QUE algebras, corresponding to GNC α , β , γ with two of the deformation parameters approaching zero, is found to be in agreement with the existing results of the literature on quantum Heisenberg group. Finally, we dualize the underlying QUE algebra to obtain an expression for the underlying star-product between smooth functions on GNC α , β , γ .

  7. 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.

  8. Matrix quantum mechanics from qubits

    NASA Astrophysics Data System (ADS)

    Hartnoll, Sean A.; Huijse, Liza; Mazenc, Edward A.

    2017-01-01

    We introduce a transverse field Ising model with order N 2 spins interacting via a nonlocal quartic interaction. The model has an O( N, ℤ), hyperoctahedral, symmetry. We show that the large N partition function admits a saddle point in which the symmetry is enhanced to O( N). We further demonstrate that this `matrix saddle' correctly computes large N observables at weak and strong coupling. The matrix saddle undergoes a continuous quantum phase transition at intermediate couplings. At the transition the matrix eigenvalue distribution becomes disconnected. The critical excitations are described by large N matrix quantum mechanics. At the critical point, the low energy excitations are waves propagating in an emergent 1 + 1 dimensional spacetime.

  9. Quantum-mechanical twin paradox

    NASA Astrophysics Data System (ADS)

    Franson, J. D.

    2016-10-01

    In the twin paradox of special relativity, an observer that travels along an accelerated trajectory at a high velocity will experience a smaller amount of elapsed time than an observer that remains at rest. This illustrates the fact that time is relative unlike the situation in classical physics where time is absolute. In a recent paper, Bushev et al (2016 New J. Phys. 18 093050) showed that the twin paradox can also be demonstrated using a single electron that functions as a quantum-mechanical clock. The wave function of the electron can travel along two different paths simultaneously, which allows a measurement of the difference in proper times along the two trajectories using a single particle. Quantum interference effects show that time cannot be thought of as a classical parameter even when associated with a single clock or observer.

  10. Mechanism for quantum speedup in open quantum systems

    NASA Astrophysics Data System (ADS)

    Liu, Hai-Bin; Yang, W. L.; An, Jun-Hong; Xu, Zhen-Yu

    2016-02-01

    The quantum speed limit (QSL) time for open system characterizes the most efficient response of the system to the environmental influences. Previous results showed that the non-Markovianity governs the quantum speedup. Via studying the dynamics of a dissipative two-level system, we reveal that the non-Markovian effect is only the dynamical way of the quantum speedup, while the formation of the system-environment bound states is the essential reason for the quantum speedup. Our attribution of the quantum speedup to the energy-spectrum character can supply another vital path for experiments when the quantum speedup shows up without any dynamical calculations. The potential experimental observation of our quantum speedup mechanism in the circuit QED system is discussed. Our results may be of both theoretical and experimental interest in exploring the ultimate QSL in realistic environments, and may open new perspectives for devising active quantum speedup devices.

  11. 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.

  12. A quantum mechanical/molecular mechanical study of the aspartic protease plasmepsin IV complexed with allophenylnorstatine-based inhibitor

    NASA Astrophysics Data System (ADS)

    Silva, Natália de Farias; Lameira, Jerônimo; Alves, Cláudio Nahum

    2011-06-01

    Plasmepsin IV (PM IV) is a potential target for developing drugs against malaria. This Letter presents results of QM/MM dynamic simulations applied to the study of the protonation state of two aspartates (Asp34 and Asp214) catalytic residues of PM IV in complex with KNI-764 inhibitor. The potential of mean force profile was used to assign the protonation state of the two catalytic aspartates in PM IV-KNI-764 complex. The results indicate that protonation of the 214 residue is more favorable. In addition, energy terms decomposition was used to explore key interactions between the main residues and KNI-764 inhibitor.

  13. Quantum mechanical/molecular mechanical/continuum style solvation model: Linear response theory, variational treatment, and nuclear gradients

    NASA Astrophysics Data System (ADS)

    Li, Hui

    2009-11-01

    Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S0→S1 excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

  14. Quantum mechanics in complex systems

    NASA Astrophysics Data System (ADS)

    Hoehn, Ross Douglas

    This document should be considered in its separation; there are three distinct topics contained within and three distinct chapters within the body of works. In a similar fashion, this abstract should be considered in three parts. Firstly, we explored the existence of multiply-charged atomic ions by having developed a new set of dimensional scaling equations as well as a series of relativistic augmentations to the standard dimensional scaling procedure and to the self-consistent field calculations. Secondly, we propose a novel method of predicting drug efficacy in hopes to facilitate the discovery of new small molecule therapeutics by modeling the agonist-protein system as being similar to the process of Inelastic Electron Tunneling Spectroscopy. Finally, we facilitate the instruction in basic quantum mechanical topics through the use of quantum games; this method of approach allows for the generation of exercises with the intent of conveying the fundamental concepts within a first year quantum mechanics classroom. Furthermore, no to be mentioned within the body of the text, yet presented in appendix form, certain works modeling the proliferation of cells types within the confines of man-made lattices for the purpose of facilitating artificial vascular transplants. In Chapter 2, we present a theoretical framework which describes multiply-charged atomic ions, their stability within super-intense laser fields, also lay corrections to the systems due to relativistic effects. Dimensional scaling calculations with relativistic corrections for systems: H, H-, H 2-, He, He-, He2-, He3- within super-intense laser fields were completed. Also completed were three-dimensional self consistent field calculations to verify the dimensionally scaled quantities. With the aforementioned methods the system's ability to stably bind 'additional' electrons through the development of multiple isolated regions of high potential energy leading to nodes of high electron density is shown

  15. Propagators in polymer quantum mechanics

    NASA Astrophysics Data System (ADS)

    Flores-González, Ernesto; Morales-Técotl, Hugo A.; Reyes, Juan D.

    2013-09-01

    Polymer Quantum Mechanics is based on some of the techniques used in the loop quantization of gravity that are adapted to describe systems possessing a finite number of degrees of freedom. It has been used in two ways: on one hand it has been used to represent some aspects of the loop quantization in a simpler context, and, on the other, it has been applied to each of the infinite mechanical modes of other systems. Indeed, this polymer approach was recently implemented for the free scalar field propagator. In this work we compute the polymer propagators of the free particle and a particle in a box; amusingly, just as in the non polymeric case, the one of the particle in a box may be computed also from that of the free particle using the method of images. We verify the propagators hereby obtained satisfy standard properties such as: consistency with initial conditions, composition and Green's function character. Furthermore they are also shown to reduce to the usual Schrödinger propagators in the limit of small parameter μ0, the length scale introduced in the polymer dynamics and which plays a role analog of that of Planck length in Quantum Gravity.

  16. Bridging classical and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Haddad, D.; Seifert, F.; Chao, L. S.; Li, S.; Newell, D. B.; Pratt, J. R.; Williams, C.; Schlamminger, S.

    2016-10-01

    Using a watt balance and a frequency comb, a mass-energy equivalence is derived. The watt balance compares mechanical power measured in terms of the meter, the second, and the kilogram to electrical power measured in terms of the volt and the ohm. A direct link between mechanical action and the Planck constant is established by the practical realization of the electrical units derived from the Josephson and the quantum Hall effects. By using frequency combs to measure velocities and acceleration of gravity, the unit of mass can be realized from a set of three defining constants: the Planck constant h, the speed of light c, and the hyperfine splitting frequency of 133Cs.

  17. 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).

  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. 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.

  20. 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.

  1. Towards a Constructive Foundation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Smilga, Walter

    2016-11-01

    I describe a constructive foundation for quantum mechanics, based on the discreteness of the degrees of freedom of quantum objects and on the Principle of Relativity. Taking Einstein's historical construction of Special Relativity as a model, the construction is carried out in close contact with a simple quantum mechanical Gedanken experiment. This leads to the standard axioms of quantum mechanics. The quantum mechanical description is identified as a mathematical tool that allows describing objects, whose degree of freedom in space-time has a discrete spectrum, relative to classical observers in space-time. This description is covariant with respect to (continuous) coordinate transformations and meets the requirement that the spectrum is the same in every inertial system. The construction gives detailed answers to controversial questions, such as the measurement problem, the informational content of the wave function, and the completeness of quantum mechanics.

  2. Towards a Constructive Foundation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Smilga, Walter

    2017-01-01

    I describe a constructive foundation for quantum mechanics, based on the discreteness of the degrees of freedom of quantum objects and on the Principle of Relativity. Taking Einstein's historical construction of Special Relativity as a model, the construction is carried out in close contact with a simple quantum mechanical Gedanken experiment. This leads to the standard axioms of quantum mechanics. The quantum mechanical description is identified as a mathematical tool that allows describing objects, whose degree of freedom in space-time has a discrete spectrum, relative to classical observers in space-time. This description is covariant with respect to (continuous) coordinate transformations and meets the requirement that the spectrum is the same in every inertial system. The construction gives detailed answers to controversial questions, such as the measurement problem, the informational content of the wave function, and the completeness of quantum mechanics.

  3. Bohmian mechanics and quantum field theory.

    PubMed

    Dürr, Detlef; Goldstein, Sheldon; Tumulka, Roderich; Zanghì, Nino

    2004-08-27

    We discuss a recently proposed extension of Bohmian mechanics to quantum field theory. For more or less any regularized quantum field theory there is a corresponding theory of particle motion, which, in particular, ascribes trajectories to the electrons or whatever sort of particles the quantum field theory is about. Corresponding to the nonconservation of the particle number operator in the quantum field theory, the theory describes explicit creation and annihilation events: the world lines for the particles can begin and end.

  4. A Bit of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Oss, Stefano; Rosi, Tommaso

    2015-04-01

    We have developed an app for iOS-based smart-phones/tablets that allows a 3-D, complex phase-based colorful visualization of hydrogen atom wave functions. Several important features of the quantum behavior of atomic orbitals can easily be made evident, thus making this app a useful companion in introductory modern physics classes. There are many reasons why quantum mechanical systems and phenomena are difficult both to teach and deeply understand. They are described by equations that are generally hard to visualize, and they often oppose the so-called "common sense" based on the human perception of the world, which is built on mental images such as locality and causality. Moreover students cannot have direct experience of those systems and solutions, and generally do not even have the possibility to refer to pictures, videos, or experiments to fill this gap. Teachers often encounter quite serious troubles in finding out a sensible way to speak about the wonders of quantum physics at the high school level, where complex formalisms are not accessible at all. One should however consider that this is quite a common issue in physics and, more generally, in science education. There are plenty of natural phenomena whose models (not only at microscopic and atomic levels) are of difficult, if not impossible, visualization. Just think of certain kinds of waves, fields of forces, velocities, energy, angular momentum, and so on. One should also notice that physical reality is not the same as the images we make of it. Pictures (formal, abstract ones, as well as artists' views) are a convenient bridge between these two aspects.

  5. 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

  6. Quantum mechanics without potential function

    SciTech Connect

    Alhaidari, A. D.; 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 is 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.

  7. Quantum mechanics of Proca fields

    NASA Astrophysics Data System (ADS)

    Zamani, Farhad; Mostafazadeh, Ali

    2009-05-01

    We construct the most general physically admissible positive-definite inner product on the space of Proca fields. Up to a trivial scaling this defines a five-parameter family of Lorentz invariant inner products that we use to construct a genuine Hilbert space for the quantum mechanics of Proca fields. If we identify the generator of time translations with the Hamiltonian, we obtain a unitary quantum system that describes first-quantized Proca fields and does not involve the conventional restriction to the positive-frequency fields. We provide a rather comprehensive analysis of this system. In particular, we examine the conserved current density responsible for the conservation of the probabilities, explore the global gauge symmetry underlying the conservation of the probabilities, obtain a probability current density, construct position, momentum, helicity, spin, and angular momentum operators, and determine the localized Proca fields. We also compute the generalized parity (P), generalized time-reversal (T), and generalized charge or chirality (C) operators for this system and offer a physical interpretation for its PT-, C-, and CPT-symmetries.

  8. Kindergarten Quantum Mechanics: Lecture Notes

    SciTech Connect

    Coecke, Bob

    2006-01-04

    These lecture notes survey some joint work with Samson Abramsky as it was presented by me at several conferences in the summer of 2005. It concerns 'doing quantum mechanics using only pictures of lines, squares, triangles and diamonds'. This picture calculus can be seen as a very substantial extension of Dirac's notation, and has a purely algebraic counterpart in terms of so-called Strongly Compact Closed Categories (introduced by Abramsky and I which subsumes my Logic of Entanglement. For a survey on the 'what', the 'why' and the 'hows' I refer to a previous set of lecture notes. In a last section we provide some pointers to the body of technical literature on the subject.

  9. Quantum mechanics, relativity and time

    NASA Astrophysics Data System (ADS)

    Basini, Giuseppe; Capozziello, Salvatore

    2005-01-01

    A discussion on quantum mechanics, general relativity and their relations is introduced. The assumption of the absolute validity of conservation laws and the extension to a 5D-space lead to reconsider several shortcomings and paradoxes of modern physics under a new light without the necessity to take into account symmetry breakings. In this picture, starting from first principles, and after a reduction procedure from 5D to 4D, dynamics leads to the natural emergence of two time arrows and ofa scalar-tensor theory of gravity. In this framework, phenomena like entanglement of systems and topology changes can be naturally accounted and, furthermore, several experimental evidences as gamma ray bursts, sizes of astrophysical structures and the observed values of cosmological parameters can be explained. The identification, thanks to conservation laws, of a covariant symplectic structure as a general feature also for gravity can be seen as a deep link common to all the interactions.

  10. 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.

  11. Quantum Mechanics and physical calculations

    NASA Astrophysics Data System (ADS)

    Karayan, H. S.

    2014-03-01

    We suggest to realize the computer simulation and calculation by the algebraic structure built on the basis of the logic inherent to processes in physical systems (called physical computing). We suggest a principle for the construction of quantum algorithms of neuroinformatics of quantum neural networks. The role of academician Sahakyan is emphasized in the development of quantum physics in Armenia.

  12. 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.

  13. Quantum Mechanics with a Little Less Mystery

    ERIC Educational Resources Information Center

    Cropper, William H.

    1969-01-01

    Suggests the "route of the inquiring mind in presenting the esoteric quantum mechanical postulates and concepts in an understandable form. Explains that the quantum mechanical postulates are but useful mathematical forms to express thebroader principles of superposition and correspondence. Briefly describes some of the features which makes the…

  14. 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.

  15. Quantum Mechanical Models Of The Fermi Shuttle

    SciTech Connect

    Sternberg, James

    2011-06-01

    The Fermi shuttle is a mechanism in which high energy electrons are produced in an atomic collision by multiple collisions with a target and a projectile atom. It is normally explained purely classically in terms of the electron's orbits prescribed in the collision. Common calculations to predict the Fermi shuttle use semi-classical methods, but these methods still rely on classical orbits. In reality such collisions belong to the realm of quantum mechanics, however. In this paper we discuss several purely quantum mechanical calculations which can produce the Fermi shuttle. Being quantum mechanical in nature, these calculations produce these features by wave interference, rather than by classical orbits.

  16. Strange Bedfellows: Quantum Mechanics and Data Mining

    SciTech Connect

    Weinstein, Marvin; /SLAC

    2009-12-16

    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.

  17. Quantum mechanics and the generalized uncertainty principle

    SciTech Connect

    Bang, Jang Young; Berger, Micheal S.

    2006-12-15

    The generalized uncertainty principle has been described as a general consequence of incorporating a minimal length from a theory of quantum gravity. We consider a simple quantum mechanical model where the operator corresponding to position has discrete eigenvalues and show how the generalized uncertainty principle results for minimum uncertainty wave packets.

  18. Principles and Dynamics of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Efthimiades, Spyros

    2009-05-01

    Quantum mechanics can be founded on three principles: particle waves, concurrent states and averaged energy relations. The Schrodinger, time-evolution and Dirac equations are derived to be the conditions the wavefunction must satisfy in order to fulfill the corresponding averaged energy relations. Adopting a particle and wave balanced approach we attain a clear, consistent and justified quantum theory.

  19. Dynamics of nonrelativistic quantum mechanics

    NASA Astrophysics Data System (ADS)

    Efthimiades, Spyros

    2017-01-01

    We show that the wavefunction of an electron interacting with an electric potential is accurately represented by the superposition of plane waves that fulfills the total energy relation. As a result, we explicitly derive the Schrödinger, Pauli, Klein-Gordon, and Dirac equations. While the traditional nonrelativistic quantum dynamics is based on postulates, the dynamics we introduce is theoretically justified, in agreement with experimental measurements, and consistent with the fundamental theory of quantum electrodynamics.

  20. 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)

  1. 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.

  2. Quantum mechanical stabilization of Minkowski signature wormholes

    SciTech Connect

    Visser, M.

    1989-05-19

    When one attempts to construct classical wormholes in Minkowski signature Lorentzian spacetimes violations of both the weak energy hypothesis and averaged weak energy hypothesis are encountered. Since the weak energy hypothesis is experimentally known to be violated quantum mechanically, this suggests that a quantum mechanical analysis of Minkowski signature wormholes is in order. In this note I perform a minisuperspace analysis of a simple class of Minkowski signature wormholes. By solving the Wheeler-de Witt equation for pure Einstein gravity on this minisuperspace the quantum mechanical wave function of the wormhole is obtained in closed form. The wormhole is shown to be quantum mechanically stabilized with an average radius of order the Planck length. 8 refs.

  3. 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.

  4. On the geometrization of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Tavernelli, Ivano

    2016-08-01

    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 induced 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.

  5. Macroscopic quantum mechanics in a classical spacetime.

    PubMed

    Yang, Huan; Miao, Haixing; Lee, Da-Shin; Helou, Bassam; Chen, Yanbei

    2013-04-26

    We apply the many-particle Schrödinger-Newton equation, which describes the coevolution of a many-particle quantum wave function and a classical space-time geometry, to macroscopic mechanical objects. By averaging over motions of the objects' internal degrees of freedom, we obtain an effective Schrödinger-Newton equation for their centers of mass, which can be monitored and manipulated at quantum levels by state-of-the-art optomechanics experiments. For a single macroscopic object moving quantum mechanically within a harmonic potential well, its quantum uncertainty is found to evolve at a frequency different from its classical eigenfrequency-with a difference that depends on the internal structure of the object-and can be observable using current technology. For several objects, the Schrödinger-Newton equation predicts semiclassical motions just like Newtonian physics, yet quantum uncertainty cannot be transferred from one object to another.

  6. Geometric Hamiltonian quantum mechanics and applications

    NASA Astrophysics Data System (ADS)

    Pastorello, Davide

    2016-08-01

    Adopting a geometric point of view on Quantum Mechanics is an intriguing idea since, we know that geometric methods are very powerful in Classical Mechanics then, we can try to use them to study quantum systems. In this paper, we summarize the construction of a general prescription to set up a well-defined and self-consistent geometric Hamiltonian formulation of finite-dimensional quantum theories, where phase space is given by the Hilbert projective space (as Kähler manifold), in the spirit of celebrated works of Kibble, Ashtekar and others. Within geometric Hamiltonian formulation quantum observables are represented by phase space functions, quantum states are described by Liouville densities (phase space probability densities), and Schrödinger dynamics is induced by a Hamiltonian flow on the projective space. We construct the star-product of this phase space formulation and some applications of geometric picture are discussed.

  7. On the geometrization of quantum mechanics

    SciTech Connect

    Tavernelli, Ivano

    2016-08-15

    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 induced 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.

  8. Antonio Gramsci's Reflection on Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Tassani, Isabella

    2006-06-01

    As the first step of a wider historical reconstruction of the reception of quantum mechanics in the nineteenth-century philosophy, we are going to consider Antonio Gramsci's philosophy. He asks himself about the nature of quantum objects, if their existence depends on the act of measuring by the experimenter and if this kind of relationship can be interpreted as an argument in favour of an immaterialistic philosophy. We will remark how an idealistic interpretation of quantum mechanics found a fertile field in the Italian culture, characterized by an antiscientific attitude and at the same time needing to find in science a term of comparison.

  9. Quantum mechanics near closed timelike lines

    NASA Astrophysics Data System (ADS)

    Deutsch, David

    1991-11-01

    The methods of the quantum theory of computation are used to analyze the physics of closed timelike lines. This is dominated, even at the macroscopic level, by quantum mechanics. In classical physics the existence of such lines in a spacetime imposes ``paradoxical'' constraints on the state of matter in their past and also provides means for knowledge to be created in ways that conflict with the principles of the philosophy of science. In quantum mechanics the first of these pathologies does not occur. The second is mitigated, and may be avoidable without such spacetimes being ruled out. Several novel and distinctive (but nonparadoxical) quantum-mechanical effects occur on and near closed timelike lines, including violations of the correspondence principle and of unitarity. It becomes possible to ``clone'' quantum systems and to measure the state of a quantum system. A new experimental test of the Everett interpretation against all others becomes possible. Consideration of these and other effects sheds light on the nature of quantum mechanics.

  10. Quantum Mechanical Molecular Interactions for Calculating the Excitation Energy in Molecular Environments: A First-Order Interacting Space Approach

    PubMed Central

    Hasegawa, Jun-ya; Yanai, Kazuma; Ishimura, Kazuya

    2015-01-01

    Intermolecular interactions regulate the molecular properties in proteins and solutions such as solvatochromic systems. Some of the interactions have to be described at an electronic-structure level. In this study, a commutator for calculating the excitation energy is used for deriving a first-order interacting space (FOIS) to describe the environmental response to solute excitation. The FOIS wave function for a solute-in-solvent cluster is solved by second-order perturbation theory. The contributions to the excitation energy are decomposed into each interaction and for each solvent. PMID:25393373

  11. Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study

    NASA Astrophysics Data System (ADS)

    Voityuk, Alexander A.

    2008-03-01

    The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15ns MD trajectories for several DNA oligomers, we calculate the average coupling squares ⟨V2⟩ and the energies of basepair triplets XG +Y and XA +Y, where X, Y =G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B-DNA structure and show that in several important cases the couplings calculated for the idealized B-DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ˜0.07eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The XG +Y are by 0.5eV more stable than XA +Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA.

  12. Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study.

    PubMed

    Voityuk, Alexander A

    2008-03-21

    The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the pi stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares V(2) and the energies of basepair triplets XG(+)Y and XA(+)Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15,000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B-DNA structure and show that in several important cases the couplings calculated for the idealized B-DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, approximately 0.07 eV, while the interstrand couplings are quite different. The energies of hole states G(+) and A(+) in the stack depend on the nature of the neighboring pairs. The XG(+)Y are by 0.5 eV more stable than XA(+)Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA.

  13. A "Bit" of Quantum Mechanics

    ERIC Educational Resources Information Center

    Oss, Stefano; Rosi, Tommaso

    2015-01-01

    We have developed an app for iOS-based smart-phones/tablets that allows a 3-D, complex phase-based colorful visualization of hydrogen atom wave functions. Several important features of the quantum behavior of atomic orbitals can easily be made evident, thus making this app a useful companion in introductory modern physics classes. There are many…

  14. 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.

  15. 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.

  16. Understanding formation mechanism of ZnO diatomic chain and multi-shell structure using physical mechanics: Molecular dynamics and first-principle simulations?

    NASA Astrophysics Data System (ADS)

    Wang, BinBin; Wang, FengChao; Zhao, YaPu

    2012-06-01

    In this paper, the possibility of the monatomic chain (MC) formation for ZnO material was studied by molecular dynamics (MD) simulation. The process of MC formation and the effects of temperature, strain rate and size were studied extensively. The tensile process can be divided to be five stages and the ZnO diatomic chain (DC) can be found. The MD results show that most atoms in MC came from the original surface of ZnO nanowires (NWs). Temperature and strain rate are two important factors affecting the process, and both high temperature and low strain rate in a certain range would be beneficial to the formation of DC. Moreover, the effects of strain rate and temperature could attribute to the Arrhenius model and the energy release mechanism. Furthermore, multi-shell structure was found for the samples under tensile strain and the layer-layer distance was about 3 Å. Our studies based on density functional theory showed that the most stable structure of ZnO DC was confirmed to be linear, and the I-V curve was also got using ATK.

  17. 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.

  18. Photon Quantum Mechanics in the Undergraduate Curriculum

    NASA Astrophysics Data System (ADS)

    Pearson, Brett; Carson, Zack; Jackson, David

    2011-05-01

    Although it has been discussed for centuries, the true nature of light is still being debated. In fact, the quantum mechanical aspects of light have only been observed within the past 30 years. Recent advances in technology have decreased the complexity of such tests, and the Department of Physics and Astronomy at Dickinson College has worked to infuse various quantum optics experiments throughout our curriculum. We describe a set of experiments that includes the existence of photons, single-photon interference, the quantum eraser, and tests of Bell's theorem. A primary motivation is bringing undergraduate students face to face with some of the fascinating and subtle aspects of quantum mechanics in a hands-on setting. Supported by Dickinson College and NSF DUE-0737230.

  19. Optimal guidance law in quantum mechanics

    SciTech Connect

    Yang, Ciann-Dong Cheng, Lieh-Lieh

    2013-11-15

    Following de Broglie’s idea of a pilot wave, this paper treats quantum mechanics as a problem of stochastic optimal guidance law design. The guidance scenario considered in the quantum world is that an electron is the flight vehicle to be guided and its accompanying pilot wave is the guidance law to be designed so as to guide the electron to a random target driven by the Wiener process, while minimizing a cost-to-go function. After solving the stochastic optimal guidance problem by differential dynamic programming, we point out that the optimal pilot wave guiding the particle’s motion is just the wavefunction Ψ(t,x), a solution to the Schrödinger equation; meanwhile, the closed-loop guidance system forms a complex state–space dynamics for Ψ(t,x), from which quantum operators emerge naturally. Quantum trajectories under the action of the optimal guidance law are solved and their statistical distribution is shown to coincide with the prediction of the probability density function Ψ{sup ∗}Ψ. -- Highlights: •Treating quantum mechanics as a pursuit-evasion game. •Reveal an interesting analogy between guided flight motion and guided quantum motion. •Solve optimal quantum guidance problem by dynamic programming. •Gives a formal proof of de Broglie–Bohm’s idea of a pilot wave. •The optimal pilot wave is shown to be a wavefunction solved from Schrödinger equation.

  20. Computations in quantum mechanics made easy

    NASA Astrophysics Data System (ADS)

    Korsch, H. J.; Rapedius, K.

