Bohm's Quantum Potential and the Visualization of Molecular Structure

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

Transient Evolutional Dynamics of Quantum-Dot Molecular Phase Coherence for Sensitive Optical Switching

NASA Astrophysics Data System (ADS)

Shen, Jian Qi; Gu, Jing

2018-04-01

Atomic phase coherence (quantum interference) in a multilevel atomic gas exhibits a number of interesting phenomena. Such an atomic quantum coherence effect can be generalized to a quantum-dot molecular dielectric. Two quantum dots form a quantum-dot molecule, which can be described by a three-level Λ-configuration model { |0> ,|1> ,|2> } , i.e., the ground state of the molecule is the lower level |0> and the highly degenerate electronic states in the two quantum dots are the two upper levels |1> ,|2> . The electromagnetic characteristics due to the |0>-|1> transition can be controllably manipulated by a tunable gate voltage (control field) that drives the |2>-|1> transition. When the gate voltage is switched on, the quantum-dot molecular state can evolve from one steady state (i.e., |0>-|1> two-level dressed state) to another steady state (i.e., three-level coherent-population-trapping state). In this process, the electromagnetic characteristics of a quantum-dot molecular dielectric, which is modified by the gate voltage, will also evolve. In this study, the transient evolutional behavior of the susceptibility of a quantum-dot molecular thin film and its reflection spectrum are treated by using the density matrix formulation of the multilevel systems. The present field-tunable and frequency-sensitive electromagnetic characteristics of a quantum-dot molecular thin film, which are sensitive to the applied gate voltage, can be utilized to design optical switching devices.

Enhancing quantum annealing performance for the molecular similarity problem

NASA Astrophysics Data System (ADS)

Hernandez, Maritza; Aramon, Maliheh

2017-05-01

Quantum annealing is a promising technique which leverages quantum mechanics to solve hard optimization problems. Considerable progress has been made in the development of a physical quantum annealer, motivating the study of methods to enhance the efficiency of such a solver. In this work, we present a quantum annealing approach to measure similarity among molecular structures. Implementing real-world problems on a quantum annealer is challenging due to hardware limitations such as sparse connectivity, intrinsic control error, and limited precision. In order to overcome the limited connectivity, a problem must be reformulated using minor-embedding techniques. Using a real data set, we investigate the performance of a quantum annealer in solving the molecular similarity problem. We provide experimental evidence that common practices for embedding can be replaced by new alternatives which mitigate some of the hardware limitations and enhance its performance. Common practices for embedding include minimizing either the number of qubits or the chain length and determining the strength of ferromagnetic couplers empirically. We show that current criteria for selecting an embedding do not improve the hardware's performance for the molecular similarity problem. Furthermore, we use a theoretical approach to determine the strength of ferromagnetic couplers. Such an approach removes the computational burden of the current empirical approaches and also results in hardware solutions that can benefit from simple local classical improvement. Although our results are limited to the problems considered here, they can be generalized to guide future benchmarking studies.

Will spin-relaxation times in molecular magnets permit quantum information processing?

NASA Astrophysics Data System (ADS)

Ardavan, Arzhang

2007-03-01

Certain computational tasks can be efficiently implemented using quantum logic, in which the information-carrying elements are permitted to exist in quantum superpositions. To achieve this in practice, a physical system that is suitable for embodying quantum bits (qubits) must be identified. Some proposed scenarios employ electron spins in the solid state, for example phosphorous donors in silicon, quantum dots, heterostructures and endohedral fullerenes, motivated by the long electron-spin relaxation times exhibited by these systems. An alternative electron-spin based proposal exploits the large number of quantum states and the non-degenerate transitions available in high spin molecular magnets. Although these advantages have stimulated vigorous research in molecular magnets, the key question of whether the intrinsic spin relaxation times are long enough has hitherto remained unaddressed. Using X-band pulsed electron spin resonance, we measure the intrinsic spin-lattice (T1) and phase coherence (T2) relaxation times in molecular nanomagnets for the first time. In Cr7M heterometallic wheels, with M = Ni and Mn, phase coherence relaxation is dominated by the coupling of the electron spin to protons within the molecule. In deuterated samples T2 reaches 3 μs at low temperatures, which is several orders of magnitude longer than the duration of spin manipulations, satisfying a prerequisite for the deployment of molecular nanomagnets in quantum information applications.

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.

Simulation and understanding of atomic and molecular quantum crystals

NASA Astrophysics Data System (ADS)

Cazorla, Claudio; Boronat, Jordi

2017-07-01

Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

Molecular nanomagnets with switchable coupling for quantum simulation

DOE PAGES

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

2014-12-11

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

Preparation of a pure molecular quantum gas.

PubMed

Herbig, Jens; Kraemer, Tobias; Mark, Michael; Weber, Tino; Chin, Cheng; Nägerl, Hanns-Christoph; Grimm, Rudolf

2003-09-12

An ultracold molecular quantum gas is created by application of a magnetic field sweep across a Feshbach resonance to a Bose-Einstein condensate of cesium atoms. The ability to separate the molecules from the atoms permits direct imaging of the pure molecular sample. Magnetic levitation enables study of the dynamics of the ensemble on extended time scales. We measured ultralow expansion energies in the range of a few nanokelvin for a sample of 3000 molecules. Our observations are consistent with the presence of a macroscopic molecular matter wave.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Combined quantum and molecular mechanics (QM/MM).

PubMed

Friesner, Richard A

2004-12-01

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

Ultrarelativistic electrons and solar flare gamma-radiation

NASA Technical Reports Server (NTRS)

Semukhin, P. E.; Kovaltsov, G. A.

1985-01-01

Ten solar flares with gamma radiation in excess of 10 MeV were observed. Almost all took place within a heliolatitude greater than 60 deg, close to the solar limb, an indication of the essential anisotropy of high-energy gamma radiation. This high-energy solar flare gamma radiation can be explained by the specific features of the bremsstrahlung of ultrarelativistic electrons trapped within the magnetic arc of the solar atmosphere, even if the acceleration of the electrons is anisotropic.

Acetylcholine molecular arrays enable quantum information processing

NASA Astrophysics Data System (ADS)

Tamulis, Arvydas; Majauskaite, Kristina; Talaikis, Martynas; Zborowski, Krzysztof; Kairys, Visvaldas

2017-09-01

We have found self-assembly of four neurotransmitter acetylcholine (ACh) molecular complexes in a water molecules environment by using geometry optimization with DFT B97d method. These complexes organizes to regular arrays of ACh molecules possessing electronic spins, i.e. quantum information bits. These spin arrays could potentially be controlled by the application of a non-uniform external magnetic field. The proper sequence of resonant electromagnetic pulses would then drive all the spin groups into the 3-spin entangled state and proceed large scale quantum information bits.

Free Quantum Field Theory from Quantum Cellular Automata

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Quantum-dots-encoded-microbeads based molecularly imprinted polymer.

PubMed

Liu, Yixi; Liu, Le; He, Yonghong; He, Qinghua; Ma, Hui

2016-03-15

Quantum dots encoded microbeads have various advantages such as large surface area, superb optical properties and the ability of multiplexing. Molecularly imprinted polymer that can mimic the natural recognition entities has high affinity and selectivity for the specific analyte. Here, the concept of utilizing the quantum dots encoded microbeads as the supporting material and the polydopamine as the functional monomer to form the core-shell molecular imprinted polymer was proposed for the first time. The resulted imprinted polymer can provide various merits: polymerization can complete in aqueous environment; fabrication procedure is facile and universal; the obvious economic advantage; the thickness of the imprinting layer is highly controllable; polydopamine coating can improve the biocompatibility of the quantum dot encoded microbeads. The rabbit IgG binding and flow cytometer experiment result showed the distinct advantages of this strategy: cost-saving, facile and fast preparation procedure. Most importantly, the ability for the multichannel detection, which makes the imprinted polydopamine modified encoded-beads very attractive in protein pre-concentration, recognition, separation and biosensing. Copyright © 2015 Elsevier B.V. All rights reserved.

Formation of Ultrarelativistic Electron Rings from a Laser-Wakefield Accelerator.

PubMed

Pollock, B B; Tsung, F S; Albert, F; Shaw, J L; Clayton, C E; Davidson, A; Lemos, N; Marsh, K A; Pak, A; Ralph, J E; Mori, W B; Joshi, C

2015-07-31

Ultrarelativistic-energy electron ring structures have been observed from laser-wakefield acceleration experiments in the blowout regime. These electron rings had 170-280 MeV energies with 5%-25% energy spread and ∼10  pC of charge and were observed over a range of plasma densities and compositions. Three-dimensional particle-in-cell simulations show that laser intensity enhancement in the wake leads to sheath splitting and the formation of a hollow toroidal pocket in the electron density around the wake behind the first wake period. If the laser propagates over a distance greater than the ideal dephasing length, some of the dephasing electrons in the second period can become trapped within the pocket and form an ultrarelativistic electron ring that propagates in free space over a meter-scale distance upon exiting the plasma. Such a structure acts as a relativistic potential well, which has applications for accelerating positively charged particles such as positrons.

Search for ultrarelativistic magnetic monopoles with the Pierre Auger observatory

NASA Astrophysics Data System (ADS)

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

2016-10-01

We present a search for ultrarelativistic magnetic monopoles with the Pierre Auger observatory. Such particles, possibly a relic of phase transitions in the early Universe, would deposit a large amount of energy along their path through the atmosphere, comparable to that of ultrahigh-energy cosmic rays (UHECRs). The air-shower profile of a magnetic monopole can be effectively distinguished by the fluorescence detector from that of standard UHECRs. No candidate was found in the data collected between 2004 and 2012, with an expected background of less than 0.1 event from UHECRs. The corresponding 90% confidence level (C.L.) upper limits on the flux of ultrarelativistic magnetic monopoles range from 10-19(cm2 sr s )-1 for a Lorentz factor γ =1 09 to 2.5 ×10-21(cm2 sr s )-1 for γ =1 012. These results—the first obtained with a UHECR detector—improve previously published limits by up to an order of magnitude.

Quantum Landauer erasure with a molecular nanomagnet

NASA Astrophysics Data System (ADS)

Gaudenzi, R.; Burzurí, E.; Maegawa, S.; van der Zant, H. S. J.; Luis, F.

2018-06-01

The erasure of a bit of information is an irreversible operation whose minimal entropy production of kB ln 2 is set by the Landauer limit1. This limit has been verified in a variety of classical systems, including particles in traps2,3 and nanomagnets4. Here, we extend it to the quantum realm by using a crystal of molecular nanomagnets as a quantum spin memory and showing that its erasure is still governed by the Landauer principle. In contrast to classical systems, maximal energy efficiency is achieved while preserving fast operation owing to its high-speed spin dynamics. The performance of our spin register in terms of energy-time cost is orders of magnitude better than existing memory devices to date. The result shows that thermodynamics sets a limit on the energy cost of certain quantum operations and illustrates a way to enhance classical computations by using a quantum system.

Molecular Model of a Quantum Dot Beyond the Constant Interaction Approximation

NASA Astrophysics Data System (ADS)

Temirov, Ruslan; Green, Matthew F. B.; Friedrich, Niklas; Leinen, Philipp; Esat, Taner; Chmielniak, Pawel; Sarwar, Sidra; Rawson, Jeff; Kögerler, Paul; Wagner, Christian; Rohlfing, Michael; Tautz, F. Stefan

2018-05-01

We present a physically intuitive model of molecular quantum dots beyond the constant interaction approximation. It accurately describes their charging behavior and allows the extraction of important molecular properties that are otherwise experimentally inaccessible. The model is applied to data recorded with a noncontact atomic force microscope on three different molecules that act as a quantum dot when attached to the microscope tip. The results are in excellent agreement with first-principles simulations.

Quantum tomography of a molecular bond in ice.

PubMed

Goldschleger, I U; Golschleger, I U; van Staveren, M N; Apkarian, V Ara

2013-07-21

We present the moving picture of a molecular bond, in phase-space, in real-time, at resolution limited by quantum uncertainty. The images are tomographically reconstructed Wigner distribution functions (WDF) obtained from four-wave mixing measurements on Br2-doped ice. The WDF completely characterizes the dissipative quantum evolution of the system, which despite coupling to the environment retains quantum coherence, as evidenced by its persistent negative Wigner hole. The spectral decomposition of the WDF allows a direct visualization of wavefunctions and spatiotemporal coherences of the system and the system-bath interaction. The measurements vividly illustrate nonclassical wave mechanics in a many-body system, in ordinary condensed matter.

A quantum spin-probe molecular microscope

NASA Astrophysics Data System (ADS)

Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

2016-10-01

Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

Preparation and coherent manipulation of pure quantum states of a single molecular ion

NASA Astrophysics Data System (ADS)

Chou, Chin-Wen; Kurz, Christoph; Hume, David B.; Plessow, Philipp N.; Leibrandt, David R.; Leibfried, Dietrich

2017-05-01

Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH+) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

Preparation and coherent manipulation of pure quantum states of a single molecular ion.

PubMed

Chou, Chin-Wen; Kurz, Christoph; Hume, David B; Plessow, Philipp N; Leibrandt, David R; Leibfried, Dietrich

2017-05-10

Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH + ) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

Anticipatory dynamics of biological systems: from molecular quantum states to evolution

NASA Astrophysics Data System (ADS)

Igamberdiev, Abir U.

2015-08-01

Living systems possess anticipatory behaviour that is based on the flexibility of internal models generated by the system's embedded description. The idea was suggested by Aristotle and is explicitly introduced to theoretical biology by Rosen. The possibility of holding the embedded internal model is grounded in the principle of stable non-equilibrium (Bauer). From the quantum mechanical view, this principle aims to minimize energy dissipation in expense of long relaxation times. The ideas of stable non-equilibrium were developed by Liberman who viewed living systems as subdivided into the quantum regulator and the molecular computer supporting coherence of the regulator's internal quantum state. The computational power of the cell molecular computer is based on the possibility of molecular rearrangements according to molecular addresses. In evolution, the anticipatory strategies are realized both as a precession of phylogenesis by ontogenesis (Berg) and as the anticipatory search of genetic fixation of adaptive changes that incorporates them into the internal model of genetic system. We discuss how the fundamental ideas of anticipation can be introduced into the basic foundations of theoretical biology.

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

NASA Astrophysics Data System (ADS)

Sinitskiy, Anton V.; Voth, Gregory A.

2018-01-01

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

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

PubMed

Sinitskiy, Anton V; Voth, Gregory A

2018-01-07

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

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

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

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

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

PubMed

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

2017-07-21

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

Activation of molecular catalysts using semiconductor quantum dots

DOEpatents

Meyer, Thomas J [Chapel Hill, NC; Sykora, Milan [Los Alamos, NM; Klimov, Victor I [Los Alamos, NM

2011-10-04

Photocatalytic materials based on coupling of semiconductor nanocrystalline quantum dots (NQD) and molecular catalysts. These materials have capability to drive or catalyze non-spontaneous chemical reactions in the presence of visible radiation, ultraviolet radiation, or both. The NQD functions in these materials as a light absorber and charge generator. Following light absorption, the NQD activates a molecular catalyst adsorbed on the surface of the NQD via transfer of one or more charges (either electrons or electron-holes) from the NQD to the molecular catalyst. The activated molecular catalyst can then drive a chemical reaction. A photoelectrolytic device that includes such photocatalytic materials is also described.

Experimental evidence of quantum radiation reaction in aligned crystals.

PubMed

Wistisen, Tobias N; Di Piazza, Antonino; Knudsen, Helge V; Uggerhøj, Ulrik I

2018-02-23

Quantum radiation reaction is the influence of multiple photon emissions from a charged particle on the particle's dynamics, characterized by a significant energy-momentum loss per emission. Here we report experimental radiation emission spectra from ultrarelativistic positrons in silicon in a regime where quantum radiation reaction effects dominate the positron's dynamics. Our analysis shows that while the widely used quantum approach is overall the best model, it does not completely describe all the data in this regime. Thus, these experimental findings may prompt seeking more generally valid methods to describe quantum radiation reaction. This experiment is a fundamental test of quantum electrodynamics in a regime where the dynamics of charged particles is strongly influenced not only by the external electromagnetic fields but also by the radiation field generated by the charges themselves and where each photon emission may significantly reduce the energy of the charge.

Molecular spectrum of laterally coupled quantum rings under intense terahertz radiation.

PubMed

Baghramyan, Henrikh M; Barseghyan, Manuk G; Laroze, David

2017-09-05

We study the influence of intense THz laser radiation and electric field on molecular states of laterally coupled quantum rings. Laser radiation shows the capability to dissociate quantum ring molecule and add 2-fold degeneracy to the molecular states at the fixed value of the overlapping size between rings. It is shown that coupled to decoupled molecular states phase transition points form almost a straight line with a slope equal to two. In addition, the electric field direction dependent energy spectrum shows unexpected oscillations, demonstrating strong coupling between molecular states. Besides, intraband absorption is considered, showing both blue and redshifts in its spectrum. The obtained results can be useful for the controlling of degeneracy of the discrete energy spectrum of nanoscale structures and in the tunneling effects therein.

Towards the simulation of molecular collisions with a superconducting quantum computer

NASA Astrophysics Data System (ADS)

Geller, Michael

2013-05-01

I will discuss the prospects for the use of large-scale, error-corrected quantum computers to simulate complex quantum dynamics such as molecular collisions. This will likely require millions qubits. I will also discuss an alternative approach [M. R. Geller et al., arXiv:1210.5260] that is ideally suited for today's superconducting circuits, which uses the single-excitation subspace (SES) of a system of n tunably coupled qubits. The SES method allows many operations in the unitary group SU(n) to be implemented in a single step, bypassing the need for elementary gates, thereby making large computations possible without error correction. The method enables universal quantum simulation, including simulation of the time-dependent Schrodinger equation, and we argue that a 1000-qubit SES processor should be capable of achieving quantum speedup relative to a petaflop supercomputer. We speculate on the utility and practicality of such a simulator for atomic and molecular collision physics. Work supported by the US National Science Foundation CDI program.

Coherent spin transfer between molecularly bridged quantum dots.

PubMed

Ouyang, Min; Awschalom, David D

2003-08-22

Femtosecond time-resolved Faraday rotation spectroscopy reveals the instantaneous transfer of spin coherence through conjugated molecular bridges spanning quantum dots of different size over a broad range of temperature. The room-temperature spin-transfer efficiency is approximately 20%, showing that conjugated molecules can be used not only as interconnections for the hierarchical assembly of functional networks but also as efficient spin channels. The results suggest that this class of structures may be useful as two-spin quantum devices operating at ambient temperatures and may offer promising opportunities for future versatile molecule-based spintronic technologies.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Vertical resonant tunneling transistors with molecular quantum dots for large-scale integration.

PubMed

Hayakawa, Ryoma; Chikyow, Toyohiro; Wakayama, Yutaka

2017-08-10

Quantum molecular devices have a potential for the construction of new data processing architectures that cannot be achieved using current complementary metal-oxide-semiconductor (CMOS) technology. The relevant basic quantum transport properties have been examined by specific methods such as scanning probe and break-junction techniques. However, these methodologies are not compatible with current CMOS applications, and the development of practical molecular devices remains a persistent challenge. Here, we demonstrate a new vertical resonant tunneling transistor for large-scale integration. The transistor channel is comprised of a MOS structure with C 60 molecules as quantum dots, and the structure behaves like a double tunnel junction. Notably, the transistors enabled the observation of stepwise drain currents, which originated from resonant tunneling via the discrete molecular orbitals. Applying side-gate voltages produced depletion layers in Si substrates, to achieve effective modulation of the drain currents and obvious peak shifts in the differential conductance curves. Our device configuration thus provides a promising means of integrating molecular functions into future CMOS applications.

Modeling the Impenetrable Barrier to Inward Transport of Ultra-relativistic Radiation Belt Electrons

NASA Astrophysics Data System (ADS)

Tu, W.; Cunningham, G.; Chen, Y.; Baker, D. N.; Henderson, M. G.; Reeves, G. D.

2014-12-01

It has long been considered that the inner edge of the Earth's outer radiation belt is closely correlated with the minimum plasmapause location. However, recent discoveries by Baker et al. [1] show that it is not the case for ultra-relativistic electrons (2-10 MeV) in the radiation belt. Based on almost two years of Van Allen Probes/REPT data, they find that the inner edge of highly relativistic electrons is rarely collocated with the plasmapause; and more interestingly, there is a clear, persistent, and nearly impenetrable barrier to inward transport of high energy electrons, observed to locate at L~2.8. The presence of such an impenetrable barrier at this very specific location poses a significant puzzle. Using our DREAM3D diffusion model, which includes radial, pitch angle, and momentum diffusion, we are able to simulate the observed impenetrable barrier of ultra-relativistic electrons. The simulation demonstrates that during strong geomagnetic storms the plasmapause can be compressed to very low L region (sometimes as low as L~3), then strong chorus waves just outside the plasmapause can locally accelerate electrons up to multiple-MeV; when storm recovers, plasmapause moves back to large L, while the highly-relativistic electrons generated at low L continue to diffuse inward and slow decay by pitch angle diffusion from plasmaspheric hiss. The delicate balance between slow inward radial diffusion and weak pitch angle scattering creates a fixed inner boundary or barrier for ultra-relativistic electrons. The barrier is found to locate at a fixed L location, independent of the initial penetration depth of electrons that is correlated with the plasmapause location. Our simulation results quantitatively reproduce the evolution of the flux versus L profile, the L location of the barrier, and the decay rate of highly energetic electrons right outside the barrier. 1Baker, D. N., et al. (2014), Nearly Impenetrable Barrier to Inward Ultra-relativistic Magnetospheric

Tuning Electrostatic Potentials for Imaging the Quantum Properties of Massless Dirac Fermions in Graphene

NASA Astrophysics Data System (ADS)

Wong, Dillon

Graphene, a two-dimensional (2D) honeycomb lattice of sp 2-bonded carbon atoms, is renowned for its many extraordinary properties. Not only does it have an extremely high carrier mobility, exceptional mechanical strength, and fascinating optical behavior, graphene additionally has an interesting energy-momentum relationship that is emergent from its space group symmetry. Graphene's low-energy electronic excitations consist of quasiparticles whose energies disperse linearly with wavevector and obey a 2D massless Dirac equation with a modified speed of light. This fortuitous circumstance allows for the exploration of ultra-relativistic phenomena using conventional tabletop techniques common to solid state physics and material science. Here I discuss experiments that probe these ultra-relativistic effects via application of scanning tunneling microscopy (STM) and spectroscopy (STS) to graphene field-effect transistors (FETs) in proximity with charged impurities. The first part of this dissertation focuses on the ultra-relativistic Coulomb problem. Depending on the strength of the potential, the Coulomb problem for massless Dirac particles is divided into two regimes: the subcritical and the supercritical. The subcritical regime is characterized by an electron-hole asymmetry in the local density of states (LDOS) and, unlike in nonrelativistic quantum mechanics, does not support bound states. In contrast, the supercritical regime hosts quasi-bound states that are analogous to "atomic collapse" orbits predicted to occur in atoms with nuclear charge Z > 170. By using an STM tip to directly position calcium (Ca) impurities on a graphene surface, we assembled "artificial nuclei" and observed a transition between the subcritical and supercritical regimes with increasing nuclear charge. We also investigated the screening of these charged impurities by massless Dirac fermions while varying the graphene carrier concentration with an electrostatic gate. The second part of this

Two-dimensional cylindrical ion-acoustic solitary and rogue waves in ultrarelativistic plasmas

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

Ata-ur-Rahman; National Centre for Physics at QAU Campus, Shahdrah Valley Road, Islamabad 44000; Ali, S.

2013-07-15

The propagation of ion-acoustic (IA) solitary and rogue waves is investigated in a two-dimensional ultrarelativistic degenerate warm dense plasma. By using the reductive perturbation technique, the cylindrical Kadomtsev–Petviashvili (KP) equation is derived, which can be further transformed into a Korteweg–de Vries (KdV) equation. The latter admits a solitary wave solution. However, when the frequency of the carrier wave is much smaller than the ion plasma frequency, the KdV equation can be transferred to a nonlinear Schrödinger equation to study the nonlinear evolution of modulationally unstable modified IA wavepackets. The propagation characteristics of the IA solitary and rogue waves are stronglymore » influenced by the variation of different plasma parameters in an ultrarelativistic degenerate dense plasma. The present results might be helpful to understand the nonlinear electrostatic excitations in astrophysical degenerate dense plasmas.« less

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

PubMed

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

2006-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

Search for Ultra-relativistic Magnetic Monopoles with the Pierre Auger Observatory

DOE PAGES

Aab, Alexander

2016-10-03

In this paper, we present a search for ultra-relativistic magnetic monopoles with the Pierre Auger Observatory. Such particles, possibly a relic of phase transitions in the early universe, would deposit a large amount of energy along their path through the atmosphere, comparable to that of ultrahigh-energy cosmic rays (UHECRs). The air shower profile of a magnetic monopole can be effectively distinguished by the fluorescence detector from that of standard UHECRs. No candidate was found in the data collected between 2004 and 2012, with an expected background of less than 0.1 event from UHECRs. The corresponding 90% confidence level (C.L.) upper limits on the flux of ultra-relativistic magnetic monopoles range frommore » $$10^{-19}$$ (cm$$^{2}$$ sr s)$$^{-1}$$ for a Lorentz factor $$\\gamma=10^9$$ to $$2.5 \\times10^{-21}$$ (cm$$^{2}$$ sr s)$$^{-1}$$ for $$\\gamma=10^{12}$$. Lastly, these results - the first obtained with a UHECR detector - improve previously published limits by up to an order of magnitude.« less

Quasi-classical modeling of molecular quantum-dot cellular automata multidriver gates

NASA Astrophysics Data System (ADS)

Rahimi, Ehsan; Nejad, Shahram Mohammad

2012-05-01

Molecular quantum-dot cellular automata (mQCA) has received considerable attention in nanoscience. Unlike the current-based molecular switches, where the digital data is represented by the on/off states of the switches, in mQCA devices, binary information is encoded in charge configuration within molecular redox centers. The mQCA paradigm allows high device density and ultra-low power consumption. Digital mQCA gates are the building blocks of circuits in this paradigm. Design and analysis of these gates require quantum chemical calculations, which are demanding in computer time and memory. Therefore, developing simple models to probe mQCA gates is of paramount importance. We derive a semi-classical model to study the steady-state output polarization of mQCA multidriver gates, directly from the two-state approximation in electron transfer theory. The accuracy and validity of this model are analyzed using full quantum chemistry calculations. A complete set of logic gates, including inverters and minority voters, are implemented to provide an appropriate test bench in the two-dot mQCA regime. We also briefly discuss how the QCADesigner tool could find its application in simulation of mQCA devices.

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

Magnetic torque anomaly in the quantum limit of Weyl semimetals

PubMed Central

Moll, Philip J. W.; Potter, Andrew C.; Nair, Nityan L.; Ramshaw, B. J.; Modic, K. A.; Riggs, Scott; Zeng, Bin; Ghimire, Nirmal J.; Bauer, Eric D.; Kealhofer, Robert; Ronning, Filip; Analytis, James G.

2016-01-01

Electrons in materials with linear dispersion behave as massless Weyl- or Dirac-quasiparticles, and continue to intrigue due to their close resemblance to elusive ultra-relativistic particles as well as their potential for future electronics. Yet the experimental signatures of Weyl-fermions are often subtle and indirect, in particular if they coexist with conventional, massive quasiparticles. Here we show a pronounced anomaly in the magnetic torque of the Weyl semimetal NbAs upon entering the quantum limit state in high magnetic fields. The torque changes sign in the quantum limit, signalling a reversal of the magnetic anisotropy that can be directly attributed to the topological nature of the Weyl electrons. Our results establish that anomalous quantum limit torque measurements provide a direct experimental method to identify and distinguish Weyl and Dirac systems. PMID:27545105

Coherent manipulation of quantum spin states in a single molecular nanomagnet

NASA Astrophysics Data System (ADS)

Wernsdorfer, Wolfgang

The endeavour of quantum electronics is driven by one of the most ambitious technological goals of today's scientists: the realization of an operational quantum computer (http://qurope.eu). We started to address this goal by the new research field of molecular quantum spintronics. The building blocks are magnetic molecules, i.e. well-defined spin qubits. We will discuss this still largely unexplored field and present our first results: For example, using a molecular spin-transistor, we achieved the electronic read-out of the nuclear spin of an individual metal atom embedded in an SMM. We could show very long spin lifetimes (>10 s). Using the hyperfine Stark effect, which transforms electric fields into local effective magnetic fields, we could not only tune the resonance frequency by several MHz, but also perform coherent quantum manipulations on a single nuclear qubit faster than a μs by means of electrical fields only, establishing the individual addressability of identical nuclear qubits. Using three different microwave frequencies, we could implement a simple four-level Grover algorithm. S. Thiele, F. Balestro, R. Ballou, S. Klyatskaya, M. Ruben, W. Wernsdorfer, Science 344, 1135 (2014).

Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

NASA Technical Reports Server (NTRS)

Menon, Madhu

1998-01-01

In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.

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.

Quantum tunneling of magnetization and related phenomena in molecular materials.

PubMed

Gatteschi, Dante; Sessoli, Roberta

2003-01-20

Molecules comprising a large number of coupled paramagnetic centers are attracting much interest because they may show properties which are intermediate between those of simple paramagnets and classical bulk magnets and provide unambiguous evidence of quantum size effects in magnets. To date, two cluster families, usually referred to as Mn12 and Fe8, have been used to test theories. However, it is reasonable to predict that other classes of molecules will be discovered which have similar or superior properties. To do this it is necessary that synthetic chemists have a good understanding of the correlation between the structure and properties of the molecules, for this it is necessary that concepts such as quantum tunneling, quantum coherence, quantum oscillations are understood. The goal of this article is to review the fundamental concepts needed to understand quantum size effects in molecular magnets and to critically report what has been done in the field to date.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Explaining the dynamics of the ultra-relativistic third Van Allen radiation belt

DOE PAGES

Mann, I. R.; Ozeke, L. G.; Murphy, K. R.; ...

2016-06-20

Since the discovery of the Van Allen radiation belts over 50 years ago, an explanation for their complete dynamics has remained elusive. Especially challenging is understanding the recently discovered ultra-relativistic third electron radiation belt. Current theory asserts that loss in the heart of the outer belt, essential to the formation of the third belt, must be controlled by high-frequency plasma wave–particle scattering into the atmosphere, via whistler mode chorus, plasmaspheric hiss, or electromagnetic ion cyclotron waves. However, this has failed to accurately reproduce the third belt. In this paper, using a data-driven, time-dependent specification of ultra-low-frequency (ULF) waves we showmore » for the first time how the third radiation belt is established as a simple, elegant consequence of storm-time extremely fast outward ULF wave transport. High-frequency wave–particle scattering loss into the atmosphere is not needed in this case. Finally, when rapid ULF wave transport coupled to a dynamic boundary is accurately specified, the sensitive dynamics controlling the enigmatic ultra-relativistic third radiation belt are naturally explained.« less

Explaining the dynamics of the ultra-relativistic third Van Allen radiation belt

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

Mann, I. R.; Ozeke, L. G.; Murphy, K. R.

Since the discovery of the Van Allen radiation belts over 50 years ago, an explanation for their complete dynamics has remained elusive. Especially challenging is understanding the recently discovered ultra-relativistic third electron radiation belt. Current theory asserts that loss in the heart of the outer belt, essential to the formation of the third belt, must be controlled by high-frequency plasma wave–particle scattering into the atmosphere, via whistler mode chorus, plasmaspheric hiss, or electromagnetic ion cyclotron waves. However, this has failed to accurately reproduce the third belt. In this paper, using a data-driven, time-dependent specification of ultra-low-frequency (ULF) waves we showmore » for the first time how the third radiation belt is established as a simple, elegant consequence of storm-time extremely fast outward ULF wave transport. High-frequency wave–particle scattering loss into the atmosphere is not needed in this case. Finally, when rapid ULF wave transport coupled to a dynamic boundary is accurately specified, the sensitive dynamics controlling the enigmatic ultra-relativistic third radiation belt are naturally explained.« less

Magnetic torque anomaly in the quantum limit of Weyl semimetals

DOE PAGES

Moll, Philip J. W.; Potter, Andrew C.; Nair, Nityan L.; ...

2016-08-22

Electrons in materials with linear dispersion behave as massless Weyl- or Dirac-quasiparticles, and continue to intrigue due to their close resemblance to elusive ultra-relativistic particles as well as their potential for future electronics. Yet the experimental signatures of Weyl-fermions are often subtle and indirect, in particular if they coexist with conventional, massive quasiparticles. Here we show a pronounced anomaly in the magnetic torque of the Weyl semimetal NbAs upon entering the quantum limit state in high magnetic fields. The torque changes sign in the quantum limit, signalling a reversal of the magnetic anisotropy that can be directly attributed to themore » topological nature of the Weyl electrons. Our results establish that anomalous quantum limit torque measurements provide a direct experimental method to identify and distinguish Weyl and Dirac systems.« less

Molecular engineering with artificial atoms: designing a material platform for scalable quantum spintronics and photonics

NASA Astrophysics Data System (ADS)

Doty, Matthew F.; Ma, Xiangyu; Zide, Joshua M. O.; Bryant, Garnett W.