    2016-09-01

    Convenient and simple numerical techniques for performing quantum computations based on matrix representations of Hilbert space operators are presented and illustrated by various examples. The applications include the calculations of spectral and dynamical properties for one-dimensional and two-dimensional single-particle systems as well as bosonic many-particle and open quantum systems. Due to their technical simplicity these methods are well suited as a tool for teaching quantum mechanics to undergraduates and graduates. Explicit implementations of the presented numerical methods in Matlab are given.

  1. Emergent quantum mechanics of finances

    NASA Astrophysics Data System (ADS)

    Nastasiuk, Vadim A.

    2014-06-01

    This paper is an attempt at understanding the quantum-like dynamics of financial markets in terms of non-differentiable price-time continuum having fractal properties. The main steps of this development are the statistical scaling, the non-differentiability hypothesis, and the equations of motion entailed by this hypothesis. From perspective of the proposed theory the dynamics of S&P500 index are analyzed.

  2. Multichannel framework for singular quantum mechanics

    SciTech Connect

    Camblong, Horacio E.; Epele, Luis N.; Fanchiotti, Huner; García Canal, Carlos A.; Ordóñez, Carlos R.

    2014-01-15

    A multichannel S-matrix framework for singular quantum mechanics (SQM) subsumes the renormalization and self-adjoint extension methods and resolves its boundary-condition ambiguities. In addition to the standard channel accessible to a distant (“asymptotic”) observer, one supplementary channel opens up at each coordinate singularity, where local outgoing and ingoing singularity waves coexist. The channels are linked by a fully unitary S-matrix, which governs all possible scenarios, including cases with an apparent nonunitary behavior as viewed from asymptotic distances. -- Highlights: •A multichannel framework is proposed for singular quantum mechanics and analogues. •The framework unifies several established approaches for singular potentials. •Singular points are treated as new scattering channels. •Nonunitary asymptotic behavior is subsumed in a unitary multichannel S-matrix. •Conformal quantum mechanics and the inverse quartic potential are highlighted.

  3. An Axiomatic Basis for Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Cassinelli, Gianni; Lahti, Pekka

    2016-10-01

    In this paper we use the framework of generalized probabilistic theories to present two sets of basic assumptions, called axioms, for which we show that they lead to the Hilbert space formulation of quantum mechanics. The key results in this derivation are the co-ordinatization of generalized geometries and a theorem of Solér which characterizes Hilbert spaces among the orthomodular spaces. A generalized Wigner theorem is applied to reduce some of the assumptions of Solér's theorem to the theory of symmetry in quantum mechanics. Since this reduction is only partial we also point out the remaining open questions.

  4. Two basic Uncertainty Relations in Quantum Mechanics

    SciTech Connect

    Angelow, Andrey

    2011-04-07

    In the present article, we discuss two types of uncertainty relations in Quantum Mechanics-multiplicative and additive inequalities for two canonical observables. The multiplicative uncertainty relation was discovered by Heisenberg. Few years later (1930) Erwin Schroedinger has generalized and made it more precise than the original. The additive uncertainty relation is based on the three independent statistical moments in Quantum Mechanics-Cov(q,p), Var(q) and Var(p). We discuss the existing symmetry of both types of relations and applicability of the additive form for the estimation of the total error.

  5. Two basic Uncertainty Relations in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Angelow, Andrey

    2011-04-01

    In the present article, we discuss two types of uncertainty relations in Quantum Mechanics-multiplicative and additive inequalities for two canonical observables. The multiplicative uncertainty relation was discovered by Heisenberg. Few years later (1930) Erwin Schrödinger has generalized and made it more precise than the original. The additive uncertainty relation is based on the three independent statistical moments in Quantum Mechanics-Cov(q,p), Var(q) and Var(p). We discuss the existing symmetry of both types of relations and applicability of the additive form for the estimation of the total error.

  6. Quantum Mechanical Aspects of Free Electron Lasers.

    NASA Astrophysics Data System (ADS)

    Saritepe, Selcuk

    Scope of study. A 2-D quantum theory of the Free Electron Laser (FEL) has been developed based on the solutions of Dirac equation for the motion of electrons moving in various wiggler geometries, uniform, tapered and enhanced by an axial guide field. It is shown that these solutions can be written in terms of Mathieu functions of fractional order. Using these solutions a perturbational analysis is carried out to calculate the frequencies and the gain of the FEL in each magnet configuration. Finally, an optical model for the FEL interaction is developed to explain the saturation behaviour and the short-pulse effects such as Laser Lethargy. Findings and conclusions. It is found that the quantum mechanical effects due to transverse momentum correction were gamma (Lorentz factor) times larger than the quantum recoil and spin effects and therefore important for the short wavelength FELs. These quantum mechanical effects cause a broadening in the spontaneous emission lineshape, a decrease in gain and an increase in the rate of harmonic frequency generation. In the presence of an axial field, gain is increased, harmonic frequency rate is reduced and Dirac solutions exhibit instability. The optical model developed in this thesis correctly predicts the oscillator rise time and uses a simpler algorithm to calculate the nonlinear saturation behaviour. Optical model also incorporates inhomogeneous broadening and quantum mechanical effects and explains the Laser Lethargy effect as an optical pulse compression phenomenon.

  7. A new introductory quantum mechanics curriculum

    NASA Astrophysics Data System (ADS)

    Kohnle, Antje; Bozhinova, Inna; Browne, Dan; Everitt, Mark; Fomins, Aleksejs; Kok, Pieter; Kulaitis, Gytis; Prokopas, Martynas; Raine, Derek; Swinbank, Elizabeth

    2014-01-01

    The Institute of Physics New Quantum Curriculum consists of freely available online learning and teaching materials (quantumphysics.iop.org) for a first course in university quantum mechanics starting from two-level systems. This approach immediately immerses students in inherently quantum-mechanical aspects by focusing on experiments that have no classical explanation. It allows from the start a discussion of the interpretive aspects of quantum mechanics and quantum information theory. This paper gives an overview of the resources available from the IOP website. The core text includes around 80 articles which are co-authored by leading experts, arranged in themes, and can be used flexibly to provide a range of alternative approaches. Many of the articles include interactive simulations with accompanying activities and problem sets that can be explored by students to enhance their understanding. Much of the linear algebra needed for this approach is included in the resource. Solutions to activities are available to instructors. The resources can be used in a variety of ways, from being supplemental to existing courses to forming a complete programme.

  8. Statistical mechanics based on fractional classical and quantum mechanics

    SciTech Connect

    Korichi, Z.; Meftah, M. T.

    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.

  9. Quantum Mechanics in the Light of Quantum Cosmology

    NASA Astrophysics Data System (ADS)

    Gell-Mann, Murray; Hartle, James B.

    We sketch a quantum-mechanical framework for the universe as a whole. Within that framework we propose a program for describing the ultimate origin in quantum cosmology of the "quasiclassical domain" of familiar experience and for characterizing the process of measurement. Predictions in quantum mechanics are made from probabilities for sets of alternative histories. Probabilities (approximately obeying the rules of probability theory) can be assigned only to sets of histories that approximately decohere. Decoherence is defined and the mechanism of decoherence is reviewed. Decoherence requires a sufficiently coarse-grained description of alternative histories of the universe. A quasiclassical domain consists of a branching set of alternative decohering histories, described by a coarse graining that is, in an appropriate sense, maximally refined consistent with decoherence, with individual branches that exhibit a high level of classical correlation in time. We pose the problem of making these notions precise and quantitative. A quasiclassical domain is emergent in the universe as a consequence of the initial condition and the action function of the elementary particles. It is an important question whether all the quasiclassical domains are roughly equivalent or whether there are various essentially inequivalent ones. A measurement is a correlation with variables in a quasiclassical domain. An "observer" (or information gathering and utilizing system) is a complex adaptive system that has evolved to exploit the relative predictability of a quasiclassical domain, or rather a set of such domains among which it cannot discriminate because of its own very coarse graining. We suggest that resolution of many of the problems of interpretation presented by quantum mechanics is to be accomplished, not by further scrutiny of the subject as it applies to reproducible laboratory situations, but rather by an examination of alternative histories of the universe, stemming from its

  10. Consistent interpretations of quantum mechanics

    SciTech Connect

    Omnes, R. )

    1992-04-01

    Within the last decade, significant progress has been made towards a consistent and complete reformulation of the Copenhagen interpretation (an interpretation consisting in a formulation of the experimental aspects of physics in terms of the basic formalism; it is consistent if free from internal contradiction and complete if it provides precise predictions for all experiments). The main steps involved decoherence (the transition from linear superpositions of macroscopic states to a mixing), Griffiths histories describing the evolution of quantum properties, a convenient logical structure for dealing with histories, and also some progress in semiclassical physics, which was made possible by new methods. The main outcome is a theory of phenomena, viz., the classically meaningful properties of a macroscopic system. It shows in particular how and when determinism is valid. This theory can be used to give a deductive form to measurement theory, which now covers some cases that were initially devised as counterexamples against the Copenhagen interpretation. These theories are described, together with their applications to some key experiments and some of their consequences concerning epistemology.

  11. 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).

  12. 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)

  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.

  14. Quantum mechanics is compatible with realism

    SciTech Connect

    Burgos, M.E.

    1987-08-01

    A new paradox of quantum mechanics has recently been proposed by an author claiming that any attempt to inject realism in physical theory is bound to lead to inconsistencies. In this paper the author shows that the mentioned paradox is not such a one and that at present there are no reasons to reject realism.

  15. Holism, physical theories and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Seevinck, M. P.

    Motivated by the question what it is that makes quantum mechanics a holistic theory (if so), I try to define for general physical theories what we mean by `holism'. For this purpose I propose an epistemological criterion to decide whether or not a physical theory is holistic, namely: a physical theory is holistic if and only if it is impossible in principle to infer the global properties, as assigned in the theory, by local resources available to an agent. I propose that these resources include at least all local operations and classical communication. This approach is contrasted with the well-known approaches to holism in terms of supervenience. The criterion for holism proposed here involves a shift in emphasis from ontology to epistemology. I apply this epistemological criterion to classical physics and Bohmian mechanics as represented on a phase and configuration space respectively, and for quantum mechanics (in the orthodox interpretation) using the formalism of general quantum operations as completely positive trace non-increasing maps. Furthermore, I provide an interesting example from which one can conclude that quantum mechanics is holistic in the above mentioned sense, although, perhaps surprisingly, no entanglement is needed.

  16. 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.

  17. The Compton effect: Transition to quantum mechanics

    NASA Astrophysics Data System (ADS)

    Stuewer, R. H.

    2000-11-01

    The discovery of the Compton effect at the end of 1922 was a decisive event in the transition to the new quantum mechanics of 1925-1926 because it stimulated physicists to examine anew the fundamental problem of the interaction between radiation and matter. I first discuss Albert Einstein's light-quantum hypothesis of 1905 and why physicists greeted it with extreme skepticism, despite Robert A. Millikan's confirmation of Einstein's equation of the photoelectric effect in 1915. I then follow in some detail the experimental and theoretical research program that Arthur Holly Compton pursued between 1916 and 1922 at the University of Minnesota, the Westinghouse Lamp Company, the Cavendish Laboratory, and Washington University that culminated in his discovery of the Compton effect. Surprisingly, Compton was not influenced directly by Einstein's light-quantum hypothesis, in contrast to Peter Debye and H.A. Kramers, who discovered the quantum theory of scattering independently. I close by discussing the most significant response to that discovery, the Bohr-Kramers-Slater theory of 1924, its experimental refutation, and its influence on the emerging new quantum mechanics.

  18. Time in classical and in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Elçi, A.

    2010-07-01

    This paper presents an analysis of the time concept in classical mechanics from the perspective of the invariants of a motion. The analysis shows that there is a conceptual gap concerning time in the Dirac-Heisenberg-von Neumann formalism and that Bohr's complementarity principle does not fill the gap. In the Dirac-Heisenberg-von Neumann formalism, a particle's properties are represented by Heisenberg matrices. This axiom is the source of the time problem in quantum mechanics.

  19. Quantum mechanical studies of carbon structures

    SciTech Connect

    Bartelt, Norman Charles; Ward, Donald; Zhou, Xiaowang; Foster, Michael E.; Schultz, Peter A.; Wang, Bryan M.; McCarty, Kevin F.

    2015-10-01

    Carbon nanostructures, such as nanotubes and graphene, are of considerable interest due to their unique mechanical and electrical properties. The materials exhibit extremely high strength and conductivity when defects created during synthesis are minimized. Atomistic modeling is one technique for high resolution studies of defect formation and mitigation. To enable simulations of the mechanical behavior and growth mechanisms of C nanostructures, a high-fidelity analytical bond-order potential for the C is needed. To generate inputs for developing such a potential, we performed quantum mechanical calculations of various C structures.

  20. Quantum mechanics of 4-derivative theories.

    PubMed

    Salvio, Alberto; Strumia, Alessandro

    2016-01-01

    A renormalizable theory of gravity is obtained if the dimension-less 4-derivative kinetic term of the graviton, which classically suffers from negative unbounded energy, admits a sensible quantization. We find that a 4-derivative degree of freedom involves a canonical coordinate with unusual time-inversion parity, and that a correspondingly unusual representation must be employed for the relative quantum operator. The resulting theory has positive energy eigenvalues, normalizable wavefunctions, unitary evolution in a negative-norm configuration space. We present a formalism for quantum mechanics with a generic norm.

  1. A Primer on Resonances in Quantum Mechanics

    SciTech Connect

    Rosas-Ortiz, Oscar; Fernandez-Garcia, Nicolas; Cruz y Cruz, Sara

    2008-11-13

    After a pedagogical introduction to the concept of resonance in classical and quantum mechanics, some interesting applications are discussed. The subject includes resonances occurring as one of the effects of radiative reaction, the resonances involved in the refraction of electromagnetic waves by a medium with a complex refractive index, and quantum decaying systems described in terms of resonant states of the energy (Gamow-Siegert functions). Some useful mathematical approaches like the Fourier transform, the complex scaling method and the Darboux transformation are also reviewed.

  2. Quantum mechanical coherence, resonance, and mind

    SciTech Connect

    Stapp, H.P.

    1995-03-26

    Norbert Wiener and J.B.S. Haldane suggested during the early thirties that the profound changes in our conception of matter entailed by quantum theory opens the way for our thoughts, and other experiential or mind-like qualities, to play a role in nature that is causally interactive and effective, rather than purely epiphenomenal, as required by classical mechanics. The mathematical basis of this suggestion is described here, and it is then shown how, by giving mind this efficacious role in natural process, the classical character of our perceptions of the quantum universe can be seen to be a consequence of evolutionary pressures for the survival of the species.

  3. Global and local horizon quantum mechanics

    NASA Astrophysics Data System (ADS)

    Casadio, Roberto; Giugno, Andrea; Giusti, Andrea

    2017-02-01

    Horizons are classical causal structures that arise in systems with sharply defined energy and corresponding gravitational radius. A global gravitational radius operator can be introduced for a static and spherically symmetric quantum mechanical matter state by lifting the classical "Hamiltonian" constraint that relates the gravitational radius to the ADM mass, thus giving rise to a "horizon wave-function". This minisuperspace-like formalism is shown here to be able to consistently describe also the local gravitational radius related to the Misner-Sharp mass function of the quantum source, provided its energy spectrum is determined by spatially localised modes.

  4. Neutrino oscillations: Quantum mechanics vs. quantum field theory

    SciTech Connect

    Akhmedov, Evgeny Kh.; Kopp, Joachim

    2010-01-01

    A consistent description of neutrino oscillations requires either the quantum-mechanical (QM) wave packet approach or a quantum field theoretic (QFT) treatment. We compare these two approaches to neutrino oscillations and discuss the correspondence between them. In particular, we derive expressions for the QM neutrino wave packets from QFT and relate the free parameters of the QM framework, in particular the effective momentum uncertainty of the neutrino state, to the more fundamental parameters of the QFT approach. We include in our discussion the possibilities that some of the neutrino's interaction partners are not detected, that the neutrino is produced in the decay of an unstable parent particle, and that the overlap of the wave packets of the particles involved in the neutrino production (or detection) process is not maximal. Finally, we demonstrate how the properly normalized oscillation probabilities can be obtained in the QFT framework without an ad hoc normalization procedure employed in the QM approach.

  5. ``the Human BRAIN & Fractal quantum mechanics''

    NASA Astrophysics Data System (ADS)

    Rosary-Oyong, Se, Glory

    In mtDNA ever retrieved from Iman Tuassoly, et.al:Multifractal analysis of chaos game representation images of mtDNA''.Enhances the price & valuetales of HE. Prof. Dr-Ing. B.J. HABIBIE's N-219, in J. Bacteriology, Nov 1973 sought:'' 219 exist as separate plasmidDNA species in E.coli & Salmonella panama'' related to ``the brain 2 distinct molecular forms of the (Na,K)-ATPase..'' & ``neuron maintains different concentration of ions(charged atoms'' thorough Rabi & Heisenber Hamiltonian. Further, after ``fractal space time are geometric analogue of relativistic quantum mechanics''[Ord], sought L.Marek Crnjac: ``Chaotic fractals at the root of relativistic quantum physics''& from famous Nottale: ``Scale relativity & fractal space-time:''Application to Quantum Physics , Cosmology & Chaotic systems'',1995. Acknowledgements to HE. Mr. H. TUK SETYOHADI, Jl. Sriwijaya Raya 3, South-Jakarta, INDONESIA.

  6. Dummett vs Bell on quantum mechanics

    NASA Astrophysics Data System (ADS)

    Ben-Menahem, Yemima

    The purpose of this paper is to cast doubt on the common allegation that quantum mechanics (QM) is incompatible with realism. I argue that the results usually considered inimical to realism, notably the violation of Bells inequality, in fact play the opposite role-they support realism. The argument is not intended, however, to demonstrate realism or refute its alternatives as general metaphysical positions. It is directed specifically at the view that QM differs from classical mechanics in that, unlike classical mechanics, it is not amenable to a realist interpretation.

  7. Hidden variables and nonlocality in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Hemmick, Douglas Lloyd

    1997-05-01

    Most physicists hold a skeptical attitude toward a 'hidden variables' interpretation of quantum theory, despite David Bohm's successful construction of such a theory and John S. Bell's strong arguments in favor of the idea. The first reason for doubt concerns certain mathematical theorems (von Neumann's, Gleason's, Kochen and Specker's, and Bell's) which can be applied to the hidden variables issue. These theorems are often credited with proving that hidden variables are indeed 'impossible', in the sense that they cannot replicate the predictions of quantum mechanics. Many who do not draw such a strong conclusion nevertheless accept that hidden variables have been shown to exhibit prohibitively complicated features. The second concern is that the most sophisticated example of a hidden variables theory-that of David Bohm-exhibits non-locality, i.e., consequences of events at one place can propagate to other places instantaneously. However, neither the mathematical theorems in question nor the attribute of nonlocality detract from the importance of a hidden variables interpretation of quantum theory. Nonlocality is present in quantum mechanics itself, and is a required characteristic of any theory that agrees with the quantum mechanical predictions. We first discuss the earliest analysis of hidden variables-that of von Neumann's theorem-and review John S. Bell's refutation of von Neumann's 'impossibility proof'. We recall and elaborate on Bell's arguments regarding the theorems of Gleason, and Kochen and Specker. According to Bell, these latter theorems do not imply that hidden variables interpretations are untenable, but instead that such theories must exhibit contextuality, i.e., they must allow for the dependence of measurement results on the characteristics of both measured system and measuring apparatus. We demonstrate a new way to understand the implications of both Gleason's theorem and Kochen and Specker's theorem by noting that they prove a result we call

  8. Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation.

    PubMed

    Suardíaz, Reynier; Jambrina, Pablo G; Masgrau, Laura; González-Lafont, Àngels; Rosta, Edina; Lluch, José M

    2016-04-12

    Lipoxygenases (LOXs) are a family of enzymes involved in the biosynthesis of several lipid mediators. In the case of human 15-LOX, the 15-LOX-1 and 15-LOX-2 isoforms show slightly different reaction regiospecificity and substrate specificity, indicating that substrate binding and recognition may be different, a fact that could be related to their different biological role. Here, we have used long molecular dynamics simulations, QM(DFT)/MM potential energy and free energy calculations (using the newly developed DHAM method), to investigate the binding mode of the arachidonic acid (AA) substrate into 15-LOX-2 and the rate-limiting hydrogen-abstraction reaction 15-LOX-2 catalyzes. Our results strongly indicate that hydrogen abstraction from C13 in 15-LOX-2 is only consistent with the "tail-first" orientation of AA, with its carboxylate group interacting with Arg429, and that only the pro-S H13 hydrogen will be abstracted (being the pro-R H13 and H10 too far from the acceptor oxygen atom). At the B3LYP/6-31G(d) level the potential and free energy barriers for the pro-S H13 abstraction of AA by 15-LOX-2 are 18.0 and 18.6 kcal/mol, respectively. To analyze the kinetics of the hydrogen abstraction process, we determined a Markov model corresponding to the unbiased simulations along the state-discretized reaction coordinate. The calculated rates based on the second largest eigenvalue of the Markov matrices agree well with experimental measurements, and also provide the means to directly determine the pre-exponential factor for the reaction by comparing with the free energy barrier height. Our calculated pre-exponential factor is close to the value of kBT/h. On the other hand, our results suggest that the spin inversion of the complete system (including the O2 molecule) that is required to happen at some point along the full process to lead to the final hydroperoxide product, is likely to take place during the hydrogen transfer, which is a proton coupled electron transfer. Overall, a different binding mode from the one accepted for 15-LOX-1 is proposed, which provides a molecular basis for 15-LOX-2 exclusive 15-HPETE production in front of the double (although highly 15-) 12/15 regiospecificity of 15-LOX-1. Understanding how these different isoenzymes achieve their regiospecificity is expected to help in specific inhibitor design.

  9. Quantum statistical mechanics in arithmetic topology

    NASA Astrophysics Data System (ADS)

    Marcolli, Matilde; Xu, Yujie

    2017-04-01

    This paper provides a construction of a quantum statistical mechanical system associated to knots in the 3-sphere and cyclic branched coverings of the 3-sphere, which is an analog, in the sense of arithmetic topology, of the Bost-Connes system, with knots replacing primes, and cyclic branched coverings of the 3-sphere replacing abelian extensions of the field of rational numbers. The operator algebraic properties of this system differ significantly from the Bost-Connes case, due to the properties of the action of the semigroup of knots on a direct limit of knot groups. The resulting algebra of observables is a noncommutative Bernoulli product. We describe the main properties of the associated quantum statistical mechanical system and of the relevant partition functions, which are obtained from simple knot invariants like genus and crossing number.

  10. Quantum-Mechanical Prediction of Nanoscale Photovoltaics.

    PubMed

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

    2014-04-03

    Previous simulations of photovoltaic devices are based on classical models, which neglect the atomistic details and quantum-mechanical effects besides the dependence on many empirical parameters. Here, within the nonequilibrium Green's function formalism, we present a quantum-mechanical study of the performance of inorganic nanowire-based photovoltaic devices. On the basis of density-functional tight-binding theory, the method allows simulation of current-voltage characteristics and optical properties of photovoltaic devices without relying on empirical parameters. Numerical studies of silicon nanowire-based devices of realistic sizes with 10 000 atoms are performed, and the results indicate that atomistic details and nonequilibrium conditions have a clear impact on the photoresponse of the devices.

  11. Applications of computational quantum mechanics

    NASA Astrophysics Data System (ADS)

    Temel, Burcin

    This original research dissertation is composed of a new numerical technique based on Chebyshev polynomials that is applied on scattering problems, a phenomenological kinetics study for CO oxidation on RuO2 surface, and an experimental study on methanol coupling with doped metal oxide catalysts. Minimum Error Method (MEM), a least-squares minimization method, provides an efficient and accurate alternative to solve systems of ordinary differential equations. Existing methods usually utilize matrix methods which are computationally costful. MEM, which is based on the Chebyshev polynomials as a basis set, uses the recursion relationships and fast Chebyshev transforms which scale as O(N). For large basis set calculations this provides an enormous computational efficiency in the calculations. Chebyshev polynomials are also able to represent non-periodic problems very accurately. We applied MEM on elastic and inelastic scattering problems: it is more efficient and accurate than traditionally used Kohn variational principle, and it also provides the wave function in the interaction region. Phenomenological kinetics (PK) is widely used in industry to predict the optimum conditions for a chemical reaction. PK neglects the fluctuations, assumes no lateral interactions, and considers an ideal mix of reactants. The rate equations are tested by fitting the rate constants to the results of the experiments. Unfortunately, there are numerous examples where a fitted mechanism was later shown to be erroneous. We have undertaken a thorough comparison between the phenomenological equations and the results of kinetic Monte Carlo (KMC) simulations performed on the same system. The PK equations are qualitatively consistent with the KMC results but are quantitatively erroneous as a result of interplays between the adsorption and desorption events. The experimental study on methanol coupling with doped metal oxide catalysts demonstrates the doped metal oxides as a new class of catalysts

  12. Probing pores using elementary quantum mechanics.

    PubMed

    Ryu, S

    2001-01-01

    The relaxation of polarized spins in a porous medium has been utilized as a probe of its structure. We note that the governing diffusion problem has a close parallel to that of a particle in a box, an elementary Quantum mechanics toy model. Following the spirits of "free electron" model, we use generic properties of the eigen spectrum to understand features common to a wide variety of pore geometry, consistent with large scale numerical simulations and experimental data.

  13. A quantum mechanics glimpse to standard cosmology

    SciTech Connect

    Barbosa-Cendejas, N.; Reyes, M.

    2010-07-12

    In this work we present a connection between a standard cosmology model for inflation and quantum mechanics. We consider a time independent Schroedinger type equation derived from the equations of motion for a single scalar field in a flat space time with a FRW metric and a cosmological constant; the fact that the equation of motion is precisely a Schroedinger equation allows us to investigate on the algebraic relations between the two models and probe the consequences derived from this point of view.

  14. Grounding quantum probability in psychological mechanism.

    PubMed

    Love, Bradley C

    2013-06-01

    Pothos & Busemeyer (P&B) provide a compelling case that quantum probability (QP) theory is a better match to human judgment than is classical probability (CP) theory. However, any theory (QP, CP, or other) phrased solely at the computational level runs the risk of being underconstrained. One suggestion is to ground QP accounts in mechanism, to leverage a wide range of process-level data.