2017-09-01

Self-assembled InAs Quantum Dots (QDs) are often called "artificial atoms" and have long been of interest as components of quantum photonic and spintronic devices. Although there has been substantial progress in demonstrating optical control of both single spins confined to a single QD and entanglement between two separated QDs, the path toward scalable quantum photonic devices based on spins remains challenging. Quantum Dot Molecules, which consist of two closely-spaced InAs QDs, have unique properties that can be engineered with the solid state analog of molecular engineering in which the composition, size, and location of both the QDs and the intervening barrier are controlled during growth. Moreover, applied electric, magnetic, and optical fields can be used to modulate, in situ, both the spin and optical properties of the molecular states. We describe how the unique photonic properties of engineered Quantum Dot Molecules can be leveraged to overcome long-standing challenges to the creation of scalable quantum devices that manipulate single spins via photonics.

Spintronic characteristics of self-assembled neurotransmitter acetylcholine molecular complexes enable quantum information processing in neural networks and brain

NASA Astrophysics Data System (ADS)

Tamulis, Arvydas; Majauskaite, Kristina; Kairys, Visvaldas; Zborowski, Krzysztof; Adhikari, Kapil; Krisciukaitis, Sarunas

2016-09-01

Implementation of liquid state quantum information processing based on spatially localized electronic spin in the neurotransmitter stable acetylcholine (ACh) neutral molecular radical is discussed. Using DFT quantum calculations we proved that this molecule possesses stable localized electron spin, which may represent a qubit in quantum information processing. The necessary operating conditions for ACh molecule are formulated in self-assembled dimer and more complex systems. The main quantum mechanical research result of this paper is that the neurotransmitter ACh systems, which were proposed, include the use of quantum molecular spintronics arrays to control the neurotransmission in neural networks.

Electrically tunable g factors in quantum dot molecular spin states.

PubMed

Doty, M F; Scheibner, M; Ponomarev, I V; Stinaff, E A; Bracker, A S; Korenev, V L; Reinecke, T L; Gammon, D

2006-11-10

We present a magnetophotoluminescence study of individual vertically stacked InAs/GaAs quantum dot pairs separated by thin tunnel barriers. As an applied electric field tunes the relative energies of the two dots, we observe a strong resonant increase or decrease in the g factors of different spin states that have molecular wave functions distributed over both quantum dots. We propose a phenomenological model for the change in g factor based on resonant changes in the amplitude of the wave function in the barrier due to the formation of bonding and antibonding orbitals.

Electrically Tunable g Factors in Quantum Dot Molecular Spin States

NASA Astrophysics Data System (ADS)

Doty, M. F.; Scheibner, M.; Ponomarev, I. V.; Stinaff, E. A.; Bracker, A. S.; Korenev, V. L.; Reinecke, T. L.; Gammon, D.

2006-11-01

We present a magnetophotoluminescence study of individual vertically stacked InAs/GaAs quantum dot pairs separated by thin tunnel barriers. As an applied electric field tunes the relative energies of the two dots, we observe a strong resonant increase or decrease in the g factors of different spin states that have molecular wave functions distributed over both quantum dots. We propose a phenomenological model for the change in g factor based on resonant changes in the amplitude of the wave function in the barrier due to the formation of bonding and antibonding orbitals.

Communication: Probing the interaction of infrared antenna arrays and molecular films with ultrafast quantum dynamics

NASA Astrophysics Data System (ADS)

Cohn, Bar; Prasad, Amit K.; Chuntonov, Lev

2018-04-01

Narrowband vibrational molecular transitions interacting with the broadband resonance of infrared plasmonic antennas lead to Fano lineshapes observed in linear (FTIR) and third-order (transient absorption and 2DIR) spectroscopic experiments. Both molecular and plasmonic components are inherently dissipative, and the effects associated with their coupling can be observed, in principle, when measuring the corresponding ultrafast quantum dynamics. We used 2DIR spectroscopy to study the waiting time evolution of quantum coherence excited in the carbonyl stretching modes of rhodium (acetylacetonato) dicarbonyl molecules, which were embedded in an 80 nm-thick polymer film spin-coated on an array of infrared half-wavelength gold antennas. Despite the pronounced Fano lineshapes obtained for the molecular transitions, and up to a four order of magnitude enhancement of the third-order signals, which taken together, indicate the coupling between the plasmonic and molecular transitions, the dynamics of the quantum coherence were identical to that obtained with 3 μm-thick film without the interaction with the plamson mode. This suggests that the coupling rate between the molecular and plasmonic excitations is significantly smaller than the relaxation rates of the molecular excitations monitored in the experiment. Here, the Fano lineshape, observed at the frequency of the molecular transition, can result from the mutual radiation damping of the molecular and plasmon modes.

Quantum molecular dynamics simulation of shock-wave experiments in aluminum

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

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

PubMed

Hendry, Robin Findlay

2003-05-01

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

The classical and quantum dynamics of molecular spins on graphene

PubMed Central

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2015-01-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019

The classical and quantum dynamics of molecular spins on graphene.

PubMed

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

The classical and quantum dynamics of molecular spins on graphene

NASA Astrophysics Data System (ADS)

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

Molecular basis of quantitative structure-properties relationships (QSPR): a quantum similarity approach.

PubMed

Ponec, R; Amat, L; Carbó-Dorca, R

1999-05-01

Since the dawn of quantitative structure-properties relationships (QSPR), empirical parameters related to structural, electronic and hydrophobic molecular properties have been used as molecular descriptors to determine such relationships. Among all these parameters, Hammett sigma constants and the logarithm of the octanol-water partition coefficient, log P, have been massively employed in QSPR studies. In the present paper, a new molecular descriptor, based on quantum similarity measures (QSM), is proposed as a general substitute of these empirical parameters. This work continues previous analyses related to the use of QSM to QSPR, introducing molecular quantum self-similarity measures (MQS-SM) as a single working parameter in some cases. The use of MQS-SM as a molecular descriptor is first confirmed from the correlation with the aforementioned empirical parameters. The Hammett equation has been examined using MQS-SM for a series of substituted carboxylic acids. Then, for a series of aliphatic alcohols and acetic acid esters, log P values have been correlated with the self-similarity measure between density functions in water and octanol of a given molecule. And finally, some examples and applications of MQS-SM to determine QSAR are presented. In all studied cases MQS-SM appeared to be excellent molecular descriptors usable in general QSPR applications of chemical interest.

Molecular basis of quantitative structure-properties relationships (QSPR): A quantum similarity approach

NASA Astrophysics Data System (ADS)

Ponec, Robert; Amat, Lluís; Carbó-dorca, Ramon

1999-05-01

Since the dawn of quantitative structure-properties relationships (QSPR), empirical parameters related to structural, electronic and hydrophobic molecular properties have been used as molecular descriptors to determine such relationships. Among all these parameters, Hammett σ constants and the logarithm of the octanol- water partition coefficient, log P, have been massively employed in QSPR studies. In the present paper, a new molecular descriptor, based on quantum similarity measures (QSM), is proposed as a general substitute of these empirical parameters. This work continues previous analyses related to the use of QSM to QSPR, introducing molecular quantum self-similarity measures (MQS-SM) as a single working parameter in some cases. The use of MQS-SM as a molecular descriptor is first confirmed from the correlation with the aforementioned empirical parameters. The Hammett equation has been examined using MQS-SM for a series of substituted carboxylic acids. Then, for a series of aliphatic alcohols and acetic acid esters, log P values have been correlated with the self-similarity measure between density functions in water and octanol of a given molecule. And finally, some examples and applications of MQS-SM to determine QSAR are presented. In all studied cases MQS-SM appeared to be excellent molecular descriptors usable in general QSPR applications of chemical interest.

Topology, localization, and quantum information in atomic, molecular and optical systems

NASA Astrophysics Data System (ADS)

Yao, Norman Ying

The scientific interface between atomic, molecular and optical (AMO) physics, condensed matter, and quantum information science has recently led to the development of new insights and tools that bridge the gap between macroscopic quantum behavior and detailed microscopic intuition. While the dialogue between these fields has sharpened our understanding of quantum theory, it has also raised a bevy of new questions regarding the out-of-equilibrium dynamics and control of many-body systems. This thesis is motivated by experimental advances that make it possible to produce and probe isolated, strongly interacting ensembles of disordered particles, as found in systems ranging from trapped ions and Rydberg atoms to ultracold polar molecules and spin defects in the solid state. The presence of strong interactions in these systems underlies their potential for exploring correlated many-body physics and this thesis presents recent results on realizing fractionalization and localization. From a complementary perspective, the controlled manipulation of individual quanta can also enable the bottom-up construction of quantum devices. To this end, this thesis also describes blueprints for a room-temperature quantum computer, quantum credit cards and nanoscale quantum thermometry.

Head-on collision of ultrarelativistic particles in ghost-free theories of gravity

NASA Astrophysics Data System (ADS)

Frolov, Valeri P.; Zelnikov, Andrei

2016-03-01

We study linearized equations of a ghost-free gravity in four- and higher-dimensional spacetimes. We consider versions of such a theory where the nonlocal modification of the □ operator has the form □exp [(-□/μ2)N] , where N =1 or N =2 n . We first obtain the Newtonian gravitational potential for a point mass for such models and demonstrate that it is finite and regular in any number of spatial dimensions d ≥3 . The second result of the paper is calculation of the gravitational field of an ultrarelativistic particle in such theories. And finally, we study a head-on collision of two ultrarelativistic particles. We formulated conditions of the apparent horizon formation and showed that there exists a mass gap for mini-black-hole production in the ghost-free theory of gravity. In the case when the center-of-mass energy is sufficient for the formation of the apparent horizon, the latter has two branches, the outer and the inner ones. When the energy increases the outer horizon tends to the Schwarzschild-Tangherlini limit, while the inner horizon becomes closer to r =0 .

Manipulation of Molecular Quantum Wavepackets with Ultrashort Laser Pulses for Non-destructive Detection of Volatile Explosives

DTIC Science & Technology

2013-02-01

DTRA-TR-12-65 Manipulation of Molecular Quantum Wavepackets with Ultrashort Laser Pulses for Non-destructive Detection of Volatile Explosives ...Manipulation of Molecular Quantum Wavepackets with Ultrashort Laser Pulses for Non-destructive Detection of Volatile Explosives HDTRA1-09-1-0021 Valery...destructive detection of volatile explosives . Moshe Shapiro1, Valery Milner1 and Jun Ye2 1University of British Columbia, Vancouver, Canada 2JILA

Quantum molecular dynamics simulation of shock-wave experiments in aluminum

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

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

2014-06-14

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

Quantum Dot Enabled Molecular Sensing and Diagnostics

PubMed Central

Zhang, Yi; Wang, Tza-Huei

2012-01-01

Since its emergence, semiconductor nanoparticles known as quantum dots (QDs) have drawn considerable attention and have quickly extended their applicability to numerous fields within the life sciences. This is largely due to their unique optical properties such as high brightness and narrow emission band as well as other advantages over traditional organic fluorophores. New molecular sensing strategies based on QDs have been developed in pursuit of high sensitivity, high throughput, and multiplexing capabilities. For traditional biological applications, QDs have already begun to replace traditional organic fluorophores to serve as simple fluorescent reporters in immunoassays, microarrays, fluorescent imaging applications, and other assay platforms. In addition, smarter, more advanced QD probes such as quantum dot fluorescence resonance energy transfer (QD-FRET) sensors, quenching sensors, and barcoding systems are paving the way for highly-sensitive genetic and epigenetic detection of diseases, multiplexed identification of infectious pathogens, and tracking of intracellular drug and gene delivery. When combined with microfluidics and confocal fluorescence spectroscopy, the detection limit is further enhanced to single molecule level. Recently, investigations have revealed that QDs participate in series of new phenomena and exhibit interesting non-photoluminescent properties. Some of these new findings are now being incorporated into novel assays for gene copy number variation (CNV) studies and DNA methylation analysis with improved quantification resolution. Herein, we provide a comprehensive review on the latest developments of QD based molecular diagnostic platforms in which QD plays a versatile and essential role. PMID:22916072

Study of nuclear multifragmentation induced by ultrarelativistic μ-mesons in nuclear track emulsion

NASA Astrophysics Data System (ADS)

Artemenkov, D. A.; Bradnova, V.; Firu, E.; Kornegrutsa, N. K.; Haiduc, M.; Mamatkulov, K. Z.; Kattabekov, R. R.; Neagu, A.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.

2016-02-01

Exposures of test samples of nuclear track emulsion were analyzed. The formation of high-multiplicity nuclear stars was observed upon irradiating nuclear track emulsions with ultrarelativistic muons. Kinematical features studied in this exposure of nuclear track emulsions for events of the muon-induced splitting of carbon nuclei to three α-particles are indicative of the nuclear-diffraction interaction mechanism.

Quantum Dots for Molecular Diagnostics of Tumors

PubMed Central

Zdobnova, T.A.; Lebedenko, E.N.; Deyev, S.М.

2011-01-01

Semiconductor quantum dots (QDs) are a new class of fluorophores with unique physical and chemical properties, which allow to appreciably expand the possibilities for the current methods of fluorescent imaging and optical diagnostics. Here we discuss the prospects of QD application for molecular diagnostics of tumors ranging from cancer-specific marker detection on microplates to non-invasive tumor imagingin vivo. We also point out the essential problems that require resolution in order to clinically promote QD, and we indicate innovative approaches to oncology which are implementable using QD. PMID:22649672

Inelastic electron tunneling mediated by a molecular quantum rotator

NASA Astrophysics Data System (ADS)

Sugimoto, Toshiki; Kunisada, Yuji; Fukutani, Katsuyuki

2017-12-01

Inelastic electron tunneling (IET) accompanying nuclear motion is not only of fundamental physical interest but also has strong impacts on chemical and biological processes in nature. Although excitation of rotational motion plays an important role in enhancing electric conductance at a low bias, the mechanism of rotational excitation remains veiled. Here, we present a basic theoretical framework of IET that explicitly takes into consideration quantum angular momentum, focusing on a molecular H2 rotator trapped in a nanocavity between two metallic electrodes as a model system. It is shown that orientationally anisotropic electrode-rotator coupling is the origin of angular-momentum exchange between the electron and molecule; we found that the anisotropic coupling imposes rigorous selection rules in rotational excitation. In addition, rotational symmetry breaking induced by the anisotropic potential lifts the degeneracy of the energy level of the degenerated rotational state of the quantum rotator and tunes the threshold bias voltage that triggers rotational IET. Our theoretical results provide a paradigm for physical understanding of the rotational IET process and spectroscopy, as well as molecular-level design of electron-rotation coupling in nanoelectronics.

Solvent fluctuations and nuclear quantum effects modulate the molecular hyperpolarizability of water

NASA Astrophysics Data System (ADS)

Liang, Chungwen; Tocci, Gabriele; Wilkins, David M.; Grisafi, Andrea; Roke, Sylvie; Ceriotti, Michele

2017-07-01

Second-harmonic scattering (SHS) experiments provide a unique approach to probe noncentrosymmetric environments in aqueous media, from bulk solutions to interfaces, living cells, and tissue. A central assumption made in analyzing SHS experiments is that each molecule scatters light according to a constant molecular hyperpolarizability tensor β(2 ). Here, we investigate the dependence of the molecular hyperpolarizability of water on its environment and internal geometric distortions, in order to test the hypothesis of constant β(2 ). We use quantum chemistry calculations of the hyperpolarizability of a molecule embedded in point-charge environments obtained from simulations of bulk water. We demonstrate that both the heterogeneity of the solvent configurations and the quantum mechanical fluctuations of the molecular geometry introduce large variations in the nonlinear optical response of water. This finding has the potential to change the way SHS experiments are interpreted: In particular, isotopic differences between H2O and D2O could explain recent SHS observations. Finally, we show that a machine-learning framework can predict accurately the fluctuations of the molecular hyperpolarizability. This model accounts for the microscopic inhomogeneity of the solvent and represents a step towards quantitative modeling of SHS experiments.

Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

PubMed

Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

2012-11-28

Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

NASA Astrophysics Data System (ADS)

Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

2016-12-01

Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

Carboxylate-based molecular magnet: One path toward achieving stable quantum correlations at room temperature

DOE PAGES

Cruz, C.; Soares-Pinto, D. O.; Brandão, P.; ...

2016-03-07

The control of quantum correlations in solid-state systems by means of material engineering is a broad avenue to be explored, since it makes possible steps toward the limits of quantum mechanics and the design of novel materials with applications on emerging quantum technologies. This letter explores the potential of molecular magnets to be prototypes of materials for quantum information technology in this context. More precisely, we engineered a material and from its geometric quantum discord we found significant quantum correlations up to 9540 K (even without entanglement); and, a pure singlet state occupied up to around 80 K (above liquidmore » nitrogen temperature), additionally. Our results could only be achieved due to the carboxylate group promoting a metal-to-metal huge magnetic interaction.« less

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.

Spatiotemporal distributions of pair production and cascade in solid targets irradiated by ultra-relativistic lasers with different polarizations

NASA Astrophysics Data System (ADS)

Yuan, T.; Yu, J. Y.; Liu, W. Y.; Weng, S. M.; Yuan, X. H.; Luo, W.; Chen, M.; Sheng, Z. M.; Zhang, J.

2018-06-01

Two-dimensional particle-in-cell simulations have been performed to study electron-positron pair production and cascade development in single ultra-relativistic laser interaction with solid targets. The spatiotemporal distributions of particles produced via QED processes are illustrated and their dependence on laser polarizations is investigated. The evolution of particle generation displays clear QED cascade characters. Studies show that although a circularly polarized laser delays the QED process due to the effective ion acceleration, it can reduce the target heating and confine high-energy charged particles, which leads to deeper QED cascade order and denser pair plasma production than linearly polarized lasers. These findings may benefit the understanding of the coming experimental studies of ultra-relativistic laser target interaction in the QED dominated regime.

Cyto-molecular Tuning of Quantum Dots

NASA Astrophysics Data System (ADS)

Lee, Bong; Suresh, Sindhuja; Ekpenyong, Andrew

Quantum dots (QDs) are semiconductor nanoparticles composed of groups II-VI or III-V elements, with physical dimensions smaller than the exciton Bohr radius, and between 1-10 nm. Their applications and promising myriad applications in photovoltaic cells, biomedical imaging, targeted drug delivery, quantum computing, etc, have led to much research on their interactions with other systems. For biological systems, research has focused on biocompatibility and cytotoxicity of QDs in the context of imaging/therapy. However, there is a paucity of work on how biological systems might be used to tune QDs. Here, we hypothesize that the photo-electronic properties of QDs can be tuned by biological macromolecules following controlled changes in cellular activities. Using CdSe/ZnS core-shell QDs, we perform spectroscopic analysis of optically excited colloidal QDs with and without promyelocytic HL60 cells. Preliminary results show shifts in the emission spectra of the colloidal dispersions with and without cells. We will present results for activated HL60-derived cells where specific macromolecules produced by these cells perturb the electric dipole moments of the excited QDs and the associated electric fields, in ways that constitute what we describe as cyto-molecular tuning. Startup funds from the College of Arts and Sciences, Creighton University (to AEE).

Anharmonic and Quantum Fluctuations in Molecular Crystals from Ab Initio Simulations

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

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

Quantum mechanical force fields for condensed phase molecular simulations

NASA Astrophysics Data System (ADS)

Giese, Timothy J.; York, Darrin M.

2017-09-01

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

Quantum nuclear effects in water using centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kondratyuk, N. D.; Norman, G. E.; Stegailov, V. V.

2018-01-01

The quantum nuclear effects are studied in water using the method of centroid molecular dynamics (CMD). The aim is the calibration of CMD implementation in LAMMPS. The calculated intramolecular energy, atoms gyration radii and radial distribution functions are shown in comparison with previous works. The work is assumed to be the step toward to solution of the discrepancy between the simulation results and the experimental data of liquid n-alkane properties in our previous works.

Quantum Chemically Estimated Abraham Solute Parameters Using Multiple Solvent-Water Partition Coefficients and Molecular Polarizability.

PubMed

Liang, Yuzhen; Xiong, Ruichang; Sandler, Stanley I; Di Toro, Dominic M

2017-09-05

Polyparameter Linear Free Energy Relationships (pp-LFERs), also called Linear Solvation Energy Relationships (LSERs), are used to predict many environmentally significant properties of chemicals. A method is presented for computing the necessary chemical parameters, the Abraham parameters (AP), used by many pp-LFERs. It employs quantum chemical calculations and uses only the chemical's molecular structure. The method computes the Abraham E parameter using density functional theory computed molecular polarizability and the Clausius-Mossotti equation relating the index refraction to the molecular polarizability, estimates the Abraham V as the COSMO calculated molecular volume, and computes the remaining AP S, A, and B jointly with a multiple linear regression using sixty-five solvent-water partition coefficients computed using the quantum mechanical COSMO-SAC solvation model. These solute parameters, referred to as Quantum Chemically estimated Abraham Parameters (QCAP), are further adjusted by fitting to experimentally based APs using QCAP parameters as the independent variables so that they are compatible with existing Abraham pp-LFERs. QCAP and adjusted QCAP for 1827 neutral chemicals are included. For 24 solvent-water systems including octanol-water, predicted log solvent-water partition coefficients using adjusted QCAP have the smallest root-mean-square errors (RMSEs, 0.314-0.602) compared to predictions made using APs estimated using the molecular fragment based method ABSOLV (0.45-0.716). For munition and munition-like compounds, adjusted QCAP has much lower RMSE (0.860) than does ABSOLV (4.45) which essentially fails for these compounds.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

DNA-programmed dynamic assembly of quantum dots for molecular computation.

PubMed

He, Xuewen; Li, Zhi; Chen, Muzi; Ma, Nan

2014-12-22

Despite the widespread use of quantum dots (QDs) for biosensing and bioimaging, QD-based bio-interfaceable and reconfigurable molecular computing systems have not yet been realized. DNA-programmed dynamic assembly of multi-color QDs is presented for the construction of a new class of fluorescence resonance energy transfer (FRET)-based QD computing systems. A complete set of seven elementary logic gates (OR, AND, NOR, NAND, INH, XOR, XNOR) are realized using a series of binary and ternary QD complexes operated by strand displacement reactions. The integration of different logic gates into a half-adder circuit for molecular computation is also demonstrated. This strategy is quite versatile and straightforward for logical operations and would pave the way for QD-biocomputing-based intelligent molecular diagnostics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Kremer, Kurt; Potestio, Raffaello; Tuckerman, Mark E.

2017-12-01

Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.

Effect of diatomic molecular properties on binary laser pulse optimizations of quantum gate operations.

PubMed

Zaari, Ryan R; Brown, Alex

2011-07-28

The importance of the ro-vibrational state energies on the ability to produce high fidelity binary shaped laser pulses for quantum logic gates is investigated. The single frequency 2-qubit ACNOT(1) and double frequency 2-qubit NOT(2) quantum gates are used as test cases to examine this behaviour. A range of diatomics is sampled. The laser pulses are optimized using a genetic algorithm for binary (two amplitude and two phase parameter) variation on a discretized frequency spectrum. The resulting trends in the fidelities were attributed to the intrinsic molecular properties and not the choice of method: a discretized frequency spectrum with genetic algorithm optimization. This is verified by using other common laser pulse optimization methods (including iterative optimal control theory), which result in the same qualitative trends in fidelity. The results differ from other studies that used vibrational state energies only. Moreover, appropriate choice of diatomic (relative ro-vibrational state arrangement) is critical for producing high fidelity optimized quantum logic gates. It is also suggested that global phase alignment imposes a significant restriction on obtaining high fidelity regions within the parameter search space. Overall, this indicates a complexity in the ability to provide appropriate binary laser pulse control of diatomics for molecular quantum computing. © 2011 American Institute of Physics

Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti- resonances

NASA Astrophysics Data System (ADS)

Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevinçli, Hâldun; Gutierrez, Rafael; Cuniberti, Gianaurelio

2013-03-01

Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method to predict the appearance of quantum interference, Fano resonances or anti- resonances, and its position in the conductance spectrum by introducing a simple graphical representation (parabolic model). Using it we can easily visualize the relation between the key electronic parameters and the positions of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules and the coupling between side group and main conduction channel from transmission spectra.

Feedback quantum control of molecular electronic population transfer

NASA Astrophysics Data System (ADS)

Bardeen, Christopher J.; Yakovlev, Vladislav V.; Wilson, Kent R.; Carpenter, Scott D.; Weber, Peter M.; Warren, Warren S.

1997-11-01

Feedback quantum control, where the sample `teaches' a computer-controlled arbitrary lightform generator to find the optimal light field, is experimentally demonstrated for a molecular system. Femtosecond pulses tailored by a computer-controlled acousto-optic pulse shaper excite fluorescence from laser dye molecules in solution. Fluorescence and laser power are monitored, and the computer uses the experimental data and a genetic algorithm to optimize population transfer from ground to first excited state. Both efficiency (the ratio of excited state population to laser energy) and effectiveness (total excited state population) are optimized. Potential use as an `automated theory tester' is discussed.

Suppression of quantum phase interference in the molecular magnet Fe8 with dipolar-dipolar interaction

NASA Astrophysics Data System (ADS)

Chen, Zhi-De; Liang, J.-Q.; Shen, Shun-Qing

2002-09-01

Renormalized tunnel splitting with a finite distribution in the biaxial spin model for molecular magnets is obtained by taking into account the dipolar interaction of enviromental spins. Oscillation of the resonant tunnel splitting with a transverse magnetic field along the hard axis is smeared by the finite distribution, which subsequently affects the quantum steps of the hysteresis curve evaluated in terms of the modified Landau-Zener model of spin flipping induced by the sweeping field. We conclude that the dipolar-dipolar interaction drives decoherence of quantum tunneling in the molecular magnet Fe8, which explains why the quenching points of tunnel splitting between odd and even resonant tunneling predicted theoretically were not observed experimentally.

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

Molecular dispersion spectroscopy for chemical sensing using chirped mid-infrared quantum cascade laser.

PubMed

Wysocki, Gerard; Weidmann, Damien

2010-12-06

A spectroscopic method of molecular detection based on dispersion measurements using a frequency-chirped laser source is presented. An infrared quantum cascade laser emitting around 1912 cm(-1) is used as a tunable spectroscopic source to measure dispersion that occurs in the vicinity of molecular ro-vibrational transitions. The sample under study is a mixture of nitric oxide in dry nitrogen. Two experimental configurations based on a coherent detection scheme are investigated and discussed. The theoretical models, which describe the observed spectral signals, are developed and verified experimentally. The method is particularly relevant to optical sensing based on mid-infrared quantum cascade lasers as the high chirp rates available with those sources can significantly enhance the magnitude of the measured dispersion signals. The method relies on heterodyne beatnote frequency measurements and shows high immunity to variations in the optical power received by the photodetector.

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

PubMed

Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

2016-10-11

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

Coupling molecular spin centers to microwave resonators: steps towards the implementation of molecular qubits for hybrid quantum circuits

NASA Astrophysics Data System (ADS)

Bonizzoni, Claudio; Ghirri, Alberto; Affronte, Marco

Hybrid spin-photons quantum bits can be obtained under strong coupling regime between microwave photons and a spin ensemble, where coherent exchange of photons is realized. Molecular spins systems, thanks to their tailorable magnetic properties, are retained promising candidates for hybrid qubits. We present an experimental study of the coupling regimes between a high critical temperature YBCO superconducting resonator and different molecular spin ensembles. Three mononuclear compounds, (PPh4)2[Cu(mnt)2], [ErPc2]-TBA+ , Dy(trensal) and two organic radicals, DPPH and PyBTM, are studied. Strong coupling is found in radicals thanks to exchange narrowing. Possible strategies to achieve strong coupling with mononuclear compounds are discussed, and several hints in the design of molecular spins are given.

Abrupt acceleration of a 'cold' ultrarelativistic wind from the Crab pulsar.

PubMed

Aharonian, F A; Bogovalov, S V; Khangulyan, D

2012-02-15

Pulsars are thought to eject electron-positron winds that energize the surrounding environment, with the formation of a pulsar wind nebula. The pulsar wind originates close to the light cylinder, the surface at which the pulsar co-rotation velocity equals the speed of light, and carries away much of the rotational energy lost by the pulsar. Initially the wind is dominated by electromagnetic energy (Poynting flux) but later this is converted to the kinetic energy of bulk motion. It is unclear exactly where this takes place and to what speed the wind is accelerated. Although some preferred models imply a gradual acceleration over the entire distance from the magnetosphere to the point at which the wind terminates, a rapid acceleration close to the light cylinder cannot be excluded. Here we report that the recent observations of pulsed, very high-energy γ-ray emission from the Crab pulsar are explained by the presence of a cold (in the sense of the low energy of the electrons in the frame of the moving plasma) ultrarelativistic wind dominated by kinetic energy. The conversion of the Poynting flux to kinetic energy should take place abruptly in the narrow cylindrical zone of radius between 20 and 50 light-cylinder radii centred on the axis of rotation of the pulsar, and should accelerate the wind to a Lorentz factor of (0.5-1.0) × 10(6). Although the ultrarelativistic nature of the wind does support the general model of pulsars, the requirement of the very high acceleration of the wind in a narrow zone not far from the light cylinder challenges current models.

Molecular quantum control landscapes in von Neumann time-frequency phase space

NASA Astrophysics Data System (ADS)

Ruetzel, Stefan; Stolzenberger, Christoph; Fechner, Susanne; Dimler, Frank; Brixner, Tobias; Tannor, David J.

2010-10-01

Recently we introduced the von Neumann representation as a joint time-frequency description for femtosecond laser pulses and suggested its use as a basis for pulse shaping experiments. Here we use the von Neumann basis to represent multidimensional molecular control landscapes, providing insight into the molecular dynamics. We present three kinds of time-frequency phase space scanning procedures based on the von Neumann formalism: variation of intensity, time-frequency phase space position, and/or the relative phase of single subpulses. The shaped pulses produced are characterized via Fourier-transform spectral interferometry. Quantum control is demonstrated on the laser dye IR140 elucidating a time-frequency pump-dump mechanism.

Molecular quantum control landscapes in von Neumann time-frequency phase space.

PubMed

Ruetzel, Stefan; Stolzenberger, Christoph; Fechner, Susanne; Dimler, Frank; Brixner, Tobias; Tannor, David J

2010-10-28

Recently we introduced the von Neumann representation as a joint time-frequency description for femtosecond laser pulses and suggested its use as a basis for pulse shaping experiments. Here we use the von Neumann basis to represent multidimensional molecular control landscapes, providing insight into the molecular dynamics. We present three kinds of time-frequency phase space scanning procedures based on the von Neumann formalism: variation of intensity, time-frequency phase space position, and/or the relative phase of single subpulses. The shaped pulses produced are characterized via Fourier-transform spectral interferometry. Quantum control is demonstrated on the laser dye IR140 elucidating a time-frequency pump-dump mechanism.

Molecular profiling of single cancer cells and clinical tissue specimens with semiconductor quantum dots

PubMed Central

Xing, Yun; Smith, Andrew M; Agrawal, Amit; Ruan, Gang; Nie, Shuming

2006-01-01

Semiconductor quantum dots (QDs) are a new class of fluorescent labels with broad applications in biomedical imaging, disease diagnostics, and molecular and cell biology. In comparison with organic dyes and fluorescent proteins, quantum dots have unique optical and electronic properties such as size-tunable light emission, improved signal brightness, resistance against photobleaching, and simultaneous excitation of multiple fluorescence colors. Recent advances have led to multifunctional nanoparticle probes that are highly bright and stable under complex in vitro and in vivo conditions. New designs involve encapsulating luminescent QDs with amphiphilic block copolymers, and linking the polymer coating to tumor-targeting ligands and drug-delivery functionalities. These improved QDs have opened new possibilities for real-time imaging and tracking of molecular targets in living cells, for multiplexed analysis of biomolecular markers in clinical tissue specimens, and for ultrasensitive imaging of malignant tumors in living animal models. In this article, we briefly discuss recent developments in bioaffinity QD probes and their applications in molecular profiling of individual cancer cells and clinical tissue specimens. PMID:17722280

Exploring warm dense matter using quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Clérouin, J.; Mazevet, S.

2006-06-01

For dense plasmas produced in shock experiments, the influence of the media on the isolated atomic properties can no longer be treated as a perturbation and conventional atomic physics approaches usually fail. Recently, quantum molecular dynamics (QMD) has been used to successfully predict static, dynamical and optical properties in this regime within the framework of a first principle method. In this short report, we illustrate the usefulness of the method for dense plasmas with a few selected examples: the equation of state of liquid deuterium, the electrical properties of expanded metals, the optical properties of shocked insulators, and the interaction of femto-second lasers with gold thin films.

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.

Passivation Using Molecular Halides Increases Quantum Dot Solar Cell Performance.

PubMed

Lan, Xinzheng; Voznyy, Oleksandr; Kiani, Amirreza; García de Arquer, F Pelayo; Abbas, Abdullah Saud; Kim, Gi-Hwan; Liu, Mengxia; Yang, Zhenyu; Walters, Grant; Xu, Jixian; Yuan, Mingjian; Ning, Zhijun; Fan, Fengjia; Kanjanaboos, Pongsakorn; Kramer, Illan; Zhitomirsky, David; Lee, Philip; Perelgut, Alexander; Hoogland, Sjoerd; Sargent, Edward H

2016-01-13

A solution-based passivation scheme is developed featuring the use of molecular iodine and PbS colloidal quantum dots (CQDs). The improved passivation translates into a longer carrier diffusion length in the solid film. This allows thicker solar-cell devices to be built while preserving efficient charge collection, leading to a certified power conversion efficiency of 9.9%, which is a new record in CQD solar cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamical evolution of spectator systems produced in ultrarelativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Mazurek, K.; Szczurek, A.; Schmitt, C.; Nadtochy, P. N.

2018-02-01

In peripheral heavy-ion collisions at ultrarelativistic energies, usually only parts of the colliding nuclei effectively interact with each other. In the overlapping zone, a fireball or quark-gluon plasma is produced. The excitation energy of the heavy remnant can range from a few tens to several hundreds of MeV, depending on the impact parameter. The decay of these excited spectators is investigated in this work for the first time within a dynamical approach based on the multidimensional stochastic Langevin equation. The potential of this exploratory work to understand the connection between electromagnetic fields generated by the heavy spectators and measured pion distributions is discussed.

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

PubMed

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

2018-06-13

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

Molecular Dynamics Simulation of the Thermophysical Properties of Quantum Liquid Helium Using the Feynman-Hibbs Potential

NASA Astrophysics Data System (ADS)

Liu, J.; Lu, W. Q.

2010-03-01

This paper presents the detailed MD simulation on the properties including the thermal conductivities and viscosities of the quantum fluid helium at different state points. The molecular interactions are represented by the Lennard-Jones pair potentials supplemented by quantum corrections following the Feynman-Hibbs approach and the properties are calculated using the Green-Kubo equations. A comparison is made among the numerical results using LJ and QFH potentials and the existing database and shows that the LJ model is not quantitatively correct for the supercritical liquid helium, thereby the quantum effect must be taken into account when the quantum fluid helium is studied. The comparison of the thermal conductivity is also made as a function of temperatures and pressure and the results show quantum effect correction is an efficient tool to get the thermal conductivities.

On the maximum energy of shock-accelerated cosmic rays at ultra-relativistic shocks

NASA Astrophysics Data System (ADS)

Reville, B.; Bell, A. R.

2014-04-01

The maximum energy to which cosmic rays can be accelerated at weakly magnetised ultra-relativistic shocks is investigated. We demonstrate that for such shocks, in which the scattering of energetic particles is mediated exclusively by ion skin-depth scale structures, as might be expected for a Weibel-mediated shock, there is an intrinsic limit on the maximum energy to which particles can be accelerated. This maximum energy is determined from the requirement that particles must be isotropized in the downstream plasma frame before the mean field transports them far downstream, and falls considerably short of what is required to produce ultra-high-energy cosmic rays. To circumvent this limit, a highly disorganized field is required on larger scales. The growth of cosmic ray-induced instabilities on wavelengths much longer than the ion-plasma skin depth, both upstream and downstream of the shock, is considered. While these instabilities may play an important role in magnetic field amplification at relativistic shocks, on scales comparable to the gyroradius of the most energetic particles, the calculated growth rates have insufficient time to modify the scattering. Since strong modification is a necessary condition for particles in the downstream region to re-cross the shock, in the absence of an alternative scattering mechanism, these results imply that acceleration to higher energies is ruled out. If weakly magnetized ultra-relativistic shocks are disfavoured as high-energy particle accelerators in general, the search for potential sources of ultra-high-energy cosmic rays can be narrowed.

Current rectification by self-assembled molecular quantum dots from first principles

NASA Astrophysics Data System (ADS)

Larade, Brian; Bratkovsky, Alexander

2003-03-01

We present results of first-principles calculations of the current rectification by self-assembled molecular quantum dots. Molecules of that kind should be synthesized with a central conjugated (narrow band-gap) part, and two peripheral saturated (wide band-gap) barrier groups of substantially different lengths L1 and L_2. The peripheral groups must end with chemical Â"anchorÂ" groups, enabling attachment of the molecule to the electrodes. In such molecules, if they are not longer than about 2-3 nm, the electron transport is likely to proceed by resonant tunneling through molecular orbitals (MO) centered on the conjugated part of the molecule (Â"quantum dotÂ") [1,2]. Generally, either LUMO (lowest unoccupied MO) or HOMO (highest occupied MO) will be most transparent to the tunneling electrons because of their different coupling to electrodes. We have studied (i) single benzene ring C6H6 [2] and (ii) naphthalene C10H8, separated from gold electrodes by alkane chains of different lengths with the use of the non-equilibrium Green's function method and self-consistent density-functional theory. The results show significant changes in electron density and potential distribution in the vicinity of molecule-electrode contact. In the case of a naphthalene quantum dot, separated from electrodes by asymmetric alkane groups (CH2)2 and (CH2)6, the I-V curve shows current rectification on the order of ˜ 10^2. [1] A.M. Bratkovsky and P.E. Kornilovitch, Phys. Rev. B (2002), to be published. [2] P. E. Kornilovitch, A.M. Bratkovsky, and R.S. Williams, Phys. Rev. B 66, 165436 (2002).

Tuning of quantum entanglement in molecular quantum cellular automata based on mixed-valence tetrameric units.

PubMed

Palii, Andrew; Tsukerblat, Boris

2016-10-25

In this article we consider two coupled tetrameric mixed-valence (MV) units accommodating electron pairs, which play the role of cells in molecular quantum cellular automata. It is supposed that the Coulombic interaction between instantly localized electrons within the cell markedly inhibits the transfer processes between the redox centers. Under this condition, as well as due to the vibronic localization of the electron pair, the cell can encode binary information, which is controlled by neighboring cells. We show that under certain conditions the two low-lying vibronic spin levels of the cell (ground and first excited states) can be regarded as originating from an effective spin-spin interaction. This is shown to depend on the internal parameters of the cell as well as on the induced polarization. Within this simplified two-level picture we evaluate the quantum entanglement in the system represented by the two electrons in the cell and show how the entanglement within the cell and concurrence can be controlled via polarization of the neighboring cells and temperature.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Explaining the Diverse Response of the Ultra-relativistic Van Allen Radiation Belt to Solar Wind Forcing

NASA Astrophysics Data System (ADS)

Mann, I. R.; Ozeke, L.; Murphy, K. R.; Claudepierre, S. G.; Rae, J.; Milling, D. K.; Kale, A.; Baker, D. N.

2017-12-01

The NASA Van Allen Probes have opened a new window on the dynamics of ultra-relativistic electrons in the Van Allen radiation belts. Under different solar wind forcing the outer belt is seen to respond in a variety of apparently diverse and sometimes remarkable ways. For example, sometimes a third radiation belt is carved out (e.g., September 2012), or the belts can remain depleted for 10 days or more (September 2014). More usually there is a sequential response of a strong and sometimes rapid depletion followed by a re-energization, the latter increasing outer belt electron flux by orders of magnitude on hour timescales during some of the strongest storms of this solar cycle (e.g., March 2013, March 2015). Such dynamics also appear to be often bounded at low-L by an apparently impenetrable barrier at L 2.8 through which ultra-relativistic electrons do not penetrate. Many studies in the Van Allen Probes era have sought explanations for these apparently diverse features, often incorporating the effects from multiple plasma waves. In contrast, we show how this apparently diverse behaviour can instead be explained by one dominant process: ULF wave radial transport. Once ULF wave transport rates are accurately specified by observations, and coupled to the dynamical variation of the outer boundary condition at the edge of the outer belt, the observed diverse responses can all be explained. However, in order to get good agreement with observations, the modeling reveals the importance of still currently unexplained very fast loss in the main phase which results in an almost total extinction of the belts and decouples pre- and post-storm ultra-relativistic electron flux on hour timescales. Similarly, varying plasmasheet source populations are seen to be of critical importance such that near-tail dynamics play a crucial role in Van Allen belt dynamics. Nonetheless, simple models incorporating accurate transport rates derived directly from ULF wave measurements are shown to

Coherent coupling between Vanadyl Phthalocyanine spin ensemble and microwave photons: towards integration of molecular spin qubits into quantum circuits.

PubMed

Bonizzoni, C; Ghirri, A; Atzori, M; Sorace, L; Sessoli, R; Affronte, M

2017-10-12

Electron spins are ideal two-level systems that may couple with microwave photons so that, under specific conditions, coherent spin-photon states can be realized. This represents a fundamental step for the transfer and the manipulation of quantum information. Along with spin impurities in solids, molecular spins in concentrated phases have recently shown coherent dynamics under microwave stimuli. Here we show that it is possible to obtain high cooperativity regime between a molecular Vanadyl Phthalocyanine (VOPc) spin ensemble and a high quality factor superconducting YBa 2 Cu 3 O 7 (YBCO) coplanar resonator at 0.5 K. This demonstrates that molecular spin centers can be successfully integrated in hybrid quantum devices.

Molecular-beam epitaxy of 7-8 μm range quantum-cascade laser heterostructures

NASA Astrophysics Data System (ADS)

Babichev, A. V.; Denisov, D. V.; Filimonov, A. V.; Nevedomsky, V. N.; Kurochkin, A. S.; Gladyshev, A. G.; Karachinsky, L. Ya; Sokolovskii, G. S.; Novikov, I. I.; Bousseksou, A.; Egorov, A. Yu

2017-11-01

The method of molecular beam epitaxy demonstrates the possibility to create high quality heterostructures of quantum cascade lasers in a spectral range of 7-8 μm containing 50 quantum cascades in an active region. Design based on the principle of two-phonon resonant scattering is used. X-ray diffraction and transmission electron microscopy experiments confirm high structural properties of the created heterostructures, e.g. the identity of the composition and thickness of epitaxial layers in all 50 cascades. Edge-emitting lasers based on the grown heterostructure demonstrate lasing with threshold current density of 2.8 kA/cm2 at a temperature of 78 K.

A sensitive fluorescent nanosensor for chloramphenicol based on molecularly imprinted polymer-capped CdTe quantum dots.

PubMed

Amjadi, Mohammad; Jalili, Roghayeh; Manzoori, Jamshid L

2016-05-01

A novel fluorescent nanosensor using molecularly imprinted silica nanospheres embedded CdTe quantum dots (CdTe@SiO2 @MIP) was developed for detection and quantification of chloramphenicol (CAP). The imprinted sensor was prepared by synthesis of molecularly imprinting polymer (MIP) on the hydrophilic CdTe quantum dots via reverse microemulsion method using small amounts of solvents. The resulting CdTe@SiO2 @MIP nanoparticles were characterized by fluorescence, UV-vis absorption and FT-IR spectroscopy and transmission electron microscopy. They preserved 48% of fluorescence quantum yield of the parent quantum dots. CAP remarkably quenched the fluorescence of prepared CdTe@SiO2 @MIP, probably via electron transfer mechanism. Under the optimal conditions, the relative fluorescence intensity of CdTe@SiO2 @MIP decreased with increasing CAP by a Stern-Volmer type equation in the concentration range of 40-500 µg L(-1). The corresponding detection limit was 5.0 µg L(-1). The intra-day and inter-day values for the precision of the proposed method were all <4%. The developed sensor had a good selectivity and was applied to determine CAP in spiked human and bovine serum and milk samples with satisfactory results. Copyright © 2015 John Wiley & Sons, Ltd.

The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Belova, Natalya V.; Girichev, Georgiy V.; Kotova, Vitaliya E.; Korolkova, Kseniya A.; Trang, Nguyen Hoang

2018-03-01

The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in CS molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

QSAR models based on quantum topological molecular similarity.

PubMed

Popelier, P L A; Smith, P J

2006-07-01

A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

Observation of Global Hyperon Polarization in Ultrarelativistic Heavy-Ion Collisions

NASA Astrophysics Data System (ADS)

Upsal, Isaac; STAR Collaboration

2017-11-01

Collisions between heavy nuclei at ultra-relativistic energies form a color-deconfined state of matter known as the quark-gluon plasma. This state is well described by hydrodynamics, and non-central collisions are expected to produce a fluid characterized by strong vorticity in the presence of strong external magnetic fields. The STAR Collaboration at Brookhaven National Laboratory's Relativistic Heavy Ion Collider (RHIC) has measured collisions between gold nuclei at center of mass energies √{sNN} = 7.7- 200 GeV. We report the first observation of globally polarized Λ and Λ bar hyperons, aligned with the angular momentum of the colliding system. These measurements provide important information on partonic spin-orbit coupling, the vorticity of the quark-gluon plasma, and the magnetic field generated in the collision.

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

PubMed

Melkikh, Alexey V; Khrennikov, Andrei

2017-11-01

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

Compensation effects in molecular interactions and the quantum chemical le Chatelier principle.

PubMed

Mezey, Paul G

2015-05-28

Components of molecular interactions and various changes in the components of total energy changes during molecular processes typically exhibit some degrees of compensation. This may be as prominent as the over 90% compensation of the electronic energy and nuclear repulsion energy components of the total energy in some conformational changes. Some of these compensations are enhanced by solvent effects. For various arrangements of ions in a solvent, however, not only compensation but also a formal, mutual enhancement between the electronic energy and nuclear repulsion energy components of the total energy may also occur, when the tools of nuclear charge variation are applied to establish quantum chemically rigorous energy inequalities.

Vibrons in finite size molecular lattices: a route for high-fidelity quantum state transfer at room temperature.

PubMed

Pouthier, Vincent

2012-11-07

A communication protocol is proposed in which vibron-mediated quantum state transfer takes place in a molecular lattice. We consider two distant molecular groups grafted on each side of the lattice. These groups form two quantum computers where vibrational qubits are implemented and received. The lattice defines the communication channel along which a vibron delocalizes and interacts with a phonon bath. Using quasi-degenerate perturbation theory, vibron-phonon entanglement is taken into account through the effective Hamiltonian concept. A vibron is thus dressed by a virtual phonon cloud whereas a phonon is clothed by virtual vibronic transitions. It is shown that three quasi-degenerate dressed states define the relevant paths followed by a vibron to tunnel between the computers. When the coupling between the computers and the lattice is judiciously chosen, constructive interference takes place between these paths. Phonon-induced decoherence is minimized and a high-fidelity quantum state transfer occurs over a broad temperature range.

Molecular Orbitals of NO, NO[superscript+], and NO[superscript-]: A Computational Quantum Chemistry Experiment

ERIC Educational Resources Information Center

Orenha, Renato P.; Galembeck, Sérgio E.

2014-01-01

This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…

Quantum molecular dynamics simulations of dense matter

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

Collins, L.; Kress, J.; Troullier, N.

1997-12-31

The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB,more » which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.« less

Shear viscosity of an ultrarelativistic Boltzmann gas with isotropic inelastic scattering processes

NASA Astrophysics Data System (ADS)

El, A.; Lauciello, F.; Wesp, C.; Bouras, I.; Xu, Z.; Greiner, C.

2014-05-01

We derive an analytic expression for the shear viscosity of an ultra-relativistic gas in presence of both elastic 2→2 and inelastic 2↔3 processes with isotropic differential cross sections. The derivation is based on the entropy principle and Grad's approximation for the off-equilibrium distribution function. The obtained formula relates the shear viscosity coefficient η to the total cross sections σ22 and σ23 of the elastic resp. inelastic processes. The values of shear viscosity extracted using the Green-Kubo formula from kinetic transport calculations are shown to be in excellent agreement with the analytic results which demonstrates the validity of the derived formula.

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

PubMed

Tvaroška, Igor

2015-02-11

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

Molecular controlled of quantum nano systems

NASA Astrophysics Data System (ADS)

Paltiel, Yossi

2014-03-01

A century ago quantum mechanics created a conceptual revolution whose fruits are now seen in almost any aspect of our day-to-day life. Lasers, transistors and other solid state and optical devices represent the core technology of current computers, memory devices and communication systems. However, all these examples do not exploit fully the quantum revolution as they do not take advantage of the coherent wave-like properties of the quantum wave function. Controlled coherent system and devices at ambient temperatures are challenging to realize. We are developing a novel nano tool box with control coupling between the quantum states and the environment. This tool box that combines nano particles with organic molecules enables the integration of quantum properties with classical existing devices at ambient temperatures. The nano particles generate the quantum states while the organic molecules control the coupling and therefore the energy, charge, spin, or quasi particle transfer between the layers. Coherent effects at ambient temperatures can be measured in the strong coupling regime. In the talk I will present our nano tool box and show studies of charge transfer, spin transfer and energy transfer in the hybrid layers as well as collective transfer phenomena. These enable the realization of room temperature operating quantum electro optical devices. For example I will present in details, our recent development of a new type of chiral molecules based magnetless universal memory exploiting selective spin transfer.

Photoexcitation cascade and quantum-relativistic jet formation in graphene

NASA Astrophysics Data System (ADS)

Lewandowski, Cyprian; Levitov, Leonid

Interactions between ultra-relativistic particles can lead to striking behavior in which a high-energy particle creates showers of softer particles characterized by a collimated angular distribution aligned with the particle velocity. These showers, known as jets, are a generic phenomenon relevant for all quantum cascades of linearly dispersing particles. This talk will discuss jets formed upon photoexcitation in graphene, which due to its linear dispersion provides an appealing medium for exploring quantum-relativistic phenomena. We will study the cascade generated by carrier-carrier collisions in photon absorption, wherein a single photon creates an electron-hole (e-h) excitation that decays producing multiple near-collinear secondary e-h excitations. We will argue that the cascade can occur through an off-shell mechanism such that all the particles and holes involved reside outside the energy-momentum dispersion manifold, relieving the bottleneck arising in the on-shell process due to energy and momentum conservation. The characteristics of the jets such as the angular and energy distribution of the particles will be discussed. Photogenerated jets provide an interesting setting to investigate the carrier-carrier collision processes in graphene and other Dirac materials. We acknowledge support of the Center for Integrated Quantum Materials (CIQM) under NSF award DMR-1231319.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

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

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

Quantum dot-based molecular imaging of cancer cell growth using a clone formation assay.

PubMed

Geng, Xia-Fei; Fang, Min; Liu, Shao-Ping; Li, Yan

2016-10-01

This aim of the present study was to investigate clonal growth behavior and analyze the proliferation characteristics of cancer cells. The MCF‑7 human breast cancer cell line, SW480 human colon cancer cell line and SGC7901 human gastric cancer cell line were selected to investigate the morphology of cell clones. Quantum dot‑based molecular targeted imaging techniques (which stained pan‑cytokeratin in the cytoplasm green and Ki67 in the cell nucleus yellow or red) were used to investigate the clone formation rate, cell morphology, discrete tendency, and Ki67 expression and distribution in clones. From the cell clone formation assay, the MCF‑7, SW480 and SGC7901 cells were observed to form clones on days 6, 8 and 12 of cell culture, respectively. These three types of cells had heterogeneous morphology, large nuclear:cytoplasmic ratios, and conspicuous pathological mitotic features. The cells at the clone periphery formed multiple pseudopodium. In certain clones, cancer cells at the borderline were separated from the central cell clusters or presented a discrete tendency. With quantum dot‑based molecular targeted imaging techniques, cells with strong Ki67 expression were predominantly shown to be distributed at the clone periphery, or concentrated on one side of the clones. In conclusion, cancer cell clones showed asymmetric growth behavior, and Ki67 was widely expressed in clones of these three cell lines, with strong expression around the clones, or aggregated at one side. Cell clone formation assay based on quantum dots molecular imaging offered a novel method to study the proliferative features of cancer cells, thus providing a further insight into tumor biology.

Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach.

PubMed

Hyeon-Deuk, Kim; Ando, Koji

2014-05-07

Liquid para-hydrogen (p-H2) is a typical quantum liquid which exhibits strong nuclear quantum effects (NQEs) and thus anomalous static and dynamic properties. We propose a real-time simulation method of wave packet (WP) molecular dynamics (MD) based on non-empirical intra- and inter-molecular interactions of non-spherical hydrogen molecules, and apply it to condensed-phase p-H2. The NQEs, such as WP delocalization and zero-point energy, are taken into account without perturbative expansion of prepared model potential functions but with explicit interactions between nuclear and electron WPs. The developed MD simulation for 100 ps with 1200 hydrogen molecules is realized at feasible computational cost, by which basic experimental properties of p-H2 liquid such as radial distribution functions, self-diffusion coefficients, and shear viscosities are all well reproduced.

QM2017: Status and Key open Questions in Ultra-Relativistic Heavy-Ion Physics

NASA Astrophysics Data System (ADS)

Schukraft, Jurgen

2017-11-01

Almost exactly 3 decades ago, in the fall of 1986, the era of experimental ultra-relativistic E / m ≫ 1) heavy ion physics started simultaneously at the SPS at CERN and the AGS at Brookhaven with first beams of light Oxygen ions at fixed target energies of 200 GeV/A and 14.6 GeV/A, respectively. The event was announced by CERN [CERN's subatomic particle accelerators: Set up world-record in energy and break new ground for physics (CERN-PR-86-11-EN) (1986) 4 p, issued on 29 September 1986. URL (http://cds.cern.ch/record/855571)

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

PubMed

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

2013-08-28

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

Towards quantum chemistry on a quantum computer.

PubMed

Lanyon, B P; Whitfield, J D; Gillett, G G; Goggin, M E; Almeida, M P; Kassal, I; Biamonte, J D; Mohseni, M; Powell, B J; Barbieri, M; Aspuru-Guzik, A; White, A G

2010-02-01

Exact first-principles calculations of molecular properties are currently intractable because their computational cost grows exponentially with both the number of atoms and basis set size. A solution is to move to a radically different model of computing by building a quantum computer, which is a device that uses quantum systems themselves to store and process data. Here we report the application of the latest photonic quantum computer technology to calculate properties of the smallest molecular system: the hydrogen molecule in a minimal basis. We calculate the complete energy spectrum to 20 bits of precision and discuss how the technique can be expanded to solve large-scale chemical problems that lie beyond the reach of modern supercomputers. These results represent an early practical step toward a powerful tool with a broad range of quantum-chemical applications.

A molecular-field approximation for quantum crystals. Ph.D. Thesis; [considering ground state properties

NASA Technical Reports Server (NTRS)

Danilowicz, R.

1973-01-01

Ground-state properties of quantum crystals have received considerable attention from both theorists and experimentalists. The theoretical results have varied widely with the Monte Carlo calculations being the most successful. The molecular field approximation yields ground-state properties which agree closely with the Monte Carlo results. This approach evaluates the dynamical behavior of each pair of molecules in the molecular field of the other N-2 molecules. In addition to predicting ground-state properties that agree well with experiment, this approach yields data on the relative importance of interactions of different nearest neighbor pairs.

Simulation with quantum mechanics/molecular mechanics for drug discovery.

PubMed

Barbault, Florent; Maurel, François

2015-10-01

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

Simulation with quantum mechanics/molecular mechanics for drug discovery.

PubMed

Barbault, Florent; Maurel, François

2015-08-08

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

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

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

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

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.

Molecularly Engineered Organic-Inorganic Hybrid Perovskite with Multiple Quantum Well Structure for Multicolored Light-Emitting Diodes

PubMed Central

Hu, Hongwei; Salim, Teddy; Chen, Bingbing; Lam, Yeng Ming

2016-01-01

Organic-inorganic hybrid perovskites have the potential to be used as a new class of emitters with tunable emission, high color purity and good ease of fabrication. Recent studies have so far been focused on three-dimensional (3D) perovskites, such as CH3NH3PbBr3 and CH3NH3PbI3 for green and infrared emission. Here, we explore a new series of hybrid perovskite emitters with a general formula of (C4H9NH3)2(CH3NH3)n−1PbnI3n+1 (where n = 1, 2, 3), which possesses a multiple quantum well structure. The quantum well thickness of these materials is adjustable through simple molecular engineering which results in a continuously tunable bandgap and emission spectra. Deep saturated red emission was obtained with a peak external quantum efficiency of 2.29% and a maximum luminance of 214 cd/m2. Green and blue LEDs were also demonstrated through halogen substitutions in these hybrid perovskites. We expect these results to open up the way towards high performance perovskite LEDs through molecular-structure engineering of these perovskite emitters. PMID:27633084

Electrically Tunable g Factors in Quantum Dot Molecular Spin States

DTIC Science & Technology

2006-11-10

Electrically Tunable g Factors in Quantum Dot Molecular Spin States M. F. Doty,1,* M. Scheibner,1 I. V. Ponomarev,1 E. A. Stinaff,1 A. S . Bracker,1 V...L. Korenev ,2 T. L. Reinecke,1 and D. Gammon1 1Naval Research Laboratory, Washington, D.C. 20375, USA 2A.F. Ioffe Physical Technical Institute, St...on the applied electric field (F). PRL 97, 197202 (2006) P H Y S I C A L R E V I E W L E T T E R S week ending 10 NOVEMBER 2006 0031-9007=06=97(19

Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach

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

Hyeon-Deuk, Kim, E-mail: kim@kuchem.kyoto-u.ac.jp; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012; Ando, Koji

2014-05-07

Liquid para-hydrogen (p-H{sub 2}) is a typical quantum liquid which exhibits strong nuclear quantum effects (NQEs) and thus anomalous static and dynamic properties. We propose a real-time simulation method of wave packet (WP) molecular dynamics (MD) based on non-empirical intra- and inter-molecular interactions of non-spherical hydrogen molecules, and apply it to condensed-phase p-H{sub 2}. The NQEs, such as WP delocalization and zero-point energy, are taken into account without perturbative expansion of prepared model potential functions but with explicit interactions between nuclear and electron WPs. The developed MD simulation for 100 ps with 1200 hydrogen molecules is realized at feasible computationalmore » cost, by which basic experimental properties of p-H{sub 2} liquid such as radial distribution functions, self-diffusion coefficients, and shear viscosities are all well reproduced.« less

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

PubMed

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

2011-06-23

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

Optical characteristics of the nanoparticle coupled to a quantum molecular aggregate

NASA Astrophysics Data System (ADS)

Ropakova, I. Yu.; Zvyagin, A. A.

2017-11-01

Optical characteristics of a single nanoparticle, coupled to the one-dimensional quantum molecular aggregate is studied. Depending on the values of the coupling of the particle and its own frequency, with respect to the own frequency of the aggregated molecules, and the strength of the aggregation, the dynamical relative permittivity of the nanoparticle manifests the contribution from the exciton band, or/and the ones from the local level(s) caused by the particle. The refractive index and the extinction coefficient of the nanoparticle is also calculated.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE PAGES

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

2018-03-22

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

NASA Astrophysics Data System (ADS)

Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

2018-05-01

One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

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

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

A modular design of molecular qubits to implement universal quantum gates

PubMed Central

Ferrando-Soria, Jesús; Moreno Pineda, Eufemio; Chiesa, Alessandro; Fernandez, Antonio; Magee, Samantha A.; Carretta, Stefano; Santini, Paolo; Vitorica-Yrezabal, Iñigo J.; Tuna, Floriana; Timco, Grigore A.; McInnes, Eric J.L.; Winpenny, Richard E.P.

2016-01-01

The physical implementation of quantum information processing relies on individual modules—qubits—and operations that modify such modules either individually or in groups—quantum gates. Two examples of gates that entangle pairs of qubits are the controlled NOT-gate (CNOT) gate, which flips the state of one qubit depending on the state of another, and the gate that brings a two-qubit product state into a superposition involving partially swapping the qubit states. Here we show that through supramolecular chemistry a single simple module, molecular {Cr7Ni} rings, which act as the qubits, can be assembled into structures suitable for either the CNOT or gate by choice of linker, and we characterize these structures by electron spin resonance spectroscopy. We introduce two schemes for implementing such gates with these supramolecular assemblies and perform detailed simulations, based on the measured parameters including decoherence, to demonstrate how the gates would operate. PMID:27109358

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

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

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

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

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

None, None

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

CheckDen, a program to compute quantum molecular properties on spatial grids.

PubMed

Pacios, Luis F; Fernandez, Alberto

2009-09-01

CheckDen, a program to compute quantum molecular properties on a variety of spatial grids is presented. The program reads as unique input wavefunction files written by standard quantum packages and calculates the electron density rho(r), promolecule and density difference function, gradient of rho(r), Laplacian of rho(r), information entropy, electrostatic potential, kinetic energy densities G(r) and K(r), electron localization function (ELF), and localized orbital locator (LOL) function. These properties can be calculated on a wide range of one-, two-, and three-dimensional grids that can be processed by widely used graphics programs to render high-resolution images. CheckDen offers also other options as extracting separate atom contributions to the property computed, converting grid output data into CUBE and OpenDX volumetric data formats, and perform arithmetic combinations with grid files in all the recognized formats.

Manipulating molecular quantum states with classical metal atom inputs: demonstration of a single molecule NOR logic gate.

PubMed

Soe, We-Hyo; Manzano, Carlos; Renaud, Nicolas; de Mendoza, Paula; De Sarkar, Abir; Ample, Francisco; Hliwa, Mohamed; Echavarren, Antonio M; Chandrasekhar, Natarajan; Joachim, Christian

2011-02-22

Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.

Quantum origins of molecular recognition and olfaction in Drosophila.

PubMed

Bittner, Eric R; Madalan, Adrian; Czader, Arkadiusz; Roman, Gregg

2012-12-14

The standard model for molecular recognition of an odorant is that receptor sites discriminate by molecular geometry as evidenced that two chiral molecules may smell very differently. However, recent studies of isotopically labeled olfactants indicate that there may be a molecular vibration-sensing component to olfactory reception, specifically in the spectral region around 2300 cm(-1). Here, we present a donor-bridge-acceptor model for olfaction which attempts to explain this effect. Our model, based upon accurate quantum chemical calculations of the olfactant (bridge) in its neutral and ionized states, posits that internal modes of the olfactant are excited impulsively during hole transfer from a donor to acceptor site on the receptor, specifically those modes that are resonant with the tunneling gap. By projecting the impulsive force onto the internal modes, we can determine which modes are excited at a given value of the donor-acceptor tunneling gap. Only those modes resonant with the tunneling gap and are impulsively excited will give a significant contribution to the inelastic transfer rate. Using acetophenone as a test case, our model and experiments on D. melanogaster suggest that isotopomers of a given olfactant give rise to different odorant qualities. These results support the notion that inelastic scattering effects may play a role in discriminating between isotopomers but that this is not a general spectroscopic effect.

Smoothed Particle Hydrodynamics Simulations of Ultrarelativistic Shocks with Artificial Viscosity

NASA Astrophysics Data System (ADS)

Siegler, S.; Riffert, H.

2000-03-01

We present a fully Lagrangian conservation form of the general relativistic hydrodynamic equations for perfect fluids with artificial viscosity in a given arbitrary background spacetime. This conservation formulation is achieved by choosing suitable Lagrangian time evolution variables, from which the generic fluid variables of rest-mass density, 3-velocity, and thermodynamic pressure have to be determined. We present the corresponding equations for an ideal gas and show the existence and uniqueness of the solution. On the basis of the Lagrangian formulation we have developed a three-dimensional general relativistic smoothed particle hydrodynamics (SPH) code using the standard SPH formalism as known from nonrelativistic fluid dynamics. One-dimensional simulations of a shock tube and a wall shock are presented together with a two-dimensional test calculation of an inclined shock tube. With our method we can model ultrarelativistic fluid flows including shocks with Lorentz factors of even 1000.