  15. Hunting for Snarks in Quantum Mechanics

    SciTech Connect

    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 is 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}.

  16. A molecular dynamics study of the conformation of the alanine dipeptide in aqueous solution using a quantum mechanical potential

    NASA Astrophysics Data System (ADS)

    Buesnel, Robert; Hillier, Ian H.; Masters, Andrew J.

    Molecular dynamics simulations of the aqueous solution of alanine dipeptide have been carried out for seven configurations characteristic of important regions of the Ramachandran plot. A hybrid quantum mechanical-molecular mechanical potential was used that describes the solute using the AM1 Hamiltonian and the solvent using the TIP3P model. The importance of differential solute polarization and the preferential stabilization of the extended structures alphaL, alphaR and beta have been identified. The results are compared with experiment and with the predictions of the ab initio polarizable continuum model of solvation.

  17. Classical and quantum-mechanical state reconstruction

    NASA Astrophysics Data System (ADS)

    Khanna, F. C.; Mello, P. A.; Revzen, M.

    2012-07-01

    The aim of this paper is to present the subject of state reconstruction in classical and in quantum physics, a subject that deals with the experimentally acquired information that allows the determination of the physical state of a system. Our first purpose is to explain a method for retrieving a classical state in phase space, similar to that used in medical imaging known as computer-aided tomography. It is remarkable that this method can be taken over to quantum mechanics, where it leads to a description of the quantum state in terms of the Wigner function which, although it may take on negative values, plays the role of the probability density in phase space in classical physics. We then present another approach to quantum state reconstruction based on the notion of mutually unbiased bases—a notion of current research interest, for which we give explanatory remarks—and indicate the relation between these two approaches. Since the subject of state reconstruction is rarely considered at the level of textbooks, the presentation in this paper is aimed at graduate-level readers.

  18. Quantum mechanics with coordinate dependent noncommutativity

    NASA Astrophysics Data System (ADS)

    Kupriyanov, V. G.

    2013-11-01

    Noncommutative quantum mechanics can be considered as a first step in the construction of quantum field theory on noncommutative spaces of generic form, when the commutator between coordinates is a function of these coordinates. In this paper we discuss the mathematical framework of such a theory. The noncommutativity is treated as an external antisymmetric field satisfying the Jacobi identity. First, we propose a symplectic realization of a given Poisson manifold and construct the Darboux coordinates on the obtained symplectic manifold. Then we define the star product on a Poisson manifold and obtain the expression for the trace functional. The above ingredients are used to formulate a nonrelativistic quantum mechanics on noncommutative spaces of general form. All considered constructions are obtained as a formal series in the parameter of noncommutativity. In particular, the complete algebra of commutation relations between coordinates and conjugated momenta is a deformation of the standard Heisenberg algebra. As examples we consider a free particle and an isotropic harmonic oscillator on the rotational invariant noncommutative space.

  19. An approach to nonstandard quantum mechanics

    NASA Astrophysics Data System (ADS)

    Raab, A.

    2004-12-01

    We use nonstandard analysis to formulate quantum mechanics in hyperfinite-dimensional spaces. Self-adjoint operators on hyperfinite-dimensional spaces have complete eigensets, and bound states and continuum states of a Hamiltonian can thus be treated on an equal footing. We show that the formalism extends the standard formulation of quantum mechanics. To this end we develop the Loeb-function calculus in nonstandard hulls. The idea is to perform calculations in a hyperfinite-dimensional space, but to interpret expectation values in the corresponding nonstandard hull. We further apply the framework to nonrelativistic quantum scattering theory. For time-dependent scattering theory, we identify the starting time and the finishing time of a scattering experiment, and we obtain a natural separation of time scales on which the preparation process, the interaction process, and the detection process take place. For time-independent scattering theory, we derive rigorously explicit formulas for the Mo/ller wave operators and the S-matrix.

  20. Bohmian Mechanics In A Macroscopic Quantum System

    NASA Astrophysics Data System (ADS)

    Haven, Emmanuel

    2006-01-01

    In the so called `causal' interpretation of quantum mechanics, an electron is considered as a particle and such particle is influenced not only by a classical but also by a so called quantum potential. This idea was developed by Professor Bohm in an important paper. In this paper we use some of the basics of this interpretation in a financial option pricing environment. The causal interpretation allows for trajectories. Path breaking work by Professors Bohm and Hiley and Khrennikov and Choustova have made that the causal interpretation is a step closer to potential applications in social science. In this paper we consider the wave function as a wave of information. We consider the gradient of the phase of this wave function and show how the option price could be influenced by this gradient.

  1. Indirect Acquisition of Information in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Ballesteros, M.; Fraas, M.; Fröhlich, J.; Schubnel, B.

    2016-02-01

    Long sequences of successive direct (projective) measurements or observations of just a few "uninteresting" physical quantities pertaining to a quantum system, such as clicks of some detectors, may reveal indirect, but precise and unambiguous information on the values of some very "interesting" observables of the system. In this paper, the mathematics underlying this claim is developed; i.e., we attempt to contribute to a mathematical theory of indirect and, in particular, non-demolition observations and measurements in quantum mechanics. Our attempt leads us to make some novel uses of classical notions and results of probability theory, such as the "algebra of functions measurable at infinity", the Central Limit Theorem, results concerning relative entropy and its role in the theory of large deviations, etc.

  2. Quantum mechanical hamiltonian models of turing machines

    NASA Astrophysics Data System (ADS)

    Benioff, Paul

    1982-11-01

    Quantum mechanical Hamiltonian models, which represent an aribtrary but finite number of steps of any Turing machine computation, are constructed here on a finite lattice of spin-1/2 systems. Different regions of the lattice correspond to different components of the Turing machine (plus recording system). Successive states of any machine computation are represented in the model by spin configuration states. Both time-independent and time-dependent Hamiltonian models are constructed here. The time-independent models do not dissipate energy or degrade the system state as they evolve. They operate close to the quantum limit in that the total system energy uncertainty/computation speed is close to the limit given by the time-energy uncertainty relation. However, the model evolution is time global and the Hamiltonian is more complex. The time-dependent models do not degrade the system state. Also they are time local and the Hamiltonian is less complex.

  3. Unstable trajectories and the quantum mechanical uncertainty

    SciTech Connect

    Moser, Hans R.

    2008-08-15

    There is still an ongoing discussion about various seemingly contradictory aspects of classical particle motion and its quantum mechanical counterpart. One of the best accepted viewpoints that intend to bridge the gap is the so-called Copenhagen Interpretation. A major issue there is to regard wave functions as probability amplitudes (usually for the position of a particle). However, the literature also reports on approaches that claim a trajectory for any quantum mechanical particle, Bohmian mechanics probably being the most prominent one among these ideas. We introduce a way to calculate trajectories as well, but our crucial ingredient is their well controlled local (thus also momentaneous) degree of instability. By construction, at every moment their unpredictability, i.e., their local separation rates of neighboring trajectories, is governed by the local value of the given modulus square of a wave function. We present extensive numerical simulations of the H and He atom, and for some velocity-related quantities, namely angular momentum and total energy, we inspect their agreement with the values appearing in wave mechanics. Further, we interpret the archetypal double slit interference experiment in the spirit of our findings. We also discuss many-particle problems far beyond He, which guides us to a variety of possible applications.

  4. Quantum mechanics. Mechanically detecting and avoiding the quantum fluctuations of a microwave field.

    PubMed

    Suh, J; Weinstein, A J; Lei, C U; Wollman, E E; Steinke, S K; Meystre, P; Clerk, A A; Schwab, K C

    2014-06-13

    Quantum fluctuations of the light field used for continuous position detection produce stochastic back-action forces and ultimately limit the sensitivity. To overcome this limit, the back-action forces can be avoided by giving up complete knowledge of the motion, and these types of measurements are called "back-action evading" or "quantum nondemolition" detection. We present continuous two-tone back-action evading measurements with a superconducting electromechanical device, realizing three long-standing goals: detection of back-action forces due to the quantum noise of a microwave field, reduction of this quantum back-action noise by 8.5 ± 0.4 decibels (dB), and measurement imprecision of a single quadrature of motion 2.4 ± 0.7 dB below the mechanical zero-point fluctuations. Measurements of this type will find utility in ultrasensitive measurements of weak forces and nonclassical states of motion.

  5. 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.

  6. The Simpson's paradox in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Selvitella, Alessandro

    2017-03-01

    In probability and statistics, the Simpson's paradox is a paradox in which a trend that appears in different groups of data disappears when these groups are combined, while the reverse trend appears for the aggregate data. In this paper, we give some results about the occurrence of the Simpson's paradox in quantum mechanics. In particular, we prove that the Simpson's paradox occurs for solutions of the quantum harmonic oscillator both in the stationary case and in the non-stationary case. In the non-stationary case, the Simpson's paradox is persistent: if it occurs at any time t =t ˜ , then it occurs at any time t ≠t ˜ . Moreover, we prove that the Simpson's paradox is not an isolated phenomenon, namely, that, close to initial data for which it occurs, there are lots of initial data (a open neighborhood), for which it still occurs. Differently from the case of the quantum harmonic oscillator, we also prove that the paradox appears (asymptotically) in the context of the nonlinear Schrödinger equation but at intermittent times.

  7. BiHermitian supersymmetric quantum mechanics

    NASA Astrophysics Data System (ADS)

    Zucchini, Roberto

    2007-04-01

    BiHermitian geometry, discovered long ago by Gates, Hull and Rocek, is the most general sigma model target space geometry allowing for (2, 2) world sheet supersymmetry. In this paper, we work out supersymmetric quantum mechanics for a biHermitian target space. We display the full supersymmetry of the model and illustrate in detail its quantization procedure. Finally, we show that the quantized model reproduces the Hodge theory for compact twisted generalized Kähler manifolds recently developed by Gualtieri in [33]. This allows us to recover and put in a broader context the results on the biHermitian topological sigma models obtained by Kapustin and Li in [9].

  8. 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

  9. Quantitative analysis of surface tension of liquid nano-film with thickness: Two stage stability mechanism, molecular dynamics and thermodynamics approach

    NASA Astrophysics Data System (ADS)

    Peng, Tiefeng; Li, Qibin; Chen, Jie; Gao, Xuechao

    2016-11-01

    The effects of thickness on surface tension of aqueous nano-films under the same lateral size were studied by molecular dynamics (MD) simulations. The surface tension was found to decrease with decreasing thickness when film thickness is below 1.5 nm. Between 4 and 1.5 nm, the trend is for the surface tension to decrease but this is not as significant as between 1.5 and 1.2 nm. For the surface tension of salt nano-films, with low temperatures resulting in monotonous decreasing with thickness, while high temperature (e.g. 479 K) exhibited a first increase then decrease for surface tension with thickness. Filippini et al. (2014) suggested that surface tension is constant with the thickness as long as the sheet remains in one piece, also the decrease observed and as proposed by Werth et al. (2013) is not due to a confinement effect on Lennard-Jones systems. However, in this study for aqueous nano-films, a two stage mechanism was proposed to interpret this effect, for which the stability was classified according to thickness range and validated by disjoining pressure. The results are important in describing the role of surface tension in determining the behaviour of disjoining pressure.

  10. Nonequilibrium quantum mechanics: A "hot quantum soup" of paramagnons

    NASA Astrophysics Data System (ADS)

    Scammell, H. D.; Sushkov, O. P.

    2017-01-01

    Motivated by recent measurements of the lifetime (decay width) of paramagnons in quantum antiferromagnet TlCuCl3, we investigate paramagnon decay in a heat bath and formulate an appropriate quantum theory. Our formulation can be split into two regimes: (i) a nonperturbative, "hot quantum soup" regime where the paramagnon width is comparable to its energy; (ii) a usual perturbative regime where the paramagnon width is significantly lower than its energy. Close to the Neel temperature, the paramagnon width becomes comparable to its energy and falls into the hot quantum soup regime. To describe this regime, we develop a new finite frequency, finite temperature technique for a nonlinear quantum field theory; the "golden rule of quantum kinetics." The formulation is generic and applicable to any three-dimensional quantum antiferromagnet in the vicinity of a quantum critical point. Specifically, we apply our results to TlCuCl3 and find agreement with experimental data. Additionally, we show that logarithmic running of the coupling constant in the upper critical dimension changes the commonly accepted picture of the quantum disordered and quantum critical regimes.

  11. The formal path integral and quantum mechanics

    SciTech Connect

    Johnson-Freyd, Theo

    2010-11-15

    Given an arbitrary Lagrangian function on R{sup d} and a choice of classical path, one can try to define Feynman's path integral supported near the classical path as a formal power series parameterized by 'Feynman diagrams', although these diagrams may diverge. We compute this expansion and show that it is (formally, if there are ultraviolet divergences) invariant under volume-preserving changes of coordinates. We prove that if the ultraviolet divergences cancel at each order, then our formal path integral satisfies a 'Fubini theorem' expressing the standard composition law for the time evolution operator in quantum mechanics. Moreover, we show that when the Lagrangian is inhomogeneous quadratic in velocity such that its homogeneous-quadratic part is given by a matrix with constant determinant, then the divergences cancel at each order. Thus, by 'cutting and pasting' and choosing volume-compatible local coordinates, our construction defines a Feynman-diagrammatic 'formal path integral' for the nonrelativistic quantum mechanics of a charged particle moving in a Riemannian manifold with an external electromagnetic field.

  12. 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.

  13. Mathematical model I. Electron and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Gadre, Nitin Ramchandra

    2011-03-01

    The basic particle electron obeys various theories like electrodynamics, quantum mechanics and special relativity. Particle under different experimental conditions behaves differently, allowing us to observe different characteristics which become basis for these theories. In this paper, we have made an attempt to suggest a classical picture by studying the requirements of these three modern theories. The basic presumption is: There must be certain structural characteristics in a particle like electron which make it obey postulates of modern theories. As it is `difficult' to find structure of electron experimentally, we make a mathematical attempt. For a classical approach, we require well defined systems and we have studied a system with two charged particles, proton and electron in a hydrogen atom. An attempt has been made to give a model to describe electron as seen by the proton. We then discuss how the model can satisfy the requirements of the three modern theories in a classical manner. The paper discusses basic aspects of relativity and electrodynamics. However the focus of the paper is on quantum mechanics.

  14. Differentiability of correlations in realistic quantum mechanics

    SciTech Connect

    Cabrera, Alejandro; Faria, Edson de; Pujals, Enrique; Tresser, Charles

    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 assumed 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.

  15. 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.

  16. Molecular model with quantum mechanical bonding information.

    PubMed

    Bohórquez, Hugo J; Boyd, Russell J; Matta, Chérif F

    2011-11-17

    The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.

  17. 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…

  18. Anyons in quantum mechanics with a minimal length

    NASA Astrophysics Data System (ADS)

    Buisseret, Fabien

    2017-02-01

    The existence of anyons, i.e. quantum states with an arbitrary spin, is a generic feature of standard quantum mechanics in (2 + 1) -dimensional Minkowski spacetime. Here it is shown that relativistic anyons may exist also in quantum theories where a minimal length is present. The interplay between minimal length and arbitrary spin effects are discussed.

  19. Surveying Instructors' Attitudes and Approaches to Teaching Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Siddiqui, Shabnam; Singh, Chandralekha

    2010-10-01

    Understanding instructors' attitudes and approaches to teaching quantum mechanics can be helpful in developing research-based learning tools. Here we discuss the findings from a survey in which 13 instructors reflected on issues related to quantum mechanics teaching. Topics included opinions about the goals of a quantum mechanics course, general challenges in teaching the subject, students' preparation for the course, comparison between their own learning of quantum mechanics vs. how they teach it and the extent to which contemporary topics are incorporated into the syllabus.

  20. 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.

  1. Statistical origin of classical mechanics and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Chu, Shu-Yuan

    1993-11-01

    The classical action for interacting strings, obtained by generalizing the time-symmetric electrodynamics of Wheeler and Feynman, is exactly additive. The additivity of the string action suggests a connection between the area of the string world sheets and entropy. We find that the action principle of classical mechanics is the condition that the total entropy of the strings be at an extremum, and the path-integral representation of the quantum density matrix element is an approximation to the partition function of the string theory.

  2. Testing quantum mechanics using third-order correlations

    NASA Astrophysics Data System (ADS)

    Kinsler, Paul

    1996-04-01

    Semiclassical theories similar to stochastic electrodynamics are widely used in optics. The distinguishing feature of such theories is that the quantum uncertainty is represented by random statistical fluctuations. They can successfully predict some quantum-mechanical phenomena; for example, the squeezing of the quantum uncertainty in the parametric oscillator. However, since such theories are not equivalent to quantum mechanics, they will not always be useful. Complex number representations can be used to exactly model the quantum uncertainty, but care has to be taken that approximations do not reduce the description to a hidden variable one. This paper helps show the limitations of ``semiclassical theories,'' and helps show where a true quantum-mechanical treatment needs to be used. Third-order correlations are a test that provides a clear distinction between quantum and hidden variable theories in a way analogous to that provided by the ``all or nothing'' Greenberger-Horne-Zeilinger test of local hidden variable theories.

  3. Harmonizing General Relativity with Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Alfonso-Faus, Antonio

    2007-04-01

    Gravitation is the common underlying texture between General Relativity and Quantum Mechanics. We take gravitation as the link that can make possible the marriage between these two sciences. We use here the duality of Nature for gravitation: A continuous warped space, wave-like, and a discrete quantum gas, particle-like, both coexistent and producing an equilibrium state in the Universe. The result is a static, non expanding, spherical, unlimited and finite Universe, with no cosmological constant and no dark energy. Macht's Principle is reproduced here by the convergence of the two cosmological equations of Einstein. From this a Mass Boom concept is born given by M = t, M the mass of the Universe and t its age. Also a decreasing speed of light is the consequence of the Mass Boom, c = 1/t, which explains the Supernovae Type Ia observations without the need of expansion (nor, of course, accelerated expansion). Our Mass Boom model completely wipes out the problems and paradoxes built in the Big Bang model, like the horizon, monopole, entropy, flatness, fine tuning, etc. It also eliminates the need for inflation.

  4. Dynamical phase transitions in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Rotter, Ingrid

    2012-02-01

    The nucleus is described as an open many-body quantum system with a non-Hermitian Hamilton operator the eigenvalues of which are complex, in general. The eigenvalues may cross in the complex plane (exceptional points), the phases of the eigenfunctions are not rigid in approaching the crossing points and the widths bifurcate. By varying only one parameter, the eigenvalue trajectories usually avoid crossing and width bifurcation occurs at the critical value of avoided crossing. An analog spectroscopic redistribution takes place for discrete states below the particle decay threshold. By this means, a dynamical phase transition occurs in the many-level system starting at a critical value of the level density. Hence the properties of the low-lying nuclear states (described well by the shell model) and those of highly excited nuclear states (described by random ensembles) differ fundamentally from one another. The statement of Niels Bohr on the collective features of compound nucleus states at high level density is therefore not in contradiction to the shell-model description of nuclear (and atomic) states at low level density. Dynamical phase transitions are observed experimentally in different quantum mechanical systems by varying one or two parameters.

  5. Causal localizations in relativistic quantum mechanics

    SciTech Connect

    Castrigiano, Domenico P. L. Leiseifer, Andreas D.

    2015-07-15

    Causal localizations describe the position of quantum systems moving not faster than light. They are constructed for the systems with finite spinor dimension. At the center of interest are the massive relativistic systems. For every positive mass, there is the sequence of Dirac tensor-localizations, which provides a complete set of inequivalent irreducible causal localizations. They obey the principle of special relativity and are fully Poincaré covariant. The boosters are determined by the causal position operator and the other Poincaré generators. The localization with minimal spinor dimension is the Dirac localization. Thus, the Dirac equation is derived here as a mere consequence of the principle of causality. Moreover, the higher tensor-localizations, not known so far, follow from Dirac’s localization by a simple construction. The probability of localization for positive energy states results to be described by causal positive operator valued (PO-) localizations, which are the traces of the causal localizations on the subspaces of positive energy. These causal Poincaré covariant PO-localizations for every irreducible massive relativistic system were, all the more, not known before. They are shown to be separated. Hence, the positive energy systems can be localized within every open region by a suitable preparation as accurately as desired. Finally, the attempt is made to provide an interpretation of the PO-localization operators within the frame of conventional quantum mechanics attributing an important role to the negative energy states.

  6. Causal localizations in relativistic quantum mechanics

    NASA Astrophysics Data System (ADS)

    Castrigiano, Domenico P. L.; Leiseifer, Andreas D.

    2015-07-01

    Causal localizations describe the position of quantum systems moving not faster than light. They are constructed for the systems with finite spinor dimension. At the center of interest are the massive relativistic systems. For every positive mass, there is the sequence of Dirac tensor-localizations, which provides a complete set of inequivalent irreducible causal localizations. They obey the principle of special relativity and are fully Poincaré covariant. The boosters are determined by the causal position operator and the other Poincaré generators. The localization with minimal spinor dimension is the Dirac localization. Thus, the Dirac equation is derived here as a mere consequence of the principle of causality. Moreover, the higher tensor-localizations, not known so far, follow from Dirac's localization by a simple construction. The probability of localization for positive energy states results to be described by causal positive operator valued (PO-) localizations, which are the traces of the causal localizations on the subspaces of positive energy. These causal Poincaré covariant PO-localizations for every irreducible massive relativistic system were, all the more, not known before. They are shown to be separated. Hence, the positive energy systems can be localized within every open region by a suitable preparation as accurately as desired. Finally, the attempt is made to provide an interpretation of the PO-localization operators within the frame of conventional quantum mechanics attributing an important role to the negative energy states.

  7. Extending quantum mechanics entails extending special relativity

    NASA Astrophysics Data System (ADS)

    Aravinda, S.; Srikanth, R.

    2016-05-01

    The complementarity between signaling and randomness in any communicated resource that can simulate singlet statistics is generalized by relaxing the assumption of free will in the choice of measurement settings. We show how to construct an ontological extension for quantum mechanics (QMs) through the oblivious embedding of a sound simulation protocol in a Newtonian spacetime. Minkowski or other intermediate spacetimes are ruled out as the locus of the embedding by virtue of hidden influence inequalities. The complementarity transferred from a simulation to the extension unifies a number of results about quantum non-locality, and implies that special relativity has a different significance for the ontological model and for the operational theory it reproduces. Only the latter, being experimentally accessible, is required to be Lorentz covariant. There may be certain Lorentz non-covariant elements at the ontological level, but they will be inaccessible at the operational level in a valid extension. Certain arguments against the extendability of QM, due to Conway and Kochen (2009) and Colbeck and Renner (2012), are attributed to their assumption that the spacetime at the ontological level has Minkowski causal structure.

  8. 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.

  9. Quantum mechanics of a generalised rigid body

    NASA Astrophysics Data System (ADS)

    Gripaios, Ben; Sutherland, Dave

    2016-05-01

    We consider the quantum version of Arnold’s generalisation of a rigid body in classical mechanics. Thus, we quantise the motion on an arbitrary Lie group manifold of a particle whose classical trajectories correspond to the geodesics of any one-sided-invariant metric. We show how the derivation of the spectrum of energy eigenstates can be simplified by making use of automorphisms of the Lie algebra and (for groups of type I) by methods of harmonic analysis. We show how the method can be extended to cosets, generalising the linear rigid rotor. As examples, we consider all connected and simply connected Lie groups up to dimension 3. This includes the universal cover of the archetypical rigid body, along with a number of new exactly solvable models. We also discuss a possible application to the topical problem of quantising a perfect fluid.

  10. Gauge invariance and reciprocity in quantum mechanics

    SciTech Connect

    Leung, P. T.; Young, K.

    2010-03-15

    Reciprocity in wave propagation usually refers to the symmetry of the Green's function under the interchange of the source and the observer coordinates, but this condition is not gauge invariant in quantum mechanics, a problem that is particularly significant in the presence of a vector potential. Several possible alternative criteria are given and analyzed with reference to different examples with nonzero magnetic fields and/or vector potentials, including the case of a multiply connected spatial domain. It is shown that the appropriate reciprocity criterion allows for specific phase factors separable into functions of the source and observer coordinates and that this condition is robust with respect to the addition of any scalar potential. In the Aharonov-Bohm effect, reciprocity beyond monoenergetic experiments holds only because of subsidiary conditions satisfied in actual experiments: the test charge is in units of e and the flux is produced by a condensate of particles with charge 2e.

  11. Waveform information from quantum mechanical entropy

    NASA Astrophysics Data System (ADS)

    Funkhouser, Scott; Suski, William; Winn, Andrew

    2016-06-01

    Although the entropy of a given signal-type waveform is technically zero, it is nonetheless desirable to use entropic measures to quantify the associated information. Several such prescriptions have been advanced in the literature but none are generally successful. Here, we report that the Fourier-conjugated `total entropy' associated with quantum-mechanical probabilistic amplitude functions (PAFs) is a meaningful measure of information in non-probabilistic real waveforms, with either the waveform itself or its (normalized) analytic representation acting in the role of the PAF. Detailed numerical calculations are presented for both adaptations, showing the expected informatic behaviours in a variety of rudimentary scenarios. Particularly noteworthy are the sensitivity to the degree of randomness in a sequence of pulses and potential for detection of weak signals.

  12. Quantum mechanical calculations to chemical accuracy

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1991-01-01

    The accuracy of current molecular-structure calculations is illustrated with examples of quantum mechanical solutions for chemical problems. Two approaches are considered: (1) the coupled-cluster singles and doubles (CCSD) with a perturbational estimate of the contribution of connected triple excitations, or CCDS(T); and (2) the multireference configuration-interaction (MRCI) approach to the correlation problem. The MRCI approach gains greater applicability by means of size-extensive modifications such as the averaged-coupled pair functional approach. The examples of solutions to chemical problems include those for C-H bond energies, the vibrational frequencies of O3, identifying the ground state of Al2 and Si2, and the Lewis-Rayleigh afterglow and the Hermann IR system of N2. Accurate molecular-wave functions can be derived from a combination of basis-set saturation studies and full configuration-interaction calculations.