Properties of an ultrarelativistic charged particle radiation in a constant homogeneous crossed electromagnetic field

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

Bogdanov, O.V., E-mail: bov@tpu.ru; Department of Higher Mathematics and Mathematical Physics, Tomsk Polytechnic University, Tomsk, 634050; Kazinski, P.O., E-mail: kpo@phys.tsu.ru

The properties of radiation created by a classical ultrarelativistic scalar charged particle in a constant homogeneous crossed electromagnetic field are described both analytically and numerically with radiation reaction taken into account in the form of the Landau–Lifshitz equation. The total radiation naturally falls into two parts: the radiation formed at the entrance point of a particle into the crossed field (the synchrotron entrance radiation), and the radiation coming from the late-time asymptotics of a particle motion (the de-excited radiation). The synchrotron entrance radiation resembles, although does not coincide with, the ultrarelativistic limit of the synchrotron radiation: its distribution over energiesmore » and angles possesses almost the same properties. The de-excited radiation is soft, not concentrated in the plane of motion of a charged particle, and almost completely circularly polarized. The photon energy delivering the maximum to its spectral angular distribution decreases with increasing the initial energy of a charged particle, while the maximum value of this distribution remains the same at the fixed photon observation angle and entrance angle of a charged particle. The ultraviolet and infrared asymptotics of the total radiation are also described. - Highlights: • Properties of an electron radiation in a crossed electromagnetic field are studied. • Spectral angular distribution of the synchrotron entrance radiation is described. • Spectral angular distribution of the de-excited radiation is described. • De-excited radiation is almost completely circularly polarized. • Photon energy at the maximum of the de-excited radiation decreases with increasing the initial energy of an electron.« less

Entanglement loss in molecular quantum-dot qubits due to interaction with the environment.

PubMed

Blair, Enrique P; Tóth, Géza; Lent, Craig S

2018-05-16

We study quantum entanglement loss due to environmental interaction in a condensed matter system with a complex geometry relevant to recent proposals for computing with single electrons at the nanoscale. We consider a system consisting of two qubits, each realized by an electron in a double quantum dot, which are initially in an entangled Bell state. The qubits are widely separated and each interacts with its own environment. The environment for each is modeled by surrounding double quantum dots placed at random positions with random orientations. We calculate the unitary evolution of the joint system and environment. The global state remains pure throughout. We examine the time dependence of the expectation value of the bipartite Clauser-Horne-Shimony-Holt (CHSH) and Brukner-Paunković-Rudolph-Vedral (BPRV) Bell operators and explore the emergence of correlations consistent with local realism. Though the details of this transition depend on the specific environmental geometry, we show how the results can be mapped on to a universal behavior with appropriate scaling. We determine the relevant disentanglement times based on realistic physical parameters for molecular double-dots.

Entanglement loss in molecular quantum-dot qubits due to interaction with the environment

NASA Astrophysics Data System (ADS)

Blair, Enrique P.; Tóth, Géza; Lent, Craig S.

2018-05-01

We study quantum entanglement loss due to environmental interaction in a condensed matter system with a complex geometry relevant to recent proposals for computing with single electrons at the nanoscale. We consider a system consisting of two qubits, each realized by an electron in a double quantum dot, which are initially in an entangled Bell state. The qubits are widely separated and each interacts with its own environment. The environment for each is modeled by surrounding double quantum dots placed at random positions with random orientations. We calculate the unitary evolution of the joint system and environment. The global state remains pure throughout. We examine the time dependence of the expectation value of the bipartite Clauser–Horne–Shimony–Holt (CHSH) and Brukner–Paunković–Rudolph–Vedral (BPRV) Bell operators and explore the emergence of correlations consistent with local realism. Though the details of this transition depend on the specific environmental geometry, we show how the results can be mapped on to a universal behavior with appropriate scaling. We determine the relevant disentanglement times based on realistic physical parameters for molecular double-dots.

Destructive quantum interference in electron transport: A reconciliation of the molecular orbital and the atomic orbital perspective

NASA Astrophysics Data System (ADS)

Zhao, Xin; Geskin, Victor; Stadler, Robert

2017-03-01

Destructive quantum interference (DQI) in single molecule electronics is a purely quantum mechanical effect and is entirely defined by the inherent properties of the molecule in the junction such as its structure and symmetry. This definition of DQI by molecular properties alone suggests its relation to other more general concepts in chemistry as well as the possibility of deriving simple models for its understanding and molecular device design. Recently, two such models have gained a wide spread attention, where one was a graphical scheme based on visually inspecting the connectivity of the carbon sites in conjugated π systems in an atomic orbital (AO) basis and the other one puts the emphasis on the amplitudes and signs of the frontier molecular orbitals (MOs). There have been discussions on the range of applicability for these schemes, but ultimately conclusions from topological molecular Hamiltonians should not depend on whether they are drawn from an AO or a MO representation, as long as all the orbitals are taken into account. In this article, we clarify the relation between both models in terms of the zeroth order Green's function and compare their predictions for a variety of systems. From this comparison, we conclude that for a correct description of DQI from a MO perspective, it is necessary to include the contributions from all MOs rather than just those from the frontier orbitals. The cases where DQI effects can be successfully predicted within a frontier orbital approximation we show them to be limited to alternant even-membered hydrocarbons, as a direct consequence of the Coulson-Rushbrooke pairing theorem in quantum chemistry.

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.

Quantum soldering of individual quantum dots.

PubMed

Roy, Xavier; Schenck, Christine L; Ahn, Seokhoon; Lalancette, Roger A; Venkataraman, Latha; Nuckolls, Colin; Steigerwald, Michael L

2012-12-07

Making contact to a quantum dot: Single quantum-dot electronic circuits are fabricated by wiring atomically precise metal chalcogenide clusters with conjugated molecular connectors. These wired clusters can couple electronically to nanoscale electrodes and be tuned to control the charge-transfer characteristics (see picture). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

NASA Astrophysics Data System (ADS)

Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

2014-05-01

The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

An exceptional kinetic quantum sieving separation effect of hydrogen isotopes on commercially available carbon molecular sieves.

PubMed

Xing, Yanlong; Cai, Jinjun; Li, Liangjun; Yang, Menglong; Zhao, Xuebo

2014-08-14

The quantum sieving effect of H2/D2 at 77 K on commercially available carbon molecular sieves (1.5GN-H and 3KT-172) was studied. An exceptional reverse kinetic quantum effect is observed on 1.5GN-H where D2 diffuses much faster than H2 with a ratio of up to 5.83 at low pressure, and the difference is still very evident even as the pressure increases up to 1 bar. D2 also diffuses faster than H2 on 3KT-172 with a ratio of up to 1.86. However, the reverse kinetic sieving disappears in a polymer-based carbon (PC). The present kinetic quantum sieving effect of H2 and D2 at 77 K on 1.5GN-H is the highest to date.

Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation.

PubMed

Rahimi, Ehsan; Reimers, Jeffrey R

2018-06-20

The use of molecules to enact quantum cellular automata (QCA) cells has been proposed as a new way for performing electronic logic operations at sub-nm dimensions. A key question that arises concerns whether chemical or physical processes are to be exploited. The use of chemical reactions allows the state of a switch element to be latched in molecular form, making the output of a cell independent of its inputs, but costs energy to do the reaction. Alternatively, if purely electronic polarization is manipulated then no internal latching occurs, but no power is dissipated provided the fields from the inputs change slowly compared to the molecular response times. How these scenarios pan out is discussed by considering calculated properties of the 1,4-diallylbutane cation, a species often used as a paradigm for molecular electronic switching. Utilized are results from different calculation approaches that depict the ion either as a charge-localized mixed-valence compound functioning as a bistable switch, or else as an extremely polarizable molecule with a delocalized electronic structure. Practical schemes for using molecular cells in QCA and other devices emerge.

Nucleon matter equation of state, particle number fluctuations, and shear viscosity within UrQMD box calculations

NASA Astrophysics Data System (ADS)

Motornenko, A.; Bravina, L.; Gorenstein, M. I.; Magner, A. G.; Zabrodin, E.

2018-03-01

Properties of equilibrated nucleon system are studied within the ultra-relativistic quantum molecular dynamics (UrQMD) transport model. The UrQMD calculations are done within a finite box with periodic boundary conditions. The system achieves thermal equilibrium due to nucleon-nucleon elastic scattering. For the UrQMD-equilibrium state, nucleon energy spectra, equation of state, particle number fluctuations, and shear viscosity η are calculated. The UrQMD results are compared with both, statistical mechanics and Chapman-Enskog kinetic theory, for a classical system of nucleons with hard-core repulsion.

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

A device-oriented optimizer for solving ground state problems on an approximate quantum computer, Part II: Experiments for interacting spin and molecular systems

NASA Astrophysics Data System (ADS)

Kandala, Abhinav; Mezzacapo, Antonio; Temme, Kristan; Bravyi, Sergey; Takita, Maika; Chavez-Garcia, Jose; Córcoles, Antonio; Smolin, John; Chow, Jerry; Gambetta, Jay

Hybrid quantum-classical algorithms can be used to find variational solutions to generic quantum problems. Here, we present an experimental implementation of a device-oriented optimizer that uses superconducting quantum hardware. The experiment relies on feedback between the quantum device and classical optimization software which is robust to measurement noise. Our device-oriented approach uses naturally available interactions for the preparation of trial states. We demonstrate the application of this technique for solving interacting spin and molecular structure problems.

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

PubMed

Schiffmann, Christoph; Sebastiani, Daniel

2011-05-10

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

Performance of quantum Monte Carlo for calculating molecular bond lengths

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

Cleland, Deidre M., E-mail: deidre.cleland@csiro.au; Per, Manolo C., E-mail: manolo.per@csiro.au

2016-03-28

This work investigates the accuracy of real-space quantum Monte Carlo (QMC) methods for calculating molecular geometries. We present the equilibrium bond lengths of a test set of 30 diatomic molecules calculated using variational Monte Carlo (VMC) and diffusion Monte Carlo (DMC) methods. The effect of different trial wavefunctions is investigated using single determinants constructed from Hartree-Fock (HF) and Density Functional Theory (DFT) orbitals with LDA, PBE, and B3LYP functionals, as well as small multi-configurational self-consistent field (MCSCF) multi-determinant expansions. When compared to experimental geometries, all DMC methods exhibit smaller mean-absolute deviations (MADs) than those given by HF, DFT, and MCSCF.more » The most accurate MAD of 3 ± 2 × 10{sup −3} Å is achieved using DMC with a small multi-determinant expansion. However, the more computationally efficient multi-determinant VMC method has a similar MAD of only 4.0 ± 0.9 × 10{sup −3} Å, suggesting that QMC forces calculated from the relatively simple VMC algorithm may often be sufficient for accurate molecular geometries.« less

Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems.

PubMed

Liu, Xinzijian; Liu, Jian

2018-03-14

An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties. Its application to several representative one-dimensional and multi-dimensional models demonstrates that MES-PIMD in principle offers a practical tool in either of the diabatic and adiabatic representations for studying exact quantum statistics of complex/large MES systems when the Born-Oppenheimer approximation, Condon approximation, and harmonic bath approximation are broken.

Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems

NASA Astrophysics Data System (ADS)

Liu, Xinzijian; Liu, Jian

2018-03-01

An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties. Its application to several representative one-dimensional and multi-dimensional models demonstrates that MES-PIMD in principle offers a practical tool in either of the diabatic and adiabatic representations for studying exact quantum statistics of complex/large MES systems when the Born-Oppenheimer approximation, Condon approximation, and harmonic bath approximation are broken.

Electron Tunneling, a Quantum Probe for the Quantum World of Nanotechnology

ERIC Educational Resources Information Center

Hipps, K. W.; Scudiero, L.

2005-01-01

A quantum-mechanical probe is essential to study the quantum world, which is provided by electron tunneling. A spectroscopic mapping to image the electron-transport pathways on a sub-molecular scale is used.

A modified gradient approach for the growth of low-density InAs quantum dot molecules by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Sharma, Nandlal; Reuter, Dirk

2017-11-01

Two vertically stacked quantum dots that are electronically coupled, so called quantum dot molecules, are of great interest for the realization of solid state building blocks for quantum communication networks. We present a modified gradient approach to realize InAs quantum dot molecules with a low areal density so that single quantum dot molecules can be optically addressed. The individual quantum dot layers were prepared by solid source molecular beam epitaxy depositing InAs on GaAs(100). The bottom quantum dot layer has been grown without substrate rotation resulting in an In-gradient across the surface, which translated into a density gradient with low quantum dot density in a certain region of the wafer. For the top quantum dot layer, separated from the bottom quantum dot layer by a 6 nm thick GaAs barrier, various InAs amounts were deposited without an In-gradient. In spite of the absence of an In-gradient, a pronounced density gradient is observed for the top quantum dots. Even for an In-amount slightly below the critical thickness for a single dot layer, a density gradient in the top quantum dot layer, which seems to reproduce the density gradient in the bottom layer, is observed. For more or less In, respectively, deviations from this behavior occur. We suggest that the obvious influence of the bottom quantum dot layer on the growth of the top quantum dots is due to the strain field induced by the buried dots.

Molecular-Barrier-Enhanced Aromatic Fluorophores in Cocrystals with Unity Quantum Efficiency.

PubMed

Ye, Huanqing; Liu, Guangfeng; Liu, Sheng; Casanova, David; Ye, Xin; Tao, Xutang; Zhang, Qichun; Xiong, Qihua

2018-02-12

Singlet-triplet conversion in organic light-emitting materials introduces non-emissive (dark) and long-lived triplet states, which represents a significant challenge in constraining the optical properties. There have been considerable attempts at separating singlets and triplets in long-chain polymers, scavenging triplets, and quenching triplets with heavy metals; nonetheless, such triplet-induced loss cannot be fully eliminated. Herein, a new strategy of crafting a periodic molecular barrier into the π-conjugated matrices of organic aromatic fluorophores is reported. The molecular barriers effectively block the singlet-to-triplet pathway, resulting in near-unity photoluminescence quantum efficiency (PLQE) of the organic fluorophores. The transient optical spectroscopy measurements confirm the absence of the triplet absorption. These studies provide a general approach to preventing the formation of dark triplet states in organic semiconductors and bring new opportunities for the development of advanced organic optics and photonics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

The Alexandria library, a quantum-chemical database of molecular properties for force field development.

PubMed

Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

2018-04-10

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

The Alexandria library, a quantum-chemical database of molecular properties for force field development

NASA Astrophysics Data System (ADS)

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

2018-04-01

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

Revisiting first type self-similar solutions of explosions containing ultrarelativistic shocks

NASA Astrophysics Data System (ADS)

Tian, Jun

2018-05-01

We revisit the first type self-similar solutions for ultrarelativistic shock waves produced by explosions propagating into cold external medium whose density profile decreases with radius as ρ ∝ r-k. The first-type solutions proposed by Blandford and McKee (hereafter BM solution) conforms to the global conservation of energy and applies when k < 4. They have been found to be invalid when k > 17/4 because of the divergence of total energy contained in the shocked fluids. So far no attention has been paid to the particle number. We use the BM solution to calculate the total particle number traversed by the shock and find that it diverges when k > 3. This is inconsistent with the finite particles in the surrounding medium. We propose a possible solution when k > 3 based on the conservation of particle number and discuss its implication for the second-type solutions.

Applications of Quantum Theory of Atomic and Molecular Scattering to Problems in Hypersonic Flow

NASA Technical Reports Server (NTRS)

Malik, F. Bary

1995-01-01

The general status of a grant to investigate the applications of quantum theory in atomic and molecular scattering problems in hypersonic flow is summarized. Abstracts of five articles and eleven full-length articles published or submitted for publication are included as attachments. The following topics are addressed in these articles: fragmentation of heavy ions (HZE particles); parameterization of absorption cross sections; light ion transport; emission of light fragments as an indicator of equilibrated populations; quantum mechanical, optical model methods for calculating cross sections for particle fragmentation by hydrogen; evaluation of NUCFRG2, the semi-empirical nuclear fragmentation database; investigation of the single- and double-ionization of He by proton and anti-proton collisions; Bose-Einstein condensation of nuclei; and a liquid drop model in HZE particle fragmentation by hydrogen.

Growth of analog Al(x)Ga(1-x)As/GaAs parabolic quantum wells by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Wang, S. M.; Treideris, G.; Chen, W. Q.; Andersson, T. G.

1993-01-01

Parabolic Al(x)Ga(1-x)As/GaAs quantum wells have been grown by molecular beam epitaxy with linear ramping of the Al effusion cell temperature, where the ramping rate was carefully analyzed to avoid a flux lag. The calculated potential profile from the temperature variation was very close to the parabolic one. Low-temperature photoluminescence showed clear interband transitions up to the n = 3 sublevels. The equal energy spacing between adjacent transitions involving heavy-hole states confirmed the parabolic shape of the quantum well.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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

PubMed

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

2017-12-28

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

Ultrarelativistic bound states in the spherical well

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

Żaba, Mariusz; Garbaczewski, Piotr

2016-07-15

We address an eigenvalue problem for the ultrarelativistic (Cauchy) operator (−Δ){sup 1/2}, whose action is restricted to functions that vanish beyond the interior of a unit sphere in three spatial dimensions. We provide high accuracy spectral data for lowest eigenvalues and eigenfunctions of this infinite spherical well problem. Our focus is on radial and orbital shapes of eigenfunctions. The spectrum consists of an ordered set of strictly positive eigenvalues which naturally splits into non-overlapping, orbitally labelled E{sub (k,l)} series. For each orbital label l = 0, 1, 2, …, the label k = 1, 2, … enumerates consecutive lth seriesmore » eigenvalues. Each of them is 2l + 1-degenerate. The l = 0 eigenvalues series E{sub (k,0)} are identical with the set of even labeled eigenvalues for the d = 1 Cauchy well: E{sub (k,0)}(d = 3) = E{sub 2k}(d = 1). Likewise, the eigenfunctions ψ{sub (k,0)}(d = 3) and ψ{sub 2k}(d = 1) show affinity. We have identified the generic functional form of eigenfunctions of the spherical well which appear to be composed of a product of a solid harmonic and of a suitable purely radial function. The method to evaluate (approximately) the latter has been found to follow the universal pattern which effectively allows to skip all, sometimes involved, intermediate calculations (those were in usage, while computing the eigenvalues for l ≤ 3).« less

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

PubMed

Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

2016-07-12

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.

Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations

DOE PAGES

Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; ...

2016-06-06

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive iterative re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance ismore » obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.« less

Validation of radiative transfer computation with Monte Carlo method for ultra-relativistic background flow

NASA Astrophysics Data System (ADS)

Ishii, Ayako; Ohnishi, Naofumi; Nagakura, Hiroki; Ito, Hirotaka; Yamada, Shoichi

2017-11-01

We developed a three-dimensional radiative transfer code for an ultra-relativistic background flow-field by using the Monte Carlo (MC) method in the context of gamma-ray burst (GRB) emission. For obtaining reliable simulation results in the coupled computation of MC radiation transport with relativistic hydrodynamics which can reproduce GRB emission, we validated radiative transfer computation in the ultra-relativistic regime and assessed the appropriate simulation conditions. The radiative transfer code was validated through two test calculations: (1) computing in different inertial frames and (2) computing in flow-fields with discontinuous and smeared shock fronts. The simulation results of the angular distribution and spectrum were compared among three different inertial frames and in good agreement with each other. If the time duration for updating the flow-field was sufficiently small to resolve a mean free path of a photon into ten steps, the results were thoroughly converged. The spectrum computed in the flow-field with a discontinuous shock front obeyed a power-law in frequency whose index was positive in the range from 1 to 10 MeV. The number of photons in the high-energy side decreased with the smeared shock front because the photons were less scattered immediately behind the shock wave due to the small electron number density. The large optical depth near the shock front was needed for obtaining high-energy photons through bulk Compton scattering. Even one-dimensional structure of the shock wave could affect the results of radiation transport computation. Although we examined the effect of the shock structure on the emitted spectrum with a large number of cells, it is hard to employ so many computational cells per dimension in multi-dimensional simulations. Therefore, a further investigation with a smaller number of cells is required for obtaining realistic high-energy photons with multi-dimensional computations.

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision

Quantum chemistry simulation on quantum computers: theories and experiments.

PubMed

Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

2012-07-14

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

Dispersion characteristics of anisotropic unmagnetized ultra-relativistic transverse plasma wave with arbitrary electron degeneracy

NASA Astrophysics Data System (ADS)

Sarfraz, M.; Farooq, H.; Abbas, G.; Noureen, S.; Iqbal, Z.; Rasheed, A.

2018-03-01

Thermal momentum space anisotropy is ubiquitous in many astrophysical and laboratory plasma environments. Using Vlasov-Maxwell's model equations, a generalized polarization tensor for a collisionless ultra-relativistic unmagnetized electron plasma is derived. In particular, the tensor is obtained by considering anisotropy in the momentum space. The integral of moments of Fermi-Dirac distribution function in terms of Polylog functions is used for describing the border line plasma systems (T/e TF e ≈1 ) comprising arbitrary electron degeneracy, where Te and TF e, are thermal and Fermi temperatures, respectively. Furthermore, the effects of variation in thermal momentum space anisotropy on the electron equilibrium number density and the spectrum of electromagnetic waves are analyzed.

HYDJET++ for ultra-relativistic HIC’s: A hot cocktail of hydrodynamics, resonances and jets

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

Bravina, L. V.; Johansson, B. H. Brusheim; Crkovska, J.

An ultra-relativistic heavy-ion collision at LHC energies is a mixture of soft and hard processes. For comparison with data we employ the HYDJET++ model, which combines the description of soft processes with the treatment of hard partons propagating hot and dense nuclear medium. Importance of the interplay of ideal hydrodynamics, final state interactions and jets for the description of harmonics of the anisotropic flow is discussed. Jets are found to be the main source of violation of the number-of-constituent-quark (NCQ) scaling at LHC energies. Many features of higher flow harmonics and dihadron angular correlations, including ridge, can be described bymore » the interference of elliptic and triangular flows.« less

Standing electromagnetic solitons in hot ultra-relativistic electron-positron plasmas

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

Heidari, E., E-mail: ehphys75@iaubushehr.ac.ir; Aslaninejad, M.; Eshraghi, H.

2014-03-15

Using a one-dimensional self-consistent fluid model, we investigate standing relativistic bright solitons in hot electron-positron plasmas. The positron dynamics is taken into account. A set of nonlinear coupled differential equations describing the evolution of electromagnetic waves in fully relativistic two-fluid plasma is derived analytically and solved numerically. As a necessary condition for the existence of standing solitons the system should be relativistic. For the case of ultra-relativistic plasma, we investigate non-drifting bright solitary waves. Detailed discussions of the acceptable solutions are presented. New single hump non-trivial symmetric solutions for the scalar potential were found, and single and multi-nodal symmetric andmore » anti-symmetric solutions for the vector potential are presented. It is shown that for a fixed value of the fluid velocity excited modes with more zeros in the profile of the vector potential show a higher magnitude for the scalar potential. An increase in the plasma fluid velocity also increases the magnitude of the scalar potential. Furthermore, the Hamiltonian and the first integral of the system are given.« less

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

PubMed

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

2018-06-30

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

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.

Adiabatic quantum computing with spin qubits hosted by molecules.

PubMed

Yamamoto, Satoru; Nakazawa, Shigeaki; Sugisaki, Kenji; Sato, Kazunobu; Toyota, Kazuo; Shiomi, Daisuke; Takui, Takeji

2015-01-28

A molecular spin quantum computer (MSQC) requires electron spin qubits, which pulse-based electron spin/magnetic resonance (ESR/MR) techniques can afford to manipulate for implementing quantum gate operations in open shell molecular entities. Importantly, nuclear spins, which are topologically connected, particularly in organic molecular spin systems, are client qubits, while electron spins play a role of bus qubits. Here, we introduce the implementation for an adiabatic quantum algorithm, suggesting the possible utilization of molecular spins with optimized spin structures for MSQCs. We exemplify the utilization of an adiabatic factorization problem of 21, compared with the corresponding nuclear magnetic resonance (NMR) case. Two molecular spins are selected: one is a molecular spin composed of three exchange-coupled electrons as electron-only qubits and the other an electron-bus qubit with two client nuclear spin qubits. Their electronic spin structures are well characterized in terms of the quantum mechanical behaviour in the spin Hamiltonian. The implementation of adiabatic quantum computing/computation (AQC) has, for the first time, been achieved by establishing ESR/MR pulse sequences for effective spin Hamiltonians in a fully controlled manner of spin manipulation. The conquered pulse sequences have been compared with the NMR experiments and shown much faster CPU times corresponding to the interaction strength between the spins. Significant differences are shown in rotational operations and pulse intervals for ESR/MR operations. As a result, we suggest the advantages and possible utilization of the time-evolution based AQC approach for molecular spin quantum computers and molecular spin quantum simulators underlain by sophisticated ESR/MR pulsed spin technology.

Optical signatures of coupled quantum dots.

PubMed

Stinaff, E A; Scheibner, M; Bracker, A S; Ponomarev, I V; Korenev, V L; Ware, M E; Doty, M F; Reinecke, T L; Gammon, D

2006-02-03

An asymmetric pair of coupled InAs quantum dots is tuned into resonance by applying an electric field so that a single hole forms a coherent molecular wave function. The optical spectrum shows a rich pattern of level anticrossings and crossings that can be understood as a superposition of charge and spin configurations of the two dots. Coulomb interactions shift the molecular resonance of the optically excited state (charged exciton) with respect to the ground state (single charge), enabling light-induced coupling of the quantum dots. This result demonstrates the possibility of optically coupling quantum dots for application in quantum information processing.

Optical Signatures of Coupled Quantum Dots

NASA Astrophysics Data System (ADS)

Stinaff, E. A.; Scheibner, M.; Bracker, A. S.; Ponomarev, I. V.; Korenev, V. L.; Ware, M. E.; Doty, M. F.; Reinecke, T. L.; Gammon, D.

2006-02-01

An asymmetric pair of coupled InAs quantum dots is tuned into resonance by applying an electric field so that a single hole forms a coherent molecular wave function. The optical spectrum shows a rich pattern of level anticrossings and crossings that can be understood as a superposition of charge and spin configurations of the two dots. Coulomb interactions shift the molecular resonance of the optically excited state (charged exciton) with respect to the ground state (single charge), enabling light-induced coupling of the quantum dots. This result demonstrates the possibility of optically coupling quantum dots for application in quantum information processing.

A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

NASA Astrophysics Data System (ADS)

Simon, Sílvia; Duran, Miquel

1997-08-01

Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.

Nanoheterostructures with CdTe/ZnMgSeTe Quantum Dots for Single-Photon Emitters Grown by Molecular Beam Epitaxy

NASA Astrophysics Data System (ADS)

Sorokin, S. V.; Sedova, I. V.; Belyaev, K. G.; Rakhlin, M. V.; Yagovkina, M. A.; Toropov, A. A.; Ivanov, S. V.

2018-03-01

Data on the molecular beam epitaxy (MBE) technology, design, and luminescent properties of heterostructures with CdTe/Zn(Mg)(Se)Te quantum dots on InAs(001) substrates are presented. X-ray diffraction has been used to study short-period ZnTe/MgTe/MgSe superlattices used as wide-bandgap barriers in structures with CdTe/ZnTe quantum dots for the effective confinement of holes. It is shown that the design of these superlattices must take into account the replacement of Te atoms by selenium on MgSe/ZnTe and MgTe/MgSe heterointerfaces. Heterostructures with CdTe/Zn(Mg)(Se)Te quantum dots exhibit photoluminescence at temperatures up to 300 K. The spectra of microphotoluminescence at T = 10 K display a set of emission lines from separate CdTe/ZnTe quantum dots, the surface density of which is estimated at 1010 cm-2.

Nuclear quantum fluctuations in ice I(h).

PubMed

Moreira, Pedro Augusto Franco Pinheiro; de Koning, Maurice

2015-10-14

We discuss the role of nuclear quantum fluctuations in ice Ih, focusing on the hydrogen-bond (HB) structure and the molecular dipole-moment distribution. For this purpose we carry out DFT-based first-principles molecular dynamics and path-integral molecular dynamics simulations at T = 100 K. We analyze the HB structure in terms of a set of parameters previously employed to characterize molecular structures in the liquid phase and compute the molecular dipole moments using the maximally-localized Wannier functions. The results show that the protons experience very large digressions driven by quantum fluctuations, accompanied by major rearrangements in the electronic density. As a result of these protonic quantum fluctuations the molecular dipole-moment distribution is substantially broadened as well as shifted to a larger mean value when compared to the results obtained when such fluctuations are neglected. In terms of dielectric constants, the reconciliation between the greater mean dipole moment and experimental indications that the dielectric constant of H2O ice is lower than that of D2O ice would indicate that the topology of the HB network is sensitive to protonic quantum fluctuations.

Quantum indistinguishability in chemical reactions.

PubMed

Fisher, Matthew P A; Radzihovsky, Leo

2018-05-15

Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high-temperature processes, particularly for ionic coordinates, implicitly assumed to be distinguishable, incoherent, and thus well approximated classically. We explore enzymatic chemical reactions involving small symmetric molecules and argue that in many situations a full quantum treatment of collective nuclear degrees of freedom is essential. Supported by several physical arguments, we conjecture a "quantum dynamical selection" (QDS) rule for small symmetric molecules that precludes chemical processes that involve direct transitions from orbitally nonsymmetric molecular states. As we propose and discuss, the implications of the QDS rule include ( i ) a differential chemical reactivity of para- and orthohydrogen, ( ii ) a mechanism for inducing intermolecular quantum entanglement of nuclear spins, ( iii ) a mass-independent isotope fractionation mechanism, ( iv ) an explanation of the enhanced chemical activity of "reactive oxygen species", ( v ) illuminating the importance of ortho-water molecules in modulating the quantum dynamics of liquid water, and ( vi ) providing the critical quantum-to-biochemical linkage in the nuclear spin model of the (putative) quantum brain, among others.

Quantum Effects in Molecule-Based Nanomagnets

NASA Astrophysics Data System (ADS)

Hill, Stephen

2005-11-01

Research into molecule-based-magnets has made immense strides in recent years, with the discoveries of all organic molecular magnets, room temperature 3D ordered permanent magnets, and single-molecule magnets (SMMs), the latter exhibiting a host of spectacular quantum phenomena; for a review, see ref. [1]. SMMs represent a molecular approach to nanoscale and sub-nanoscale magnetic particles. They offer all of the advantages of molecular chemistry as well as displaying the superparamagnetic properties of mesoscale magnetic particles of much larger dimensions. They also straddle the interface between classical and quantum behavior; for example, they exhibit quantum tunneling of their magnetization. I will give a general introduction to this area of research, followed by an overview of recent results obtained using high-frequency (40-800 GHz) electron paramagnetic resonance techniques developed at the University of Florida. These results include: an elucidation of the role of molecular symmetry in the magnetic quantum tunneling phenomenon [2]; and the observation of quantum entanglement between pairs of nanomagnets within a supramolecular dimer [3]. 1. D. Gatteschi and R. Sessoli, Angew. Chem. 42, 268 (2003). 2. E. del Barco et al., J. Low Temp. Phys. 140, 119-174 (2005). 3. S. Hill et al., Science 302, 1015 (2003).

Surface induced molecular dynamics of thin lipid films confined to submicron cavities: A 1H multiple-quantum NMR study

NASA Astrophysics Data System (ADS)

Jagadeesh, B.; Prabhakar, A.; Demco, D. E.; Buda, A.; Blümich, B.

2005-03-01

The dynamics and molecular order of thin lipid (lecithin) films confined to 200, 100 and 20 nm cylindrical pores with varying surface coverage, were investigated by 1H multiple-quantum NMR. The results show that the molecular dynamics in the surface controlled layers are less hindered compared to those in the bulk. Dynamic heterogeneity among terminal CH 3 groups is evident. Enhanced dynamic freedom is observed for films with area per molecule, ˜ 128 Å 2. The results are discussed in terms of changes in the lipid molecular organization with respect to surface concentration, its plausible motional modes and dynamic heterogeneity.

Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.

D2+ Molecular complex in non-uniform height quantum ribbon under crossed electric and magnetic fields

NASA Astrophysics Data System (ADS)

Suaza, Y. A.; Laroze, D.; Fulla, M. R.; Marín, J. H.

2018-05-01

The D2+ molecular complex fundamental properties in a uniform and multi-hilled semiconductor quantum ribbon under orthogonal electric and magnetic fields are theoretically studied. The energy structure is calculated by using adiabatic approximation combined with diagonalization procedure. The D2+ energy structure is more strongly controlled by the geometrical structural hills than the Coulomb interaction. The formation of vibrational and rotational states is discussed. Aharanov-Bohm oscillation patterns linked to rotational states as well as the D2+ molecular complex stability are highly sensitive to the number of hills while electric field breaks the electron rotational symmetry and removes the energy degeneration between low-lying states.

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.

The detection of ultra-relativistic electrons in low Earth orbit

NASA Astrophysics Data System (ADS)

Katsiyannis, Athanassios C.; Dominique, Marie; Pierrard, Viviane; Rosson, Graciela Lopez; Keyser, Johan De; Berghmans, David; Kruglanski, Michel; Dammasch, Ingolf E.; Donder, Erwin De

2018-01-01

Aims: To better understand the radiation environment in low Earth orbit (LEO), the analysis of in-situ observations of a variety of particles, at different atmospheric heights, and in a wide range of energies, is needed. Methods: We present an analysis of energetic particles, indirectly detected by the large yield radiometer (LYRA) instrument on board ESA's project for on-board autonomy 2 (PROBA2) satellite as background signal. Combining energetic particle telescope (EPT) observations with LYRA data for an overlapping period of time, we identified these particles as electrons with an energy range of 2 to 8 MeV. Results: The observed events are strongly correlated to geo-magnetic activity and appear even during modest disturbances. They are also well confined geographically within the L = 4-6 McIlwain zone, which makes it possible to identify their source. Conclusions: Although highly energetic particles are commonly perturbing data acquisition of space instruments, we show in this work that ultra-relativistic electrons with energies in the range of 2-8 MeV are detected only at high latitudes, while not present in the South Atlantic Anomaly region.

Quantum autoencoders for efficient compression of quantum data

NASA Astrophysics Data System (ADS)

Romero, Jonathan; Olson, Jonathan P.; Aspuru-Guzik, Alan

2017-12-01

Classical autoencoders are neural networks that can learn efficient low-dimensional representations of data in higher-dimensional space. The task of an autoencoder is, given an input x, to map x to a lower dimensional point y such that x can likely be recovered from y. The structure of the underlying autoencoder network can be chosen to represent the data on a smaller dimension, effectively compressing the input. Inspired by this idea, we introduce the model of a quantum autoencoder to perform similar tasks on quantum data. The quantum autoencoder is trained to compress a particular data set of quantum states, where a classical compression algorithm cannot be employed. The parameters of the quantum autoencoder are trained using classical optimization algorithms. We show an example of a simple programmable circuit that can be trained as an efficient autoencoder. We apply our model in the context of quantum simulation to compress ground states of the Hubbard model and molecular Hamiltonians.

Molecular machines operating on the nanoscale: from classical to quantum

PubMed Central

2016-01-01

Summary The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed. PMID:27335728

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.

Electron-positron pair production by ultrarelativistic electrons in a soft photon field

NASA Technical Reports Server (NTRS)

Mastichiadis, A.; Marscher, A. P.; Brecher, K.

1986-01-01

The fully differential cross section for photon-electron pair production is integrated numerically over phase space. Results are obtained for the astrophysically interesting case in which the interaction between an ultrarelativistic electron and a soft photon results in electron-positron pair production. The positron spectrum is a function of the energies of both the photon and the electron, as well as the angle of interaction. It is found that the energy at which the positron distribution peaks is inversely proportional to the photon energy and independent of the electron energy. The positron spectrum is integrated once more over initial electron energies for a power-law energy distribution of primary electrons. The same procedure is repeated for the recoil particle; it is shown that the peak of the recoil energy distribution depends linearly on the energy of the primary electron. Finally, semianalytical expressions are obtained for the energy losses of the primary electrons.

Quantum Dots for Molecular Pathology

PubMed Central

True, Lawrence D.; Gao, Xiaohu

2007-01-01

Assessing malignant tumors for expression of multiple biomarkers provides data that are critical for patient management. Quantum dot-conjugated probes to specific biomarkers are powerful tools that can be applied in a multiplex manner to single tissue sections of biopsies to measure expression levels of multiple biomarkers. PMID:17251330

Cold molecules: Progress in quantum engineering of chemistry and quantum matter

NASA Astrophysics Data System (ADS)

Bohn, John L.; Rey, Ana Maria; Ye, Jun

2017-09-01

Cooling atoms to ultralow temperatures has produced a wealth of opportunities in fundamental physics, precision metrology, and quantum science. The more recent application of sophisticated cooling techniques to molecules, which has been more challenging to implement owing to the complexity of molecular structures, has now opened the door to the longstanding goal of precisely controlling molecular internal and external degrees of freedom and the resulting interaction processes. This line of research can leverage fundamental insights into how molecules interact and evolve to enable the control of reaction chemistry and the design and realization of a range of advanced quantum materials.

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

PubMed

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

NASA Astrophysics Data System (ADS)

Adli, E.; Lindstrøm, C. A.; Allen, J.; Clarke, C. I.; Frederico, J.; Gessner, S. J.; Green, S. Z.; Hogan, M. J.; Litos, M. D.; O'Shea, B.; Yakimenko, V.; An, W.; Clayton, C. E.; Marsh, K. A.; Mori, W. B.; Joshi, C.; Vafaei-Najafabadi, N.; Corde, S.; Lu, W.

2016-10-01

We report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. The attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam-plasma interactions in general and plasma wakefield accelerator technology in particular.

Spintronics: The molecular way

NASA Astrophysics Data System (ADS)

Cornia, Andrea; Seneor, Pierre

2017-05-01

Molecular spintronics is an interdisciplinary field at the interface between organic spintronics, molecular magnetism, molecular electronics and quantum computing, which is advancing fast and promises large technological payoffs.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

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

Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu, E-mail: okazaki@apchem.nagoya-u.ac.jp

2014-08-28

In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfermore » process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −1}. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.« less

Quantum Sensors for the Generating Functional of Interacting Quantum Field Theories

NASA Astrophysics Data System (ADS)

Bermudez, A.; Aarts, G.; Müller, M.

2017-10-01

Difficult problems described in terms of interacting quantum fields evolving in real time or out of equilibrium abound in condensed-matter and high-energy physics. Addressing such problems via controlled experiments in atomic, molecular, and optical physics would be a breakthrough in the field of quantum simulations. In this work, we present a quantum-sensing protocol to measure the generating functional of an interacting quantum field theory and, with it, all the relevant information about its in- or out-of-equilibrium phenomena. Our protocol can be understood as a collective interferometric scheme based on a generalization of the notion of Schwinger sources in quantum field theories, which make it possible to probe the generating functional. We show that our scheme can be realized in crystals of trapped ions acting as analog quantum simulators of self-interacting scalar quantum field theories.

Operating Quantum States in Single Magnetic Molecules: Implementation of Grover's Quantum Algorithm.

PubMed

Godfrin, C; Ferhat, A; Ballou, R; Klyatskaya, S; Ruben, M; Wernsdorfer, W; Balestro, F

2017-11-03

Quantum algorithms use the principles of quantum mechanics, such as, for example, quantum superposition, in order to solve particular problems outperforming standard computation. They are developed for cryptography, searching, optimization, simulation, and solving large systems of linear equations. Here, we implement Grover's quantum algorithm, proposed to find an element in an unsorted list, using a single nuclear 3/2 spin carried by a Tb ion sitting in a single molecular magnet transistor. The coherent manipulation of this multilevel quantum system (qudit) is achieved by means of electric fields only. Grover's search algorithm is implemented by constructing a quantum database via a multilevel Hadamard gate. The Grover sequence then allows us to select each state. The presented method is of universal character and can be implemented in any multilevel quantum system with nonequal spaced energy levels, opening the way to novel quantum search algorithms.

Operating Quantum States in Single Magnetic Molecules: Implementation of Grover's Quantum Algorithm

NASA Astrophysics Data System (ADS)

Godfrin, C.; Ferhat, A.; Ballou, R.; Klyatskaya, S.; Ruben, M.; Wernsdorfer, W.; Balestro, F.

2017-11-01

Quantum algorithms use the principles of quantum mechanics, such as, for example, quantum superposition, in order to solve particular problems outperforming standard computation. They are developed for cryptography, searching, optimization, simulation, and solving large systems of linear equations. Here, we implement Grover's quantum algorithm, proposed to find an element in an unsorted list, using a single nuclear 3 /2 spin carried by a Tb ion sitting in a single molecular magnet transistor. The coherent manipulation of this multilevel quantum system (qudit) is achieved by means of electric fields only. Grover's search algorithm is implemented by constructing a quantum database via a multilevel Hadamard gate. The Grover sequence then allows us to select each state. The presented method is of universal character and can be implemented in any multilevel quantum system with nonequal spaced energy levels, opening the way to novel quantum search algorithms.

Application of JAERI quantum molecular dynamics model for collisions of heavy nuclei

NASA Astrophysics Data System (ADS)

Ogawa, Tatsuhiko; Hashimoto, Shintaro; Sato, Tatsuhiko; Niita, Koji

2016-06-01

The quantum molecular dynamics (QMD) model incorporated into the general-purpose radiation transport code PHITS was revised for accurate prediction of fragment yields in peripheral collisions. For more accurate simulation of peripheral collisions, stability of the nuclei at their ground state was improved and the algorithm to reject invalid events was modified. In-medium correction on nucleon-nucleon cross sections was also considered. To clarify the effect of this improvement on fragmentation of heavy nuclei, the new QMD model coupled with a statistical decay model was used to calculate fragment production cross sections of Ag and Au targets and compared with the data of earlier measurement. It is shown that the revised version can predict cross section more accurately.

Quantum molecular dynamics simulation of structural and thermodynamic properties of NiAl

NASA Astrophysics Data System (ADS)

Karchevskaya, E. S.; Minakov, D. V.; Levashov, P. R.

2018-01-01

In this work, structural and thermodynamic properties of a solid and liquid Ni-Al compound are studied using an ab initio method of quantum molecular dynamics (QMD). Simulations were carried out in 700-3000 K temperature range at atmospheric pressure. Radial distribution functions are analyzed to determine the presence of Ni-Al chemical bonds. Diffusion coefficients for individual components are also calculated. Another goal of this work is the investigation of the reaction propagation in thermally-initiated Ni-Al foils. For this purpose, we performed QMD simulations of Ni-Al layers in the microcanonical ensemble. An exothermic reaction between the solid Ni-Al layers is observed in our simulations at temperature less than the melting temperatures of the components.

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

PubMed

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

2017-05-05

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

Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

2016-09-01

Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

Recommender engine for continuous-time quantum Monte Carlo methods

NASA Astrophysics Data System (ADS)

Huang, Li; Yang, Yi-feng; Wang, Lei

2017-03-01

Recommender systems play an essential role in the modern business world. They recommend favorable items such as books, movies, and search queries to users based on their past preferences. Applying similar ideas and techniques to Monte Carlo simulations of physical systems boosts their efficiency without sacrificing accuracy. Exploiting the quantum to classical mapping inherent in the continuous-time quantum Monte Carlo methods, we construct a classical molecular gas model to reproduce the quantum distributions. We then utilize powerful molecular simulation techniques to propose efficient quantum Monte Carlo updates. The recommender engine approach provides a general way to speed up the quantum impurity solvers.

Exciton Fine-Structure Splitting in Self-Assembled Lateral InAs/GaAs Quantum-Dot Molecular Structures.

PubMed

Fillipov, Stanislav; Puttisong, Yuttapoom; Huang, Yuqing; Buyanova, Irina A; Suraprapapich, Suwaree; Tu, Charles W; Chen, Weimin M

2015-06-23

Fine-structure splitting (FSS) of excitons in semiconductor nanostructures is a key parameter that has significant implications in photon entanglement and polarization conversion between electron spins and photons, relevant to quantum information technology and spintronics. Here, we investigate exciton FSS in self-organized lateral InAs/GaAs quantum-dot molecular structures (QMSs) including laterally aligned double quantum dots (DQDs), quantum-dot clusters (QCs), and quantum rings (QRs), by employing polarization-resolved microphotoluminescence (μPL) spectroscopy. We find a clear trend in FSS between the studied QMSs depending on their geometric arrangements, from a large FSS in the DQDs to a smaller FSS in the QCs and QRs. This trend is accompanied by a corresponding difference in the optical polarization directions of the excitons between these QMSs, namely, the bright-exciton lines are linearly polarized preferably along or perpendicular to the [11̅0] crystallographic axis in the DQDs that also defines the alignment direction of the two constituting QDs, whereas in the QCs and QRs, the polarization directions are randomly oriented. We attribute the observed trend in the FSS to a significant reduction of the asymmetry in the lateral confinement potential of the excitons in the QRs and QCs as compared with the DQDs, as a result of a compensation between the effects of lateral shape anisotropy and piezoelectric field. Our work demonstrates that FSS strongly depends on the geometric arrangements of the QMSs, which effectively tune the degree of the compensation effects and are capable of reducing FSS even in a strained QD system to a limit similar to strain-free QDs. This approach provides a pathway in obtaining high-symmetry quantum emitters desirable for realizing photon entanglement and spintronic devices based on such nanostructures, utilizing an uninterrupted epitaxial growth procedure without special requirements for lattice-matched materials combinations

Enhanced Hole Mobility and Density in GaSb Quantum Wells

DTIC Science & Technology

2013-01-01

Keywords: Molecular beam epitaxy Quantum wells Semiconducting III–V materials Field-effect transistors GaSb a b s t r a c t Modulation-doped quantum wells...QWs) of GaSb clad by AlAsSb were grown by molecular beam epitaxy on InP substrates. By virtue of quantum confinement and compressive strain of the...heterostructures studied here are grown by molecular beam epitaxy (MBE) on semi-insulating (001) InP substrates using a Riber Compact 21T MBE system. A cross

Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations

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

Giorgi, G.L., E-mail: g.giorgi@inrim.it; Roncaglia, M.; Raffa, F.A.

2015-10-15

During the long course of evolution, nature has learnt how to exploit quantum effects. In fact, recent experiments reveal the existence of quantum processes whose coherence extends over unexpectedly long time and space ranges. In particular, photosynthetic processes in light-harvesting complexes display a typical oscillatory dynamics ascribed to quantum coherence. Here, we consider the simple model where a dimer made of two chromophores is strongly coupled with a quasi-resonant vibrational mode. We observe the occurrence of wide oscillations of genuine quantum correlations, between electronic excitations and the environment, represented by vibrational bosonic modes. Such a quantum dynamics has been unveiledmore » through the calculation of the negativity of entanglement and the discord, indicators widely used in quantum information for quantifying the resources needed to realize quantum technologies. We also discuss the possibility of approximating additional weakly-coupled off-resonant vibrational modes, simulating the disturbances induced by the rest of the environment, by a single vibrational mode. Within this approximation, one can show that the off-resonant bath behaves like a classical source of noise.« less

Diagonal and off-diagonal susceptibilities of conserved quantities in relativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Chatterjee, Arghya; Chatterjee, Sandeep; Nayak, Tapan K.; Ranjan Sahoo, Nihar

2016-12-01

Susceptibilities of conserved quantities, such as baryon number, strangeness and electric charge are sensitive to the onset of quantum chromodynamics phase transition, and are expected to provide information on the matter produced in heavy-ion collision experiments. A comprehensive study of the second order diagonal susceptibilities and cross correlations has been made within a thermal model approach of the hadron resonance gas model as well as with a hadronic transport model, ultra-relativistic quantum molecular dynamics. We perform a detailed analysis of the effect of detector acceptances and choice of particle species in the experimental measurements of the susceptibilities for heavy-ion collisions corresponding to \\sqrt{{s}{NN}} = 4 GeV to 200 GeV. The transverse momentum cutoff dependence of suitably normalised susceptibilities are proposed as useful observables to probe the properties of the medium at freezeout.

Car-Parrinello molecular dynamics study of the melting behaviors of n-atom (n = 6, 10) graphene quantum dots

NASA Astrophysics Data System (ADS)

Shekaari, Ashkan; Abolhassani, Mohammad Reza

2017-06-01

First-principles molecular dynamics has been applied to inquire into the melting behaviors of n-atom (n = 6, 10) graphene quantum dots (GQD6 and zigzag GQD10) within the temperature range of T = 0-500 K. The temperature dependence of the geometry of each quantum dot is thoroughly evaluated via calculating the related shape deformation parameters and the eigenvalues of the quadrupole tensors. Examining the variations of some phase-transition indicators such as root-mean-square bond length fluctuations and mean square displacements broadly proposes the value of Tm = 70 K for the melting point of GQD6 while a continuous, two-stage phase transition has been concluded for zigzag GQD10.

Dynamics of plasmonic field polarization induced by quantum coherence in quantum dot-metallic nanoshell structures.

PubMed

Sadeghi, S M

2014-09-01

When a hybrid system consisting of a semiconductor quantum dot and a metallic nanoparticle interacts with a laser field, the plasmonic field of the metallic nanoparticle can be normalized by the quantum coherence generated in the quantum dot. In this Letter, we study the states of polarization of such a coherent-plasmonic field and demonstrate how these states can reveal unique aspects of the collective molecular properties of the hybrid system formed via coherent exciton-plasmon coupling. We show that transition between the molecular states of this system can lead to ultrafast polarization dynamics, including sudden reversal of the sense of variations of the plasmonic field and formation of circular and elliptical polarization.

Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Motta, Mario; Zhang, Shiwei

2018-05-01

We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

Electron-phonon interaction in quantum transport through quantum dots and molecular systems

NASA Astrophysics Data System (ADS)

Ojeda, J. H.; Duque, C. A.; Laroze, D.

2016-12-01

The quantum transport and effects of decoherence properties are studied in quantum dots systems and finite homogeneous chains of aromatic molecules connected to two semi-infinite leads. We study these systems based on the tight-binding approach through Green's function technique within a real space renormalization and polaron transformation schemes. In particular, we calculate the transmission probability following the Landauer-Büttiker formalism, the I - V characteristics and the noise power of current fluctuations taken into account the decoherence. Our results may explain the inelastic effects through nanoscopic systems.

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

DOE PAGES

Adli, Erik; Lindstrom, C. A.; Allen, J.; ...

2016-10-12

Here, we report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. Themore » attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam–plasma interactions in general and plasma wakefield accelerator technology in particular.« less

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

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

Adli, Erik; Lindstrom, C. A.; Allen, J.

Here, we report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. Themore » attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam–plasma interactions in general and plasma wakefield accelerator technology in particular.« less

Molecular Magnetic Quantum Cellular Automata

DTIC Science & Technology

2004-06-01

Folting K, Gatteschi D, Christou G, Hendrickson D N 1993a, High-Spin Molecules - [Mn12O12(O2CR)16(H2O)4], J. Am. Chem. Soc. 115 1804 Sessoli R... Gatteschi D, Caneschi A and Novak M A 1993b, Magnetic bistability in a metal-ion cluster, Nature 365 141 Twamely J 2003, Quantum-cellular-automata

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.

Single-molecule quantum dot as a Kondo simulator

NASA Astrophysics Data System (ADS)

Hiraoka, R.; Minamitani, E.; Arafune, R.; Tsukahara, N.; Watanabe, S.; Kawai, M.; Takagi, N.

2017-06-01

Structural flexibility of molecule-based systems is key to realizing the novel functionalities. Tuning the structure in the atomic scale enables us to manipulate the quantum state in the molecule-based system. Here we present the reversible Hamiltonian manipulation in a single-molecule quantum dot consisting of an iron phthalocyanine molecule attached to an Au electrode and a scanning tunnelling microscope tip. We precisely controlled the position of Fe2+ ion in the molecular cage by using the tip, and tuned the Kondo coupling between the molecular spins and the Au electrode. Then, we realized the crossover between the strong-coupling Kondo regime and the weak-coupling regime governed by spin-orbit interaction in the molecule. The results open an avenue to simulate low-energy quantum many-body physics and quantum phase transition through the molecular flexibility.

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

PubMed

Dyekjaer, Jane Dannow; Jónsdóttir, Svava Osk

2004-01-22

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

Quantum Dynamics in Biological Systems

NASA Astrophysics Data System (ADS)

Shim, Sangwoo

In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

Preferential sites for InAsP/InP quantum wire nucleation using molecular dynamics

NASA Astrophysics Data System (ADS)

Nuñez-Moraleda, Bernardo; Pizarro, Joaquin; Guerrero, Elisa; Guerrero-Lebrero, Maria P.; Yáñez, Andres; Molina, Sergio Ignacio; Galindo, Pedro Luis

2014-11-01

In this paper, stress fields at the surface of the capping layer of self-assembled InAsP quantum wires grown on an InP (001) substrate have been determined from atomistic models using molecular dynamics and Stillinger-Weber potentials. To carry out these calculations, the quantum wire compositional distribution was extracted from previous works, where the As and P distributions were determined by electron energy loss spectroscopy and high-resolution aberration-corrected Z-contrast imaging. Preferential sites for the nucleation of wires on the surface of the capping layer were studied and compared with (i) previous simulations using finite element analysis to solve anisotropic elastic theory equations and (ii) experimentally measured locations of stacked wires. Preferential nucleation sites of stacked wires were determined by the maximum stress location at the MD model surface in good agreement with experimental results and those derived from finite element analysis. This indicates that MD simulations based on empirical potentials provide a suitable and flexible tool to study strain dependent atom processes.

Quantum probability ranking principle for ligand-based virtual screening.

PubMed

Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

2017-04-01

Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

Quantum probability ranking principle for ligand-based virtual screening

NASA Astrophysics Data System (ADS)

Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

2017-04-01

Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

A Quantum-Based Similarity Method in Virtual Screening.

PubMed

Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

2015-10-02

One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.

Bioconjugated Quantum Dots for In Vivo Molecular and Cellular Imaging

PubMed Central

Smith, Andrew M.; Duan, Hongwei; Mohs, Aaron M.; Nie, Shuming

2008-01-01

Semiconductor quantum dots (QDs) are tiny light-emitting particles on the nanometer scale, and are emerging as a new class of fluorescent labels for biology and medicine. In comparison with organic dyes and fluorescent proteins, they have unique optical and electronic properties, with size-tunable light emission, superior signal brightness, resistance to photobleaching, and broad absorption spectra for simultaneous excitation of multiple fluorescence colors. QDs also provide a versatile nanoscale scaffold for designing multifunctional nanoparticles with both imaging and therapeutic functions. When linked with targeting ligands such as antibodies, peptides or small molecules, QDs can be used to target tumor biomarkers as well as tumor vasculatures with high affinity and specificity. Here we discuss the synthesis and development of state-of-the-art QD probes and their use for molecular and cellular imaging. We also examine key issues for in vivo imaging and therapy, such as nanoparticle biodistribution, pharmacokinetics, and toxicology. PMID:18495291

Quantum Chemical Molecular Dynamics Simulations of 1,3-Dichloropropene Combustion.

PubMed

Ahubelem, Nwakamma; Shah, Kalpit; Moghtaderi, Behdad; Page, Alister J

2015-09-03

Oxidative decomposition of 1,3-dichloropropene was investigated using quantum chemical molecular dynamics (QM/MD) at 1500 and 3000 K. Thermal oxidation of 1,3-dichloropropene was initiated by (1) abstraction of allylic H/Cl by O2 and (2) intra-annular C-Cl bond scission and elimination of allylic Cl. A kinetic analysis shows that (2) is the more dominant initiation pathway, in agreement with QM/MD results. These QM/MD simulations reveal new routes to the formation of major products (H2O, CO, HCl, CO2), which are propagated primarily by the chloroperoxy (ClO2), OH, and 1,3-dichloropropene derived radicals. In particular, intra-annular C-C/C-H bond dissociation reactions of intermediate aldehydes/ketones are shown to play a dominant role in the formation of CO and CO2. Our simulations demonstrate that both combustion temperature and radical concentration can influence the product yield, however not the combustion mechanism.

Molecular structure, vibrational analysis (IR and Raman) and quantum chemical investigations of 1-aminoisoquinoline

NASA Astrophysics Data System (ADS)

Sivaprakash, S.; Prakash, S.; Mohan, S.; Jose, Sujin P.

2017-12-01

Quantum chemical calculations of energy and geometrical parameters of 1-aminoisoquinoline [1-AIQ] were carried out by using DFT/B3LYP method using 6-311G (d,p), 6-311G++(d,p) and cc-pVTZ basis sets. The vibrational wavenumbers were computed for the energetically most stable, optimized geometry. The vibrational assignments were performed on the basis of potential energy distribution (PED) using VEDA program. The NBO analysis was done to investigate the intra molecular charge transfer of the molecule. The frontier molecular orbital (FMO) analysis was carried out and the chemical reactivity descriptors of the molecule were studied. The Mulliken charge analysis, molecular electrostatic potential (MEP), HOMO-LUMO energy gap and the related properties were also investigated at B3LYP level. The absorption spectrum of the molecule was studied from UV-Visible analysis by using time-dependent density functional theory (TD-DFT). Fourier Transform Infrared spectrum (FT-IR) and Raman spectrum of 1-AIQ compound were analyzed and recorded in the range 4000-400 cm-1 and 3500-100 cm-1 respectively. The experimentally determined wavenumbers were compared with those calculated theoretically and they complement each other.

High external quantum efficiency and fill-factor InGaN/GaN heterojunction solar cells grown by NH3-based molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Lang, J. R.; Neufeld, C. J.; Hurni, C. A.; Cruz, S. C.; Matioli, E.; Mishra, U. K.; Speck, J. S.

2011-03-01

High external quantum efficiency (EQE) p-i-n heterojunction solar cells grown by NH3-based molecular beam epitaxy are presented. EQE values including optical losses are greater than 50% with fill-factors over 72% when illuminated with a 1 sun AM0 spectrum. Optical absorption measurements in conjunction with EQE measurements indicate an internal quantum efficiency greater than 90% for the InGaN absorbing layer. By adjusting the thickness of the top p-type GaN window contact layer, it is shown that the short-wavelength (<365 nm) quantum efficiency is limited by the minority carrier diffusion length in highly Mg-doped p-GaN.

Zero-Point Energy Leakage in Quantum Thermal Bath Molecular Dynamics Simulations.

PubMed

Brieuc, Fabien; Bronstein, Yael; Dammak, Hichem; Depondt, Philippe; Finocchi, Fabio; Hayoun, Marc

2016-12-13

The quantum thermal bath (QTB) has been presented as an alternative to path-integral-based methods to introduce nuclear quantum effects in molecular dynamics simulations. The method has proved to be efficient, yielding accurate results for various systems. However, the QTB method is prone to zero-point energy leakage (ZPEL) in highly anharmonic systems. This is a well-known problem in methods based on classical trajectories where part of the energy of the high-frequency modes is transferred to the low-frequency modes leading to a wrong energy distribution. In some cases, the ZPEL can have dramatic consequences on the properties of the system. Thus, we investigate the ZPEL by testing the QTB method on selected systems with increasing complexity in order to study the conditions and the parameters that influence the leakage. We also analyze the consequences of the ZPEL on the structural and vibrational properties of the system. We find that the leakage is particularly dependent on the damping coefficient and that increasing its value can reduce and, in some cases, completely remove the ZPEL. When using sufficiently high values for the damping coefficient, the expected energy distribution among the vibrational modes is ensured. In this case, the QTB method gives very encouraging results. In particular, the structural properties are well-reproduced. The dynamical properties should be regarded with caution although valuable information can still be extracted from the vibrational spectrum, even for large values of the damping term.

Adiabatic Quantum Simulation of Quantum Chemistry

PubMed Central

Babbush, Ryan; Love, Peter J.; Aspuru-Guzik, Alán

2014-01-01

We show how to apply the quantum adiabatic algorithm directly to the quantum computation of molecular properties. We describe a procedure to map electronic structure Hamiltonians to 2-body qubit Hamiltonians with a small set of physically realizable couplings. By combining the Bravyi-Kitaev construction to map fermions to qubits with perturbative gadgets to reduce the Hamiltonian to 2-body, we obtain precision requirements on the coupling strengths and a number of ancilla qubits that scale polynomially in the problem size. Hence our mapping is efficient. The required set of controllable interactions includes only two types of interaction beyond the Ising interactions required to apply the quantum adiabatic algorithm to combinatorial optimization problems. Our mapping may also be of interest to chemists directly as it defines a dictionary from electronic structure to spin Hamiltonians with physical interactions. PMID:25308187

Adiabatic quantum simulation of quantum chemistry.

PubMed

Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

2014-10-13

We show how to apply the quantum adiabatic algorithm directly to the quantum computation of molecular properties. We describe a procedure to map electronic structure Hamiltonians to 2-body qubit Hamiltonians with a small set of physically realizable couplings. By combining the Bravyi-Kitaev construction to map fermions to qubits with perturbative gadgets to reduce the Hamiltonian to 2-body, we obtain precision requirements on the coupling strengths and a number of ancilla qubits that scale polynomially in the problem size. Hence our mapping is efficient. The required set of controllable interactions includes only two types of interaction beyond the Ising interactions required to apply the quantum adiabatic algorithm to combinatorial optimization problems. Our mapping may also be of interest to chemists directly as it defines a dictionary from electronic structure to spin Hamiltonians with physical interactions.

Quantum microbiology.

PubMed

Trevors, J T; Masson, L

2011-01-01

During his famous 1943 lecture series at Trinity College Dublin, the reknown physicist Erwin Schrodinger discussed the failure and challenges of interpreting life by classical physics alone and that a new approach, rooted in Quantum principles, must be involved. Quantum events are simply a level of organization below the molecular level. This includes the atomic and subatomic makeup of matter in microbial metabolism and structures, as well as the organic, genetic information code of DNA and RNA. Quantum events at this time do not elucidate, for example, how specific genetic instructions were first encoded in an organic genetic code in microbial cells capable of growth and division, and its subsequent evolution over 3.6 to 4 billion years. However, due to recent technological advances, biologists and physicists are starting to demonstrate linkages between various quantum principles like quantum tunneling, entanglement and coherence in biological processes illustrating that nature has exerted some level quantum control to optimize various processes in living organisms. In this article we explore the role of quantum events in microbial processes and endeavor to show that after nearly 67 years, Schrödinger was prophetic and visionary in his view of quantum theory and its connection with some of the fundamental mechanisms of life.

Radiative transfer calculations of ultra-relativistic shock breakout in circumstellar medium: Dependence on the central engine activity

NASA Astrophysics Data System (ADS)

Ohtani, Yukari; Suzuki, Akihiro; Shigeyama, Toshikazu

2015-08-01

Core collapse supernovae radiate bright X-ray or UV flashes imediately after their explosion, because shock waves emerge on the surfaces of the progenitors. Due to their short duration, a very small number of such events (so called shock breakouts) have been observed, and the maximum shock velocities are likely to be significantly smaller than the speed of light. In principle, we can consider the shocks with ultra-relativistic velocities breakout stellar surfaces and generate gamma-ray photons. A recently popular theory of gamma-ray bursts argues that the thermal radiation produced in the jet may play important roles in the prompt emission. Therefore, for understanding of the relation between jets and the central engine, studying properties of breakouts in the relativistic limit will be interesting. To obtain some information concerning the temporal evolution of the photospheric emission from jets, we make a radiative transfer calculation of ultra-relativistic shock breakout in circumstellar medium by using a Monte Carlo method. We use a self-similar solution constructed by Blandford & McKee (1976), in which the shock Lorentz factor is assumed to follow a simple power law relation determined by the central engine activity. By comparing the calculation results of the accelerating shock and the decelerating shock, we find that influence of the beaming effect and the scattering angular distribution cause two apparent differences in light curves and temporal spectral evolution. One is that the ratio of the time between the onset and the peak to the duration is much smaller in light curves of decelerating shocks. The other one is that the spectral shape does not significantly change with time if the shock accelerates, otherwise the first half of the emerging photons contains much more high energy photons (above 1 MeV) than the second half.

Effect of growth interruption in 1.55 μm InAs/InAlGaAs quantum dots on InP grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Jung, Daehwan; Ironside, Daniel J.; Bank, Seth R.; Gossard, Arthur C.; Bowers, John E.

2018-05-01

We report the effect of growth interruptions on the structural and optical properties of InAs/InAlGaAs/InP quantum dots using molecular beam epitaxy. We find that the surface quantum dots experience an unintended ripening process during the sample cooling stage, which reshapes the uncapped InAs nanostructures. To prevent this, we performed a partial capping experiment to effectively inhibit structural reconfiguration of surface InAs nanostructures during the cooling stage, revealing that InAs nanostructures first form quantum dashes and then transform into quantum dots via a ripening process. Our result suggests that the appearance of buried InAs/InAlGaAs nanostructures can be easily misunderstood by surface analysis.

Quantum kernel applications in medicinal chemistry.

PubMed

Huang, Lulu; Massa, Lou

2012-07-01

Progress in the quantum mechanics of biological molecules is being driven by computational advances. The notion of quantum kernels can be introduced to simplify the formalism of quantum mechanics, making it especially suitable for parallel computation of very large biological molecules. The essential idea is to mathematically break large biological molecules into smaller kernels that are calculationally tractable, and then to represent the full molecule by a summation over the kernels. The accuracy of the kernel energy method (KEM) is shown by systematic application to a great variety of molecular types found in biology. These include peptides, proteins, DNA and RNA. Examples are given that explore the KEM across a variety of chemical models, and to the outer limits of energy accuracy and molecular size. KEM represents an advance in quantum biology applicable to problems in medicine and drug design.