  13. On some hydrodynamical aspects of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Spera, Mauro

    2010-02-01

    In this note we first set up an analogy between spin and vorticity of a perfect 2d-fluid flow, based on the complex polynomial ( i.e. Borel-Weil) realization of the irreducible unitary representations of SU(2), and looking at the Madelung-Bohm velocity attached to the ensuing spin wave functions. We also show that, in the framework of finite dimensional geometric quantum mechanics, the Schrödinger velocity field on projective Hilbert space is divergence-free (being Killing with respect to the Fubini-Study metric) and fulfils the stationary Euler equation, with pressure proportional to the Hamiltonian uncertainty (squared). We explicitly determine the critical points of the pressure of this “Schrödinger fluid”, together with its vorticity, which turns out to depend on the spacings of the energy levels. These results follow from hydrodynamical properties of Killing vector fields valid in any (finite dimensional) Riemannian manifold, of possible independent interest.

  14. On some hydrodynamical aspects of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Spera, Mauro

    2010-02-01

    In this note we first set up an analogy between spin and vorticity of a perfect 2d-fluid flow, based on the complex polynomial (i.e. Borel-Weil) realization of the irreducible unitary representations of SU(2), and looking at the Madelung-Bohm velocity attached to the ensuing spin wave functions. We also show that, in the framework of finite dimensional geometric quantum mechanics, the Schrödinger velocity field on projective Hilbert space is divergence-free (being Killing with respect to the Fubini-Study metric) and fulfils the stationary Euler equation, with pressure proportional to the Hamiltonian uncertainty (squared). We explicitly determine the critical points of the pressure of this "Schrödinger fluid", together with its vorticity, which turns out to depend on the spacings of the energy levels. These results follow from hydrodynamical properties of Killing vector fields valid in any (finite dimensional) Riemannian manifold, of possible independent interest.

  15. New methods for quantum mechanical reaction dynamics

    SciTech Connect

    Thompson, Ward Hugh

    1996-12-01

    Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L2) representation of the outgoing wave scattering Green`s function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green`s function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC- can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC- geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H3O- system, providing information about the potential energy surface for the OH + H2 reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the

  16. Categorical quantum mechanics II: Classical-quantum interaction

    NASA Astrophysics Data System (ADS)

    Coecke, Bob; Kissinger, Aleks

    2016-08-01

    This is the second part of a three-part overview, in which we derive the category-theoretic backbone of quantum theory from a process ontology, treating quantum theory as a theory of systems, processes and their interactions. In this part, we focus on classical-quantum interaction. Classical and quantum systems are treated as distinct types, of which the respective behavioral properties are specified in terms of processes and their compositions. In particular, classicality is witnessed by ‘spiders’ which fuse together whenever they connect. We define mixedness and show that pure processes are extremal in the space of all processes, and we define entanglement and show that quantum theory indeed exhibits entanglement. We discuss the classification of tripartite qubit entanglement and show that both the GHZ-state and the W-state come from spider-like families of processes, which differ only in how they behave when they are connected by two or more wires. We define measurements and provide fully comprehensive descriptions of several quantum protocols involving classical data flow. Finally, we give a notion of ‘genuine quantumness’, from which special processes called ‘phase spiders’ arise, and get a first glimpse of quantum nonlocality.

  17. Reverse Causation and the Transactional Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Cramer, John G.

    2006-10-01

    In the first part of the paper we present the transactional interpretation of quantum mechanics, a method of viewing the formalism of quantum mechanics that provides a way of visualizing quantum events and experiments. In the second part, we present an EPR gedankenexperiment that appears to lead to observer-level reverse causation. A transactional analysis of the experiment is presented. It easily accounts for the reported observations but does not reveal any barriers to its modification for reverse causation.

  18. 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…

  19. 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…

  20. Do Free Quantum-Mechanical Wave Packets Always Spread?

    ERIC Educational Resources Information Center

    Klein, James R.

    1980-01-01

    The spreading or shrinking of free three-dimensional quantum-mechanical wave packets is addressed. A seeming paradox concerning the time evolution operator and nonspreading wave packets is discussed, and the necessity of taking into account the appropriate mathematical structure of quantum mechanics is emphasized. Teaching implications are given.…

  1. 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…

  2. 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…

  3. 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…

  4. Quantum Mechanics from Periodic Dynamics: the bosonic case

    SciTech Connect

    Dolce, Donatello

    2010-05-04

    Enforcing the periodicity hypothesis of the 'old' formulation of Quantum Mechanics we show the possibility for a new scenario where Special Relativity and Quantum Mechanics are unified in a deterministic field theory. A novel interpretation of the AdS/CFT conjecture is discussed.

  5. Fragment quantum mechanical calculation of proteins and its applications.

    PubMed

    He, Xiao; Zhu, Tong; Wang, Xianwei; Liu, Jinfeng; Zhang, John Z H

    2014-09-16

    Conspectus The desire to study molecular systems that are much larger than what the current state-of-the-art ab initio or density functional theory methods could handle has naturally led to the development of novel approximate methods, including semiempirical approaches, reduced-scaling methods, and fragmentation methods. The major computational limitation of ab initio methods is the scaling problem, because the cost of ab initio calculation scales nth power or worse with system size. In the past decade, the fragmentation approach based on chemical locality has opened a new door for developing linear-scaling quantum mechanical (QM) methods for large systems and for applications to large molecular systems such as biomolecules. The fragmentation approach is highly attractive from a computational standpoint. First, the ab initio calculation of individual fragments can be conducted almost independently, which makes it suitable for massively parallel computations. Second, the electron properties, such as density and energy, are typically combined in a linear fashion to reproduce those for the entire molecular system, which makes the overall computation scale linearly with the size of the system. In this Account, two fragmentation methods and their applications to macromolecules are described. They are the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method and the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. The EE-GMFCC method is developed from the MFCC approach, which was initially used to obtain accurate protein-ligand QM interaction energies. The main idea of the MFCC approach is that a pair of conjugate caps (concaps) is inserted at the location where the subsystem is divided by cutting the chemical bond. In addition, the pair of concaps is fused to form molecular species such that the overcounted effect from added concaps can be properly removed. By introducing the electrostatic

  6. A snapshot of foundational attitudes toward quantum mechanics

    NASA Astrophysics Data System (ADS)

    Schlosshauer, Maximilian; Kofler, Johannes; Zeilinger, Anton

    2013-08-01

    Foundational investigations in quantum mechanics, both experimental and theoretical, gave birth to the field of quantum information science. Nevertheless, the foundations of quantum mechanics themselves remain hotly debated in the scientific community, and no consensus on essential questions has been reached. Here, we present the results of a poll carried out among 33 participants of a conference on the foundations of quantum mechanics. The participants completed a questionnaire containing 16 multiple-choice questions probing opinions on quantum-foundational issues. Participants included physicists, philosophers, and mathematicians. We describe our findings, identify commonly held views, and determine strong, medium, and weak correlations between the answers. Our study provides a unique snapshot of current views in the field of quantum foundations, as well as an analysis of the relationships between these views.

  7. Chirality, quantum mechanics, and biological determinism

    NASA Astrophysics Data System (ADS)

    Davies, P. C. W.

    2006-08-01

    life with biochemical make-up resembling that of known life. Whilst the experimental search for a second sample of life - possibly by detecting a chiral "anomaly" - continues, some theoretical investigations may be pursued to narrow down the options. Chiral determinism would be an intrinsically quantum process. There are hints that quantum mechanics plays a key role in biology, but the claim remains contentious. Here I review some of the evidence for quantum aspects of biology. I also summarize some proposals for testing biological determinism by seeking evidence for a multiple genesis events on Earth, and for identifying extant "alien microbes" - micro-organisms descended from an independent origin from familiar life.

  8. 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

  9. Statistical mechanics of quantum-classical systems with holonomic constraints.

    PubMed

    Sergi, Alessandro

    2006-01-14

    The statistical mechanics of quantum-classical systems with holonomic constraints is formulated rigorously by unifying the classical Dirac bracket and the quantum-classical bracket in matrix form. The resulting Dirac quantum-classical theory, which conserves the holonomic constraints exactly, is then used to formulate time evolution and statistical mechanics. The correct momentum-jump approximation for constrained systems arises naturally from this formalism. Finally, in analogy with what was found in the classical case, it is shown that the rigorous linear-response function of constrained quantum-classical systems contains nontrivial additional terms which are absent in the response of unconstrained systems.

  10. High-efficiency quantum state transfer and quantum memory using a mechanical oscillator

    NASA Astrophysics Data System (ADS)

    Sete, Eyob A.; Eleuch, H.

    2015-03-01

    We analyze an optomechanical system that can be used to efficiently transfer a quantum state between an optical cavity and a distant mechanical oscillator coupled to a second optical cavity. We show that for a moderate mechanical Q factor it is possible to achieve a transfer efficiency of 99.4 % by using adjustable cavity damping rates and destructive interference. We also show that the quantum mechanical oscillator can be used as a quantum memory device with an efficiency of 96 % employing a pulsed optomechanical coupling. Although the mechanical dissipation slightly decreases the efficiency, its effect can be significantly reduced by designing a high-Q mechanical oscillator.

  11. 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 .

  12. Review of student difficulties in upper-level quantum mechanics

    NASA Astrophysics Data System (ADS)

    Singh, Chandralekha; Marshman, Emily

    2015-12-01

    [This paper is part of the Focused Collection on Upper Division Physics Courses.] 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 mechanics and quantum mechanics are very different. Here, we review research on student reasoning difficulties in learning upper-level quantum mechanics and research on students' problem-solving and metacognitive skills in these courses. Some of these studies were multiuniversity investigations. The investigations suggest that there is large diversity in student performance in upper-level quantum mechanics regardless of the university, textbook, or instructor, and many students in these courses have not acquired a functional understanding of the fundamental concepts. The nature of reasoning difficulties in learning quantum mechanics is analogous to reasoning difficulties found via research in introductory physics courses. The reasoning difficulties were often due to overgeneralizations of concepts learned in one context to another context where they are not directly applicable. Reasoning difficulties in distinguishing between closely related concepts and in making sense of the formalism of quantum mechanics were common. We conclude with a brief summary of the research-based approaches that take advantage of research on student difficulties in order to improve teaching and learning of quantum mechanics.

  13. Observation and superselection in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Landsman, N. P.

    We attempt to clarify the main conceptual issues in approaches to 'objectification' or 'measurement' in quantum mechanics which are based on superselection rules. Such approaches venture to derive the emergence of classical 'reality' relative to a class of observers; those believing that the classical world exists intrinsically and absolutely are advised against reading this paper. The prototype approach (K. Hepp, Helv. Phys. Acta 45 (1972), 237-248) where superselection sectors are assumed in the state space of the apparatus is shown to be untenable. Instead, one should couple system and apparatus to an environment, and postulate superselection rules for the latter. These are motivated by the locality of any observer or other (actual or virtual) monitoring system. In this way 'environmental' solutions to the measurement problem (H.D. Zeh, Found. Phys. 1 (1970), 69-76; W. H. Zurek, Phys. Rev. D26 (1982), 1862-1880 and Progr. Theor. Phys. 89 (1993), 281-312) become consistent and acceptable, too. Points of contact with the modal interpretation are briefly discussed. We propose a minimal value attribution to observables in theories with superselection rules, in which only central observables have properties. In particular, the eigenvector-eigenvalue link is dropped. This is mainly motivated by Ockham's razor.

  14. "Mysticism" in Quantum Mechanics: The Forgotten Controversy

    ERIC Educational Resources Information Center

    Marin, Juan Miguel

    2009-01-01

    This paper argues that a European controversy over a "mystical" hypothesis, one assigning the mind a role to play at the material level of reality, shaped much of the debate over the interpretation of the quantum equations. It traces back the controversy to the past two decades, beginning in the late 1920s--birth of quantum theory--and concluding…

  15. The physical principles of quantum mechanics. A critical review

    NASA Astrophysics Data System (ADS)

    Strocchi, F.

    2012-01-01

    The standard presentation of the principles of quantum mechanics is critically reviewed both from the experimental/operational point and with respect to the request of mathematical consistency and logical economy. A simpler and more physically motivated formulation is discussed. The existence of non commuting observables, which characterizes quantum mechanics with respect to classical mechanics, is related to operationally testable complementarity relations, rather than to uncertainty relations. The drawbacks of Dirac argument for canonical quantization are avoided by a more geometrical approach.

  16. Quantum Hamilton mechanics: Hamilton equations of quantum motion, origin of quantum operators, and proof of quantization axiom

    SciTech Connect

    Yang, C.-D. . E-mail: cdyang@mail.ncku.edu.tw

    2006-12-15

    This paper gives a thorough investigation on formulating and solving quantum problems by extended analytical mechanics that extends canonical variables to complex domain. With this complex extension, we show that quantum mechanics becomes a part of analytical mechanics and hence can be treated integrally with classical mechanics. Complex canonical variables are governed by Hamilton equations of motion, which can be derived naturally from Schroedinger equation. Using complex canonical variables, a formal proof of the quantization axiom p {sup {yields}} p = -ih{nabla}, which is the kernel in constructing quantum-mechanical systems, becomes a one-line corollary of Hamilton mechanics. The derivation of quantum operators from Hamilton mechanics is coordinate independent and thus allows us to derive quantum operators directly under any coordinate system without transforming back to Cartesian coordinates. Besides deriving quantum operators, we also show that the various prominent quantum effects, such as quantization, tunneling, atomic shell structure, Aharonov-Bohm effect, and spin, all have the root in Hamilton mechanics and can be described entirely by Hamilton equations of motion.

  17. Ruling out multi-order interference in quantum mechanics.

    PubMed

    Sinha, Urbasi; Couteau, Christophe; Jennewein, Thomas; Laflamme, Raymond; Weihs, Gregor

    2010-07-23

    Quantum mechanics and gravitation are two pillars of modern physics. Despite their success in describing the physical world around us, they seem to be incompatible theories. There are suggestions that one of these theories must be generalized to achieve unification. For example, Born's rule--one of the axioms of quantum mechanics--could be violated. Born's rule predicts that quantum interference, as shown by a double-slit diffraction experiment, occurs from pairs of paths. A generalized version of quantum mechanics might allow multipath (i.e., higher-order) interference, thus leading to a deviation from the theory. We performed a three-slit experiment with photons and bounded the magnitude of three-path interference to less than 10(-2) of the expected two-path interference, thus ruling out third- and higher-order interference and providing a bound on the accuracy of Born's rule. Our experiment is consistent with the postulate both in semiclassical and quantum regimes.

  18. Bell operator and Gaussian squeezed states in noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Bastos, Catarina; Bernardini, Alex E.; Bertolami, Orfeu; Dias, Nuno Costa; Prata, João Nuno

    2016-05-01

    We examine putative corrections to the Bell operator due to the noncommutativity in the phase space. Starting from a Gaussian squeezed envelope whose time evolution is driven by commutative (standard quantum mechanics) and noncommutative dynamics, respectively, we conclude that although the time-evolving covariance matrix in the noncommutative case is different from the standard case, the squeezing parameter dominates and there are no noticeable noncommutative corrections to the Bell operator. This indicates that, at least for squeezed states, the privileged states to test Bell correlations, noncommutativity versions of quantum mechanics remain as nonlocal as quantum mechanics itself.

  19. Predicting crystal structure by merging data mining with quantum mechanics.

    PubMed

    Fischer, Christopher C; Tibbetts, Kevin J; Morgan, Dane; Ceder, Gerbrand

    2006-08-01

    Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an algorithm to direct the search through the large space of possible structures is found. We present a new approach to the prediction of structure that rigorously mines correlations embodied within experimental data and uses them to direct quantum mechanical techniques efficiently towards the stable crystal structure of materials.

  20. 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.

  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. On Heat in a Quantum Mechanical Process

    NASA Astrophysics Data System (ADS)

    Deesuwan, Tanapat; Anders, Janet

    2013-05-01

    Heat is the portion of energy exchange between systems in thermodynamic process which, unlike work, is always associated with the change of the entropies of the systems. In the context of quantum thermodynamics, heat process is described by an incoherent generalised quantum evolution, which is a map between two quantum states that does not preserve the entropy. Based on an information-theoretic reasoning, we propose that heat involving in a general quantum thermodynamic process can be separated into two types: one that is due to the unital subclass of the evolutions and another one that is due to the others. According to these categories, we show how the former type of heat can be incorporated into Jarzynski equality, resulting in a generalised version of the equality. We also derive a Jarzynski inequality which incorporates all heat into the picture and show that this situation is just equivalent to the presence of Maxwell's demon.

  3. Quantum Mechanics in Biology: Photoexcitations in DNA

    NASA Astrophysics Data System (ADS)

    Bittner, Eric R.; Czader, Arkadiusz

    We consider here the theoretical and quantum chemical description of the photoexcitated states in DNA duplexes. We discuss the motivation and limitations of an exciton model and use this as the starting point for more detailed excited state quantum chemical evaluations. In particular, we focus upon the role of interbase proton transfer between Watson/Crick pairs in localizing an excitation and then quenching it through intersystem crossing and charge transfer.

  4. Why are probabilistic laws governing quantum mechanics and neurobiology?

    NASA Astrophysics Data System (ADS)

    Kröger, Helmut

    2005-08-01

    We address the question: Why are dynamical laws governing in quantum mechanics and in neuroscience of probabilistic nature instead of being deterministic? We discuss some ideas showing that the probabilistic option offers advantages over the deterministic one.

  5. 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.

  6. Probabilistic Approach to Teaching the Principles of Quantum Mechanics

    ERIC Educational Resources Information Center

    Santos, Emilio

    1976-01-01

    Approaches the representation of quantum mechanics through Hilbert space postulates. Demonstrates that if the representation is to be accurate, an evolution operator of the form of a Hamiltonian must be used. (CP)

  7. 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)

  8. Macroscopic test of quantum mechanics versus stochastic electrodynamics

    NASA Astrophysics Data System (ADS)

    Chaturvedi, S.; Drummond, Peter D.

    1997-02-01

    We identify a test of quantum mechanics versus macroscopic local realism in the form of stochastic electrodynamics. The test uses the steady-state triple quadrature correlations of a parametric oscillator below threshold.

  9. A Simplified Quantum Mechanical Model of Diatomic Molecules

    ERIC Educational Resources Information Center

    Nielsen, Lars Drud

    1978-01-01

    Introduces a simple one-dimensional model of a diatomic molecule that can explain all the essential features of a real two particle quantum mechanical system and gives quantitative results in fair agreement with those of a hydrogen molecule. (GA)

  10. Quantum mechanics of the inverted oscillator potential

    NASA Astrophysics Data System (ADS)

    Barton, G.

    1986-02-01

    The Hamiltonian ( 1/2m)p 2 - 1/2mω 2x 2 yields equations solvable in closed form; one is led to them by questions about the longest mean sojourn time T allowed by quantum mechanics to a system near unstable equilibrium. These equations are then studied further in their own right. After criticism of earlier arguments, one finds, by aid of the Green's function, that T ˜ ω -1log{ l/( {h̷}/{mω) 1/2}} for sojourn in the region | x| < l, where l is the resolving power of the detector. Without appeal to some parameter like l one would get nonsense estimates T ˜ ω-1 (e.g., from the nondecay probability familiar in the decay of metastable states). in this potential wavepackets Gaussian in position do not split on impact: their peaks are either transmitted or reflected, depending on the sign of the energy E ≷ 0; however, they spread so fast that not all the probability ends up on the same side of the origin as the peak. The energy eigenfunctions (parabolic cylinder functions) identify the transmission and reflection amplitudes as T = (1 + e -2πE) -1/2eiφ, R = -i(1 + e -2πE) -1/2 e -πE e iφ, where φ = arg Γ( 1/2 - iE) (in units where 2m = 1 = ω = h̷). The density of states for the interval | x| ≤ L is 2π -1 log L + π -1ϕ'( E). Wavepackets that are peaked sharply enough in energy travel without dispersion in the asymptotic region | x| > | E|, and do split on impact in the usual way. The travel times and time delays of these packets are determined. For both reflection and transmission, and for both E ≷ 0, the time delays are given by φ'( E), which is a symmetric function of E, with a positive maximum at E = 0. In particular, packets tunneling under the barrier reemerge sooner if their energy is more negative. This paradox (which occurs also in other tunneling problems) is elucidated as far as possible. Coherent states are constructed by analogy to those of the ordinary oscillator. Though not integrable, their probability distributions do have a

  11. Contexts, Systems and Modalities: A New Ontology for Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Auffèves, Alexia; Grangier, Philippe

    2016-02-01

    In this article we present a possible way to make usual quantum mechanics fully compatible with physical realism, defined as the statement that the goal of physics is to study entities of the natural world, existing independently from any particular observer's perception, and obeying universal and intelligible rules. Rather than elaborating on the quantum formalism itself, we propose a new quantum ontology, where physical properties are attributed jointly to the system, and to the context in which it is embedded. In combination with a quantization principle, this non-classical definition of physical reality sheds new light on counter-intuitive features of quantum mechanics such as the origin of probabilities, non-locality, and the quantum-classical boundary.

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

    SciTech Connect

    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 chaotic 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.

  14. Structure and dynamics of the uranyl tricarbonate complex in aqueous solution: insights from quantum mechanical charge field molecular dynamics.

    PubMed

    Tirler, Andreas O; Hofer, Thomas S

    2014-11-13

    This investigation presents the characterization of structural and dynamical properties of uranyl tricarbonate in aqueous solution employing an extended hybrid quantum mechanical/molecular mechanical (QM/MM) approach. It is shown that the inclusion of explicit solvent molecules in the quantum chemical treatment is essential to mimic the complex interaction occurring in an aqueous environment. Thus, in contrast to gas phase cluster calculations on a quantum chemical level proposing a 6-fold coordination of the three carbonates, the QMCF MD simulation proposes a 5-fold coordination. An extensive comparison of the simulation results to structural and dynamical data available in the literature was found to be in excellent agreement. Furthermore, this work is the first theoretical study on a quantum chemical level of theory able to observe the conversion of carbonate (CO₃²⁻) to bicarbonate (HCO₃⁻) in the equatorial coordination sphere of the uranyl ion. From a comparison of the free energy ΔG values for the unprotonated educt [UO₂(CO₃)₃]⁴⁻ and the protonated [UO₂(CO₃)₂(HCO₃)]³⁻, it could be concluded that the reaction equilibrium is strongly shifted toward the product state confirming the benignity for the observed protonation reaction. Structural properties and the three-dimensional arrangement of carbonate ligands were analyzed via pair-, three-body, and angular distributions, the dynamical properties were evaluated by hydrogen-bond correlation functions and vibrational power spectra.

  15. $\\cN$-FOLD SUPERSYMMETRY IN QUANTUM MECHANICAL MATRIX MODELS

    NASA Astrophysics Data System (ADS)

    Tanaka, Toshiaki

    2012-03-01

    We formulate Ņ-fold supersymmetry in quantum mechanical matrix models. As an example, we construct general two-by-two Hermitian matrix two-fold supersymmetric quantum mechanical systems. We find that there are two inequivalent such systems, both of which are characterized by two arbitrary scalar functions, and one of which does not reduce to the scalar system. The obtained systems are all weakly quasi-solvable.

  16. Geometrical description of algebraic structures: Applications to Quantum Mechanics

    SciTech Connect

    Carinena, J. F.; Ibort, A.; Marmo, G.; Morandi, G.

    2009-05-06

    Geometrization of physical theories have always played an important role in their analysis and development. In this contribution we discuss various aspects concerning the geometrization of physical theories: from classical mechanics to quantum mechanics. We will concentrate our attention into quantum theories and we will show how to use in a systematic way the transition from algebraic to geometrical structures to explore their geometry, mainly its Jordan-Lie structure.

  17. Bohmian mechanics with complex action: A new trajectory-based formulation of quantum mechanics

    SciTech Connect

    Goldfarb, Yair; Degani, Ilan; Tannor, David J.

    2006-12-21

    In recent years there has been a resurgence of interest in Bohmian mechanics as a numerical tool because of its local dynamics, which suggest the possibility of significant computational advantages for the simulation of large quantum systems. However, closer inspection of the Bohmian formulation reveals that the nonlocality of quantum mechanics has not disappeared--it has simply been swept under the rug into the quantum force. In this paper we present a new formulation of Bohmian mechanics in which the quantum action, S, is taken to be complex. This leads to a single equation for complex S, and ultimately complex x and p but there is a reward for this complexification - a significantly higher degree of localization. The quantum force in the new approach vanishes for Gaussian wave packet dynamics, and its effect on barrier tunneling processes is orders of magnitude lower than that of the classical force. In fact, the current method is shown to be a rigorous extension of generalized Gaussian wave packet dynamics to give exact quantum mechanics. We demonstrate tunneling probabilities that are in virtually perfect agreement with the exact quantum mechanics down to 10{sup -7} calculated from strictly localized quantum trajectories that do not communicate with their neighbors. The new formulation may have significant implications for fundamental quantum mechanics, ranging from the interpretation of non-locality to measures of quantum complexity.

  18. Bohmian mechanics with complex action: a new trajectory-based formulation of quantum mechanics.

    PubMed

    Goldfarb, Yair; Degani, Ilan; Tannor, David J

    2006-12-21

    In recent years there has been a resurgence of interest in Bohmian mechanics as a numerical tool because of its local dynamics, which suggest the possibility of significant computational advantages for the simulation of large quantum systems. However, closer inspection of the Bohmian formulation reveals that the nonlocality of quantum mechanics has not disappeared-it has simply been swept under the rug into the quantum force. In this paper we present a new formulation of Bohmian mechanics in which the quantum action, S, is taken to be complex. This leads to a single equation for complex S, and ultimately complex x and p but there is a reward for this complexification-a significantly higher degree of localization. The quantum force in the new approach vanishes for Gaussian wave packet dynamics, and its effect on barrier tunneling processes is orders of magnitude lower than that of the classical force. In fact, the current method is shown to be a rigorous extension of generalized Gaussian wave packet dynamics to give exact quantum mechanics. We demonstrate tunneling probabilities that are in virtually perfect agreement with the exact quantum mechanics down to 10(-7) calculated from strictly localized quantum trajectories that do not communicate with their neighbors. The new formulation may have significant implications for fundamental quantum mechanics, ranging from the interpretation of non-locality to measures of quantum complexity.

  19. Quantum mechanical effects in plasmonic structures with subnanometre gaps

    PubMed Central

    Zhu, Wenqi; Esteban, Ruben; Borisov, Andrei G.; Baumberg, Jeremy J.; Nordlander, Peter; Lezec, Henri J.; Aizpurua, Javier; Crozier, Kenneth B.