Quantum dot formation by molecular beam epitaxy of Ge on Si(100)

NASA Astrophysics Data System (ADS)

Chaparro, Sergio Arturo

1999-11-01

A new technique for producing electron systems with quantum confinement in three dimensions, quantum dots, has been studied. These quantum dots are coherent islands spontaneously formed at the early stages of Ge/Si(100) epitaxy due to the misfit of the system. Our goal is to gain understanding and control of the growth process so uniform quantum dot ensembles can be created for possible use in optoelectronic devices. A UHV Molecular Beam Epitaxy (MBE) growth system was built and calibrated to grow our samples. The samples were prepared by depositing Ge onto a Si(100) surface cleaned by flash desorption of the native oxides. Varying the growth rates from 0.6 ML/min to 4.0 ML/min, the substrate temperature from 450°C to 600°C, and the coverage from 3.5 ML to 14 ML produces different sample morphologies. After growth, the samples were analyzed both in situ and ex situ. The in situ analysis consisted of Auger electron spectroscopy for elemental analysis and reflection high energy electron diffraction, for surface structure analysis. The ex situ analysis included atomic force microscopy (AFM), transmission electron microscopy (TEM) and/or scanning electron microscopy (SEM). Many digital images were obtained from the microscope analysis. A novel, computer based, analysis was developed to extract the islands parameters from the microscope images. This data, which includes island area and average height for each island on every image, was used for a statistical analysis. Also from the data, island size distributions (histograms of island size) were generated. These measurements confirm that islands form after growth of a 3 ML wetting layer and that islands evolve as they grow. As more Ge is deposited these islands grow and as they grow they evolve from huts, square based pyramids, to domes, truncated pyramids, to dislocated domes. Our results show that the substrate temperature, deposition rate, and amount of deposited material are factors that affect the growth

Epigenetics: Biology's Quantum Mechanics

PubMed Central

Jorgensen, Richard A.

2011-01-01

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

Optical properties of a-plane (Al, Ga)N/GaN multiple quantum wells grown on strain engineered Zn1-xMgxO layers by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Xia, Y.; Brault, J.; Nemoz, M.; Teisseire, M.; Vinter, B.; Leroux, M.; Chauveau, J.-M.

2011-12-01

Nonpolar (112¯0) Al0.2Ga0.8N/GaN multiple quantum wells (MQWs) have been grown by molecular beam epitaxy on (112¯0) Zn0.74Mg0.26O templates on r-plane sapphire substrates. The quantum wells exhibit well-resolved photoluminescence peaks in the ultra-violet region, and no sign of quantum confined Stark effect is observed in the complete multiple quantum well series. The results agree well with flat band quantum well calculations. Furthermore, we show that the MQW structures are strongly polarized along the [0001] direction. The origin of the polarization is discussed in terms of the strain anisotropy dependence of the exciton optical oscillator strengths.

Short wavelength (visible) GaAs quantum well lasers grown by molecular beam epitaxy

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

Woodbridge, K.; Blood, P.; Fletcher, E.D.

1984-07-01

GaAs-AlGaAs multiple quantum well (MQW) injection lasers with well widths from 55 to 13 A have been grown by molecular beam epitaxy and operated at room temperature, showing emission at wavelengths down to 704 nm, the shortest reported for a MQW injection laser with GaAs wells. In a device with 25-A wells some evidence of coupling was apparent when barrier widths were reduced to 40 A. For devices with 80-A barriers there is a difference of about 20 nm between the calculated n = 1 (e--hh) transition wavelength and the lasing wavelength, whereas the calculation agrees with photovoltage absorption measurementsmore » on the same structures.« less

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.

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.

A molecular orbital study of the energy spectrum, exchange interaction and gate crosstalk of a four-quantum-dot system

NASA Astrophysics Data System (ADS)

Yang, Xu-Chen; Wang, Xin

The manipulation of coupled quantum dot devices is crucial to scalable, fault-tolerant quantum computation. We present a theoretical study of a four-electron four-quantum-dot system based on molecular orbital methods, which depicts a pair of singlet-triplet (S-T) qubits. We find that while the two S-T qubits are coupled by the capacitive interaction when they are sufficiently far away, the admixture of wave functions undergoes a substantial change as the two S-T qubits get closer. We find that in certain parameter regime the exchange interaction may only be defined in the sense of an effective one when the computational basis states no longer dominate the eigenstates. We further discuss the gate crosstalk as a consequence of this wave function mixing. This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, China (No. CityU 21300116) and the National Natural Science Foundation of China (No. 11604277).

Fluorescence quantum yield measurements of fluorescent proteins: a laboratory experiment for a biochemistry or molecular biophysics laboratory course.

PubMed

Wall, Kathryn P; Dillon, Rebecca; Knowles, Michelle K

2015-01-01

Fluorescent proteins are commonly used in cell biology to assess where proteins are within a cell as a function of time and provide insight into intracellular protein function. However, the usefulness of a fluorescent protein depends directly on the quantum yield. The quantum yield relates the efficiency at which a fluorescent molecule converts absorbed photons into emitted photons and it is necessary to know for assessing what fluorescent protein is the most appropriate for a particular application. In this work, we have designed an upper-level, biochemistry laboratory experiment where students measure the fluorescence quantum yields of fluorescent proteins relative to a standard organic dye. Four fluorescent protein variants, enhanced cyan fluorescent protein (ECFP), enhanced green fluorescent protein (EGFP), mCitrine, and mCherry, were used, however the methods described are useful for the characterization of any fluorescent protein or could be expanded to fluorescent quantum yield measurements of organic dye molecules. The laboratory is designed as a guided inquiry project and takes two, 4 hr laboratory periods. During the first day students design the experiment by selecting the excitation wavelength, choosing the standard, and determining the concentration needed for the quantum yield experiment that takes place in the second laboratory period. Overall, this laboratory provides students with a guided inquiry learning experience and introduces concepts of fluorescence biophysics into a biochemistry laboratory curriculum. © 2014 The International Union of Biochemistry and Molecular Biology.

Photoluminescence of ZnTe/ZnMgTe multiple quantum well structures grown on ZnTe substrates by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Tanaka, Tooru; Ohshita, Hiroshi; Saito, Katsuhiko; Guo, Qixin

2018-02-01

Photoluminescence (PL) properties of ZnTe/ZnMgTe quantum well (QW) structures grown by molecular beam epitaxy (MBE) were investigated systematically with respect to well widths and Mg contents. Observed PL peak energies were consistent well with the calculated emission energies of the QWs considering a lattice distortion in the ZnTe well. From the temperature dependence of PL intensity, it was found that a suppression of a carrier escape from QW is crucial to obtain a PL at higher temperature in the ZnTe/ZnMgTe QW. Based on the results, multiple quantum well structures were designed and fabricated, which exhibited a green PL at room temperature.

EDITORIAL: Focus on Quantum Control

NASA Astrophysics Data System (ADS)

Rabitz, Herschel

2009-10-01

Control of quantum phenomena has grown from a dream to a burgeoning field encompassing wide-ranging experimental and theoretical activities. Theoretical research in this area primarily concerns identification of the principles for controlling quantum phenomena, the exploration of new experimental applications and the development of associated operational algorithms to guide such experiments. Recent experiments with adaptive feedback control span many applications including selective excitation, wave packet engineering and control in the presence of complex environments. Practical procedures are also being developed to execute real-time feedback control considering the resultant back action on the quantum system. This focus issue includes papers covering many of the latest advances in the field. Focus on Quantum Control Contents Control of quantum phenomena: past, present and future Constantin Brif, Raj Chakrabarti and Herschel Rabitz Biologically inspired molecular machines driven by light. Optimal control of a unidirectional rotor Guillermo Pérez-Hernández, Adam Pelzer, Leticia González and Tamar Seideman Simulating quantum search algorithm using vibronic states of I2 manipulated by optimally designed gate pulses Yukiyoshi Ohtsuki Efficient coherent control by sequences of pulses of finite duration Götz S Uhrig and Stefano Pasini Control by decoherence: weak field control of an excited state objective Gil Katz, Mark A Ratner and Ronnie Kosloff Multi-qubit compensation sequences Y Tomita, J T Merrill and K R Brown Environment-invariant measure of distance between evolutions of an open quantum system Matthew D Grace, Jason Dominy, Robert L Kosut, Constantin Brif and Herschel Rabitz Simplified quantum process tomography M P A Branderhorst, J Nunn, I A Walmsley and R L Kosut Achieving 'perfect' molecular discrimination via coherent control and stimulated emission Stephen D Clow, Uvo C Holscher and Thomas C Weinacht A convenient method to simulate and visually

Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes

DOE PAGES

Sjostrom, Travis; Daligault, Jerome

2014-10-10

Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lowermore » temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.« less

Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-03-01

Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

Quantum molecular dynamics and multistep-direct analyses of multiple preequilibrium emission

NASA Astrophysics Data System (ADS)

Chadwick, M. B.; Chiba, S.; Niita, K.; Maruyama, T.; Iwamoto, A.

1995-11-01

We study multiple preequilibrium emission in nucleon induced reactions at intermediate energies, and compare quantum molecular dynamics (QMD) calculations with multistep-direct Feshbach-Kerman-Koonin results [M. B. Chadwick, P. G. Young, D. C. George, and Y. Watanabe, Phys. Rev. C 50, 996 (1994)]. When the theoretical expressions of this reference are reformulated so that the definitions of primary and multiple emission correspond to those used in QMD, the two theories yield similar results for primary and multiple preequilibrium emission. We use QMD as a tool to determine the multiplicities of fast preequilibrium nucleons as a function of incident energy. For fast particle cross sections to exceed 5% of the inclusive preequilibrium emission cross sections we find that two particles should be included in reactions above 50 MeV, three above about 180 MeV, and four are only needed when the incident energy exceeds about 400 MeV.

Studying fundamental physics using quantum enabled technologies with trapped molecular ions

NASA Astrophysics Data System (ADS)

Segal, D. M.; Lorent, V.; Dubessy, R.; Darquié, B.

2018-03-01

The text below was written during two visits that Daniel Segal made at Université Paris 13. Danny stayed at Laboratoire de Physique des Lasers the summers of 2008 and 2009 to participate in the exploration of a novel lead in the field of ultra-high resolution spectroscopy. Our idea was to probe trapped molecular ions using Quantum Logic Spectroscopy (QLS) in order to advance our understanding of a variety of fundamental processes in nature. At that time, QLS, a ground-breaking spectroscopic technique, had only been demonstrated with atomic ions. Our ultimate goals were new approaches to the observation of parity violation in chiral molecules and tests of time variations of the fundamental constants. This text is the original research proposal written eight years ago. We have added a series of notes to revisit it in the light of what has been since realized in the field.

Quantum cascade light emitting diodes based on type-2 quantum wells

NASA Technical Reports Server (NTRS)

Lin, C. H.; Yang, R. Q.; Zhang, D.; Murry, S. J.; Pei, S. S.; Allerman, A. A.; Kurtz, S. R.

1997-01-01

The authors have demonstrated room-temperature CW operation of type-2 quantum cascade (QC) light emitting diodes at 4.2 (micro)m using InAs/InGaSb/InAlSb type-2 quantum wells. The type-2 QC configuration utilizes sequential multiple photon emissions in a staircase of coupled type-2 quantum wells. The device was grown by molecular beam epitaxy on a p-type GaSb substrate and was compared of 20 periods of active regions separated by digitally graded quantum well injection regions. The maximum average output power is about 250 (micro)W at 80 K, and 140 (micro)W at 300 K at a repetition rate of 1 kHz with a duty cycle of 50%.

Distribution of tunnelling times for quantum electron transport.

PubMed

Rudge, Samuel L; Kosov, Daniel S

2016-03-28

In electron transport, the tunnelling time is the time taken for an electron to tunnel out of a system after it has tunnelled in. We define the tunnelling time distribution for quantum processes in a dissipative environment and develop a practical approach for calculating it, where the environment is described by the general Markovian master equation. We illustrate the theory by using the rate equation to compute the tunnelling time distribution for electron transport through a molecular junction. The tunnelling time distribution is exponential, which indicates that Markovian quantum tunnelling is a Poissonian statistical process. The tunnelling time distribution is used not only to study the quantum statistics of tunnelling along the average electric current but also to analyse extreme quantum events where an electron jumps against the applied voltage bias. The average tunnelling time shows distinctly different temperature dependence for p- and n-type molecular junctions and therefore provides a sensitive tool to probe the alignment of molecular orbitals relative to the electrode Fermi energy.

Signatures of α clustering in ultrarelativistic collisions with light nuclei

NASA Astrophysics Data System (ADS)

Rybczyński, Maciej; Piotrowska, Milena; Broniowski, Wojciech

2018-03-01

We explore possible observable signatures of α clustering of light nuclei in ultrarelativistic nuclear collisions involving Be,97, 12C, and 16O. The clustering leads to specific spatial correlations of the nucleon distributions in the ground state, which are manifest in the earliest stage of the ultrahigh energy reaction. The formed initial state of the fireball is sensitive to these correlations, and the effect influences, after the collective evolution of the system, the hadron production in the final stage. Specifically, we study effects on the harmonic flow in collisions of light clustered nuclei with a heavy target (208Pb), showing that measures of the elliptic flow are sensitive to clusterization in Be,97, whereas triangular flow is sensitive to clusterization in 12C and 16O. Specific predictions are made for model collisions at energies available at the CERN Super Proton Synchrotron. In another exploratory development we also examine proton-beryllium collisions, where the 3 /2- ground state of Be,97 nuclei is polarized by an external magnetic field. Clusterization leads to multiplicity distributions of participant nucleons which depend on the orientation of the polarization with respect to the collision axis, as well as on the magnetic number of the state. The obtained effects on multiplicities reach a factor of a few for collisions with a large number of participant nucleons.

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

PubMed

Álvarez-Barcia, Sonia; Kästner, Johannes

2017-06-01

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

The Development of Rigorously Correct, Dynamical Pseudopotentials for Use in Mixed Quantum/Classical Molecular Dynamics Simulations in the Condensed Phase

NASA Astrophysics Data System (ADS)

Kahros, Argyris

Incorporating quantum mechanics into an atomistic simulation necessarily involves solving the Schrodinger equation. Unfortunately, the computational expense associated with solving this equation scales miserably with the number of included quantum degrees of freedom (DOF). The situation is so dire, in fact, that a molecular dynamics (MD) simulation cannot include more than a small number of quantum DOFs before it becomes computationally intractable. Thus, if one were to simulate a relatively large system, such as one containing several hundred atoms or molecules, it would be unreasonable to attempt to include the effects of all of the electrons associated with all of the components of the system. The mixed quantum/classical (MQC) approach provides a way to circumvent this issue. It involves treating the vast majority of the system classically, which incurs minimal computational expense, and reserves the consideration of quantum mechanical effects for only the few degrees of freedom more directly involved in the chemical phenomenon being studied. For example, if one were to study the bonding of a single diatomic molecule in the gas phase, one could employ a MQC approach by treating the nuclei of the molecule's two atoms classically---including the deeply bound, low-energy electrons that change relatively little---and solving the Schrodinger equation only for the high energy electron(s) directly involved in the bonding of the classical cores. In such a way, one could study the bonding of this molecule in a rigorous fashion while treating only the directly related degrees of freedom quantum mechanically. Pseudopotentials are then responsible for dictating the interactions between the quantum and classical degrees of freedom. As these potentials are the sole link between the quantum and classical DOFs, their proper development is of the utmost importance. This Thesis is concerned primarily with my work on the development of novel, rigorous and dynamical

Making a molecular gas in the quantum regime

NASA Astrophysics Data System (ADS)

Ni, Kang-Kuen

2017-04-01

Ultracold molecules are exciting systems for a large range of scientific explorations including studies of novel phases of matter and precision measurement. In this talk, I will present a brief story of the first quantum gas of molecules, KRb, created under my PhD advisor, Deborah Jin, in 2008. A complete surprise was finding ultracold chemistry in such a system through measurements of reactant losses. In particular, long-range physics that determines KRb reactant collision rates, including van der Waals interactions, quantum statistics, and dipolar interactions, were studied extensively. However, the short-range behavior of these chemical reactions remains unknown. A legacy of her work is carried out in my lab at Harvard, where we are integrating physical chemistry tools with cold atom techniques to study ultracold chemistry with KRb molecules. In particular, we aim to elucidate the four-center reaction 2 KRb ->K2 + Rb2 by detecting the reaction products through ionization - both identify the product species and mapping out their complete quantum states.

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

PubMed

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

2015-01-01

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

Thermal quantum time-correlation functions from classical-like dynamics

NASA Astrophysics Data System (ADS)

Hele, Timothy J. H.

2017-07-01

Thermal quantum time-correlation functions are of fundamental importance in quantum dynamics, allowing experimentally measurable properties such as reaction rates, diffusion constants and vibrational spectra to be computed from first principles. Since the exact quantum solution scales exponentially with system size, there has been considerable effort in formulating reliable linear-scaling methods involving exact quantum statistics and approximate quantum dynamics modelled with classical-like trajectories. Here, we review recent progress in the field with the development of methods including centroid molecular dynamics , ring polymer molecular dynamics (RPMD) and thermostatted RPMD (TRPMD). We show how these methods have recently been obtained from 'Matsubara dynamics', a form of semiclassical dynamics which conserves the quantum Boltzmann distribution. We also apply the Matsubara formalism to reaction rate theory, rederiving t → 0+ quantum transition-state theory (QTST) and showing that Matsubara-TST, like RPMD-TST, is equivalent to QTST. We end by surveying areas for future progress.

Quantum interference in coherent tunneling through branched molecular junctions containing ferrocene centers

NASA Astrophysics Data System (ADS)

Zhao, Xin; Kastlunger, Georg; Stadler, Robert

2017-08-01

In our theoretical study where we combine a nonequilibrium Green's function approach with density functional theory we investigate branched compounds containing ferrocene moieties in both branches which, due to their metal centers, are designed to allow for asymmetry induced by local charging. In these compounds the ferrocene moieties are connected to pyridyl anchor groups either directly or via acetylenic spacers in a metaconnection, where we also compare our results with those obtained for the respective single-branched molecules with both meta- and paraconnections between the metal center and the anchors. We find a destructive quantum interference (DQI) feature in the transmission function slightly below the lowest unoccupied molecular orbital, which dominates the conductance even for the uncharged branched compound with spacer groups inserted. In an analysis based on mapping the structural characteristics of the range of molecules in our article onto tight-binding models, we identify the structural source of the DQI minimum as the through-space coupling between the pyridyl anchor groups. We also find that local charging in one of the branches changes the conductance only by about one order of magnitude, which we explain in terms of the spatial distributions of the relevant molecular orbitals for the branched compounds.

Multi-Excitonic Quantum Dot Molecules

NASA Astrophysics Data System (ADS)

Scheibner, M.; Stinaff, E. A.; Doty, M. F.; Ware, M. E.; Bracker, A. S.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2006-03-01

With the ability to create coupled pairs of quantum dots, the next step towards the realization of semiconductor based quantum information processing devices can be taken. However, so far little knowledge has been gained on these artificial molecules. Our photoluminescence experiments on single InAs/GaAs quantum dot molecules provide the systematics of coupled quantum dots by delineating the spectroscopic features of several key charge configurations in such quantum systems, including X, X^+,X^2+, XX, XX^+ (with X being the neutral exciton). We extract general rules which determine the formation of molecular states of coupled quantum dots. These include the fact that quantum dot molecules provide the possibility to realize various spin configurations and to switch the electron hole exchange interaction on and off by shifting charges inside the molecule. This knowledge will be valuable in developing implementations for quantum information processing.

Molecular dynamics in an optical trap of glutamate receptors labeled with quantum-dots on living neurons

NASA Astrophysics Data System (ADS)

Kishimoto, Tatsunori; Maezawa, Yasuyo; Kudoh, Suguru N.; Taguchi, Takahisa; Hosokawa, Chie

2017-04-01

Molecular dynamics of glutamate receptor, which is major neurotransmitter receptor at excitatory synapse located on neuron, is essential for synaptic plasticity in the complex neuronal networks. Here we studied molecular dynamics in an optical trap of AMPA-type glutamate receptor (AMPAR) labeled with quantum-dot (QD) on living neuronal cells with fluorescence imaging and fluorescence correlation spectroscopy (FCS). When a 1064-nm laser beam for optical trapping was focused on QD-AMPARs located on neuronal cells, the fluorescence intensity of QD-AMPARs gradually increased at the focal spot. Using single-particle tracking of QD-AMPARs on neurons, the average diffusion coefficient decreased in an optical trap. Moreover, the decay time obtained from FCS analysis increased with the laser power and the initial assembling state of AMPARs depended on culturing day, suggesting that the motion of QD-AMPAR was constrained in an optical trap.

Vibrational Heat Transport in Molecular Junctions

NASA Astrophysics Data System (ADS)

Segal, Dvira; Agarwalla, Bijay Kumar

2016-05-01

We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.

An ultra-relativistic outflow from a neutron star accreting gas from a companion.

PubMed

Fender, Rob; Wu, Kinwah; Johnston, Helen; Tzioumis, Tasso; Jonker, Peter; Spencer, Ralph; Van Der Klis, Michiel

2004-01-15

Collimated relativistic outflows-also known as jets-are amongst the most energetic phenomena in the Universe. They are associated with supermassive black holes in distant active galactic nuclei, accreting stellar-mass black holes and neutron stars in binary systems and are believed to be responsible for gamma-ray bursts. The physics of these jets, however, remains something of a mystery in that their bulk velocities, compositions and energetics remain poorly determined. Here we report the discovery of an ultra-relativistic outflow from a neutron star accreting gas within a binary stellar system. The velocity of the outflow is comparable to the fastest-moving flows observed from active galactic nuclei, and its strength is modulated by the rate of accretion of material onto the neutron star. Shocks are energized further downstream in the flow, which are themselves moving at mildly relativistic bulk velocities and are the sites of the observed synchrotron emission from the jet. We conclude that the generation of highly relativistic outflows does not require properties that are unique to black holes, such as an event horizon.

Numerical solution of special ultra-relativistic Euler equations using central upwind scheme

NASA Astrophysics Data System (ADS)

Ghaffar, Tayabia; Yousaf, Muhammad; Qamar, Shamsul

2018-06-01

This article is concerned with the numerical approximation of one and two-dimensional special ultra-relativistic Euler equations. The governing equations are coupled first-order nonlinear hyperbolic partial differential equations. These equations describe perfect fluid flow in terms of the particle density, the four-velocity and the pressure. A high-resolution shock-capturing central upwind scheme is employed to solve the model equations. To avoid excessive numerical diffusion, the considered scheme avails the specific information of local propagation speeds. By using Runge-Kutta time stepping method and MUSCL-type initial reconstruction, we have obtained 2nd order accuracy of the proposed scheme. After discussing the model equations and the numerical technique, several 1D and 2D test problems are investigated. For all the numerical test cases, our proposed scheme demonstrates very good agreement with the results obtained by well-established algorithms, even in the case of highly relativistic 2D test problems. For validation and comparison, the staggered central scheme and the kinetic flux-vector splitting (KFVS) method are also implemented to the same model. The robustness and efficiency of central upwind scheme is demonstrated by the numerical results.

Transport Properties of the Nuclear Pasta Phase with Quantum Molecular Dynamics

NASA Astrophysics Data System (ADS)

Nandi, Rana; Schramm, Stefan

2018-01-01

We study the transport properties of nuclear pasta for a wide range of density, temperature, and proton fractions, relevant for different astrophysical scenarios adopting a quantum molecular dynamics model. In particular, we estimate the values of shear viscosity as well as electrical and thermal conductivities by calculating the static structure factor S(q) using simulation data. In the density and temperature range where the pasta phase appears, the static structure factor shows irregular behavior. The presence of a slab phase greatly enhances the peak in S(q). However, the effect of irregularities in S(q) on the transport coefficients is not very dramatic. The values of all three transport coefficients are found to have the same orders of magnitude as found in theoretical calculations for the inner crust matter of neutron stars without the pasta phase; therefore, the values are in contrast to earlier speculations that a pasta layer might be highly resistive, both thermally and electrically.

Synthesis of a Neutral Mixed-Valence Diferrocenyl Carborane for Molecular Quantum-Dot Cellular Automata Applications.

PubMed

Christie, John A; Forrest, Ryan P; Corcelli, Steven A; Wasio, Natalie A; Quardokus, Rebecca C; Brown, Ryan; Kandel, S Alex; Lu, Yuhui; Lent, Craig S; Henderson, Kenneth W

2015-12-14

The preparation of 7-Fc(+) -8-Fc-7,8-nido-[C2 B9 H10 ](-) (Fc(+) FcC2 B9 (-) ) demonstrates the successful incorporation of a carborane cage as an internal counteranion bridging between ferrocene and ferrocenium units. This neutral mixed-valence Fe(II) /Fe(III) complex overcomes the proximal electronic bias imposed by external counterions, a practical limitation in the use of molecular switches. A combination of UV/Vis-NIR spectroscopic and TD-DFT computational studies indicate that electron transfer within Fc(+) FcC2 B9 (-) is achieved through a bridge-mediated mechanism. This electronic framework therefore provides the possibility of an all-neutral null state, a key requirement for the implementation of quantum-dot cellular automata (QCA) molecular computing. The adhesion, ordering, and characterization of Fc(+) FcC2 B9 (-) on Au(111) has been observed by scanning tunneling microscopy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

DTIC Science & Technology

2016-06-06

Understanding Molecular Ion-Neutral Atom Collisions for the Production of Utracold Molecular Ions In the last five years, the study of ultracold...U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 molecular ion, quantum chemistry, atom ion interaction...Molecular Ion-Neutral Atom Collisions for the Production of Utracold Molecular Ions Report Title In the last five years, the study of ultracold molecular

Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Laskin, A.

2017-12-01

Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

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

PubMed

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

2018-03-13

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

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

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

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

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

Role of wave packet width in quantum molecular dynamics in fusion reactions near barrier

NASA Astrophysics Data System (ADS)

Cao, X. G.; Ma, Y. G.; Zhang, G. Q.; Wang, H. W.; Anastasi, A.; Curciarello, F.; De Leo, V.

2014-05-01

The dynamical fusion process of 48Ca + 144Sm with different impact parameters near barrier is studied by an extended quantum molecular dynamics (EQMD) model, where width of wavepacket is dynamically treated based on variational principle. The time evolution of different energy components such as potential energy, kinetic energy, Coulomb energy and Pauli potential are analyzed when dynamical or fixed width is assumed in calculation. It is found that the dynamical wavepacket width can enhance the dissipation of incident energy and the fluctuations, which are important to form compound nuclei. Moreover, we compare the fusion barrier dependence on the incident energy when it is determined by both dynamical and fixed wavepacket width.

Intermediate-band photosensitive device with quantum dots having tunneling barrier embedded in organic matrix

DOEpatents

Forrest, Stephen R.

2008-08-19

A plurality of quantum dots each have a shell. The quantum dots are embedded in an organic matrix. At least the quantum dots and the organic matrix are photoconductive semiconductors. The shell of each quantum dot is arranged as a tunneling barrier to require a charge carrier (an electron or a hole) at a base of the tunneling barrier in the organic matrix to perform quantum mechanical tunneling to reach the respective quantum dot. A first quantum state in each quantum dot is between a lowest unoccupied molecular orbital (LUMO) and a highest occupied molecular orbital (HOMO) of the organic matrix. Wave functions of the first quantum state of the plurality of quantum dots may overlap to form an intermediate band.

Luminescent N-polar (In,Ga)N/GaN quantum wells achieved by plasma-assisted molecular beam epitaxy at temperatures exceeding 700 °C

NASA Astrophysics Data System (ADS)

Chèze, C.; Feix, F.; Lähnemann, J.; Flissikowski, T.; Kryśko, M.; Wolny, P.; Turski, H.; Skierbiszewski, C.; Brandt, O.

2018-01-01

Previously, we found that N-polar (In,Ga)N/GaN quantum wells prepared on freestanding GaN substrates by plasma-assisted molecular beam epitaxy at conventional growth temperatures of about 650 °C do not exhibit any detectable luminescence even at 10 K. In the present work, we investigate (In,Ga)N/GaN quantum wells grown on Ga- and N-polar GaN substrates at a constant temperature of 730 °C . This exceptionally high temperature results in a vanishing In incorporation for the Ga-polar sample. In contrast, quantum wells with an In content of 20% and abrupt interfaces are formed on N-polar GaN. Moreover, these quantum wells exhibit a spatially uniform green luminescence band up to room temperature, but the intensity of this band is observed to strongly quench with temperature. Temperature-dependent photoluminescence transients show that this thermal quenching is related to a high density of nonradiative Shockley-Read-Hall centers with large capture coefficients for electrons and holes.

Quantum physics meets biology

PubMed Central

Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko

2009-01-01

Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a “pedestrian guide” to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future “quantum biology,” its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena. PMID:20234806

Quantum physics meets biology.

PubMed

Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko

2009-12-01

Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a "pedestrian guide" to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future "quantum biology," its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.

From transistor to trapped-ion computers for quantum chemistry.

PubMed

Yung, M-H; Casanova, J; Mezzacapo, A; McClean, J; Lamata, L; Aspuru-Guzik, A; Solano, E

2014-01-07

Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology.

From transistor to trapped-ion computers for quantum chemistry

PubMed Central

Yung, M.-H.; Casanova, J.; Mezzacapo, A.; McClean, J.; Lamata, L.; Aspuru-Guzik, A.; Solano, E.

2014-01-01

Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology. PMID:24395054

Molecular Quantum Similarity, Chemical Reactivity and Database Screening of 3D Pharmacophores of the Protein Kinases A, B and G from Mycobacterium tuberculosis.

PubMed

Morales-Bayuelo, Alejandro

2017-06-21

Mycobacterium tuberculosis remains one of the world's most devastating pathogens. For this reason, we developed a study involving 3D pharmacophore searching, selectivity analysis and database screening for a series of anti-tuberculosis compounds, associated with the protein kinases A, B, and G. This theoretical study is expected to shed some light onto some molecular aspects that could contribute to the knowledge of the molecular mechanics behind interactions of these compounds, with anti-tuberculosis activity. Using the Molecular Quantum Similarity field and reactivity descriptors supported in the Density Functional Theory, it was possible to measure the quantification of the steric and electrostatic effects through the Overlap and Coulomb quantitative convergence (alpha and beta) scales. In addition, an analysis of reactivity indices using global and local descriptors was developed, identifying the binding sites and selectivity on these anti-tuberculosis compounds in the active sites. Finally, the reported pharmacophores to PKn A, B and G, were used to carry out database screening, using a database with anti-tuberculosis drugs from the Kelly Chibale research group (http://www.kellychibaleresearch.uct.ac.za/), to find the compounds with affinity for the specific protein targets associated with PKn A, B and G. In this regard, this hybrid methodology (Molecular Mechanic/Quantum Chemistry) shows new insights into drug design that may be useful in the tuberculosis treatment today.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Resonant transition-based quantum computation

NASA Astrophysics Data System (ADS)

Chiang, Chen-Fu; Hsieh, Chang-Yu

2017-05-01

In this article we assess a novel quantum computation paradigm based on the resonant transition (RT) phenomenon commonly associated with atomic and molecular systems. We thoroughly analyze the intimate connections between the RT-based quantum computation and the well-established adiabatic quantum computation (AQC). Both quantum computing frameworks encode solutions to computational problems in the spectral properties of a Hamiltonian and rely on the quantum dynamics to obtain the desired output state. We discuss how one can adapt any adiabatic quantum algorithm to a corresponding RT version and the two approaches are limited by different aspects of Hamiltonians' spectra. The RT approach provides a compelling alternative to the AQC under various circumstances. To better illustrate the usefulness of the novel framework, we analyze the time complexity of an algorithm for 3-SAT problems and discuss straightforward methods to fine tune its efficiency.

Phase transition between quantum and classical regimes for the escape rate of dimeric molecular nanomagnets in a staggered magnetic field

NASA Astrophysics Data System (ADS)

Owerre, S. A.; Paranjape, M. B.

2014-04-01

We study the phase transition of the escape rate of exchange-coupled dimer of single-molecule magnets which are coupled either ferromagnetically or antiferromagnetically in a staggered magnetic field and an easy z-axis anisotropy. The Hamiltonian for this system has been used to study dimeric molecular nanomagnet [Mn4]2 which is comprised of two single molecule magnets coupled antiferromagnetically. We generalize the method of mapping a single-molecule magnetic spin problem onto a quantum-mechanical particle to dimeric molecular nanomagnets. The problem is mapped to a single particle quantum-mechanical Hamiltonian in terms of the relative coordinate and a coordinate dependent reduced mass. It is shown that the presence of the external staggered magnetic field creates a phase boundary separating the first- from the second-order transition. With the set of parameters used by R. Tiron et al. (2003) [25] and S. Hill et al. (2003) [20] to fit experimental data for [Mn4]2 dimer we find that the critical temperature at the phase boundary is T0(c)=0.29K. Therefore, thermally activated transitions should occur for temperatures greater than T0(c).

Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

PubMed

Kantardjiev, Alexander A

2012-07-01

Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

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

DOE PAGES

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

2017-01-24

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

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.

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

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

Huang, Jing; Mei, Ye; König, Gerhard

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

Optical Spectroscopy Of Charged Quantum Dot Molecules

NASA Astrophysics Data System (ADS)

Scheibner, M.; Bracker, A. S.; Stinaff, E. A.; Doty, M. F.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2007-04-01

Coupling between two closely spaced quantum dots is observed by means of photoluminescence spectroscopy. Hole coupling is realized by rational crystal growth and heterostructure design. We identify molecular resonances of different excitonic charge states, including the important case of a doubly charged quantum dot molecule.

Turbocharged molecular discovery of OLED emitters: from high-throughput quantum simulation to highly efficient TADF devices

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Ha, Dong-Gwang; Einzinger, Markus; Wu, Tony; Baldo, Marc A.; Aspuru-Guzik, Alán.

2016-09-01

Discovering new OLED emitters requires many experiments to synthesize candidates and test performance in devices. Large scale computer simulation can greatly speed this search process but the problem remains challenging enough that brute force application of massive computing power is not enough to successfully identify novel structures. We report a successful High Throughput Virtual Screening study that leveraged a range of methods to optimize the search process. The generation of candidate structures was constrained to contain combinatorial explosion. Simulations were tuned to the specific problem and calibrated with experimental results. Experimentalists and theorists actively collaborated such that experimental feedback was regularly utilized to update and shape the computational search. Supervised machine learning methods prioritized candidate structures prior to quantum chemistry simulation to prevent wasting compute on likely poor performers. With this combination of techniques, each multiplying the strength of the search, this effort managed to navigate an area of molecular space and identify hundreds of promising OLED candidate structures. An experimentally validated selection of this set shows emitters with external quantum efficiencies as high as 22%.

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

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

PubMed

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

2012-10-11

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

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

Magnetismo Molecular (Molecular Magentism)

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

Reis, Mario S; Moreira Dos Santos, Antonio F

The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail themore » physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.« less

Sensing of molecules using quantum dynamics

PubMed Central

Migliore, Agostino; Naaman, Ron; Beratan, David N.

2015-01-01

We design sensors where information is transferred between the sensing event and the actuator via quantum relaxation processes, through distances of a few nanometers. We thus explore the possibility of sensing using intrinsically quantum mechanical phenomena that are also at play in photobiology, bioenergetics, and information processing. Specifically, we analyze schemes for sensing based on charge transfer and polarization (electronic relaxation) processes. These devices can have surprising properties. Their sensitivity can increase with increasing separation between the sites of sensing (the receptor) and the actuator (often a solid-state substrate). This counterintuitive response and other quantum features give these devices favorable characteristics, such as enhanced sensitivity and selectivity. Using coherent phenomena at the core of molecular sensing presents technical challenges but also suggests appealing schemes for molecular sensing and information transfer in supramolecular structures. PMID:25911636

Sensing of molecules using quantum dynamics

DOE PAGES

Migliore, Agostino; Naaman, Ron; Beratan, David N.

2015-04-24

In this study, we design sensors where information is transferred between the sensing event and the actuator via quantum relaxation processes, through distances of a few nanometers. We thus explore the possibility of sensing using intrinsically quantum mechanical phenomena that are also at play in photobiology, bioenergetics, and information processing. Specifically, we analyze schemes for sensing based on charge transfer and polarization (electronic relaxation) processes. These devices can have surprising properties. Their sensitivity can increase with increasing separation between the sites of sensing (the receptor) and the actuator (often a solid-state substrate). This counterintuitive response and other quantum features givemore » these devices favorable characteristics, such as enhanced sensitivity and selectivity. Finally, using coherent phenomena at the core of molecular sensing presents technical challenges but also suggests appealing schemes for molecular sensing and information transfer in supramolecular structures.« less

WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard; Lorenz, Ulf

2017-04-01

WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. The graphical capabilities allow visualization of quantum dynamics 'on the fly', including Wigner phase space representations. Being easy to use and highly versatile, WavePacket is well suited for the teaching of quantum mechanics as well as for research projects in atomic, molecular and optical physics or in physical or theoretical chemistry. The present Part I deals with the description of closed quantum systems in terms of Schrödinger equations. The emphasis is on discrete variable representations for spatial discretization as well as various techniques for temporal discretization. The upcoming Part II will focus on open quantum systems and dimension reduction; it also describes the codes for optimal control of quantum dynamics. The present work introduces the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge platform, where extensive Wiki-documentation as well as worked-out demonstration examples can be found.

Biocompatible Quantum Dots for Biological Applications

PubMed Central

Rosenthal, Sandra J.; Chang, Jerry C.; Kovtun, Oleg; McBride, James R.; Tomlinson, Ian D.

2011-01-01

Semiconductor quantum dots are quickly becoming a critical diagnostic tool for discerning cellular function at the molecular level. Their high brightness, long-lasting, sizetunable, and narrow luminescence set them apart from conventional fluorescence dyes. Quantum dots are being developed for a variety of biologically oriented applications, including fluorescent assays for drug discovery, disease detection, single protein tracking, and intracellular reporting. This review introduces the science behind quantum dots and describes how they are made biologically compatible. Several applications are also included, illustrating strategies toward target specificity, and are followed by a discussion on the limitations of quantum dot approaches. The article is concluded with a look at the future direction of quantum dots. PMID:21276935

Electron transport in unipolar InGaN/GaN multiple quantum well structures grown by NH 3 molecular beam epitaxy

DOE PAGES

Browne, David A.; Wu, Yuh -Renn; Speck, James S.; ...

2015-05-08

Unipolar-light emitting diode like structures were grown by NH 3 molecular beam epitaxy on c plane (0001) GaN on sapphire templates. Studies were performed to experimentally examine the effect of random alloy fluctuations on electron transport through quantum well active regions. These unipolar structures served as a test vehicle to test our 2D model of the effect of compositional fluctuations on polarization-induced barriers. Variables that were systematically studied included varying quantum well number from 0 to 5, well thickness of 1.5 nm, 3 nm, and 4.5 nm, and well compositions of In 0.14Ga 0.86N and In 0.19Ga 0.81N. Diode-like currentmore » voltage behavior was clearly observed due to the polarization-induced conduction band barrier in the quantum well region. Increasing quantum well width and number were shown to have a significant impact on increasing the turn-on voltage of each device. Temperature dependent IV measurements clearly revealed the dominant effect of thermionic behavior for temperatures from room temperature and above. Atom probe tomography was used to directly analyze parameters of the alloy fluctuations in the quantum wells including amplitude and length scale of compositional variation. Furthermore, a drift diffusion Schrodinger Poisson method accounting for two dimensional indium fluctuations (both in the growth direction and within the wells) was used to correctly model the turn-on voltages of the devices as compared to traditional 1D simulation models.« less

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

PubMed

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

2009-04-01

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

Explaining the apparent impenetrable barrier to ultra-relativistic electrons in the outer Van Allen belt.

PubMed

Ozeke, Louis G; Mann, Ian R; Murphy, Kyle R; Degeling, Alex W; Claudepierre, Seth G; Spence, Harlan E

2018-05-10

Recent observations have shown the existence of an apparent impenetrable barrier at the inner edge of the ultra-relativistic outer electron radiation belt. This apparent impenetrable barrier has not been explained. However, recent studies have suggested that fast loss, such as associated with scattering into the atmosphere from man-made very-low frequency transmissions, is required to limit the Earthward extent of the belt. Here we show that the steep flux gradient at the implied barrier location is instead explained as a natural consequence of ultra-low frequency wave radial diffusion. Contrary to earlier claims, sharp boundaries in fast loss processes at the barrier are not needed. Moreover, we show that penetration to the barrier can occur on the timescale of days rather than years as previously reported, with the Earthward extent of the belt being limited by the finite duration of strong solar wind driving, which can encompass only a single geomagnetic storm.

Ultrarelativistic boost of a black hole in the magnetic universe of Levi-Civita-Bertotti-Robinson

NASA Astrophysics Data System (ADS)

Ortaggio, Marcello; Astorino, Marco

2018-05-01

We consider an exact Einstein-Maxwell solution constructed by Alekseev and Garcia, which describes a Schwarzschild black hole immersed in the magnetic universe of Levi-Civita, Bertotti, and Robinson (LCBR). After reviewing the basic properties of this spacetime, we study the ultrarelativistic limit in which the black hole is boosted to the speed of light, while sending its mass to 0. This results in a nonexpanding impulsive wave traveling in the LCBR universe. The wave front is a 2-sphere carrying two null point particles at its poles—a remnant of the structure of the original static spacetime. It is also shown that the obtained line element belongs to the Kundt class of spacetimes, and the relation with the known family of exact gravitational waves of finite duration propagating in the LCBR background is clarified. In the limit of a vanishing electromagnetic field, one point particle is pushed away to infinity and the single-particle Aichelburg-Sexl p p -wave propagating in Minkowski space is recovered.

Data mining techniques for scientific computing: Application to asymptotic paraxial approximations to model ultrarelativistic particles

NASA Astrophysics Data System (ADS)

Assous, Franck; Chaskalovic, Joël

2011-06-01

We propose a new approach that consists in using data mining techniques for scientific computing. Indeed, data mining has proved to be efficient in other contexts which deal with huge data like in biology, medicine, marketing, advertising and communications. Our aim, here, is to deal with the important problem of the exploitation of the results produced by any numerical method. Indeed, more and more data are created today by numerical simulations. Thus, it seems necessary to look at efficient tools to analyze them. In this work, we focus our presentation to a test case dedicated to an asymptotic paraxial approximation to model ultrarelativistic particles. Our method directly deals with numerical results of simulations and try to understand what each order of the asymptotic expansion brings to the simulation results over what could be obtained by other lower-order or less accurate means. This new heuristic approach offers new potential applications to treat numerical solutions to mathematical models.

Systematic study of 16O-induced fusion with the improved quantum molecular dynamics model

NASA Astrophysics Data System (ADS)

Wang, Ning; Zhao, Kai; Li, Zhuxia

2014-11-01

The heavy-ion fusion reactions with 16O bombarding on 62Ni,65Cu,74Ge,148Nd,180Hf,186W,208Pb,238U are systematically investigated with the improved quantum molecular dynamics model. The fusion cross sections at energies near and above the Coulomb barriers can be reasonably well reproduced by using this semiclassical microscopic transport model with the parameter sets SkP* and IQ3a. The dynamical nucleus-nucleus potentials and the influence of Fermi constraint on the fusion process are also studied simultaneously. In addition to the mean field, the Fermi constraint also plays a key role for the reliable description of the fusion process and for improving the stability of fragments in heavy-ion collisions.

From quantum measurement to biology via retrocausality.

PubMed

Matsuno, Koichiro

2017-12-01

A reaction cycle in general or a metabolic cycle in particular owes its evolutionary emergence to the covering reaction environment acting as a measurement apparatus of a natural origin. The quantum measurement of the environmental origin underlying the molecular processes observed in the biological realm is operative cohesively between the measuring and the measured. The measuring part comes to pull in a quantum as an indivisible lump available from an arbitrary material body to be measured. The inevitable difference between the impinging quantum upon the receiving end on the part of the environment and the actual quantum pulled into the receiving end comes to effectively be nullified through the retrocausative propagation of the corresponding wave function proceeding backwards in time. The retrocausal regulation applied to the interface between the measuring and the measured is to function as the organizational agency supporting biology, and is sought in the act for the present in the immediate future within the realm of quantum phenomena. Molecular dynamics in biology owes both the evolutionary buildup and maintenance of its organization to the retrocausal operation of the unitary transformation applied to quantum phenomena proceeding backwards in time. Quantum measurement provides the cohesive agency that is pivotal for implementing the retrocausal regulation. In particular, the physical origin of Darwinian natural selection can be seen in the retrocausal regulation applied to the unitary transformation of a quantum origin. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantum-like behavior without quantum physics I : Kinematics of neural-like systems.

PubMed

Selesnick, S A; Rawling, J P; Piccinini, Gualtiero

2017-09-01

Recently there has been much interest in the possible quantum-like behavior of the human brain in such functions as cognition, the mental lexicon, memory, etc., producing a vast literature. These studies are both empirical and theoretical, the tenets of the theory in question being mainly, and apparently inevitably, those of quantum physics itself, for lack of other arenas in which quantum-like properties are presumed to obtain. However, attempts to explain this behavior on the basis of actual quantum physics going on at the atomic or molecular level within some element of brain or neuronal anatomy (other than the ordinary quantum physics that underlies everything), do not seem to survive much scrutiny. Moreover, it has been found empirically that the usual physics-like Hilbert space model seems not to apply in detail to human cognition in the large. In this paper we lay the groundwork for a theory that might explain the provenance of quantum-like behavior in complex systems whose internal structure is essentially hidden or inaccessible. The approach is via the logic obeyed by these systems which is similar to, but not identical with, the logic obeyed by actual quantum systems. The results reveal certain effects in such systems which, though quantum-like, are not identical to the kinds of quantum effects found in physics. These effects increase with the size of the system.

Quantum Tunneling of Magnetization in Ultrasmall Half-Metallic V3O4 Quantum Dots: Displaying Quantum Superparamagnetic State

PubMed Central

Xiao, Chong; Zhang, Jiajia; Xu, Jie; Tong, Wei; Cao, Boxiao; Li, Kun; Pan, Bicai; Su, Haibin; Xie, Yi

2012-01-01

Quantum tunneling of magnetization (QTMs), stemming from their importance for understanding materials with unconventional properties, has continued to attract widespread theoretical and experimental attention. However, the observation of QTMs in the most promising candidates of molecular magnets and few iron-based compounds is limited to very low temperature. Herein, we first highlight a simple system, ultrasmall half-metallic V3O4 quantum dots, as a promising candidate for the investigation of QTMs at high temperature. The quantum superparamagnetic state (QSP) as a high temperature signature of QTMs is observed at 16 K, which is beyond absolute zero temperature and much higher than that of conventional iron-based compounds due to the stronger spin-orbital coupling of V3+ ions bringing high anisotropy energy. It is undoubtedly that this ultrasmall quantum dots, V3O4, offers not only a promising candidate for theoretical understanding of QTMs but also a very exciting possibility for computers using mesoscopic magnets. PMID:23091695

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

PubMed

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

2016-02-18

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

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.

Thermally activated delayed photoluminescence from pyrenyl-functionalized CdSe quantum dots

NASA Astrophysics Data System (ADS)

Mongin, Cédric; Moroz, Pavel; Zamkov, Mikhail; Castellano, Felix N.

2018-02-01

The generation and transfer of triplet excitons across semiconductor nanomaterial-molecular interfaces will play an important role in emerging photonic and optoelectronic technologies, and understanding the rules that govern such phenomena is essential. The ability to cooperatively merge the photophysical properties of semiconductor quantum dots with those of well-understood and inexpensive molecular chromophores is therefore paramount. Here we show that 1-pyrenecarboxylic acid-functionalized CdSe quantum dots undergo thermally activated delayed photoluminescence. This phenomenon results from a near quantitative triplet-triplet energy transfer from the nanocrystals to 1-pyrenecarboxylic acid, producing a molecular triplet-state 'reservoir' that thermally repopulates the photoluminescent state of CdSe through endothermic reverse triplet-triplet energy transfer. The photoluminescence properties are systematically and predictably tuned through variation of the quantum dot-molecule energy gap, temperature and the triplet-excited-state lifetime of the molecular adsorbate. The concepts developed are likely to be applicable to semiconductor nanocrystals interfaced with molecular chromophores, enabling potential applications of their combined excited states.

Universal programmable quantum circuit schemes to emulate an operator

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

Daskin, Anmer; Grama, Ananth; Kollias, Giorgos

Unlike fixed designs, programmable circuit designs support an infinite number of operators. The functionality of a programmable circuit can be altered by simply changing the angle values of the rotation gates in the circuit. Here, we present a new quantum circuit design technique resulting in two general programmable circuit schemes. The circuit schemes can be used to simulate any given operator by setting the angle values in the circuit. This provides a fixed circuit design whose angles are determined from the elements of the given matrix-which can be non-unitary-in an efficient way. We also give both the classical and quantummore » complexity analysis for these circuits and show that the circuits require a few classical computations. For the electronic structure simulation on a quantum computer, one has to perform the following steps: prepare the initial wave function of the system; present the evolution operator U=e{sup -iHt} for a given atomic and molecular Hamiltonian H in terms of quantum gates array and apply the phase estimation algorithm to find the energy eigenvalues. Thus, in the circuit model of quantum computing for quantum chemistry, a crucial step is presenting the evolution operator for the atomic and molecular Hamiltonians in terms of quantum gate arrays. Since the presented circuit designs are independent from the matrix decomposition techniques and the global optimization processes used to find quantum circuits for a given operator, high accuracy simulations can be done for the unitary propagators of molecular Hamiltonians on quantum computers. As an example, we show how to build the circuit design for the hydrogen molecule.« less

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.

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

PubMed

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

2011-01-01

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

Physical mechanism causing rapid changes in ultrarelativistic electron pitch angle distributions right after a shock arrival: Evaluation of an electron dropout event

NASA Astrophysics Data System (ADS)

Zhang, X.-J.; Li, W.; Thorne, R. M.; Angelopoulos, V.; Ma, Q.; Li, J.; Bortnik, J.; Nishimura, Y.; Chen, L.; Baker, D. N.; Reeves, G. D.; Spence, H. E.; Kletzing, C. A.; Kurth, W. S.; Hospodarsky, G. B.; Blake, J. B.; Fennell, J. F.

2016-09-01

Three mechanisms have been proposed to explain relativistic electron flux depletions (dropouts) in the Earth's outer radiation belt during storm times: adiabatic expansion of electron drift shells due to a decrease in magnetic field strength, magnetopause shadowing and subsequent outward radial diffusion, and precipitation into the atmosphere (driven by EMIC wave scattering). Which mechanism predominates in causing electron dropouts commonly observed in the outer radiation belt is still debatable. In the present study, we evaluate the physical mechanism that may be primarily responsible for causing the sudden change in relativistic electron pitch angle distributions during a dropout event observed by Van Allen Probes during the main phase of the 27 February 2014 storm. During this event, the phase space density of ultrarelativistic (>1 MeV) electrons was depleted by more than 1 order of magnitude over the entire radial extent of the outer radiation belt (3 < L* < 5) in less than 6 h after the passage of an interplanetary shock. We model the electron pitch angle distribution under a compressed magnetic field topology based on actual solar wind conditions. Although these ultrarelativistic electrons exhibit highly anisotropic (peaked in 90°), energy-dependent pitch angle distributions, which appear to be associated with the typical EMIC wave scattering, comparison of the modeled electron distribution to electron measurements indicates that drift shell splitting is responsible for this rapid change in electron pitch angle distributions. This further indicates that magnetopause loss is the predominant cause of the electron dropout right after the shock arrival.

A novel metronidazole fluorescent nanosensor based on graphene quantum dots embedded silica molecularly imprinted polymer.

PubMed

Mehrzad-Samarin, Mina; Faridbod, Farnoush; Dezfuli, Amin Shiralizadeh; Ganjali, Mohammad Reza

2017-06-15

A novel optical nanosensor for detection of Metronidazole in biological samples was reported. Graphene quantum dots embedded silica molecular imprinted polymer (GQDs-embedded SMIP) was synthesized and used as a selective fluorescent probe for Metronidazole detection. The new synthesized GQDs-embedded SMIP showed strong fluorescent emission at 450nm excited at 365nm which quenched in presence of Metronidazole as a template molecule.. The quenching was proportional to the concentration of Metronidazole in a linear range of at least 0.2μM to 15μM. The limit of detection for metronidazole determination was obtained 0.15μM. The nanosensor successfully worked in plasma matrixes. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular Orientation of a Terbium(III)-Phthalocyaninato Double-Decker Complex for Effective Suppression of Quantum Tunneling of the Magnetization.

PubMed

Yamabayashi, Tsutomu; Katoh, Keiichi; Breedlove, Brian K; Yamashita, Masahiro

2017-06-15

Single-molecule magnet (SMM) properties of crystals of a terbium(III)-phthalocyaninato double-decker complex with different molecular packings ( 1 : TbPc₂, 2 : TbPc₂·CH₂Cl₂) were studied to elucidate the relationship between the molecular packing and SMM properties. From single crystal X-ray analyses, the high symmetry of the coordination environment of 2 suggested that the SMM properties were improved. Furthermore, the shorter intermolecular Tb-Tb distance and relative collinear alignment of the magnetic dipole in 2 indicated that the magnetic dipole-dipole interactions were stronger than those in 1 . This was confirmed by using direct current magnetic measurements. From alternating current magnetic measurements, the activation energy for spin reversal for 1 and 2 were similar. However, the relaxation time for 2 is three orders of magnitude slower than that for 1 in the low- T region due to effective suppression of the quantum tunneling of the magnetization. These results suggest that the SMM properties of TbPc₂ highly depend on the molecular packing.

Error Sensitivity to Environmental Noise in Quantum Circuits for Chemical State Preparation.

PubMed

Sawaya, Nicolas P D; Smelyanskiy, Mikhail; McClean, Jarrod R; Aspuru-Guzik, Alán

2016-07-12

Calculating molecular energies is likely to be one of the first useful applications to achieve quantum supremacy, performing faster on a quantum than a classical computer. However, if future quantum devices are to produce accurate calculations, errors due to environmental noise and algorithmic approximations need to be characterized and reduced. In this study, we use the high performance qHiPSTER software to investigate the effects of environmental noise on the preparation of quantum chemistry states. We simulated 18 16-qubit quantum circuits under environmental noise, each corresponding to a unitary coupled cluster state preparation of a different molecule or molecular configuration. Additionally, we analyze the nature of simple gate errors in noise-free circuits of up to 40 qubits. We find that, in most cases, the Jordan-Wigner (JW) encoding produces smaller errors under a noisy environment as compared to the Bravyi-Kitaev (BK) encoding. For the JW encoding, pure dephasing noise is shown to produce substantially smaller errors than pure relaxation noise of the same magnitude. We report error trends in both molecular energy and electron particle number within a unitary coupled cluster state preparation scheme, against changes in nuclear charge, bond length, number of electrons, noise types, and noise magnitude. These trends may prove to be useful in making algorithmic and hardware-related choices for quantum simulation of molecular energies.

Kondo blockade due to quantum interference in single-molecule junctions

PubMed Central

Mitchell, Andrew K.; Pedersen, Kim G. L.; Hedegård, Per; Paaske, Jens

2017-01-01

Molecular electronics offers unique scientific and technological possibilities, resulting from both the nanometre scale of the devices and their reproducible chemical complexity. Two fundamental yet different effects, with no classical analogue, have been demonstrated experimentally in single-molecule junctions: quantum interference due to competing electron transport pathways, and the Kondo effect due to entanglement from strong electronic interactions. Here we unify these phenomena, showing that transport through a spin-degenerate molecule can be either enhanced or blocked by Kondo correlations, depending on molecular structure, contacting geometry and applied gate voltages. An exact framework is developed, in terms of which the quantum interference properties of interacting molecular junctions can be systematically studied and understood. We prove that an exact Kondo-mediated conductance node results from destructive interference in exchange-cotunneling. Nonstandard temperature dependences and gate-tunable conductance peaks/nodes are demonstrated for prototypical molecular junctions, illustrating the intricate interplay of quantum effects beyond the single-orbital paradigm. PMID:28492236

Strange and non-strange particle production in antiproton-nucleus collisions in the UrQMD model

NASA Astrophysics Data System (ADS)

Limphirat, Ayut; Kobdaj, Chinorat; Bleicher, Marcus; Yan, Yupeng; Stöcker, Horst

2009-06-01

The capabilities of the ultra-relativistic quantum molecular dynamics (UrQMD) model in describing antiproton-nucleus collisions are presented. The model provides a good description of the experimental data on multiplicities, transverse momentum distributions and rapidity distributions in antiproton-nucleus collisions. Special emphasis is put on the comparison of strange particles in reactions with nuclear targets ranging from 7Li, 12C, 32S, 64Cu to 131Xe because of the important role of strangeness for the exploration of hypernuclei at PANDA-FAIR. The productions of the double strange baryons Ξ- and \\bar{\\Xi}^+ , which may be used to produce double Λ hypernuclei, are predicted in this work for the reactions \\skew2\\bar{p} + 24Mg, 64Cu and 197Au.

Quantum Dots: An Experiment for Physical or Materials Chemistry

ERIC Educational Resources Information Center

Winkler, L. D.; Arceo, J. F.; Hughes, W. C.; DeGraff, B. A.; Augustine, B. H.

2005-01-01

An experiment is conducted for obtaining quantum dots for physical or materials chemistry. This experiment serves to both reinforce the basic concept of quantum confinement and providing a useful bridge between the molecular and solid-state world.

Enhancing coherence in molecular spin qubits via atomic clock transitions

NASA Astrophysics Data System (ADS)

Shiddiq, Muhandis; Komijani, Dorsa; Duan, Yan; Gaita-Ariño, Alejandro; Coronado, Eugenio; Hill, Stephen

2016-03-01

Quantum computing is an emerging area within the information sciences revolving around the concept of quantum bits (qubits). A major obstacle is the extreme fragility of these qubits due to interactions with their environment that destroy their quantumness. This phenomenon, known as decoherence, is of fundamental interest. There are many competing candidates for qubits, including superconducting circuits, quantum optical cavities, ultracold atoms and spin qubits, and each has its strengths and weaknesses. When dealing with spin qubits, the strongest source of decoherence is the magnetic dipolar interaction. To minimize it, spins are typically diluted in a diamagnetic matrix. For example, this dilution can be taken to the extreme of a single phosphorus atom in silicon, whereas in molecular matrices a typical ratio is one magnetic molecule per 10,000 matrix molecules. However, there is a fundamental contradiction between reducing decoherence by dilution and allowing quantum operations via the interaction between spin qubits. To resolve this contradiction, the design and engineering of quantum hardware can benefit from a ‘bottom-up’ approach whereby the electronic structure of magnetic molecules is chemically tailored to give the desired physical behaviour. Here we present a way of enhancing coherence in solid-state molecular spin qubits without resorting to extreme dilution. It is based on the design of molecular structures with crystal field ground states possessing large tunnelling gaps that give rise to optimal operating points, or atomic clock transitions, at which the quantum spin dynamics become protected against dipolar decoherence. This approach is illustrated with a holmium molecular nanomagnet in which long coherence times (up to 8.4 microseconds at 5 kelvin) are obtained at unusually high concentrations. This finding opens new avenues for quantum computing based on molecular spin qubits.

Quantum control of quasi-collision states: A protocol for hybrid fusion

NASA Astrophysics Data System (ADS)

Vilela Mendes, R.

2018-04-01

When confined to small regions quantum systems exhibit electronic and structural properties different from their free space behavior. These properties are of interest, for example, for molecular insertion, hydrogen storage and the exploration of new pathways for chemical and nuclear reactions. Here, a confined three-body problem is studied, with emphasis on the study of the “quantum scars” associated to dynamical collisions. For the particular case of nuclear reactions, it is proposed that a molecular cage might simply be used as a confining device with the collision states accessed by quantum control techniques.

Nanoscale solid-state quantum computing

NASA Astrophysics Data System (ADS)

Ardavan, A.; Austwick, M.; Benjamin, S.C.; Briggs, G.A.D.; Dennis, T.J.S.; Ferguson, A.; Hasko, D.G.; Kanai, M.; Khlobystov, A.N.; Lovett, B.W.; Morley, G.W.; Oliver, R.A.; Pettifor, D.G.; Porfyrakis, K.; Reina, J.H.; Rice, J.H.; Smith, J.D.; Taylor, R.A.; Williams, D.A.; Adelmann, C.; Mariette, H.; Hamers, R.J.

2003-07-01

Most experts agree that it is too early to say how quantum computers will eventually be built, and several nanoscale solid-state schemes are being implemented in a range of materials. Nanofabricated quantum dots can be made in designer configurations, with established technology for controlling interactions and for reading out results. Epitaxial quantum dots can be grown in vertical arrays in semiconductors, and ultrafast optical techniques are available for controlling and measuring their excitations. Single-walled carbon nanotubes can be used for molecular self-assembly of endohedral fullerenes, which can embody quantum information in the electron spin. The challenges of individual addressing in such tiny structures could rapidly become intractable with increasing numbers of qubits, but these schemes are amenable to global addressing methods for computation.

Experimental methods of molecular matter-wave optics.

PubMed

Juffmann, Thomas; Ulbricht, Hendrik; Arndt, Markus

2013-08-01

We describe the state of the art in preparing, manipulating and detecting coherent molecular matter. We focus on experimental methods for handling the quantum motion of compound systems from diatomic molecules to clusters or biomolecules.Molecular quantum optics offers many challenges and innovative prospects: already the combination of two atoms into one molecule takes several well-established methods from atomic physics, such as for instance laser cooling, to their limits. The enormous internal complexity that arises when hundreds or thousands of atoms are bound in a single organic molecule, cluster or nanocrystal provides a richness that can only be tackled by combining methods from atomic physics, chemistry, cluster physics, nanotechnology and the life sciences.We review various molecular beam sources and their suitability for matter-wave experiments. We discuss numerous molecular detection schemes and give an overview over diffraction and interference experiments that have already been performed with molecules or clusters.Applications of de Broglie studies with composite systems range from fundamental tests of physics up to quantum-enhanced metrology in physical chemistry, biophysics and the surface sciences.Nanoparticle quantum optics is a growing field, which will intrigue researchers still for many years to come. This review can, therefore, only be a snapshot of a very dynamical process.

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

PubMed Central

2011-01-01

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

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

PubMed

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

2018-04-10

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

Dissipative time-dependent quantum transport theory: Quantum interference and phonon induced decoherence dynamics

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

Zhang, Yu, E-mail: zhy@yangtze.hku.hk; Chen, GuanHua, E-mail: ghc@everest.hku.hk; Yam, ChiYung

2015-04-28

A time-dependent inelastic electron transport theory for strong electron-phonon interaction is established via the equations of motion method combined with the small polaron transformation. In this work, the dissipation via electron-phonon coupling is taken into account in the strong coupling regime, which validates the small polaron transformation. The corresponding equations of motion are developed, which are used to study the quantum interference effect and phonon-induced decoherence dynamics in molecular junctions. Numerical studies show clearly quantum interference effect of the transport electrons through two quasi-degenerate states with different couplings to the leads. We also found that the quantum interference can bemore » suppressed by the electron-phonon interaction where the phase coherence is destroyed by phonon scattering. This indicates the importance of electron-phonon interaction in systems with prominent quantum interference effect.« less

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

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

Valiev, Marat; Yang, Jie; Adams, Joseph

2007-11-29

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

Quantum Stochastic Trajectories: The Fokker-Planck-Bohm Equation Driven by the Reduced Density Matrix.

PubMed

Avanzini, Francesco; Moro, Giorgio J

2018-03-15

The quantum molecular trajectory is the deterministic trajectory, arising from the Bohm theory, that describes the instantaneous positions of the nuclei of molecules by assuring the agreement with the predictions of quantum mechanics. Therefore, it provides the suitable framework for representing the geometry and the motions of molecules without neglecting their quantum nature. However, the quantum molecular trajectory is extremely demanding from the computational point of view, and this strongly limits its applications. To overcome such a drawback, we derive a stochastic representation of the quantum molecular trajectory, through projection operator techniques, for the degrees of freedom of an open quantum system. The resulting Fokker-Planck operator is parametrically dependent upon the reduced density matrix of the open system. Because of the pilot role played by the reduced density matrix, this stochastic approach is able to represent accurately the main features of the open system motions both at equilibrium and out of equilibrium with the environment. To verify this procedure, the predictions of the stochastic and deterministic representation are compared for a model system of six interacting harmonic oscillators, where one oscillator is taken as the open quantum system of interest. The undeniable advantage of the stochastic approach is that of providing a simplified and self-contained representation of the dynamics of the open system coordinates. Furthermore, it can be employed to study the out of equilibrium dynamics and the relaxation of quantum molecular motions during photoinduced processes, like photoinduced conformational changes and proton transfers.

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

PubMed

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

2015-12-03

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

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

PubMed

Ferenczy, György G

2013-04-05

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

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

PubMed

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

2014-11-18

point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

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.

Computer studies of multiple-quantum spin dynamics

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

Murdoch, J.B.

The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.

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

PubMed

Li, Hongzhi; Yang, Wei

2007-03-21

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

Can quantum approaches benefit biology of decision making?

PubMed

Takahashi, Taiki

2017-11-01

Human decision making has recently been focused in the emerging fields of quantum decision theory and neuroeconomics. The former discipline utilizes mathematical formulations developed in quantum theory, while the latter combines behavioral economics and neurobiology. In this paper, the author speculates on possible future directions unifying the two approaches, by contrasting the roles of quantum theory in the birth of molecular biology of the gene. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computation of Molecular Spectra on a Quantum Processor with an Error-Resilient Algorithm

NASA Astrophysics Data System (ADS)

Colless, J. I.; Ramasesh, V. V.; Dahlen, D.; Blok, M. S.; Kimchi-Schwartz, M. E.; McClean, J. R.; Carter, J.; de Jong, W. A.; Siddiqi, I.