    2016-01-01

    Metallic structures with nanogap features have proven highly effective as building blocks for plasmonic systems, as they can provide a wide tuning range of operating frequencies and large near-field enhancements. Recent work has shown that quantum mechanical effects such as electron tunnelling and nonlocal screening become important as the gap distances approach the subnanometre length-scale. Such quantum effects challenge the classical picture of nanogap plasmons and have stimulated a number of theoretical and experimental studies. This review outlines the findings of many groups into quantum mechanical effects in nanogap plasmons, and discusses outstanding challenges and future directions. PMID:27255556

  20. Acoustic Analog to Quantum Mechanical Level-Splitting

    NASA Astrophysics Data System (ADS)

    Hilbert, Shawn

    2010-03-01

    One difficulty in teaching quantum mechanics is the lack of classroom demonstrations. To sidestep this issue, analogies can provide an enlightening alternative. Acoustics governance by the same time-independent wave equation as quantum mechanics supports it use in such analogies. This presentation examines one such analogy for an infinite potential well with a delta potential perturbation. The physical acoustic system consists of continuous sounds waves traveling in a pair of tubes which are separated by a variable diaphragm. The level-splitting nature of the quantum system can be mimicked in the acoustic system.

  1. 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.

  2. 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.

  3. Quantum mechanics simulation of protein dynamics on long timescale.

    PubMed

    Liu, H; Elstner, M; Kaxiras, E; Frauenheim, T; Hermans, J; Yang, W

    2001-09-01

    Protein structure and dynamics are the keys to a wide range of problems in biology. In principle, both can be fully understood by using quantum mechanics as the ultimate tool to unveil the molecular interactions involved. Indeed, quantum mechanics of atoms and molecules have come to play a central role in chemistry and physics. In practice, however, direct application of quantum mechanics to protein systems has been prohibited by the large molecular size of proteins. As a consequence, there is no general quantum mechanical treatment that not only exceeds the accuracy of state-of-the-art empirical models for proteins but also maintains the efficiency needed for extensive sampling in the conformational space, a requirement mandated by the complexity of protein systems. Here we show that, given recent developments in methods, a general quantum mechanical-based treatment can be constructed. We report a molecular dynamics simulation of a protein, crambin, in solution for 350 ps in which we combine a semiempirical quantum-mechanical description of the entire protein with a description of the surrounding solvent, and solvent-protein interactions based on a molecular mechanics force field. Comparison with a recent very high-resolution crystal structure of crambin (Jelsch et al., Proc Natl Acad Sci USA 2000;102:2246-2251) shows that geometrical detail is better reproduced in this simulation than when several alternate molecular mechanics force fields are used to describe the entire system of protein and solvent, even though the structure is no less flexible. Individual atomic charges deviate in both directions from "canonical" values, and some charge transfer is found between the N and C-termini. The capability of simulating protein dynamics on and beyond the few hundred ps timescale with a demonstrably accurate quantum mechanical model will bring new opportunities to extend our understanding of a range of basic processes in biology such as molecular recognition and enzyme

  4. 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.

  5. The Möbius symmetry of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Faraggi, Alon E.; Matone, Marco

    2015-07-01

    The equivalence postulate approach to quantum mechanics aims to formulate quantum mechanics from a fundamental geometrical principle. Underlying the formulation there exists a basic cocycle condition which is invariant under D-dimensional Mobius transformations with respect to the Euclidean or Minkowski metrics. The invariance under global Mobius transformations implies that spatial space is compact. Furthermore, it implies energy quantisation and undefinability of quantum trajectories without assuming any prior interpretation of the wave function. The approach may be viewed as conventional quantum mechanics with the caveat that spatial space is compact, as dictated by the Möbius symmetry, with the classical limit corresponding to the decompactification limit. Correspondingly, there exists a finite length scale in the formalism and consequently an intrinsic regularisation scheme. Evidence for the compactness of space may exist in the cosmic microwave background radiation.

  6. 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.

  7. Optimal state discrimination and unstructured search in nonlinear quantum mechanics

    NASA Astrophysics Data System (ADS)

    Childs, Andrew M.; Young, Joshua

    2016-02-01

    Nonlinear variants of quantum mechanics can solve tasks that are impossible in standard quantum theory, such as perfectly distinguishing nonorthogonal states. Here we derive the optimal protocol for distinguishing two states of a qubit using the Gross-Pitaevskii equation, a model of nonlinear quantum mechanics that arises as an effective description of Bose-Einstein condensates. Using this protocol, we present an algorithm for unstructured search in the Gross-Pitaevskii model, obtaining an exponential improvement over a previous algorithm of Meyer and Wong. This result establishes a limitation on the effectiveness of the Gross-Pitaevskii approximation. More generally, we demonstrate similar behavior under a family of related nonlinearities, giving evidence that the ability to quickly discriminate nonorthogonal states and thereby solve unstructured search is a generic feature of nonlinear quantum mechanics.

  8. 'Mysticism' in quantum mechanics: the forgotten controversy

    NASA Astrophysics Data System (ADS)

    Marin, Juan Miguel

    2009-07-01

    This paper argues that a European controversy over a 'mystical' hypothesis, one assigning the mind a role to play at the material level of reality, shaped much of the debate over the interpretation of the quantum equations. It traces back the controversy to the past two decades, beginning in the late 1920s—birth of quantum theory—and concluding with Erwin Schrödinger's lectures published as 'Mind and Matter'. Becoming aware of the issues at stake can help us understand the historical, philosophical and cultural background from which today's physics emerged.

  9. Deformation quantization: Quantum mechanics lives and works in phase space

    NASA Astrophysics Data System (ADS)

    Zachos, Cosmas K.

    2014-09-01

    Wigner's 1932 quasi-probability Distribution Function in phase-space, his first paper in English, is a special (Weyl) representation of the density matrix. It has been useful in describing quantum flows in semiclassical limits; quantum optics; nuclear and physics; decoherence (eg, quantum computing); quantum chaos; "Welcher Weg" puzzles; molecular Talbot-Lau interferometry; atomic measurements. It is further of great importance in signal processing (time-frequency analysis). Nevertheless, a remarkable aspect of its internal logic, pioneered by H. Groenewold and J. Moyal, has only blossomed in the last quarter-century: It furnishes a third, alternate, formulation of Quantum Mechanics, independent of the conventional Hilbert Space (the gold medal), or Path Integral (the silver medal) formulations, and perhaps more intuitive, since it shares language with classical mechanics: one need not choose sides between coordinate or momentum space variables, since it is formulated simultaneously in terms of position and momentum. This bronze medal formulation is logically complete and self-standing, and accommodates the uncertainty principle in an unexpected manner, so that it offers unique insights into the classical limit of quantum theory. The observables in this formulation are cnumber functions in phase space instead of operators, with the same interpretation as their classical counterparts, only now composed together in novel algebraic ways using star products. One might then envision an imaginary world in which this formulation of quantum mechanics had preceded the conventional Hilbert-space formulation, and its own techniques and methods had arisen independently, perhaps out of generalizations of classical mechanics and statistical mechanics. A sampling of such intriguing techniques and methods has already been published in C. K. Zachos, Int Jou Mod Phys A17 297-316 (2002), and T. L. Curtright, D. B. Fairlie, and C. K. Zachos, A Concise Treatise on Quantum Mechanics in

  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. The Transactional Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Kastner, Ruth E.

    2012-10-01

    Preface; 1. Introduction: quantum peculiarities; 2. The map vs the territory; 3. The original TI: fundamentals; 4. The new possibilist TI: fundamentals; 5. Challenges, replies, and applications; 6. PTI and relativity; 7. The metaphysics of possibility; 8. PTI and 'spacetime'; 9. Epilogue: more than meets the eye; Appendixes; References; Index.

  12. Classical and Quantum-Mechanical State Reconstruction

    ERIC Educational Resources Information Center

    Khanna, F. C.; Mello, P. A.; Revzen, M.

    2012-01-01

    The aim of this paper is to present the subject of state reconstruction in classical and in quantum physics, a subject that deals with the experimentally acquired information that allows the determination of the physical state of a system. Our first purpose is to explain a method for retrieving a classical state in phase space, similar to that…

  13. Understanding the reaction mechanism and intermediate stabilization in mammalian serine racemase using multiscale quantum-classical simulations.

    PubMed

    Nitoker, Neta; Major, Dan Thomas

    2015-01-20

    Serine racemase (SerR) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the racemization of l-Ser to d-Ser. In mammals, d-Ser is an endogenous coagonist required for the activation of N-methyl-d-aspartate receptors (NMDARs), thus making SerR a promising pharmaceutical target. However, mechanistic studies of SerR are scarce, and the details of the enzymatic racemization reaction are not fully understood. In the current study we elucidate the catalytic mechanism in SerR by employing combined multiscale classical/quantum simulations. The free energy profile of a model SerR racemization reaction is first calculated in the gas phase and in aqueous solution. To obtain the free energy profile for the enzymatic reaction, hybrid quantum mechanics/molecular mechanics molecular dynamics simulations in conjunction with umbrella sampling are performed. The results suggest that in SerR, similarly to the related enzyme alanine racemase, the unprotonated PLP-substrate intermediate is stabilized mostly due to solvation effects contributed by water molecules and active-site residues, as well as long-range electrostatic interactions with the enzyme environment. In addition to a deeper understanding of the racemization mechanism in SerR, based on our simulations we propose specific mutations, which might shift the SerR equilibrium in favor of either l-Ser or d-Ser. Finally, the current studies have produced catalytically competent forms of the rat and human enzymes, which may serve as targets for future docking studies and drug design.

  14. Quantum mechanics of time travel through post-selected teleportation

    NASA Astrophysics Data System (ADS)

    Lloyd, Seth; Maccone, Lorenzo; Garcia-Patron, Raul; Giovannetti, Vittorio; Shikano, Yutaka

    2011-07-01

    This paper discusses the quantum mechanics of closed-timelike curves (CTCs) and of other potential methods for time travel. We analyze a specific proposal for such quantum time travel, the quantum description of CTCs based on post-selected teleportation (P-CTCs). We compare the theory of P-CTCs to previously proposed quantum theories of time travel: the theory is inequivalent to Deutsch’s theory of CTCs, but it is consistent with path-integral approaches (which are the best suited for analyzing quantum-field theory in curved space-time). We derive the dynamical equations that a chronology-respecting system interacting with a CTC will experience. We discuss the possibility of time travel in the absence of general-relativistic closed-timelike curves, and investigate the implications of P-CTCs for enhancing the power of computation.

  15. Analogies between optical and quantum mechanical angular momentum.

    PubMed

    Nienhuis, Gerard

    2017-02-28

    The insight that a beam of light can carry orbital angular momentum (AM) in its propagation direction came up in 1992 as a surprise. Nevertheless, the existence of momentum and AM of an electromagnetic field has been well known since the days of Maxwell. We compare the expressions for densities of AM in general three-dimensional modes and in paraxial modes. Despite their classical nature, these expressions have a suggestive quantum mechanical appearance, in terms of linear operators acting on mode functions. In addition, paraxial wave optics has several analogies with real quantum mechanics, both with the wave function of a free quantum particle and with a quantum harmonic oscillator. We discuss how these analogies can be applied.This article is part of the themed issue 'Optical orbital angular momentum'.

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

    SciTech Connect

    Strauss, Y.

    2015-07-15

    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 the 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.

  17. Quantum mechanics on profinite groups and partial order

    NASA Astrophysics Data System (ADS)

    Vourdas, A.

    2013-02-01

    Inverse limits and profinite groups are used in a quantum mechanical context. Two cases are considered: a quantum system with positions in the profinite group { {Z}}_p and momenta in the group { {Q}}_p/{ {Z}}_p, and a quantum system with positions in the profinite group {\\widehat{ {Z}}} and momenta in the group { {Q}}/{ {Z}}. The corresponding Schwatz-Bruhat spaces of wavefunctions and the Heisenberg-Weyl groups are discussed. The sets of subsystems of these systems are studied from the point of view of partial order theory. It is shown that they are directed-complete partial orders. It is also shown that they are topological spaces with T0-topologies, and this is used to define continuity of various physical quantities. The physical meaning of profinite groups, non-Archimedean metrics, partial orders and T0-topologies, in a quantum mechanical context, is discussed.

  18. Analogies between optical and quantum mechanical angular momentum

    NASA Astrophysics Data System (ADS)

    Nienhuis, Gerard

    2017-02-01

    The insight that a beam of light can carry orbital angular momentum (AM) in its propagation direction came up in 1992 as a surprise. Nevertheless, the existence of momentum and AM of an electromagnetic field has been well known since the days of Maxwell. We compare the expressions for densities of AM in general three-dimensional modes and in paraxial modes. Despite their classical nature, these expressions have a suggestive quantum mechanical appearance, in terms of linear operators acting on mode functions. In addition, paraxial wave optics has several analogies with real quantum mechanics, both with the wave function of a free quantum particle and with a quantum harmonic oscillator. We discuss how these analogies can be applied. This article is part of the themed issue 'Optical orbital angular momentum'.

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

    NASA Astrophysics Data System (ADS)

    Strauss, Y.

    2015-07-01

    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 the 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.

  20. Comment on 'Nonlocality, Counterfactuals and Quantum Mechanics'

    SciTech Connect

    Stapp, H.P.

    1999-04-14

    A recent proof [H. P. Stapp, Am. J. Phys. 65, 300 (1997)], formulated in the symbolic language of modal logic, claims to show that contemporary quantum theory, viewed as a set of rules that allow us to calculate statistical predictions among certain kinds of observations, cannot be imbedded in any rational framework that conforms to the principles that (1) the experimenters' choices of which experiments they will perform can be considered to be free choices, (2) outcomes of measurements are unique, and (3) the free choices just mentioned have no backward-in-time effects of any kind. This claim is similar to Bell's theorem, but much stronger, because no reality assumption alien to quantum philosophy is used. The paper being commented on [W. Unruh, Phys. Rev. A 59, 126 (1999)] argues that some such reality assumption has been ''smuggled'' in. That argument is examined here and shown, I believe, to be defective.

  1. Dirac particle in gravitational quantum mechanics

    NASA Astrophysics Data System (ADS)

    Pedram, Pouria

    2011-08-01

    In this Letter, we consider the effects of the Generalized (Gravitational) Uncertainty Principle (GUP) on the eigenvalues and the eigenfunctions of the Dirac equation. This form of GUP is consistent with various candidates of quantum gravity such as string theory, loop quantum gravity, doubly special relativity and black hole physics and predicts both a minimum measurable length and a maximum measurable momentum. The modified Hamiltonian contains two additional terms proportional to a( and a( where αi are Dirac matrices and a∼1/MPlc is the GUP parameter. For the case of the Dirac free particle and the Dirac particle in a box, we solve the generalized Dirac equation and find the modified energy eigenvalues and eigenfunctions.

  2. Quantum Mechanics for Beginning Physics Students

    NASA Astrophysics Data System (ADS)

    Schneider, Mark B.

    2010-10-01

    The past two decades of attention to introductory physics education has emphasized enhanced development of conceptual understanding to accompany calculational ability. Given this, it is surprising that current texts continue to rely on the Bohr model to develop a flawed intuition, and introduce correct atomic physics on an ad hoc basis. For example, Halliday, Resnick, and Walker describe the origin of atomic quantum numbers as such: "The restrictions on the values of the quantum number for the hydrogen atom, as listed in Table 39-2, are not arbitrary but come out of the solution to Schrödinger's equation." They give no further justification, but do point out the values are in conflict with the predictions of the Bohr model.

  3. Use of mathematical logical concepts in quantum mechanics: an example

    NASA Astrophysics Data System (ADS)

    Benioff, Paul

    2002-07-01

    The representation of numbers by product states in quantum mechanics can be extended to the representation of words and word sequences in languages by product states. This can be used to study quantum systems that generate text that has meaning. A simple example of such a system, based on an example described by Smullyan, is studied here. Based on a path interpretation for some word states, definitions of truth, validity, consistency and completeness are given and their properties studied. It is also shown that the relation between the potential meaning, if any, of word states and the quantum algorithmic complexity of the process generating the word states must be quite complex or nonexistent.

  4. Mathematical foundations of quantum mechanics: An advanced short course

    NASA Astrophysics Data System (ADS)

    Moretti, Valter

    2016-08-01

    This paper collects and extends the lectures I gave at the “XXIV International Fall Workshop on Geometry and Physics” held in Zaragoza (Spain) during September 2015. Within these lectures I review the formulation of Quantum Mechanics, and quantum theories in general, from a mathematically advanced viewpoint, essentially based on the orthomodular lattice of elementary propositions, discussing some fundamental ideas, mathematical tools and theorems also related to the representation of physical symmetries. The final step consists of an elementary introduction the so-called (C∗-) algebraic formulation of quantum theories.

  5. Cosmology and the pilot wave interpretation of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Tipler, Frank J.

    1984-07-01

    Bell has recently revived the pilot wave interpretation of de Broglie and Bohm as a possible scheme for interpreting wave functions in quantum cosmology. I argue that the pilot wave interpretation cannot be applied consistently to systems whose wave functions split into macroscopically distinguishable states. At some stage the pilot wave interpretation must either tacitly invoke wave function reduction in the same manner as the Copenhagen interpretation, or else abandon locality by requiring physical particles to move faster than light. Consequently, the many-worlds interpretation is the only known realist interpretation of the quantum mechanical formalism which can be extended to quantum cosmology.

  6. Models on the boundary between classical and quantum mechanics.

    PubMed

    Hooft, Gerard 't

    2015-08-06

    Arguments that quantum mechanics cannot be explained in terms of any classical theory using only classical logic seem to be based on sound mathematical considerations: there cannot be physical laws that require 'conspiracy'. It may therefore be surprising that there are several explicit quantum systems where these considerations apparently do not apply. In this report, several such counterexamples are shown. These are quantum models that do have a classical origin. The most curious of these models is superstring theory. So now the question is asked: how can such a model feature 'conspiracy', and how bad is that? Is there conspiracy in the vacuum fluctuations? Arguments concerning Bell's theorem are further sharpened.

  7. Quantum mechanics from an equivalence principle

    SciTech Connect

    Faraggi, A.E.; Matone, M.

    1997-05-15

    The authors show that requiring diffeomorphic equivalence for one-dimensional stationary states implies that the reduced action S{sub 0} satisfies the quantum Hamilton-Jacobi equation with the Planck constant playing the role of a covariantizing parameter. The construction shows the existence of a fundamental initial condition which is strictly related to the Moebius symmetry of the Legendre transform and to its involutive character. The universal nature of the initial condition implies the Schroedinger equation in any dimension.

  8. Randomness in quantum mechanics - nature's ultimate cryptogram?

    NASA Astrophysics Data System (ADS)

    Erber, T.; Putterman, S.

    1985-11-01

    The possibility that a single atom irradiated by coherent light will be equivalent to an infinite computer with regard to its ability to generate random numbers is addressed. A search for unexpected patterns of order by crypt analysis of the telegraph signal generated by the on/off time of the atom's fluorescence is described. The results will provide new experimental tests of the fundamental principles of quantum theory.

  9. Quantum mechanical models with strictly ergodic disorder

    NASA Astrophysics Data System (ADS)

    Mavi, Rajinder

    We study quantum Hamiltonians with potentials defined by strictly ergodic dynamical systems. Our interest here are models where physical properties are understood in some regimes of disorder and the extent to which they vary in alternate regimes of disorder. For Schrodinger operators we show properties known to hold in the case of analytic potentials on the torus hold even for rough potentials only required to be Holder continuous. Specifically in this case we show, assuming a positive Lyapunov exponent, dynamical localization properties hold; as well as continuity of the measure of the spectrum for all rotations. For the quantum Ising model we show for phase structure that occur in the random regime, there are similar conditions for existence under the assumption of strictly ergodic dynamics. That is, moment conditions for random disorder are paralleled by conditions on the sampling functions in deterministic disorder. We obtain conditions for existence of phase transitions given any strictly egodically defined disorder. In addition, a new multiscale analysis method is developed to show the existence of stretched exponential decay in the random cluster model generalization of the quantum Ising model where only slower decay was obainable by previous methods.

  10. Photon physics: from wave mechanics to quantum electrodynamics

    NASA Astrophysics Data System (ADS)

    Keller, Ole

    2009-05-01

    When rewritten in an appropriate manner, the microscopic Maxwell-Lorentz equations appear as a wave-mechanical theory for photons, and their quantum physical interaction with matter. A natural extension leads from photon wave mechanics to quantum electrodynamics (QED). In its modern formulation photon wave mechanics has given us valuable new insight in subjects such as spatial photon localization, near-field photon dynamics, transverse photon mass, photon eikonal theory, photon tunneling, and rim-zone electrodynamics. The present review is based on my plenary lecture at the SPIE-Europe 2009 Optics and Optoelectronics International Symposium in Prague.

  11. Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

    PubMed

    Nishimoto, Yoshio; Nakata, Hiroya; Fedorov, Dmitri G; Irle, Stephan

    2015-12-17

    The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well.

  12. The conceptual and the anecdotal history of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Beller, Mara

    1996-04-01

    The aim of this paper is to combine the intellectual and the psychosocial aspects. blurring the distinction between the conceptual and the anecdotal history of quantum mechanics. The full realization of the importance of such “anecdotal” factors leads to the revision of our understanding of the conceptual development itself. The paper concludes with the suggestion that a major part of numerous inconsistencies in the Copenhagen interpretation of quantum physics are of a psychosocial origin.

  13. Preparing a mechanical oscillator in non-gaussian quantum states.

    PubMed

    Khalili, Farid; Danilishin, Stefan; Miao, Haixing; Müller-Ebhardt, Helge; Yang, Huan; Chen, Yanbei

    2010-08-13

    We propose a protocol for coherently transferring non-Gaussian quantum states from an optical field to a mechanical oscillator. We demonstrate its experimental feasibility in future gravitational-wave detectors and tabletop optomechanical devices. This work not only outlines a feasible way to investigate nonclassicality in macroscopic optomechanical systems, but also presents a new and elegant approach for solving non-Markovian open quantum dynamics in general linear systems.

  14. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.

    PubMed

    Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L

    2016-01-01

    Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples.

  15. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

    PubMed

    Swails, Jason; Zhu, Tong; He, Xiao; Case, David A

    2015-10-01

    We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

  16. Investigations of fundamental phenomena in quantum mechanics with neutrons

    NASA Astrophysics Data System (ADS)

    Hasegawa, Yuji

    2014-04-01

    Neutron interferometer and polarimeter are used for the experimental investigations of quantum mechanical phenomena. Interferometry exhibits clear evidence of quantum-contextuality and polarimetry demonstrates conflicts of a contextual model of quantum mechanics á la Leggett. In these experiments, entanglements are achieved between degrees of freedom in a single-particle: spin, path and energy degrees of freedom are manipulated coherently and entangled. Both experiments manifest the fact that quantum contextuality is valid for phenomena with matter waves with high precision. In addition, another experiment is described which deals with error-disturbance uncertainty relation: we have experimentally tested error-disturbance uncertainty relations, one is derived by Heisenberg and the other by Ozawa. Experimental results confirm the fact that the Heisenberg's uncertainty relation is often violated and that the new relation by Ozawa is always larger than the limit. At last, as an example of a counterfactual phenomenon of quantum mechanics, observation of so-called quantum Cheshire Cat is carried out by using neutron interferometer. Experimental results suggest that pre- and post-selected neutrons travel through one of the arms of the interferometer while their magnetic moment is located in the other arm.

  17. 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.

  18. 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.

  19. Quantum mechanics, gravity and modified quantization relations.

    PubMed

    Calmet, Xavier

    2015-08-06

    In this paper, we investigate a possible energy scale dependence of the quantization rules and, in particular, from a phenomenological point of view, an energy scale dependence of an effective [Formula: see text] (reduced Planck's constant). We set a bound on the deviation of the value of [Formula: see text] at the muon scale from its usual value using measurements of the anomalous magnetic moment of the muon. Assuming that inflation has taken place, we can conclude that nature is described by a quantum theory at least up to an energy scale of about 10(16) GeV.

  20. Are nonlinear discrete cellular automata compatible with quantum mechanics?

    NASA Astrophysics Data System (ADS)

    Elze, Hans-Thomas

    2015-07-01

    We consider discrete and integer-valued cellular automata (CA). A particular class of which comprises “Hamiltonian CA” with equations of motion that bear similarities to Hamilton's equations, while they present discrete updating rules. The dynamics is linear, quite similar to unitary evolution described by the Schrödinger equation. This has been essential in our construction of an invertible map between such CA and continuous quantum mechanical models, which incorporate a fundamental discreteness scale. Based on Shannon's sampling theory, it leads, for example, to a one-to-one relation between quantum mechanical and CA conservation laws. The important issue of linearity of the theory is examined here by incorporating higher-order nonlinearities into the underlying action. These produce inconsistent nonlocal (in time) effects when trying to describe continuously such nonlinear CA. Therefore, in the present framework, only linear CA and local quantum mechanical dynamics are compatible.

  1. A deformation quantization theory for noncommutative quantum mechanics

    SciTech Connect

    Costa Dias, Nuno; Prata, Joao Nuno; Gosson, Maurice de; Luef, Franz

    2010-07-15

    We show that the deformation quantization of noncommutative quantum mechanics previously considered by Dias and Prata ['Weyl-Wigner formulation of noncommutative quantum mechanics', J. Math. Phys. 49, 072101 (2008)] and Bastos, Dias, and Prata ['Wigner measures in non-commutative quantum mechanics', e-print arXiv:math-ph/0907.4438v1; Commun. Math. Phys. (to appear)] can be expressed as a Weyl calculus on a double phase space. We study the properties of the star-product thus defined and prove a spectral theorem for the star-genvalue equation using an extension of the methods recently initiated by de Gosson and Luef ['A new approach to the *-genvalue equation', Lett. Math. Phys. 85, 173-183 (2008)].

  2. Quantum-mechanical description of in-medium fragmentation

    NASA Astrophysics Data System (ADS)

    Kopeliovich, B. Z.; Pirner, H.-J.; Potashnikova, I. K.; Schmidt, Ivan; Tarasov, A. V.; Voskresenskaya, O. O.

    2008-11-01

    We present a quantum-mechanical description of quark-hadron fragmentation in a nuclear environment. It employs the path-integral formulation of quantum mechanics, which takes care of all phases and interferences and contains all relevant time scales, such as production, coherence, and formation. The cross section includes the probability of prehadron (colorless dipole) production both inside and outside the medium. Moreover, it also includes inside-outside production, which is a typical quantum-mechanical interference effect (like twin-slit electron propagation). We observe a substantial suppression caused by the medium, even if the prehadron is produced outside the medium and no energy loss is involved. This important source of suppression is missed in the usual energy-loss scenario interpreting the effect of jet quenching observed in heavy ion collisions. This may be one reason for the too large gluon density reported by such analyses.

  3. David Bohm's Hidden Variables Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Hall, Ned; Feldman, Gary; Wulsin, Wells

    2001-04-01

    This talk presents the hidden variables interpretation of quantum mechanics as proposed by David Bohm in 1952. Using a pilot-wave, Bohm’s theory reproduces the standard predictions of quantum mechanics while at the same time postulating that particles at all times are localized at definite positions. By way of introduction, the foundational issue of the quantum mechanics measurement problem will be discussed. The talk will then focus on how Bohm’s formulation of a hidden variables theory stands up to philosophical examination. Traditional objections to the theory, such as the EPR paradox, will be addressed, as well as the deeper metaphysical implications it holds for our view of the universe.

  4. On testing for the stage of collapse in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Becker, Lon Stephen

    The question was considered whether it is possible to experimentally narrow down the time of collapse in the measurement process of quantum mechanics. A form of experiment was developed towards that end. The proof of John von Neumann that it is impossible to determine the time of collapse was analyzed, and its hidden assumptions were exploited in the design of the experiment. The reinterpretation of quantum mechanics by David Bohm was introduced to give an alternative way of looking at quantum mechanics. An objection to this view was discussed but rejected. Finally a pair of thought experiments were offered with the potential to be converted in the future into tests for whether collapse has occurred at various points in the measurement process.

  5. 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.

  6. Quantum mechanisms of density wave transport

    PubMed Central

    Miller, John H.; Wijesinghe, Asanga I.

    2012-01-01

    We report on new developments in the quantum picture of correlated electron transport in charge and spin density waves. The model treats the condensate as a quantum fluid in which charge soliton domain wall pairs nucleate above a Coulomb blockade threshold field. We employ a time-correlated soliton tunneling model, analogous to the theory of time-correlated single electron tunneling, to interpret the voltage oscillations and nonlinear current-voltage characteristics above threshold. An inverse scaling relationship between threshold field and dielectric response, originally proposed by Grüner, emerges naturally from the model. Flat dielectric and other ac responses below threshold in NbSe3 and TaS3, as well as small density wave phase displacements, indicate that the measured threshold is often much smaller than the classical depinning field. In some materials, the existence of two distinct threshold fields suggests that both soliton nucleation and classical depinning may occur. In our model, the ratio of electrostatic charging to pinning energy helps determine whether soliton nucleation or classical depinning dominates. PMID:22711979

  7. Reality in quantum mechanics, Extended Everett Concept, and consciousness

    NASA Astrophysics Data System (ADS)

    Mensky, M. B.

    2007-09-01

    Conceptual problems in quantum mechanics result from the specific quantum concept of reality and require, for their solution, including the observer’s consciousness into the quantum theory of measurements. Most naturally, this is achieved in the framework of Everett’s “many-world interpretation” of quantum mechanics. According to this interpretation, various classical alternatives are perceived by consciousness separately from each other. In the Extended Everett Concept (EEC) proposed by the present author, the separation of the alternatives is identified with the phenomenon of consciousness. This explains the classical character of the alternatives and unusual manifestations of consciousness arising “at the edge of consciousness” (i.e., in sleep or trance) when its access to “other alternative classical realities” (other Everett’s worlds) becomes feasible. Because of reversibility of quantum evolution in EEC, all time moments in the quantum world are equivalent, while the impression of flow of time appears only in consciousness. If it is assumed that consciousness may influence the probabilities of alternatives (which is consistent in case of infinitely many Everett’s worlds), EEC explains free will, “probabilistic miracles” (observing low-probability events), and decreasing entropy in the sphere of life.

  8. 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.

  9. 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.

  10. A new teaching approach to quantum mechanical tunneling

    NASA Astrophysics Data System (ADS)

    Gilfoyle, G. P.

    1999-09-01

    The transfer matrix method has been used to investigate quantum mechanical tunneling in introductory quantum mechanics. The method is applied first to calculate the transmission coefficient for tunneling through a rectangular barrier and is then extended to the problem of potential barriers of arbitrary shape, in particular, to radioactive decay. This approach uses matrix methods that are accessible to a broader range of undergraduates than other numerical techniques, the connection between the rectangular barrier problem and potential barriers of arbitrary shape is transparent, and it can be readily executed by undergraduates. The classroom experience with this approach is discussed.

  11. Study on a Possible Darwinian Origin of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Baladrón, C.

    2011-03-01

    A sketchy subquantum theory deeply influenced by Wheeler's ideas (Am. J. Phys. 51:398-404, 1983) and by the de Broglie-Bohm interpretation (Goldstein in Stanford Encyclopedia of Philosophy, 2006) of quantum mechanics is further analyzed. In this theory a fundamental system is defined as a dual entity formed by bare matter and a methodological probabilistic classical Turing machine. The evolution of the system would be determined by three Darwinian informational regulating principles. Some progress in the derivation of the postulates of quantum mechanics from these regulating principles is reported. The entanglement in a bipartite system is preliminarily considered.

  12. Unstable particles in non-relativistic quantum mechanics?

    SciTech Connect

    Hernandez-Coronado, H.

    2011-10-14

    The Schroedinger equation is up-to-a-phase invariant under the Galilei group. This phase leads to the Bargmann's superselection rule, which forbids the existence of the superposition of states with different mass and implies that unstable particles cannot be described consistently in non-relativistic quantum mechanics (NRQM). In this paper we claim that Bargmann's rule neglects physical effects and that a proper description of non-relativistic quantum mechanics requires to take into account this phase through the Extended Galilei group and the definition of its action on spacetime coordinates.

  13. The uncertainty principle determines the nonlocality of quantum mechanics.

    PubMed

    Oppenheim, Jonathan; Wehner, Stephanie

    2010-11-19

    Two central concepts of quantum mechanics are Heisenberg's uncertainty principle and a subtle form of nonlocality that Einstein famously called "spooky action at a distance." These two fundamental features have thus far been distinct concepts. We show that they are inextricably and quantitatively linked: Quantum mechanics cannot be more nonlocal with measurements that respect the uncertainty principle. In fact, the link between uncertainty and nonlocality holds for all physical theories. More specifically, the degree of nonlocality of any theory is determined by two factors: the strength of the uncertainty principle and the strength of a property called "steering," which determines which states can be prepared at one location given a measurement at another.

  14. Spacetime alternatives in the quantum mechanics of a relativistic particle

    SciTech Connect

    Whelan, J.T. Isaac Newton Institute for Mathematical Sciences, 20 Clarkson Road, Cambridge, CB3 0EH )

    1994-11-15

    Hartle's generalized quantum mechanics formalism is used to examine spacetime coarse grainings, i.e., sets of alternatives defined with respect to a region extended in time as well as space, in the quantum mechanics of a free relativistic particle. For a simple coarse graining and suitable initial conditions, tractable formulas are found for branch wave functions. Despite the nonlocality of the positive-definite version of the Klein-Gordon inner product, which means that nonoverlapping branches are not sufficient to imply decoherence, some initial conditions are found to give decoherence and allow the consistent assignment of probabilities.

  15. PREFACE: Progress in supersymmetric quantum mechanics

    NASA Astrophysics Data System (ADS)

    Aref'eva, I.; Fernández, D. J.; Hussin, V.; Negro, J.; Nieto, L. M.; Samsonov, B. F.

    2004-10-01

    The theory of integrable systems is grounded in the very beginning of theoretical physics: Kepler's system is an integrable system. This field of dynamical systems, where one looks for exact solutions of the equations of motion, has attracted most of the great figures in mathematical physics: Euler, Lagrange, Jacobi, etc. Liouville was the first to formulate the precise mathematical conditions ensuring solvability `by quadrature' of the dynamical equations, and his theorem still lies at the heart of the recent developments. The modern era started about thirty years ago with the systematic formulation of soliton solutions to nonlinear wave equations. Since then, impressive developments arose both for the classical and the quantum theory. Subtle mathematical techniques were devised for the resolution of these theories, relying on algebra (group theory), analysis and algebraic geometry (Riemann theory of surfaces). We therefore clearly see that the theory of integrable systems lies ab initio at a crossing of physics and mathematics, and that the developments of these last thirty years have strengthened this dual character, which makes it into an archetypal domain of mathematical physics. As regards the classical theory, beyond the direct connections to the various domains of classical soliton physics (hydrodynamics, condensed matter physics, laser optics, particle physics, plasma, biology or information coding), one has witnessed in these recent years more unexpected (and for some of them not yet well understood) connections to a priori farther fields of theoretical physics: string theory (through matrix models), topological field theories (two dimensional Yang--Mills, three dimensional Chern--Simons--Witten), or supersymmetric field theories (for instance the correspondence discovered by Seiberg and Witten between classical integrable models and quantum potentials). Quantum integrable theories provide examples of exactly (non perturbatively) solvable physical models

  16. Quantum mechanics concept assessment: Development and validation study

    NASA Astrophysics Data System (ADS)

    Sadaghiani, Homeyra R.; Pollock, Steven J.

    2015-06-01

    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 mechanics assessment tool (QMAT) to a multiple-choice (MC) format. Further question refinement, development of effective distractors, adding new questions, and robust statistical analysis has led to a 31-item quantum mechanics concept assessment (QMCA) test. The QMCA is used as post-test only to assess students' knowledge about five main topics of quantum measurement: the time-independent Schrödinger equation, wave functions and boundary conditions, time evolution, and probability density. During two years of testing and refinement, the QMCA has been given in alpha (N =61 ) and beta versions (N =263 ) to students in upper division quantum mechanics courses at 11 different institutions with an average post-test score of 54%. By allowing for comparisons of student learning across different populations and institutions, the QMCA provides instructors and researchers a more standard measure of effectiveness of different curricula or teaching strategies on student conceptual understanding of quantum mechanics. In this paper, we discuss the construction of effective distractors and the use of student interviews and expert feedback to revise and validate both questions and distractors. We include the results of common statistical tests of reliability and validity, which suggest the instrument is presently in a stable, usable, and promising form.

  17. Geometric control of quantum mechanical and nonlinear classical systems

    NASA Astrophysics Data System (ADS)

    Nelson, Richard Joseph

    1999-10-01

    Geometric control refers to the judicious use of the non- commuting nature of inputs and natural dynamics as the basis for control. The last few decades in control system theory have seen the application of differential geometry in proving several important properties of systems, including controllability and observability. Until recently, however, the results of this mathematical geometry have rarely been used as the basis for designing and implementing an actual controller. This thesis demonstrates the application of a judicious selection of inputs, so that if the system is proven to be controllable using geometric methods, one can design input sequences using the same geometry. A demonstration of this method is shown in simulating the attitude control of a satellite: a highly non-linear, non- holonomic control problem. Although not a practical method for large re-orientations of a typical satellite, the approach can be applied to other nonlinear systems. The method is also applied to the closed-loop performance of a quantum mechanical system to demonstrate the feasibility of coherent quantum feedback-something impossible using a conventional controller. Finally, the method is applied in the open-loop control of a quantum mechanical system: in this case, the creation of Greenberger-Horne-Zeilinger correlations among the nuclei of an ensemble of alanine molecules in a nuclear magnetic resonance spectrometer. In each case, the data demonstrate the usefulness of a geometric approach to control. In addition to demonstrations of geometric control in practice, the quantum mechanical experiments also demonstrate for the first time peculiar quantum correlations, including GHZ correlations, that have no classical analog. The quantum experiments further establish nuclear magnetic resonance as a viable and accessible testbed of quantum predictions and processes. (Copies available exclusively from MIT Libraries, Rm. 14- 0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax

  18. How Does Quantum Uncertainty Emerge from Deterministic Bohmian Mechanics?

    NASA Astrophysics Data System (ADS)

    Solé, A.; Oriols, X.; Marian, D.; Zanghì, N.

    2016-10-01

    Bohmian mechanics is a theory that provides a consistent explanation of quantum phenomena in terms of point particles whose motion is guided by the wave function. In this theory, the state of a system of particles is defined by the actual positions of the particles and the wave function of the system; and the state of the system evolves deterministically. Thus, the Bohmian state can be compared with the state in classical mechanics, which is given by the positions and momenta of all the particles, and which also evolves deterministically. However, while in classical mechanics it is usually taken for granted and considered unproblematic that the state is, at least in principle, measurable, this is not the case in Bohmian mechanics. Due to the linearity of the quantum dynamical laws, one essential component of the Bohmian state, the wave function, is not directly measurable. Moreover, it turns out that the measurement of the other component of the state — the positions of the particles — must be mediated by the wave function; a fact that in turn implies that the positions of the particles, though measurable, are constrained by absolute uncertainty. This is the key to understanding how Bohmian mechanics, despite being deterministic, can account for all quantum predictions, including quantum randomness and uncertainty.

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

    PubMed Central

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

    2013-01-01

    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 × 106 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

  20. 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

  1. Solvable time-dependent models in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Cordero-Soto, Ricardo J.

    In the traditional setting of quantum mechanics, the Hamiltonian operator does not depend on time. While some Schrodinger equations with time-dependent Hamiltonians have been solved, explicitly solvable cases are typically scarce. This thesis is a collection of papers in which this first author along with Suslov, Suazo, and Lopez, has worked on solving a series of Schrodinger equations with a time-dependent quadratic Hamiltonian that has applications in problems of quantum electrodynamics, lasers, quantum devices such as quantum dots, and external varying fields. In particular the author discusses a new completely integrable case of the time-dependent Schrodinger equation in Rn with variable coefficients for a modified oscillator, which is dual with respect to the time inversion to a model of the quantum oscillator considered by Meiler, Cordero-Soto, and Suslov. A second pair of dual Hamiltonians is found in the momentum representation. Our examples show that in mathematical physics and quantum mechanics a change in the direction of time may require a total change of the system dynamics in order to return the system back to its original quantum state. The author also considers several models of the damped oscillators in nonrelativistic quantum mechanics in a framework of a general approach to the dynamics of the time-dependent Schrodinger equation with variable quadratic Hamiltonians. The Green functions are explicitly found in terms of elementary functions and the corresponding gauge transformations are discussed. The factorization technique is applied to the case of a shifted harmonic oscillator. The time-evolution of the expectation values of the energy related operators is determined for two models of the quantum damped oscillators under consideration. The classical equations of motion for the damped oscillations are derived for the corresponding expectation values of the position operator. Finally, the author constructs integrals of motion for several models

  2. 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.

  3. 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

  4. Physics on the boundary between classical and quantum mechanics

    NASA Astrophysics Data System (ADS)

    't Hooft, Gerard

    2014-04-01

    Nature's laws in the domain where relativistic effects, gravitational effects and quantum effects are all comparatively strong are far from understood. This domain is called the Planck scale. Conceivably, a theory can be constructed where the quantum nature of phenomena at such scales can be attributed to something fundamentally simpler. However, arguments that quantum mechanics cannot be explained in terms of any classical theory using only classical logic seem to be based on sound mathematical considerations: there can't be physical laws that require "conspiracy". It may therefore be surprising that there are several explicit quantum systems where these considerations apparently do not apply. In the lecture we will show several such counterexamples. These are quantum models that do have a classical origin. The most curious of these models is superstring theory. This theory is often portrayed as to underly the quantum field theory of the subatomic particles, including the "Standard Model". So now the question is asked: how can this model feature "conspiracy", and how bad is that? Is there conspiracy in the vacuum fluctuations?

  5. Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

    SciTech Connect

    List, Nanna Holmgaard Jensen, Hans Jørgen Aagaard; Kongsted, Jacob; Beerepoot, Maarten T. P.; Gao, Bin; Ruud, Kenneth; Olsen, Jógvan Magnus Haugaard

    2015-01-21

    We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn–Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange–repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.

  6. Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone.

    PubMed

    List, Nanna Holmgaard; Beerepoot, Maarten T P; Olsen, Jógvan Magnus Haugaard; Gao, Bin; Ruud, Kenneth; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob

    2015-01-21

    We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn-Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange-repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.

  7. Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

    NASA Astrophysics Data System (ADS)

    List, Nanna Holmgaard; Beerepoot, Maarten T. P.; Olsen, Jógvan Magnus Haugaard; Gao, Bin; Ruud, Kenneth; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob

    2015-01-01

    We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn-Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange-repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.

  8. METHODOLOGICAL NOTES: Irreversibility in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Kadomtsev, Boris B.

    2003-11-01

    From the Editorial Board. November 9, 2003 would have marked the seventy-fifth birthday of Boris Borisovich Kadomtsev, were he alive. An outstanding theoretical physicist, teacher, and enlightener, a prominent scientist in plasma physics and controlled nuclear fusion, Kadomtsev was also actively involved in science organization activities. In particular, from 1976 until his untimely death on August 19, 1998, Kadomtsev was the Editor-in-Chief of Physics-Uspekhi, and it is owing to his efforts that the journal improved notably during his tenure. Now, the Editorial Board, with gratitude and sorrow, would like to celebrate his birthday and to honor his blessed memory in these pages. There is, however, a rule — indeed an immutable tradition — in the journal that, except for the Personalia section, no anniversary can be marked in any way other than in a scientific publication. This rule was strictly observed under Kadomtsev, and certainly should not be violated now, even when honoring his memory. Fortunately, there is a video which remained of a lecture on modern problems of quantum physics that Kadomtsev delivered on May 12, 1997. Prepared for publication by M B Kadomtsev, the lecture allows the reader to revisit the heritage of B B Kadomtsev, to appreciate his logic in treating this very difficult area of physics, to hear his voice as it were, to recall Boris Borisovich Kadomtsev and to honor his memory.

  9. Parity-dependent non-commutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Chung, Won Sang

    2017-01-01

    In this paper, we consider the non-commutative quantum mechanics (NCQM) with parity (or space reflection) in two dimensions. Using the parity operators Ri, we construct the deformed Heisenberg algebra with parity in the non-commutative plane. We use this algebra to discuss the isotropic harmonic Hamiltonian with parity.

  10. Efficient Integration of Quantum Mechanical Wave Equations by Unitary Transforms

    SciTech Connect

    Bauke, Heiko; Keitel, Christoph H.

    2009-08-13

    The integration of time dependent quantum mechanical wave equations is a fundamental problem in computational physics and computational chemistry. The energy and momentum spectrum of a wave function imposes fundamental limits on the performance of numerical algorithms for this problem. We demonstrate how unitary transforms can help to surmount these limitations.

  11. Time Symmetric Quantum Mechanics and Causal Classical Physics ?

    NASA Astrophysics Data System (ADS)

    Bopp, Fritz W.

    2017-02-01

    A two boundary quantum mechanics without time ordered causal structure is advocated as consistent theory. The apparent causal structure of usual "near future" macroscopic phenomena is attributed to a cosmological asymmetry and to rules governing the transition between microscopic to macroscopic observations. Our interest is a heuristic understanding of the resulting macroscopic physics.

  12. Quantum-mechanical theory of optomechanical Brillouin cooling

    SciTech Connect

    Tomes, Matthew; Bahl, Gaurav; Carmon, Tal; Marquardt, Florian

    2011-12-15

    We analyze how to exploit Brillouin scattering of light from sound for the purpose of cooling optomechanical devices and present a quantum-mechanical theory for Brillouin cooling. Our analysis shows that significant cooling ratios can be obtained with standard experimental parameters. A further improvement of cooling efficiency is possible by increasing the dissipation of the optical anti-Stokes resonance.

  13. A note on misunderstandings of Piron's axioms for quantum mechanics

    NASA Astrophysics Data System (ADS)

    Foulis, D. J.; Randall, C. H.

    1984-01-01

    Piron's axioms for a realistically interpreted quantum mechanics are analyzed in detail within the context of a formal mathematical structure expressed in the conventional set-theoretic idiom of mathematics. As a result, some of the serious misconceptions that have encouraged recent criticisms of Piron's axioms are exposed.

  14. Equivalent emergence of time dependence in classical and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Briggs, John S.

    2015-05-01

    Beginning with the principle that a closed mechanical composite system is timeless, time can be defined by the regular changes in a suitable position coordinate (clock) in the observing part, when one part of the closed composite observes another part. Translating this scenario into both classical and quantum mechanics allows a transition to be made from a time-independent mechanics for the closed composite to a time-dependent description of the observed part alone. The use of Hamilton-Jacobi theory yields a very close parallel between the derivations in classical and quantum mechanics. The time-dependent equations, Hamilton-Jacobi or Schrödinger, appear as approximations since no observed system is truly closed. The quantum case has an additional feature in the condition that the observing environment must become classical in order to define a real classical time variable. This condition leads to a removal of entanglement engendered by the interaction between the observed system and the observing environment. Comparison is made to the similar emergence of time in quantum gravity theory.

  15. 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)

  16. 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…

  17. Overcoming Misconceptions in Quantum Mechanics with the Time Evolution Operator

    ERIC Educational Resources Information Center

    Quijas, P. C. Garcia; Aguilar, L. M. Arevalo

    2007-01-01

    Recently, there have been many efforts to use the research techniques developed in the field of physics education research to improve the teaching and learning of quantum mechanics. In particular, part of this research is focusing on misconceptions held by students. For instance, a set of misconceptions is associated with the concept of stationary…

  18. Exactly Solvable Quantum Mechanical Potentials: An Alternative Approach.

    ERIC Educational Resources Information Center

    Pronchik, Jeremy N.; Williams, Brian W.

    2003-01-01

    Describes an alternative approach to finding exactly solvable, one-dimensional quantum mechanical potentials. Differs from the usual approach in that instead of starting with a particular potential and seeking solutions to the related Schrodinger equations, it begins with known solutions to second-order ordinary differential equations and seeks to…

  19. 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)

  20. Recursive representation of Wronskians in confluent supersymmetric quantum mechanics

    NASA Astrophysics Data System (ADS)

    Contreras-Astorga, Alonso; Schulze-Halberg, Axel

    2017-03-01

    A recursive form of arbitrary-order Wronskian associated with transformation functions in the confluent algorithm of supersymmetric quantum mechanics (SUSY) is constructed. With this recursive form regularity conditions for the generated potentials can be analyzed. Moreover, as byproducts we obtain new representations of solutions to Schrödinger equations that underwent a confluent SUSY-transformation.

  1. 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…

  2. 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…

  3. Hidden algebra method (quasi-exact-solvability in quantum mechanics)

    SciTech Connect

    Turbiner, Alexander

    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.

  4. 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.

  5. 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)

  6. Econophysics: from Game Theory and Information Theory to Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Jimenez, Edward; Moya, Douglas

    2005-03-01

    Rationality is the universal invariant among human behavior, universe physical laws and ordered and complex biological systems. Econophysics isboth the use of physical concepts in Finance and Economics, and the use of Information Economics in Physics. In special, we will show that it is possible to obtain the Quantum Mechanics principles using Information and Game Theory.

  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. A discrete interaction model/quantum mechanical method for describing response properties of molecules adsorbed on metal nanoparticles

    NASA Astrophysics Data System (ADS)

    Morton, Seth Michael; Jensen, Lasse

    2010-08-01

    A new polarizable quantum mechanics/molecular mechanics method for the calculation of response properties of molecules adsorbed on metal nanoparticles is presented. This method, which we denote the discrete interaction model/quantum mechanics (DIM/QM) method, represents the nanoparticle atomistically which enables the modeling of the influence of the local environment of a nanoparticle surface on the optical properties of a molecule. Using DIM/QM, we investigate the excitation energies of rhodamine-6G (R6G) and crystal violet (CV) adsorbed on silver and gold nanoparticles of different quasispherical shapes and sizes. The metal nanoparticle is characterized by its static total polarizability, a reasonable approximation for frequencies far from the plasmon resonance. We observe that for both R6G and CV, the presence of the nanoparticle shifts the strongest excitation to the red ˜40 nm and also increases the oscillator strength of that excitation. The shifts in excitation energies due to the nanoparticle surface are found to be comparable to those due to solvation. We find that these shifts decay quickly as the molecule is moved away from the surface. We also find that the wavelength shift is largest when the transition dipole moment is aligned with the edges of the nanoparticle surface where the electric field is expected to be the largest. These results show that the molecular excitations are sensitive to the local environment on the nanoparticle as well as the specific orientation of the molecule relative to the surface.

  9. 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

  10. Solvable Quantum Macroscopic Motions and Decoherence Mechanisms in Quantum Mechanics on Nonstandard Space

    NASA Technical Reports Server (NTRS)

    Kobayashi, Tsunehiro

    1996-01-01

    Quantum macroscopic motions are investigated in the scheme consisting of N-number of harmonic oscillators in terms of ultra-power representations of nonstandard analysis. Decoherence is derived from the large internal degrees of freedom of macroscopic matters.

  11. 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/.

  12. 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.

  13. Factorization in the quantum mechanics with the generalized uncertainty principle

    NASA Astrophysics Data System (ADS)

    Chung, Won Sang

    2015-07-01

    In this paper, we discuss the quantum mechanics with the generalized uncertainty principle (GUP) where the commutation relation is given by [x̂,p̂] = iℏ(1 + αp̂ + βp̂2). For this algebra, we obtain the eigenfunction of the momentum operator. We also study the GUP corrected quantum particle in a box. Finally, we apply the factorization method to the harmonic oscillator in the presence of a minimal observable length and obtain the energy eigenvalues by applying the perturbation method.

  14. 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.

  15. 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.

  16. Jarzynski Equality in PT-Symmetric Quantum Mechanics.

    PubMed

    Deffner, Sebastian; Saxena, Avadh

    2015-04-17

    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.

  17. Quantum mechanical calculation of Rydberg-Rydberg autoionization rates

    NASA Astrophysics Data System (ADS)

    Kiffner, Martin; Ceresoli, Davide; Li, Wenhui; Jaksch, Dieter

    2016-10-01

    We present quantum mechanical calculations of autoionization rates for two rubidium Rydberg atoms with weakly overlapping electron clouds. We neglect exchange effects and consider tensor products of independent atom states forming an approximate basis of the two-electron state space. We consider large sets of two-atom states with randomly chosen quantum numbers and find that the charge overlap between the two Rydberg electrons allows one to characterise the magnitude of the autoionization rates. If the electron clouds overlap by more than one percent, the autoionization rates increase approximately exponentially with the charge overlap. This finding is independent of the energy of the initial state.

  18. The geometry of real reducible polarizations in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Tejero Prieto, Carlos; Vitolo, Raffaele

    2017-03-01

    The formulation of geometric quantization contains several axioms and assumptions. We show that for real polarizations we can generalize the standard geometric quantization procedure by introducing an arbitrary connection on the polarization bundle. The existence of reducible quantum structures leads to considering the class of Liouville symplectic manifolds. Our main application of this modified geometric quantization scheme is to quantum mechanics on Riemannian manifolds. With this method we obtain an energy operator without the scalar curvature term that appears in the standard formulation, thus agreeing with the usual expression found in the physics literature.

  19. A wave equation interpolating between classical and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Schleich, W. P.; Greenberger, D. M.; Kobe, D. H.; Scully, M. O.

    2015-10-01

    We derive a ‘master’ wave equation for a family of complex-valued waves {{Φ }}\\equiv R{exp}[{{{i}}S}({cl)}/{{\\hbar }}] whose phase dynamics is dictated by the Hamilton-Jacobi equation for the classical action {S}({cl)}. For a special choice of the dynamics of the amplitude R which eliminates all remnants of classical mechanics associated with {S}({cl)} our wave equation reduces to the Schrödinger equation. In this case the amplitude satisfies a Schrödinger equation analogous to that of a charged particle in an electromagnetic field where the roles of the scalar and the vector potentials are played by the classical energy and the momentum, respectively. In general this amplitude is complex and thereby creates in addition to the classical phase {S}({cl)}/{{\\hbar }} a quantum phase. Classical statistical mechanics, as described by a classical matter wave, follows from our wave equation when we choose the dynamics of the amplitude such that it remains real for all times. Our analysis shows that classical and quantum matter waves are distinguished by two different choices of the dynamics of their amplitudes rather than two values of Planck’s constant. We dedicate this paper to the memory of Richard Lewis Arnowitt—a pioneer of many-body theory, a path finder at the interface of gravity and quantum mechanics, and a true leader in non-relativistic and relativistic quantum field theory.

  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. Quantum Mechanical Modeling of Ballistic MOSFETs

    NASA Technical Reports Server (NTRS)

    Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan (Technical Monitor)

    2001-01-01

    The objective of this project was to develop theory, approximations, and computer code to model quasi 1D structures such as nanotubes, DNA, and MOSFETs: (1) Nanotubes: Influence of defects on ballistic transport, electro-mechanical properties, and metal-nanotube coupling; (2) DNA: Model electron transfer (biochemistry) and transport experiments, and sequence dependence of conductance; and (3) MOSFETs: 2D doping profiles, polysilicon depletion, source to drain and gate tunneling, understand ballistic limit.

  2. Statistical Mechanics of Confined Quantum Particles

    NASA Astrophysics Data System (ADS)

    Bannur, Vishnu M.; Udayanandan, K. M.

    We develop statistical mechanics and thermodynamics of Bose and Fermi systems in relativistic harmonic oscillator (RHO) confining potential, which is applicable in quark gluon plasma (QGP), astrophysics, Bose-Einstein condensation (BEC) etc. Detailed study of QGP system is carried out and compared with lattice results. Furthermore, as an application, our equation of state (EoS) of QGP is used to study compact stars like quark star.

  3. Delirium Quantum Or, where I will take quantum mechanics if it will let me

    NASA Astrophysics Data System (ADS)

    Fuchs, Christopher A.

    2007-02-01

    Once again, I take advantage of the wonderfully liberal and tolerant mood Andrei Khrennikov sets at his yearly conferences by submitting a nonstandard paper for the proceedings. This pseudo-paper consists of excerpts drawn from two of my samizdats [Quantum States: What the Hell Are They? and Darwinism All the Way Down (and Probabilism All the Way Back Up)] that I think best summarize what I am aiming for on the broadest scale with my quantum foundations program. Section 1 tries to draw a picture of a physical world whose essence is "Darwinism all the way down." Section 2 outlines how quantum theory should be viewed in light of that, i.e., as being an expression of probabilism (in Bruno de Finetti or Richard Jeffrey's sense) all the way back up. Section 3 describes how the idea of "identical" quantum measurement outcomes, though sounding atomistic in character, nonetheless meshes well with a William Jamesian style "radical pluralism." Sections 4 and 5 further detail how quantum theory should not be viewed so much as a "theory of the world," but rather as a theory of decision-making for agents immersed within a quantum world—that is, a world in continual creation. Finally, Sections 6 and 7 attempt to sketch once again the very positive sense in which quantum theory is incomplete, but still just as complete is it can be. In total, I hope these heady speculations convey some of the excitement and potential I see for the malleable world quantum mechanics hints of.

  4. 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

  5. Functional methods underlying classical mechanics, relativity and quantum theory

    NASA Astrophysics Data System (ADS)

    Kryukov, A.

    2013-04-01

    The paper investigates the physical content of a recently proposed mathematical framework that unifies the standard formalisms of classical mechanics, relativity and quantum theory. In the framework states of a classical particle are identified with Dirac delta functions. The classical space is "made" of these functions and becomes a submanifold in a Hilbert space of states of the particle. The resulting embedding of the classical space into the space of states is highly non-trivial and accounts for numerous deep relations between classical and quantum physics and relativity. One of the most striking results is the proof that the normal probability distribution of position of a macroscopic particle (equivalently, position of the corresponding delta state within the classical space submanifold) yields the Born rule for transitions between arbitrary quantum states.

  6. Reflections on Zeilinger-Brukner Information Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Khrennikov, Andrei

    2016-07-01

    In this short review I present my personal reflections on Zeilinger-Brukner information interpretation of quantum mechanics (QM).In general, this interpretation is very attractive for me. However, its rigid coupling to the notion of irreducible quantum randomness is a very complicated issue which I plan to address in more detail. This note may be useful for general public interested in quantum foundations, especially because I try to analyze essentials of the information interpretation critically (i.e., not just emphasizing its advantages as it is commonly done). This review is written in non-physicist friendly manner. Experts actively exploring this interpretation may be interested in the paper as well, as in the comments of "an external observer" who have been monitoring the development of this approach to QM during the last 18 years. The last part of this review is devoted to the general methodology of science with references to views of de Finetti, Wigner, and Peres.

  7. The simplified Fermi accelerator in classical and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Karner, Gunther

    1994-11-01

    We review the simplified classical Fermi acceleration mechanism and construct a quantum counterpart by imposing time-dependent boundary conditions on solutions of the "free" Schrödinger equation at the unit interval. We find similiar dynamical features in the sense that limiting KAM curves, respectively purely singular quasienergy spectrum, exist(s) for sufficiently smooth "wall oscillations" (typically of C 2 type). In addition, we investigate quantum analogs to local approximations of the Fermi map both in its quasiperiodic and irregular phase space regions. In particular, we find pure point q.e. spectrum in the former case and conjecture that "random boundary conditions" are necessary to model a quantum analog to the chaotic regime of the classical accelerator.

  8. Quantum processes as a mechanism in olfaction for smell recognition?

    NASA Astrophysics Data System (ADS)

    Brookes, Jennifer

    2011-03-01

    The physics of smell is not well understood. The biological processes that occur following a signalling event are well understood (Buck 1991). However, the reasons how and why a signalling event occurs when a particular smell molecule and receptor combination is made, remains un-established. Luca Turin proposes a signalling mechanism which determines smell molecules by quantum mechanics (Turin 1996). Investigation of this mechanism shows it to be physically robust (Brookes,et al, 2007), and consequences of the theory provides quantitative measurements of smell and interesting potential experiments that may determine whether the recognition of smell is a quantum event. Brookes, J.C, Hartoutsiou, F, Horsfield, A.P and Stoneham, A.M. (2007). Physical Review Letters 98, no. 3 038101 Buck, L. (1991) Cell, 65, no.1 (4): 175-187. Turin, L. (1996) Chemical Sences 21, no 6. 773-791 With many thanks to the Wellcome Trust.

  9. Nonrelativistic quantum mechanics with consideration of influence of fundamental environment

    SciTech Connect

    Gevorkyan, A. S.

    2013-08-15

    Spontaneous transitions between bound states of an atomic system, the 'Lamb Shift' of energy levels and many other phenomena in real nonrelativistic quantum systems are connected with the influence of the quantum vacuum fluctuations (fundamental environment (FE)), which are impossible to consider in the framework of standard quantum-mechanical approaches. The joint system quantum system (QS) and FE is described in the framework of the stochastic differential equation (SDE) of Langevin-Schroedinger type and is defined on the extended space Double-Struck-Capital-R {sup 3} Circled-Times {Xi}{sup n}, where Double-Struck-Capital-R {sup 3} and {Xi}{sup n} are the Euclidean and functional spaces, respectively. The method of stochastic density matrix is developed and the von Neumann equation for reduced density matrix of QS with FE is generalized. The entropy of QS entangled with FE is defined and investigated. It is proved that the interaction of QS with the environment leads to emerging structures of various topologies which present new quantum-field properties of QS. It is shown that when the physical system (irrelatively to its being micro ormacro) breaks up into two fragments by means of FE, there arises between these fragments a nonpotential interaction which does not disappear at large distances.

  10. Quantum mechanics on SO(3) via noncommutative dual variables

    NASA Astrophysics Data System (ADS)

    Oriti, Daniele; Raasakka, Matti

    2011-07-01

    We formulate quantum mechanics on the group SO(3) using a noncommutative dual space representation for the quantum states, inspired by recent work in quantum gravity. The new noncommutative variables have a clear connection to the corresponding classical variables, and our analysis confirms them as the natural phase space variables, both mathematically and physically. In particular, we derive the first order (Hamiltonian) path integral in terms of the noncommutative variables, as a formulation of the transition amplitudes alternative to that based on harmonic analysis. We find that the nontrivial phase space structure gives naturally rise to quantum corrections to the action for which we find a closed expression. We then study both the semiclassical approximation of the first order path integral and the example of a free particle on SO(3). On the basis of these results, we comment on the relevance of similar structures and methods for more complicated theories with group-based configuration spaces, such as loop quantum gravity and spin foam models.

  11. Nonrelativistic quantum mechanics with consideration of influence of fundamental environment

    NASA Astrophysics Data System (ADS)

    Gevorkyan, A. S.

    2013-08-01

    Spontaneous transitions between bound states of an atomic system, the "Lamb Shift" of energy levels and many other phenomena in real nonrelativistic quantum systems are connected with the influence of the quantum vacuum fluctuations ( fundamental environment (FE)), which are impossible to consider in the framework of standard quantum-mechanical approaches. The joint system quantum system (QS) and FE is described in the framework of the stochastic differential equation (SDE) of Langevin-Schrödinger type and is defined on the extended space ℝ3⊗Ξ n , where ℝ3 and Ξ n are the Euclidean and functional spaces, respectively. The method of stochastic density matrix is developed and the von Neumann equation for reduced density matrix of QS with FE is generalized. The entropy of QS entangled with FE is defined and investigated. It is proved that the interaction of QS with the environment leads to emerging structures of various topologies which present new quantum-field properties of QS. It is shown that when the physical system (irrelatively to its being micro ormacro) breaks up into two fragments by means of FE, there arises between these fragments a nonpotential interaction which does not disappear at large distances.

  12. Non-exponential decay in Quantum Mechanics and Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Giacosa, Francesco

    2014-10-01

    We describe some salient features as well as some recent developments concerning short-time deviations from the exponential decay law in the context of Quantum Mechanics by using the Lee Hamiltonian approach and Quantum Field Theory by using relativistic Lagrangians. In particular, the case in which two decay channels are present is analyzed: the ratio of decay probability densities, which is a constant equal to the ratio of decay widths in the exponential limit, shows in general sizable fluctuations which persist also at long times.

  13. Quantum mechanical properties of graphene nano-flakes and quantum dots.

    PubMed

    Shi, Hongqing; Barnard, Amanda S; Snook, Ian K

    2012-11-07

    In recent years considerable attention has been given to methods for modifying and controlling the electronic and quantum mechanical properties of graphene quantum dots. However, as these types of properties are indirect consequences of the wavefunction of the material, a more efficient way of determining properties may be to engineer the wavefunction directly. One way of doing this may be via deliberate structural modifications, such as producing graphene nanostructures with specific sizes and shapes. In this paper we use quantum mechanical simulations to determine whether the wavefunction, quantified via the distribution of the highest occupied molecular orbital, has a direct and reliable relationship to the physical structure, and whether structural modifications can be useful for wavefunction engineering. We find that the wavefunction of small molecular graphene structures can be different from those of larger nanoscale counterparts, and the distribution of the highest occupied molecular orbital is strongly affected by the geometric shape (but only weakly by edge and corner terminations). This indicates that both size and shape may be more useful parameters in determining quantum mechanical and electronic properties, which should then be reasonably robust against variations in the chemical passivation or functionalisation around the circumference.

  14. Third emission mechanism in solid-state nanocavity quantum electrodynamics.

    PubMed

    Yamaguchi, Makoto; Asano, Takashi; Noda, Susumu

    2012-09-01

    Photonic crystal (PC) nanocavities have been receiving a great deal of attention recently because of their ability to strongly confine photons in a tiny space with a high quality factor. According to cavity quantum electrodynamics (cavity QED), such confined photons can achieve efficient interactions with excitons in semiconductors, leading to the Purcell effect in the weak coupling regime and vacuum Rabi splitting (VRS) in the strong coupling regime. These features are promising for applications such as quantum information processing, highly efficient single photon sources and ultra-low threshold lasers. In this context, the coupled system of a semiconductor quantum dot (QD) and a PC nanocavity has been intensively investigated in recent years.Although experimental reports have demonstrated such fundamental features, two anomalous phenomena have also been observed. First, photon emission from the cavity occurs even when it is significantly detuned from the QD. Second, spectral triplets are formed by additional bare-cavity lines between the VRS lines. These features cannot be explained by standard cavity QED theories and have prompted controversy regarding their physical mechanisms. In this review we describe the recent experimental and theoretical progress made in the investigation of these phenomena. Similar mechanisms will also occur in many other coupled quantum systems, and thus the findings are applicable to a wide range of fields.

  15. 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?

  16. Emergence of a New Quantum Mechanics by Multivalued Logic

    NASA Astrophysics Data System (ADS)

    de Gerlicz, Claude Gaudeau; Antoine, Mathias; Bobola, Philippe; Flawisky, Nicolas; Hebras, Xavier; Mundedi, Musa

    2013-09-01

    Quantum Mechanics associated with new logic like Multivalued Logic and Fuzzy Logic has progressed in different ways and their applications can be found in many fields of sciences and technologies. All the concepts attached to this theory are far from the classical view. Classical mechanics can be viewed as crisp limit of a Fuzzy quantum mechanics. This leads to the following interpretation: It is the consequence of an assumption that a quantum particle "reside" in different place or in every path of the continuum of paths which collapse into a single "unique" trajectory of an observed classical motion The reality is "Fuzzy" and nonlocal not only in space but also in time. In this sense, idealised pointlike particles of classical mechanics corresponding to the ultimate sharpness of the fuzziness density emerge in a process of interaction between different parts of fuzzy wholeness. This process is viewed as a continuous process of defuzzification. It transforms a fuzzy reality into a crisp one. It is clear that the emerging crisp reality as a final step of measurements carries less of information that the underlying fuzzy reality. This means that there is an irreversible loss of information usually called "collapse of the wave function". It is not so much a "collapse" as a realization of one of the many possibilities existing within a fuzzy reality. Any measurements rearrange the fuzzy reality leading to different detection outcomes.

  17. Photons and evolution: quantum mechanical processes modulate sexual differentiation.

    PubMed

    Davis, George E; Lowell, Walter E

    2009-09-01

    This paper will show that the fractional difference in the human gender ratio (GR) between the GR(at death) for those born in solar cycle peak years (maxima) and the GR(at death) in those born in solar cycle non-peak years (minima), e.g., 0.023, divided by Pi, yields a reasonable approximation of the quantum mechanical constant, alpha, or the fine structure constant (FSC) approximately 0.007297... or approximately 1/137. This finding is based on a sample of approximately 50 million cases using common, readily available demographic data, e.g., state of birth, birth date, death date, and gender. Physicists Nair, Geim et al. had found precisely the same fractional difference, 0.023, in the absorption of white light (sunlight) by a single-atom thick layer of graphene, a carbon skeleton resembling chicken wire fencing. This absorption fraction, when divided by Pi, yielded the FSC and was the first time this constant could "so directly be assessed practically by the naked eye". As the GR is a reflection of sexual differentiation, this paper reveals that a quantum mechanical process, as manifested by the FSC, is playing a role in the primordial process of replication, a necessary requirement of life. Successful replication is the primary engine driving evolution, which at a biochemical level, is a quantum mechanical process dependent upon photonic energy from the Sun. We propose that a quantum-mechanical, photon-driven chemical evolution preceded natural selection in biology and the mechanisms of mitosis and meiosis are manifestations of this chemical evolution in ancient seas over 3 billion years ago. Evolutionary processes became extant first in self-replicating molecules forced to adapt to high energy photons, mostly likely in the ultraviolet spectrum. These events led to evolution by natural selection as complex mixing of genetic material within species creating the variety needed to match changing environments reflecting the same process initiated at the dawn of life

  18. Testing Quantum Mechanics and Bell's Inequality with Astronomical Observations

    NASA Astrophysics Data System (ADS)

    Friedman, Andrew S.; Gallicchio, Jason; Kaiser, David I.; Guth, Alan H.

    2015-01-01

    We propose an experiment which would leverage cosmology to test quantum mechanics using astronomical observations. Our experiment would send entangled photons to detectors over 100 kilometers apart, whose settings would be rapidly chosen using real-time telescopic observations of distant, causally disconnected, cosmic 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, close 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 some local "hidden variables" due to unknown causal influences a mere few milliseconds prior to the experiment. Our "Cosmic Bell" experiment would push any such hidden variable conspiracy all the way back to the hot big bang, since the end of any period of inflation, 13.8 Gyr ago, an improvement of 20 orders of magnitude. We demonstrate the real world feasibility of our experimental setup. While causally disjoint patches of the cosmic microwave background radiation at redshift z ~ 1090 could be used to set the detectors, z > 3.65 quasars observed at optical wavelengths are arguably the optimal candidate source pairs using present technology. Our proposal is supported by some of the world's leading quantum experimentalists, who have begun to collaborate with us to conduct the experiment in the next 2-3 years using some of the instrumentation they have already built and used at two astronomical observatories in the Canary Islands. 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

  19. Block-adaptive quantum mechanics: an adaptive divide-and-conquer approach to interactive quantum chemistry.

    PubMed

    Bosson, Maël; Grudinin, Sergei; Redon, Stephane

    2013-03-05

    We present a novel Block-Adaptive Quantum Mechanics (BAQM) approach to interactive quantum chemistry. Although quantum chemistry models are known to be computationally demanding, we achieve interactive rates by focusing computational resources on the most active parts of the system. BAQM is based on a divide-and-conquer technique and constrains some nucleus positions and some electronic degrees of freedom on the fly to simplify the simulation. As a result, each time step may be performed significantly faster, which in turn may accelerate attraction to the neighboring local minima. By applying our approach to the nonself-consistent Atom Superposition and Electron Delocalization Molecular Orbital theory, we demonstrate interactive rates and efficient virtual prototyping for systems containing more than a thousand of atoms on a standard desktop computer.

  20. Probability and Quantum Symmetries. II. The Theorem of Noether in quantum mechanics

    SciTech Connect

    Albeverio, S.; Rezende, J.; Zambrini, J.-C.

    2006-06-15

    For the largest class of physical systems having a classical analog, a new rigorous, but not probabilistic, Lagrangian version of nonrelativistic quantum mechanics is given, in terms of a notion of regularized action function. As a consequence of the study of the symmetries of this action, an associated Noether theorem is obtained. All the quantum symmetries resulting from the canonical quantization procedure follow in this way, as well as a number of symmetries which are new even for the case of the simplest systems. The method is based on the study of a corresponding Lie algebra and an analytical continuation in the time parameter of the probabilistic construction given in paper I of this work. Generically, the associated quantum first integrals are time dependent and the probabilistic model provides a natural interpretation of the new symmetries. Various examples illustrate the physical relevance of our results.

  1. O the Verge of Collapse: Modal Interpretations of Quantum Mechanics.

    NASA Astrophysics Data System (ADS)

    Ruetsche, Laura

    1995-01-01

    The conjunction of Schrodinger dynamics and the usual way of thinking about the conditions under which quantum systems exhibit determinate values implies that measurements don't have outcomes. The orthodox fix to this quantum measurement problem is von Neumann's postulate of measurement collapse, which suspends Schrodinger dynamics in measurement contexts. Contending that the fundamental dynamical law of quantum theory breaks down every time we test the theory empirically, the collapse postulate is unsatisfactory. Recently philosophers (e.g., van Fraassen and Healey) and physicists (e.g., Kochen and Dieks) have proposed a less violent solution to the measurement problem. Their modal interpretations of quantum mechanics advocate unusual ways of thinking about the situations under which quantum systems exhibit determinate observable values, semantics which reconcile determinate measurement outcomes with universal Schrodinger dynamics. Thus modal interpretations hold out hope that quantum theory is complete and exceptionless. This dissertation tempers that hope. I consider the modal approach to the neglected problem of state preparation. A promising modal account exploits standard quantum transition probabilities. But, I claim, modal interpretations must subject these transition probabilities to a consistency constraint which they can be shown to violate. Non-standard transition probabilities might avoid this inconsistency, but they would also introduce novel dynamics, and so undo the modal triumph of taking Schrodinger dynamics to be complete and universal. Next I consider Albert and Loewer's assault on modal accounts of "error-prone" measurements. I argue that the Albert-Loewer problem is more general than Albert, Loewer, or their critics appreciate, and that the Araki-Yanase theorem implies the existence of a class of observables whose error-free measurements succumb to the Albert-Loewer problem. I review modal responses to Albert and Loewer which appeal to the

  2. Quantum mechanical calculations and mineral spectroscopy

    NASA Astrophysics Data System (ADS)

    Kubicki, J. D.

    2006-05-01

    Interpretation of spectra in systems of environmental interest is not generally straightforward due to the lack of close analogs and a clear structure of some components of the system. Computational chemistry can be used as an objective method to test interpretations of spectra. This talk will focus on applying ab initio methods to complement vibrational, NMR, and EXAFS spectroscopic information. Examples of systems studied include phosphate/Fe-hydroxides, arsenate/Al- and Fe-hydroxide, fractured silica surfaces. Phosphate interactions with Fe-hydroxides are important in controlling nutrient availability in soils and transport within streams. In addition, organo-phosphate bonding may be a key attachment mechanism for bacteria at Fe-oxide surfaces. Interpretation of IR spectra is enhanced by model predictions of vibrational frequencies for various surface complexes. Ab initio calculations were used to help explain As(V) and As(III) adsorption behavior onto amorphous Al- and Fe-hydroxides in conjunction with EXAFS measurements. Fractured silica surfaces have been implicated in silicosis. These calculations test structures that could give rise to radical formation on silica surfaces. Calculations to simulate the creation of Si and SiO radical species on sufaces and their subsequent production of OH radicals will be discussed.

  3. 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.

  4. A quantum mechanical polarizable force field for biomolecular interactions

    PubMed Central

    Donchev, A. G.; Ozrin, V. D.; Subbotin, M. V.; Tarasov, O. V.; Tarasov, V. I.

    2005-01-01

    We introduce a quantum mechanical polarizable force field (QMPFF) fitted solely to QM data at the MP2/aTZ(-hp) level. Atomic charge density is modeled by point-charge nuclei and floating exponentially shaped electron clouds. The functional form of interaction energy parallels quantum mechanics by including electrostatic, exchange, induction, and dispersion terms. Separate fitting of each term to the counterpart calculated from high-quality QM data ensures high transferability of QMPFF parameters to different molecular environments, as well as accurate fit to a broad range of experimental data in both gas and liquid phases. QMPFF, which is much more efficient than ab initio QM, is optimized for the accurate simulation of biomolecular systems and the design of drugs. PMID:15911753

  5. On the consistent effect histories approach to quantum mechanics

    NASA Astrophysics Data System (ADS)

    Rudolph, Oliver

    1996-11-01

    A formulation of the consistent histories approach to quantum mechanics in terms of generalized observables (POV measures) and effect operators is provided. The usual notion of ``history'' is generalized to the notion of ``effect history.'' The space of effect histories carries the structure of a D-poset. Recent results of J. D. Maitland Wright imply that every decoherence functional defined for ordinary histories can be uniquely extended to a bi-additive decoherence functional on the space of effect histories. Omnès' logical interpretation is generalized to the present context. The result of this work considerably generalizes and simplifies the earlier formulation of the consistent effect histories approach to quantum mechanics communicated in a previous work of this author.

  6. Approaching the standard quantum limit of mechanical torque sensing

    NASA Astrophysics Data System (ADS)

    Kim, P. H.; Hauer, B. D.; Doolin, C.; Souris, F.; Davis, J. P.

    2016-10-01

    Reducing the moment of inertia improves the sensitivity of a mechanically based torque sensor, the parallel of reducing the mass of a force sensor, yet the correspondingly small displacements can be difficult to measure. To resolve this, we incorporate cavity optomechanics, which involves co-localizing an optical and mechanical resonance. With the resulting enhanced readout, cavity-optomechanical torque sensors are now limited only by thermal noise. Further progress requires thermalizing such sensors to low temperatures, where sensitivity limitations are instead imposed by quantum noise. Here, by cooling a cavity-optomechanical torque sensor to 25 mK, we demonstrate a torque sensitivity of 2.9 yNm/. At just over a factor of ten above its quantum-limited sensitivity, such cryogenic optomechanical torque sensors will enable both static and dynamic measurements of integrated samples at the level of a few hundred spins.

  7. The black hole S-Matrix from quantum mechanics

    NASA Astrophysics Data System (ADS)

    Betzios, Panagiotis; Gaddam, Nava; Papadoulaki, Olga

    2016-11-01

    We revisit the old black hole S-Matrix construction and its new partial wave expansion of 't Hooft. Inspired by old ideas from non-critical string theory & c = 1 Matrix Quantum Mechanics, we reformulate the scattering in terms of a quantum mechanical model — of waves scattering off inverted harmonic oscillator potentials — that exactly reproduces the unitary black hole S-Matrix for all spherical harmonics; each partial wave corresponds to an inverted harmonic oscillator with ground state energy that is shifted relative to the s-wave oscillator. Identifying a connection to 2d string theory allows us to show that there is an exponential degeneracy in how a given total initial energy may be distributed among many partial waves of the 4d black hole.

  8. Some theoretical aspects of quantum mechanical equations in Rindler space

    NASA Astrophysics Data System (ADS)

    Mitra, Soma; Chakrabarty, Somenath

    2017-03-01

    In this article we have investigated theoretical aspects of the solutions of some of the quantum mechanical problems in Rindler space. We have developed formalisms for the exact analytical solutions for the relativistic equations, along with the approximate form of solutions for the Schrödinger equation. The Hamiltonian operator in Rindler space is found to be non-Hermitian in nature, whereas the energy eigen values are observed to be real in nature. We have noticed that the sole reason behind such real behavior is the PT -symmetric form of the Hamiltonian operator. We have also observed that the energy eigen values are negative, lineraly quantized and the quantum mechanical system becomes more and more bound with the increase in the strength of gravitational field strength produced by the strongly gravitating objects, e.g., black holes, which is classical in nature.

  9. Approaching the standard quantum limit of mechanical torque sensing

    PubMed Central

    Kim, P. H.; Hauer, B. D.; Doolin, C.; Souris, F.; Davis, J. P.

    2016-01-01

    Reducing the moment of inertia improves the sensitivity of a mechanically based torque sensor, the parallel of reducing the mass of a force sensor, yet the correspondingly small displacements can be difficult to measure. To resolve this, we incorporate cavity optomechanics, which involves co-localizing an optical and mechanical resonance. With the resulting enhanced readout, cavity-optomechanical torque sensors are now limited only by thermal noise. Further progress requires thermalizing such sensors to low temperatures, where sensitivity limitations are instead imposed by quantum noise. Here, by cooling a cavity-optomechanical torque sensor to 25 mK, we demonstrate a torque sensitivity of 2.9 yNm/. At just over a factor of ten above its quantum-limited sensitivity, such cryogenic optomechanical torque sensors will enable both static and dynamic measurements of integrated samples at the level of a few hundred spins. PMID:27762273

  10. 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

  11. The Problem of Representation and Experience in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Ronde, Christian De

    2014-03-01

    In this paper we discuss the problem of representation and experience in quantum mechanics. We analyze the importance of metaphysics in physical thought and its relation to empiricism and analytic philosophy. We argue against both instrumentalism and scientific realism and claim that both perspectives tend to bypass the problem of representation and justify a "common sense" type experience. Finally, we present our expressionist conception of physics.

  12. Polymer quantum mechanics some examples using path integrals

    SciTech Connect

    Parra, Lorena; Vergara, J. David

    2014-01-14

    In this work we analyze several physical systems in the context of polymer quantum mechanics using path integrals. First we introduce the group averaging method to quantize constrained systems with path integrals and later we use this procedure to compute the effective actions for the polymer non-relativistic particle and the polymer harmonic oscillator. We analyze the measure of the path integral and we describe the semiclassical dynamics of the systems.

  13. Resolution of the Klein Paradox within Relativistic Quantum Mechanics

    SciTech Connect

    Alhaidari, A. D.

    2011-10-27

    We present a resolution of the Klein paradox within the framework of one-particle relativistic quantum mechanics (no pair production). Not only reflection becomes total but the vacuum remains neutral as well. This is accomplished by replacing the pair production process with virtual negative energy ''incidence'' within the barrier in a process analogous to the introduction of image charges in electrostatic and virtual sources in optics.

  14. Effects of a scalar scaling field on quantum mechanics

    SciTech Connect

    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 each 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.

  15. A Separable, Dynamically Local Ontological Model of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Pienaar, Jacques

    2016-01-01

    A model of reality is called separable if the state of a composite system is equal to the union of the states of its parts, located in different regions of space. Spekkens has argued that it is trivial to reproduce the predictions of quantum mechanics using a separable ontological model, provided one allows for arbitrary violations of `dynamical locality'. However, since dynamical locality is strictly weaker than local causality, this leaves open the question of whether an ontological model for quantum mechanics can be both separable and dynamically local. We answer this question in the affirmative, using an ontological model based on previous work by Deutsch and Hayden. Although the original formulation of the model avoids Bell's theorem by denying that measurements result in single, definite outcomes, we show that the model can alternatively be cast in the framework of ontological models, where Bell's theorem does apply. We find that the resulting model violates local causality, but satisfies both separability and dynamical locality, making it a candidate for the `most local' ontological model of quantum mechanics.

  16. Novel symmetries in N=2 supersymmetric quantum mechanical models

    SciTech Connect

    Malik, R.P.; Khare, Avinash

    2013-07-15

    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 show 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.

  17. Computational alanine scanning with linear scaling semiempirical quantum mechanical methods.

    PubMed

    Diller, David J; Humblet, Christine; Zhang, Xiaohua; Westerhoff, Lance M

    2010-08-01

    Alanine scanning is a powerful experimental tool for understanding the key interactions in protein-protein interfaces. Linear scaling semiempirical quantum mechanical calculations are now sufficiently fast and robust to allow meaningful calculations on large systems such as proteins, RNA and DNA. In particular, they have proven useful in understanding protein-ligand interactions. Here we ask the question: can these linear scaling quantum mechanical methods developed for protein-ligand scoring be useful for computational alanine scanning? To answer this question, we assembled 15 protein-protein complexes with available crystal structures and sufficient alanine scanning data. In all, the data set contains Delta Delta Gs for 400 single point alanine mutations of these 15 complexes. We show that with only one adjusted parameter the quantum mechanics-based methods outperform both buried accessible surface area and a potential of mean force and compare favorably to a variety of published empirical methods. Finally, we closely examined the outliers in the data set and discuss some of the challenges that arise from this examination.

  18. Attosecond delays in photoionization: time and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Maquet, Alfred; Caillat, Jérémie; Taïeb, Richard

    2014-10-01

    This article addresses topics regarding time measurements performed on quantum systems. The motivation is linked to the advent of ‘attophysics’ which makes feasible to follow the motion of electrons in atoms and molecules, with time resolution at the attosecond (1 as = 10-18 s) level, i.e. at the natural scale for electronic processes in these systems. In this context, attosecond ‘time-delays’ have been recently measured in experiments on photoionization and the question arises if such advances could cast a new light on the still active discussion on the status of the time variable in quantum mechanics. One issue still debatable is how to decide whether one can define a quantum time operator with eigenvalues associated to measurable ‘time-delays’, or time is a parameter, as it is implicit in the Newtonian classical mechanics. One objective of this paper is to investigate if the recent attophysics-based measurements could shed light on this parameter-operator conundrum. To this end, we present here the main features of the theory background, followed by an analysis of the experimental schemes that have been used to evidence attosecond ‘time-delays’ in photoionization. Our conclusion is that these results reinforce the view that time is a parameter which cannot be defined without reference to classical mechanics.

  19. Principle of Least Action and Approximations in Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Kobe, Donald

    2008-03-01

    A Lagrangian together with the Principle of Least Action (PLA) is a unifying approach used in all areas of physics to derive their fundamental equations. In quantum mechanics this approach can be used to derive the Schr"odinger equation. The PLA may also be used to obtain approximate equations in quantum mechanics by using time-dependent trial wave functions. For a system with a time-independent Hamiltonian the PLA can be reduced to the Rayleigh-Ritz variational principle of time-independent quantum mechanics. For a system of many bosons a trial wave function that is a product of time-dependent single particle wave functions may be used in the PLA to obtain the time-dependent Gross-Pitaeveski equation, which is useful in describing a Bose- Einstein condensate. For a system of many fermions a trial wave function that is a product of time-dependent single particle orbitals may be used in the PLA to obtain the time-dependent Hartree-Fock equations, which are useful in atomic and nuclear physics.

  20. 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

  1. A signed particle formulation of non-relativistic quantum mechanics

    SciTech Connect

    Sellier, Jean Michel

    2015-09-15

    A formulation of non-relativistic quantum mechanics in terms of Newtonian particles is presented in the shape of a set of three postulates. In this new theory, quantum systems are described by ensembles of signed particles which behave as field-less classical objects which carry a negative or positive sign and interact with an external potential by means of creation and annihilation events only. This approach is shown to be a generalization of the signed particle Wigner Monte Carlo method which reconstructs the time-dependent Wigner quasi-distribution function of a system and, therefore, the corresponding Schrödinger time-dependent wave-function. Its classical limit is discussed and a physical interpretation, based on experimental evidences coming from quantum tomography, is suggested. Moreover, in order to show the advantages brought by this novel formulation, a straightforward extension to relativistic effects is discussed. To conclude, quantum tunnelling numerical experiments are performed to show the validity of the suggested approach.

  2. A Delayed Choice Quantum Eraser Explained by the Transactional Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Fearn, H.

    2016-01-01

    This paper explains the delayed choice quantum eraser of Kim et al. (A delayed choice quantum eraser, 1999) in terms of the transactional interpretation (TI) of quantum mechanics by Cramer (Rev Mod Phys 58:647, 1986, The quantum handshake, entanglement, nonlocality and transactions, 1986). It is kept deliberately mathematically simple to help explain the transactional technique. The emphasis is on a clear understanding of how the instantaneous "collapse" of the wave function due to a measurement at a specific time and place may be reinterpreted as a relativistically well-defined collapse over the entire path of the photon and over the entire transit time from slit to detector. This is made possible by the use of a retarded offer wave, which is thought to travel from the slits (or rather the small region within the parametric crystal where down-conversion takes place) to the detector and an advanced counter wave traveling backward in time from the detector to the slits. The point here is to make clear how simple the transactional picture is and how much more intuitive the collapse of the wave function becomes if viewed in this way. Also, any confusion about possible retro-causal signaling is put to rest. A delayed choice quantum eraser does not require any sort of backward in time communication. This paper makes the point that it is preferable to use the TI over the usual Copenhagen interpretation for a more intuitive understanding of the quantum eraser delayed choice experiment. Both methods give exactly the same end results and can be used interchangeably.

  3. 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

  4. 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

  5. A short course on quantum mechanics and methods of quantization

    NASA Astrophysics Data System (ADS)

    Ercolessi, Elisa

    2015-07-01

    These notes collect the lectures given by the author to the "XXIII International Workshop on Geometry and Physics" held in Granada (Spain) in September 2014. The first part of this paper aims at introducing a mathematical oriented reader to the realm of Quantum Mechanics (QM) and then to present the geometric structures that underline the mathematical formalism of QM which, contrary to what is usually done in Classical Mechanics (CM), are usually not taught in introductory courses. The mathematics related to Hilbert spaces and Differential Geometry are assumed to be known by the reader. In the second part, we concentrate on some quantization procedures, that are founded on the geometric structures of QM — as we have described them in the first part — and represent the ones that are more operatively used in modern theoretical physics. We will discuss first the so-called Coherent State Approach which, mainly complemented by "Feynman Path Integral Technique", is the method which is most widely used in quantum field theory. Finally, we will describe the "Weyl Quantization Approach" which is at the origin of modern tomographic techniques, originally used in optics and now in quantum information theory.

  6. PT symmetry in classical and quantum statistical mechanics.

    PubMed

    Meisinger, Peter N; Ogilvie, Michael C

    2013-04-28

    PT-symmetric Hamiltonians and transfer matrices arise naturally in statistical mechanics. These classical and quantum models often require the use of complex or negative weights and thus fall outside the conventional equilibrium statistical mechanics of Hermitian systems. PT-symmetric models form a natural class where the partition function is necessarily real, but not necessarily positive. The correlation functions of these models display a much richer set of behaviours than Hermitian systems, displaying sinusoidally modulated exponential decay, as in a dense fluid, or even sinusoidal modulation without decay. Classical spin models with PT-symmetry include Z(N) models with a complex magnetic field, the chiral Potts model and the anisotropic next-nearest-neighbour Ising model. Quantum many-body problems with a non-zero chemical potential have a natural PT-symmetric representation related to the sign problem. Two-dimensional quantum chromodynamics with heavy quarks at non-zero chemical potential can be solved by diagonalizing an appropriate PT-symmetric Hamiltonian.

  7. Quantum mechanical study of solvent effects in a prototype S{sub N}2 reaction in solution: Cl{sup −} attack on CH{sub 3}Cl

    SciTech Connect

    Kuechler, Erich R.; York, Darrin M.

    2014-02-07

    The nucleophilic attack of a chloride ion on methyl chloride is an important prototype S{sub N}2 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.

  8. Excitation transfer through open quantum networks: Three basic mechanisms

    NASA Astrophysics Data System (ADS)

    Campos Venuti, Lorenzo; Zanardi, Paolo

    2011-10-01

    A variety of open quantum networks are currently under intense examination to model energy transport in photosynthetic systems. Here, we study the coherent transfer of a quantum excitation over a network incoherently coupled with a structured and small environment that effectively models the photosynthetic reaction center. Our goal is to distill a few basic, possibly universal, mechanisms or effects that are featured in simple energy-transfer models. In particular, we identify three different phenomena: the congestion effect, the asymptotic unitarity, and the staircase effects. We begin with few-site models, in which these effects can be fully understood, and then proceed to study more complex networks similar to those employed to model energy transfer in light-harvesting complexes.

  9. Quantum mechanics on phase space and the Coulomb potential

    NASA Astrophysics Data System (ADS)

    Campos, P.; Martins, M. G. R.; Vianna, J. D. M.

    2017-04-01

    Symplectic quantum mechanics (SMQ) makes possible to derive the Wigner function without the use of the Liouville-von Neumann equation. In this formulation of the quantum theory the Galilei Lie algebra is constructed using the Weyl (or star) product with Q ˆ = q ⋆ = q +iħ/2∂p , P ˆ = p ⋆ = p -iħ/2∂q, and the Schrödinger equation is rewritten in phase space; in consequence physical applications involving the Coulomb potential present some specific difficulties. Within this context, in order to treat the Schrödinger equation in phase space, a procedure based on the Levi-Civita (or Bohlin) transformation is presented and applied to two-dimensional (2D) hydrogen atom. Amplitudes of probability in phase space and the correspondent Wigner quasi-distribution functions are derived and discussed.

  10. Deformation of supersymmetric and conformal quantum mechanics through affine transformations

    NASA Technical Reports Server (NTRS)

    Spiridonov, Vyacheslav

    1993-01-01

    Affine transformations (dilatations and translations) are used to define a deformation of one-dimensional N = 2 supersymmetric quantum mechanics. Resulting physical systems do not have conserved charges and degeneracies in the spectra. Instead, superpartner Hamiltonians are q-isospectral, i.e. the spectrum of one can be obtained from another (with possible exception of the lowest level) by q(sup 2)-factor scaling. This construction allows easily to rederive a special self-similar potential found by Shabat and to show that for the latter a q-deformed harmonic oscillator algebra of Biedenharn and Macfarlane serves as the spectrum generating algebra. A general class of potentials related to the quantum conformal algebra su(sub q)(1,1) is described. Further possibilities for q-deformation of known solvable potentials are outlined.

  11. Evanescent radiation, quantum mechanics and the Casimir effect

    NASA Technical Reports Server (NTRS)

    Schatten, Kenneth H.

    1989-01-01

    An attempt to bridge the gap between classical and quantum mechanics and to explain the Casimir effect is presented. The general nature of chaotic motion is discussed from two points of view: the first uses catastrophe theory and strange attractors to describe the deterministic view of this motion; the underlying framework for chaos in these classical dynamic systems is their extreme sensitivity to initial conditions. The second interpretation refers to randomness associated with probabilistic dynamics, as for Brownian motion. The present approach to understanding evanescent radiation and its relation to the Casimir effect corresponds to the first interpretation, whereas stochastic electrodynamics corresponds to the second viewpoint. The nonlinear behavior of the electromagnetic field is also studied. This well-understood behavior is utilized to examine the motions of two orbiting charges and shows a closeness between the classical behavior and the quantum uncertainty principle. The evanescent radiation is used to help explain the Casimir effect.

  12. Black hole thermodynamics from near-horizon conformal quantum mechanics

    SciTech Connect

    Camblong, Horacio E.; Ordonez, Carlos R.

    2005-05-15

    The thermodynamics of black holes is shown to be directly induced by their near-horizon conformal invariance. This behavior is exhibited using a scalar field as a probe of the black hole gravitational background, for a general class of metrics in D spacetime dimensions (with D{>=}4). The ensuing analysis is based on conformal quantum mechanics, within a hierarchical near-horizon expansion. In particular, the leading conformal behavior provides the correct quantum statistical properties for the Bekenstein-Hawking entropy, with the near-horizon physics governing the thermodynamics from the outset. Most importantly: (i) this treatment reveals the emergence of holographic properties; (ii) the conformal coupling parameter is shown to be related to the Hawking temperature; and (iii) Schwarzschild-like coordinates, despite their 'coordinate singularity', can be used self-consistently to describe the thermodynamics of black holes.

  13. The quantum coherent mechanism for singlet fission: experiment and theory.

    PubMed

    Chan, Wai-Lun; Berkelbach, Timothy C; Provorse, Makenzie R; Monahan, Nicholas R; Tritsch, John R; Hybertsen, Mark S; Reichman, David R; Gao, Jiali; Zhu, X-Y

    2013-06-18

    The absorption of one photon by a semiconductor material usually creates one electron-hole pair. However, this general rule breaks down in a few organic semiconductors, such as pentacene and tetracene, where one photon absorption may result in two electron-hole pairs. This process, where a singlet exciton transforms to two triplet excitons, can have quantum yields as high as 200%. Singlet fission may be useful to solar cell technologies to increase the power conversion efficiency beyond the so-called Shockley-Queisser limit. Through time-resolved two-photon photoemission (TR-2PPE) spectroscopy in crystalline pentacene and tetracene, our lab has recently provided the first spectroscopic signatures in singlet fission of a critical intermediate known as the multiexciton state (also called a correlated triplet pair). More importantly, we found that population of the multiexciton state rises at the same time as the singlet state on the ultrafast time scale upon photoexcitation. This observation does not fit with the traditional view of singlet fission involving the incoherent conversion of a singlet to a triplet pair. However, it provides an experimental foundation for a quantum coherent mechanism in which the electronic coupling creates a quantum superposition of the singlet and the multiexciton state immediately after optical excitation. In this Account, we review key experimental findings from TR-2PPE experiments and present a theoretical analysis of the quantum coherent mechanism based on electronic structural and density matrix calculations for crystalline tetracene lattices. Using multistate density functional theory, we find that the direct electronic coupling between singlet and multiexciton states is too weak to explain the experimental observation. Instead, indirect coupling via charge transfer intermediate states is two orders of magnitude stronger, and dominates the dynamics for ultrafast multiexciton formation. Density matrix calculation for the crystalline

  14. The Kantian element in the Copenhagen interpretation of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Cale, David Lee

    In Quantum Physics and the Philosophical Tradition, Aage Petersen makes the troubling claim that the entirety of the tradition of Western philosophy is "deconstructed" by quantum mechanics. This viewpoint applies, especially, to the relationship between Kantian philosophy and quantum theory. It is generally accepted that quantum mechanics, in its Copenhagen interpretation, has destroyed all validity for the classical belief in a deterministic underlying reality, a belief sustained throughout the nineteenth century through a philosophical ground in Kant's critical philosophy. This dissertation takes on the daunting task of determining what, if any, relationship can be had between contemporary physics and Kantian philosophy. It begins with a historical review of the challenges posed for Kant's arguments and proposed solutions, especially those offered by Cassirer. It then turns to the task of providing the Western philosophical tradition with an interpretation apart from Petersen's, which sees it as concerned only with the problem of being. The offered solution is the suggestion that Western philosophy be understood as a struggle, between epistemological and ontological perspectives, to provide a context for the various descriptions of nature provided by human scientific progress. Kant's philosophy is then interpreted as an effort to provide Newtonian physics with a valid context in the face of Hume's skepticism. The finding is that Kant was the first to suggest that an object does not acquire the spatio-temporal properties used in its physical description until introduced to an observer. The dissertation concludes that the authors of the Copenhagen interpretation were essentially engaged in Kant's enterprise through their attempt to provide an observer based context for the spatio-temporal descriptive principles used in the physics of their time.

  15. 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.

  16. Quantum mechanical treatment of As(3+)-thiol model compounds: implication for the core structure of As(III)-metallothionein.

    PubMed

    Garla, Roobee; Kaur, Narinder; Bansal, Mohinder Pal; Garg, Mohan Lal; Mohanty, Biraja Prasad

    2017-03-01

    Exposure to inorganic arsenic (As) is one of the major health concerns in several regions around the world. Binding of As(III) with thiols is central to the mechanisms related to its toxicity, detoxification, and therapeutic effects. Due to its high thiol content, metallothionein (MT) is presumed to play an important role in case of arsenic toxicity. Consequences of these As-thiol interactions are not yet clear due to various difficulties in the characterization of arsenic bound proteins by spectroscopic techniques. Computational modeling can be a reliable approach in predicting the molecular structures of such complexes. This paper presents the results of a systematic study on different As(III)-thiol model compounds conducted by both ab initio and DFT methods with different Gaussian type basis sets. Proficiency of these theoretical methods has been evaluated in terms of bond lengths, bond angles, free energy, partial atomic charges, computational cost, and comparison with the experimental data. It has been demonstrated that the DFT-B3LYP/6-311+G(3df) functional offers better accuracy in predicting the structure and the UV absorption spectra of As(III)-thiol complexes. The results of the present study also helps in defining the boundaries for the core of arsenic bound MT so that quantum mechanical/molecular mechanical (QM/MM) methods can be employed to predict the structural and functional aspects of the protein. Graphical Abstract Optimized structural parameters of As(3+)-thiol model compounds.

  17. Study of quantum spin correlations of relativistic electron pairs - Testing nonlocality of relativistic quantum mechanics

    SciTech Connect

    Bodek, K.; Rozpędzik, D.; Zejma, J.; Caban, P.; Rembieliński, J.; Włodarczyk, M.; Enders, J.; Köhler, A.; Kozela, A.

    2013-11-07

    The Polish-German project QUEST aims at studying relativistic quantum spin correlations of the Einstein-Rosen-Podolsky-Bohm type, through measurement of the correlation function and the corresponding probabilities for relativistic electron pairs. The results will be compared to theoretical predictions obtained by us within the framework of relativistic quantum mechanics, based on assumptions regarding the form of the relativistic spin operator. Agreement or divergence will be interpreted in the context of non-uniqueness of the relativistic spin operator in quantum mechanics as well as dependence of the correlation function on the choice of observables representing the spin. Pairs of correlated electrons will originate from the Mo/ller scattering of polarized 15 MeV electrons provided by the superconducting Darmstadt electron linear accelerator S-DALINAC, TU Darmstadt, incident on a Be target. Spin projections will be determined using the Mott polarimetry technique. Measurements (starting 2013) are planned for longitudinal and transverse beam polarizations and different orientations of the beam polarization vector w.r.t. the Mo/ller scattering plane. This is the first project to study relativistic spin correlations for particles with mass.

  18. Study of quantum spin correlations of relativistic electron pairs - Testing nonlocality of relativistic quantum mechanics

    NASA Astrophysics Data System (ADS)

    Bodek, K.; Caban, P.; Ciborowski, J.; Enders, J.; Köhler, A.; Kozela, A.; Rembieliński, J.; Rozpedzik, D.; Włodarczyk, M.; Zejma, J.

    2013-11-01

    The Polish-German project QUEST aims at studying relativistic quantum spin correlations of the Einstein-Rosen-Podolsky-Bohm type, through measurement of the correlation function and the corresponding probabilities for relativistic electron pairs. The results will be compared to theoretical predictions obtained by us within the framework of relativistic quantum mechanics, based on assumptions regarding the form of the relativistic spin operator. Agreement or divergence will be interpreted in the context of non-uniqueness of the relativistic spin operator in quantum mechanics as well as dependence of the correlation function on the choice of observables representing the spin. Pairs of correlated electrons will originate from the Mo/ller scattering of polarized 15 MeV electrons provided by the superconducting Darmstadt electron linear accelerator S-DALINAC, TU Darmstadt, incident on a Be target. Spin projections will be determined using the Mott polarimetry technique. Measurements (starting 2013) are planned for longitudinal and transverse beam polarizations and different orientations of the beam polarization vector w.r.t. the Mo/ller scattering plane. This is the first project to study relativistic spin correlations for particles with mass.

  19. Intrinsic periodicity: the forgotten lesson of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Dolce, Donatello

    2013-06-01

    Wave-particle duality, together with the concept of elementary particles, was introduced by de Broglie in terms of intrinsically periodic phenomena. However, after nearly 90 years, the physical origin of such undulatory mechanics remains unrevealed. We propose a natural realization of the de Broglie periodic phenomenon in terms of harmonic vibrational modes associated to space-time periodicities. In this way we find that, similarly to a vibrating string or a particle in a box, the intrinsic recurrence imposed as a constraint to elementary particles represents a fully consistent quantization condition. The resulting cyclic dynamics formally match ordinary relativistic Quantum Mechanics in both the canonical and Feynman formulations. Interactions are introduced in a geometrodynamical way, similarly to general relativity, by simply considering that variations of kinematical state can be equivalently described in terms of modulations of space-time recurrences, as known from undulatory mechanics. We present this novel quantization prescription from an historical prospective.

  20. Principles of Empiricism and the Interpretation of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Jaroszkiewicz, George

    The interpretation of quantum mechanics (QM) is discussed in terms of the principles and logic of empiricism. First, we list a set of issues that should be settled before any consistent interpretation is attempted. This includes questions such as whether we can use an exophysical perspective or an endophysical perspective, and whether a completely reductionist approach makes sense or are we forced to incorporate emergent laws of physics. We then list the scientific pr nciples that should be strictly adhered to in any debate on QM. We follow this with a list of cautions and warnings about misleading concepts that should be avoided, such as ignoring contextuality and the meaning of scientific truth values. These principles and warning are then used to decide on the issues we first identified, giving us a basis for an interpretation of QM from the perspective of observers and quantum signal states of apparatus, rather than in terms of qu ntum states of systems under observation. Finally, we review a proposed mathematical formalism that encodes this interpretation in terms of quantum registers.