2018-02-01

Harnessing the full power of nascent quantum processors requires the efficient management of a limited number of quantum bits with finite coherent lifetimes. Hybrid algorithms, such as the variational quantum eigensolver (VQE), leverage classical resources to reduce the required number of quantum gates. Experimental demonstrations of VQE have resulted in calculation of Hamiltonian ground states, and a new theoretical approach based on a quantum subspace expansion (QSE) has outlined a procedure for determining excited states that are central to dynamical processes. We use a superconducting-qubit-based processor to apply the QSE approach to the H2 molecule, extracting both ground and excited states without the need for auxiliary qubits or additional minimization. Further, we show that this extended protocol can mitigate the effects of incoherent errors, potentially enabling larger-scale quantum simulations without the need for complex error-correction techniques.

Growth of a delta-doped silicon layer by molecular beam epitaxy on a charge-coupled device for reflection-limited ultraviolet quantum efficiency

NASA Technical Reports Server (NTRS)

Hoenk, Michael E.; Grunthaner, Paula J.; Grunthaner, Frank J.; Terhune, R. W.; Fattahi, Masoud; Tseng, Hsin-Fu

1992-01-01

Low-temperature silicon molecular beam epitaxy is used to grow a delta-doped silicon layer on a fully processed charge-coupled device (CCD). The measured quantum efficiency of the delta-doped backside-thinned CCD is in agreement with the reflection limit for light incident on the back surface in the spectral range of 260-600 nm. The 2.5 nm silicon layer, grown at 450 C, contained a boron delta-layer with surface density of about 2 x 10 exp 14/sq cm. Passivation of the surface was done by steam oxidation of a nominally undoped 1.5 nm Si cap layer. The UV quantum efficiency was found to be uniform and stable with respect to thermal cycling and illumination conditions.

Quantum computing applied to calculations of molecular energies: CH2 benchmark.

PubMed

Veis, Libor; Pittner, Jiří

2010-11-21

Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704 (2005)] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH(2) molecule. This molecule was chosen as a benchmark, since its two lowest lying (1)A(1) states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case.

Near-Resonant Raman Amplification in the Rotational Quantum Wave Packets of Nitrogen Molecular Ions Generated by Strong Field Ionization

NASA Astrophysics Data System (ADS)

Liu, Zhaoxiang; Yao, Jinping; Chen, Jinming; Xu, Bo; Chu, Wei; Cheng, Ya

2018-02-01

The generation of laserlike narrow bandwidth emissions from nitrogen molecular ions (N2+ ) generated in intense near- and mid infrared femtosecond laser fields has aroused much interest because of the mysterious physics underlying such a phenomenon. Here, we perform a pump-probe measurement on the nonlinear interaction of rotational quantum wave packets of N2+ generated in midinfrared (e.g., at a wavelength centered at 1580 nm) femtosecond laser fields with an ultrashort probe pulse whose broad spectrum overlaps both P - and R -branch rotational transition lines between the electronic states N2+(B2Σu+,v'=0 ) and N2+(X2Σg+,v =0 ) . The results indicate the occurrence of highly efficient near-resonant stimulated Raman scattering in the quantum wave packets of N2+ ions generated in strong laser fields in the midinfrared region, of which the underlying mechanism is different from that of the air lasers generated in atmospheric environment when pumping with 800 nm intense pulses.

Computation of Molecular Spectra on a Quantum Processor with an Error-Resilient Algorithm

DOE PAGES

Colless, J. I.; Ramasesh, V. V.; Dahlen, D.; ...

2018-02-12

Harnessing the full power of nascent quantum processors requires the efficient management of a limited number of quantum bits with finite coherent lifetimes. Hybrid algorithms, such as the variational quantum eigensolver (VQE), leverage classical resources to reduce the required number of quantum gates. Experimental demonstrations of VQE have resulted in calculation of Hamiltonian ground states, and a new theoretical approach based on a quantum subspace expansion (QSE) has outlined a procedure for determining excited states that are central to dynamical processes. Here, we use a superconducting-qubit-based processor to apply the QSE approach to the H 2 molecule, extracting both groundmore » and excited states without the need for auxiliary qubits or additional minimization. Further, we show that this extended protocol can mitigate the effects of incoherent errors, potentially enabling larger-scale quantum simulations without the need for complex error-correction techniques.« less

Computation of Molecular Spectra on a Quantum Processor with an Error-Resilient Algorithm

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

Colless, J. I.; Ramasesh, V. V.; Dahlen, D.

Harnessing the full power of nascent quantum processors requires the efficient management of a limited number of quantum bits with finite coherent lifetimes. Hybrid algorithms, such as the variational quantum eigensolver (VQE), leverage classical resources to reduce the required number of quantum gates. Experimental demonstrations of VQE have resulted in calculation of Hamiltonian ground states, and a new theoretical approach based on a quantum subspace expansion (QSE) has outlined a procedure for determining excited states that are central to dynamical processes. Here, we use a superconducting-qubit-based processor to apply the QSE approach to the H 2 molecule, extracting both groundmore » and excited states without the need for auxiliary qubits or additional minimization. Further, we show that this extended protocol can mitigate the effects of incoherent errors, potentially enabling larger-scale quantum simulations without the need for complex error-correction techniques.« less

Transverse momentum fluctuations in ultrarelativistic Pb + Pb and p + Pb collisions with "wounded" quarks

NASA Astrophysics Data System (ADS)

BoŻek, Piotr; Broniowski, Wojciech

2017-07-01

We analyze the phenomenon of size-flow transmutation in ultrarelativistic nuclear collisions in a model where the initial size fluctuations are driven by the wounded quarks and the collectivity is provided by viscous hydrodynamics. It is found that the model properly reproduces the data for the transverse momentum fluctuations measured for Pb +Pb collisions at √{sN N}=2.76 TeV by the ALICE Collaboration. The agreement holds for a remarkably wide range of centralities, from 0-5 % up to 70-80 %, and displays a departure from a simple scaling with (dNch/d η ) 1 /2 in the form seen in the data. The overall agreement in the model with wounded quarks is significantly better than with nucleon participants. This feature joins the previously found wounded quark multiplicity scaling in the argumentation in favor of subnucleonic degrees of freedom in the early dynamics. We also examine in detail the correlations between measures of the initial size and final average transverse momentum of hadrons. Predictions are made for the transverse momentum fluctuations in p +Pb collisions at √{sN N}=5.02 TeV.

Quantum Entanglement and Chemical Reactivity.

PubMed

Molina-Espíritu, M; Esquivel, R O; López-Rosa, S; Dehesa, J S

2015-11-10

The water molecule and a hydrogenic abstraction reaction are used to explore in detail some quantum entanglement features of chemical interest. We illustrate that the energetic and quantum-information approaches are necessary for a full understanding of both the geometry of the quantum probability density of molecular systems and the evolution of a chemical reaction. The energy and entanglement hypersurfaces and contour maps of these two models show different phenomena. The energy ones reveal the well-known stable geometry of the models, whereas the entanglement ones grasp the chemical capability to transform from one state system to a new one. In the water molecule the chemical reactivity is witnessed through quantum entanglement as a local minimum indicating the bond cleavage in the dissociation process of the molecule. Finally, quantum entanglement is also useful as a chemical reactivity descriptor by detecting the transition state along the intrinsic reaction path in the hypersurface of the hydrogenic abstraction reaction corresponding to a maximally entangled state.

Quantum molecular dynamics of warm dense iron and a five-phase equation of state

NASA Astrophysics Data System (ADS)

Sjostrom, Travis; Crockett, Scott

2018-05-01

Through quantum molecular dynamics (QMD), utilizing both Kohn-Sham (orbital-based) and orbital-free density functional theory, we calculate the equation of state of warm dense iron in the density range 7 -30 g/cm 3 and temperatures from 1 to 100 eV. A critical examination of the iron pseudopotential is made, from which we find a significant improvement at high pressure to the previous QMD calculations of Wang et al. [Phys. Rev. E 89, 023101 (2014), 10.1103/PhysRevE.89.023101]. Our results also significantly extend the ranges of density and temperature that were attempted in that prior work. We calculate the shock Hugoniot and find very good agreement with experimental results to pressures over 20 TPa. These results are then incorporated with previous studies to generate a five-phase equation of state for iron.

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

Experimental Bayesian Quantum Phase Estimation on a Silicon Photonic Chip.

PubMed

Paesani, S; Gentile, A A; Santagati, R; Wang, J; Wiebe, N; Tew, D P; O'Brien, J L; Thompson, M G

2017-03-10

Quantum phase estimation is a fundamental subroutine in many quantum algorithms, including Shor's factorization algorithm and quantum simulation. However, so far results have cast doubt on its practicability for near-term, nonfault tolerant, quantum devices. Here we report experimental results demonstrating that this intuition need not be true. We implement a recently proposed adaptive Bayesian approach to quantum phase estimation and use it to simulate molecular energies on a silicon quantum photonic device. The approach is verified to be well suited for prethreshold quantum processors by investigating its superior robustness to noise and decoherence compared to the iterative phase estimation algorithm. This shows a promising route to unlock the power of quantum phase estimation much sooner than previously believed.

Leakage and sweet spots in triple-quantum-dot spin qubits: A molecular-orbital study

NASA Astrophysics Data System (ADS)

Zhang, Chengxian; Yang, Xu-Chen; Wang, Xin

2018-04-01

A triple-quantum-dot system can be operated as either an exchange-only qubit or a resonant-exchange qubit. While it is generally believed that the decisive advantage of the resonant-exchange qubit is the suppression of charge noise because it is operated at a sweet spot, we show that the leakage is also an important factor. Through molecular-orbital-theoretic calculations, we show that when the system is operated in the exchange-only scheme, the leakage to states with double electron occupancy in quantum dots is severe when rotations around the axis 120∘ from z ̂ is performed. While this leakage can be reduced by either shrinking the dots or separating them further, the exchange interactions are also suppressed at the same time, making the gate operations unfavorably slow. When the system is operated as a resonant-exchange qubit, the leakage is three to five orders of magnitude smaller. We have also calculated the optimal detuning point which minimizes the leakage for the resonant-exchange qubit, and have found that although it does not coincide with the double sweet spot for the charge noise, they are rather close. Our results suggest that the resonant-exchange qubit has another advantage, that leakage can be greatly suppressed compared to the exchange-only qubit, and operating at the double sweet spot point should be optimal both for reducing charge noise and suppressing leakage.

From quantum to classical modeling of radiation reaction: A focus on stochasticity effects

NASA Astrophysics Data System (ADS)

Niel, F.; Riconda, C.; Amiranoff, F.; Duclous, R.; Grech, M.

2018-04-01

Radiation reaction in the interaction of ultrarelativistic electrons with a strong external electromagnetic field is investigated using a kinetic approach in the nonlinear moderately quantum regime. Three complementary descriptions are discussed considering arbitrary geometries of interaction: a deterministic one relying on the quantum-corrected radiation reaction force in the Landau and Lifschitz (LL) form, a linear Boltzmann equation for the electron distribution function, and a Fokker-Planck (FP) expansion in the limit where the emitted photon energies are small with respect to that of the emitting electrons. The latter description is equivalent to a stochastic differential equation where the effect of the radiation reaction appears in the form of the deterministic term corresponding to the quantum-corrected LL friction force, and by a diffusion term accounting for the stochastic nature of photon emission. By studying the evolution of the energy moments of the electron distribution function with the three models, we are able to show that all three descriptions provide similar predictions on the temporal evolution of the average energy of an electron population in various physical situations of interest, even for large values of the quantum parameter χ . The FP and full linear Boltzmann descriptions also allow us to correctly describe the evolution of the energy variance (second-order moment) of the distribution function, while higher-order moments are in general correctly captured with the full linear Boltzmann description only. A general criterion for the limit of validity of each description is proposed, as well as a numerical scheme for the inclusion of the FP description in particle-in-cell codes. This work, not limited to the configuration of a monoenergetic electron beam colliding with a laser pulse, allows further insight into the relative importance of various effects of radiation reaction and in particular of the discrete and stochastic nature of high

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

NASA Astrophysics Data System (ADS)

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

2011-02-01

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

Isoscalar giant monopole resonance in Sn isotopes using a quantum molecular dynamics model

NASA Astrophysics Data System (ADS)

Tao, C.; Ma, Y. G.; Zhang, G. Q.; Cao, X. G.; Fang, D. Q.; Wang, H. W.; Xu, J.

2013-12-01

The isoscalar giant monopole resonance (GMR) in Sn isotopes and other nuclei is investigated in the framework of the isospin-dependent quantum molecular dynamics (IQMD) model. The spectrum of GMR is calculated by taking the rms radius of a nucleus as its monopole moment. The peak energy, the FWHM, and the strength of the GMR extracted by a Gaussian fit to the spectrum have been studied. The GMR peak energies for Sn isotopes from the calculations using a mass-number-dependent Gaussian wave-packet width σr for nucleons are found to be overestimated and show a weak dependence on the mass number compared with the experimental data. However, it is found that experimental data of the GMR peak energies for 56Ni, 90Zr, and 208Pb as well as Sn isotopes can be nicely reproduced after taking into account the isospin dependence in isotope chains in addition to the mass-number dependence of σr for nucleons in the IQMD model calculation.

Probing Molecular Ions With Laser-Cooled Atomic Ions

DTIC Science & Technology

2017-10-11

Sept. 23, 2015 Precision Chemical Dynamics and Quantum Control of Ultracold Molecular Ion Reactions , Cold Molecular Ions at the Quantum limit (COMIQ...ken.brown@chemistry.gatech.edu This work solved an old mystery about the lifetime of Ca+ due to reactions with background gases in laser-cooling experiments...Relative to other alkaline earths, Ca+ had a much slower reaction rate. We discovered the reason is that the Doppler cooling laser is near

Quantum dissipation theory and applications to quantum transport and quantum measurement in mesoscopic systems

NASA Astrophysics Data System (ADS)

Cui, Ping

The thesis comprises two major themes of quantum statistical dynamics. One is the development of quantum dissipation theory (QDT). It covers the establishment of some basic relations of quantum statistical dynamics, the construction of several nonequivalent complete second-order formulations, and the development of exact QDT. Another is related to the applications of quantum statistical dynamics to a variety of research fields. In particular, unconventional but novel theories of the electron transfer in Debye solvents, quantum transport, and quantum measurement are developed on the basis of QDT formulations. The thesis is organized as follows. In Chapter 1, we present some background knowledge in relation to the aforementioned two themes of this thesis. The key quantity in QDT is the reduced density operator rho(t) ≡ trBrho T(t); i.e., the partial trace of the total system and bath composite rhoT(t) over the bath degrees of freedom. QDT governs the evolution of reduced density operator, where the effects of bath are treated in a quantum statistical manner. In principle, the reduced density operator contains all dynamics information of interest. However, the conventional quantum transport theory is formulated in terms of nonequilibrium Green's function. The newly emerging field of quantum measurement in relation to quantum information and quantum computing does exploit a sort of QDT formalism. Besides the background of the relevant theoretical development, some representative experiments on molecular nanojunctions are also briefly discussed. In chapter 2, we outline some basic (including new) relations that highlight several important issues on QDT. The content includes the background of nonequilibrium quantum statistical mechanics, the general description of the total composite Hamiltonian with stochastic system-bath interaction, a novel parameterization scheme for bath correlation functions, a newly developed exact theory of driven Brownian oscillator (DBO

Size dependent bandgap of molecular beam epitaxy grown InN quantum dots measured by scanning tunneling spectroscopy

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

Kumar, Mahesh; Roul, Basanta; Central Research Laboratory, Bharat Electronics, Bangalore-560013

InN quantum dots (QDs) were grown on Si (111) by epitaxial Stranski-Krastanow growth mode using plasma-assisted molecular beam epitaxy. Single-crystalline wurtzite structure of InN QDs was verified by the x-ray diffraction and transmission electron microscopy. Scanning tunneling microscopy has been used to probe the structural aspects of QDs. A surface bandgap of InN QDs was estimated from scanning tunneling spectroscopy (STS) I-V curves and found that it is strongly dependent on the size of QDs. The observed size-dependent STS bandgap energy shifts with diameter and height were theoretical explained based on an effective mass approximation with finite-depth square-well potential model.

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

NASA Astrophysics Data System (ADS)

Shoemaker, James Richard

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

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.

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

PubMed

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

2018-01-17

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

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

PubMed

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

2018-05-28

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

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

PubMed

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

2015-03-05

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

Non-adiabatic molecular dynamics investigation of photoionization state formation and lifetime in Mn²⁺-doped ZnO quantum dots.

PubMed

Fischer, Sean A; Lingerfelt, David B; May, Joseph W; Li, Xiaosong

2014-09-07

The unique electronic structure of Mn(2+)-doped ZnO quantum dots gives rise to photoionization states that can be used to manipulate the magnetic state of the material and to generate zero-reabsorption luminescence. Fast formation and long non-radiative decay of this photoionization state is a necessary requirement for these important applications. In this work, surface hopping based non-adiabatic molecular dynamics are used to demonstrate the fast formation of a metal-to-ligand charge transfer state in a Mn(2+)-doped ZnO quantum dot. The formation occurs on an ultrafast timescale and is aided by the large density of states and significant mixing of the dopant Mn(2+) 3dt2 levels with the valence-band levels of the ZnO lattice. The non-radiative lifetime of the photoionization states is also investigated.

Photochemical Creation of Fluorescent Quantum Defects in Semiconducting Carbon Nanotube Hosts.

PubMed

Wu, Xiaojian; Kim, Mijin; Kwon, Hyejin; Wang, YuHuang

2018-01-15

Quantum defects are an emerging class of synthetic single-photon emitters that hold vast potential for near-infrared imaging, chemical sensing, materials engineering, and quantum information processing. Herein, we show that it is possible to optically direct the synthetic creation of molecularly tunable fluorescent quantum defects in semiconducting single-walled carbon nanotube hosts through photochemical reactions. By exciting the host semiconductor with light that resonates with its electronic transition, we find that halide-containing aryl groups can covalently bond to the sp 2 carbon lattice. The introduced quantum defects generate bright photoluminescence that allows tracking of the reaction progress in situ. We show that the reaction is independent of temperature but correlates strongly with the photon energy used to drive the reaction, suggesting a photochemical mechanism rather than photothermal effects. This type of photochemical reactions opens the possibility to control the synthesis of fluorescent quantum defects using light and may enable lithographic patterning of quantum emitters with electronic and molecular precision. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Bravyi-Kitaev transformation for quantum computation of electronic structure

NASA Astrophysics Data System (ADS)

Seeley, Jacob T.; Richard, Martin J.; Love, Peter J.

2012-12-01

Quantum simulation is an important application of future quantum computers with applications in quantum chemistry, condensed matter, and beyond. Quantum simulation of fermionic systems presents a specific challenge. The Jordan-Wigner transformation allows for representation of a fermionic operator by O(n) qubit operations. Here, we develop an alternative method of simulating fermions with qubits, first proposed by Bravyi and Kitaev [Ann. Phys. 298, 210 (2002), 10.1006/aphy.2002.6254; e-print arXiv:quant-ph/0003137v2], that reduces the simulation cost to O(log n) qubit operations for one fermionic operation. We apply this new Bravyi-Kitaev transformation to the task of simulating quantum chemical Hamiltonians, and give a detailed example for the simplest possible case of molecular hydrogen in a minimal basis. We show that the quantum circuit for simulating a single Trotter time step of the Bravyi-Kitaev derived Hamiltonian for H2 requires fewer gate applications than the equivalent circuit derived from the Jordan-Wigner transformation. Since the scaling of the Bravyi-Kitaev method is asymptotically better than the Jordan-Wigner method, this result for molecular hydrogen in a minimal basis demonstrates the superior efficiency of the Bravyi-Kitaev method for all quantum computations of electronic structure.

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

PubMed

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

2014-05-07

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

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

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

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

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

Entangled states in quantum mechanics

NASA Astrophysics Data System (ADS)

Ruža, Jānis

2010-01-01

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

Formation of electrostatic structures by wakefield acceleration in ultrarelativistic plasma flows: Electron acceleration to cosmic ray energies

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

Dieckmann, M.E.; Shukla, P.K.; Eliasson, B.

2006-06-15

The ever increasing performance of supercomputers is now enabling kinetic simulations of extreme astrophysical and laser produced plasmas. Three-dimensional particle-in-cell (PIC) simulations of relativistic shocks have revealed highly filamented spatial structures and their ability to accelerate particles to ultrarelativistic speeds. However, these PIC simulations have not yet revealed mechanisms that could produce particles with tera-electron volt energies and beyond. In this work, PIC simulations in one dimension (1D) of the foreshock region of an internal shock in a gamma ray burst are performed to address this issue. The large spatiotemporal range accessible to a 1D simulation enables the self-consistent evolutionmore » of proton phase space structures that can accelerate particles to giga-electron volt energies in the jet frame of reference, and to tens of tera-electron volt in the Earth's frame of reference. One potential source of ultrahigh energy cosmic rays may thus be the thermalization of relativistically moving plasma.« less

Optical properties and carrier dynamics of GaAs/GaInAs multiple-quantum-well shell grown on GaAs nanowire by molecular beam epitaxy

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

Park, Kwangwook; Ravindran, Sooraj; Ju, Gun Wu

GaAs/GaInAs multiple-quantum-well (MQW) shells having different GaInAs shell width formed on the surface of self-catalyzed GaAs core nanowires (NWs) are grown on (100) Si substrate using molecular beam epitaxy. The photoluminescence emission from GaAs/GaInAs MQW shells and the carrier lifetime could be varied by changing the width of GaInAs shell. Time-resolved photoluminescence measurements showed that the carrier lifetime had a fast and slow decay owing to the mixing of wurtzite and zinc-blende structures of the NWs. Furthermore, strain relaxation caused the carrier lifetime to decrease beyond a certain thickness of GaInAs quantum well shells.

Spectroscopy of Charged Quantum Dot Molecules

NASA Astrophysics Data System (ADS)

Stinaff, E. A.; Scheibner, M.; Bracker, A. S.; Ponomarev, I. V.; Ware, M. E.; Doty, M. F.; Reinecke, T. L.; Gammon, D.; Korenev, V. L.

2006-03-01

Spins of single charges in quantum dots are attractive for many quantum information and spintronic proposals. Scalable quantum information applications require the ability to entangle and operate on multiple spins in coupled quantum dots (CQDs). To further the understanding of these systems, we present detailed spectroscopic studies of InAs CQDs with control of the discrete electron or hole charging of the system. The optical spectrum reveals a pattern of energy anticrossings and crossings in the photoluminescence as a function of applied electric field. These features can be understood as a superposition of charge and spin configurations of the two dots and represent clear signatures of quantum mechanical coupling. The molecular resonance leading to these anticrossings is achieved at different electric fields for the optically excited (trion) states and the ground (hole) states allowing for the possibility of using the excited states for optically induced coupling of the qubits.

Simulation of a broadband nano-biosensor based on an onion-like quantum dot-quantum well structure

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

Absalan, H; SalmanOgli, A; Rostami, R

The fluorescence resonance energy transfer is studied between modified quantum-dots and quantum-wells used as a donor and an acceptor. Because of the unique properties of quantum dots, including diverse surface modification flexibility, bio-compatibility, high quantum yields and wide absorption, their use as nano-biosensors and bio-markers used in diagnosis of cancer is suggested. The fluorescence resonance energy transfer is simulated in a quantum dot-quantum well system, where the energy can flow from donor to acceptor. If the energy transfer can be either turned on or off by a specific interaction, such as interaction with any dyes, a molecular binding event ormore » a cleavage reaction, a sensor can be designed (under assumption that the healthy cells have a known effect or unyielding effect on output parameters while cancerous cells, due to their pandemic optical properties, can impact the fluorescence resonance energy transfer parameters). The developed nano-biosensor can operate in a wide range of wavelengths (310 - 760 nm). (laser applications in biology and medicine)« less

The effect of Lorentz-like force on collective flows of K + in Au+Au collisions at 1.5 GeV/nucleon

NASA Astrophysics Data System (ADS)

Du, YuShan; Wang, YongJia; Li, QingFeng; Liu, Ling

2018-06-01

Producing kaon mesons in heavy-ion collisions at beam energies below their threshold energy is an important way to investigate the properties of dense nuclear matter. In this study, based on the newly updated version of the ultrarelativistic quantum molecular dynamics model, we introduce the kaon-nucleon (KN) potential, including both the scalar and vector (also dubbed Lorentz-like) aspects. We revisit the influence of the KN potential on the collective flow of K + mesons produced in Au+Au collisions at E lab = 1.5 GeV/nucleon and find that the contribution of the newly included Lorentz-like force is very important, particulary for describing the directed flow of K +. Finally, the corresponding KaoS data of both directed and elliptic flows can be simultaneously reproduced well.

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

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

Shimojo, Fuyuki; Hattori, Shinnosuke; Department of Physics, Kumamoto University, Kumamoto 860-8555

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at themore » peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A

Multiple quantum coherence spectroscopy.

PubMed

Mathew, Nathan A; Yurs, Lena A; Block, Stephen B; Pakoulev, Andrei V; Kornau, Kathryn M; Wright, John C

2009-08-20

Multiple quantum coherences provide a powerful approach for studies of complex systems because increasing the number of quantum states in a quantum mechanical superposition state increases the selectivity of a spectroscopic measurement. We show that frequency domain multiple quantum coherence multidimensional spectroscopy can create these superposition states using different frequency excitation pulses. The superposition state is created using two excitation frequencies to excite the symmetric and asymmetric stretch modes in a rhodium dicarbonyl chelate and the dynamic Stark effect to climb the vibrational ladders involving different overtone and combination band states. A monochromator resolves the free induction decay of different coherences comprising the superposition state. The three spectral dimensions provide the selectivity required to observe 19 different spectral features associated with fully coherent nonlinear processes involving up to 11 interactions with the excitation fields. The different features act as spectroscopic probes of the diagonal and off-diagonal parts of the molecular potential energy hypersurface. This approach can be considered as a coherent pump-probe spectroscopy where the pump is a series of excitation pulses that prepares a multiple quantum coherence and the probe is another series of pulses that creates the output coherence.

Conductance and thermopower in molecular nanojunctions

NASA Astrophysics Data System (ADS)

Sen, Arijit

2013-02-01

Electronic transport through short channels in a molecular junction is an intricate quantum scattering problem [1]. To garner insight on how the structure and the electrical properties of a nanoscale junction are correlated is thus of both fundamental and technological interest [1-3]. As observed experimentally in the last couple of years by several independent research groups [4-5], a two-terminal molecular junction comprising of a simple alkane chain with varying length can exhibit high as well as low conductance. However, what causes the simultaneous unveiling of multiple conductances remained largely obscure. We have recently demonstrated [6] that the binary conductance in these heterostructures is due mainly to two distinct electrode orientations that control the electrode-molecule coupling as well as the tunneling strength through quantum interference following diversity in the electrode band structures. Our detailed analysis on the transmission spectra indicates that even a single-molecule nanojunction can potentially serve as a realistic double-quantum-dot kind of system to yield tunable Fano resonance, as often desired for nanoscale switching. In this talk, I intend to give a brief account of molecular electronics and its future applications along with the challenges and possibilities in the current perspective. A few deliberations may as well include how the inter-dot tunneling strength may affect the non-equilibrium charge transport and thermoelectricity in a myriad of molecular junctions based on different molecular conformations and electrode structures. Finally, I shall try to touch upon the effect of electron-phonon interaction on the nanoscale charge transport, and also, the phonon-mediated thermal transport in molecular nanodevices.

Computation of Ground-State Properties in Molecular Systems: Back-Propagation with Auxiliary-Field Quantum Monte Carlo.

PubMed

Motta, Mario; Zhang, Shiwei

2017-11-14

We address the computation of ground-state properties of chemical systems and realistic materials within the auxiliary-field quantum Monte Carlo method. The phase constraint to control the Fermion phase problem requires the random walks in Slater determinant space to be open-ended with branching. This in turn makes it necessary to use back-propagation (BP) to compute averages and correlation functions of operators that do not commute with the Hamiltonian. Several BP schemes are investigated, and their optimization with respect to the phaseless constraint is considered. We propose a modified BP method for the computation of observables in electronic systems, discuss its numerical stability and computational complexity, and assess its performance by computing ground-state properties in several molecular systems, including small organic molecules.

Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

PubMed

Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

2018-05-15

Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

Superabsorption of light via quantum engineering

PubMed Central

Higgins, K. D. B.; Benjamin, S. C.; Stace, T. M.; Milburn, G. J.; Lovett, B. W.; Gauger, E. M.

2014-01-01

Almost 60 years ago Dicke introduced the term superradiance to describe a signature quantum effect: N atoms can collectively emit light at a rate proportional to N2. Structures that superradiate must also have enhanced absorption, but the former always dominates in natural systems. Here we show that this restriction can be overcome by combining several well-established quantum control techniques. Our analytical and numerical calculations show that superabsorption can then be achieved and sustained in certain simple nanostructures, by trapping the system in a highly excited state through transition rate engineering. This opens the prospect of a new class of quantum nanotechnology with potential applications including photon detection and light-based power transmission. An array of quantum dots or a molecular ring structure could provide a suitable platform for an experimental demonstration. PMID:25146588

Interaction of an ultrarelativistic electron bunch train with a W-band accelerating structure: High power and high gradient

DOE PAGES

Wang, D.; Antipov, S.; Jing, C.; ...

2016-02-05

Electron beam interaction with high frequency structures (beyond microwave regime) has a great impact on future high energy frontier machines. We report on the generation of multimegawatt pulsed rf power at 91 GHz in a planar metallic accelerating structure driven by an ultrarelativistic electron bunch train. This slow-wave wakefield device can also be used for high gradient acceleration of electrons with a stable rf phase and amplitude which are controlled by manipulation of the bunch train. To achieve precise control of the rf pulse properties, a two-beam wakefield interferometry method was developed in which the rf pulse, due to themore » interference of the wakefields from the two bunches, was measured as a function of bunch separation. As a result, measurements of the energy change of a trailing electron bunch as a function of the bunch separation confirmed the interferometry method.« less

Enzymatic studies using quantum mechanical and molecular mechanical techniques

NASA Astrophysics Data System (ADS)

Faulder, Paul F.

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

Quantum criticality among entangled spin chains

DOE PAGES

Blanc, N.; Trinh, J.; Dong, L.; ...

2017-12-11

Here, an important challenge in magnetism is the unambiguous identification of a quantum spin liquid, of potential importance for quantum computing. In such a material, the magnetic spins should be fluctuating in the quantum regime, instead of frozen in a classical long-range-ordered state. While this requirement dictates systems wherein classical order is suppressed by a frustrating lattice, an ideal system would allow tuning of quantum fluctuations by an external parameter. Conventional three-dimensional antiferromagnets can be tuned through a quantum critical point—a region of highly fluctuating spins—by an applied magnetic field. Such systems suffer from a weak specific-heat peak at themore » quantum critical point, with little entropy available for quantum fluctuations. Here we study a different type of antiferromagnet, comprised of weakly coupled antiferromagnetic spin-1/2 chains as realized in the molecular salt K 2PbCu(NO 2) 6. Across the temperature–magnetic field boundary between three-dimensional order and the paramagnetic phase, the specific heat exhibits a large peak whose magnitude approaches a value suggestive of the spinon Sommerfeld coefficient of isolated quantum spin chains. These results demonstrate an alternative approach for producing quantum matter via a magnetic-field-induced shift of entropy from one-dimensional short-range order to a three-dimensional quantum critical point.« less

Quantum criticality among entangled spin chains

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

Blanc, N.; Trinh, J.; Dong, L.

Here, an important challenge in magnetism is the unambiguous identification of a quantum spin liquid, of potential importance for quantum computing. In such a material, the magnetic spins should be fluctuating in the quantum regime, instead of frozen in a classical long-range-ordered state. While this requirement dictates systems wherein classical order is suppressed by a frustrating lattice, an ideal system would allow tuning of quantum fluctuations by an external parameter. Conventional three-dimensional antiferromagnets can be tuned through a quantum critical point—a region of highly fluctuating spins—by an applied magnetic field. Such systems suffer from a weak specific-heat peak at themore » quantum critical point, with little entropy available for quantum fluctuations. Here we study a different type of antiferromagnet, comprised of weakly coupled antiferromagnetic spin-1/2 chains as realized in the molecular salt K 2PbCu(NO 2) 6. Across the temperature–magnetic field boundary between three-dimensional order and the paramagnetic phase, the specific heat exhibits a large peak whose magnitude approaches a value suggestive of the spinon Sommerfeld coefficient of isolated quantum spin chains. These results demonstrate an alternative approach for producing quantum matter via a magnetic-field-induced shift of entropy from one-dimensional short-range order to a three-dimensional quantum critical point.« less

Quantum criticality among entangled spin chains

NASA Astrophysics Data System (ADS)

Blanc, N.; Trinh, J.; Dong, L.; Bai, X.; Aczel, A. A.; Mourigal, M.; Balents, L.; Siegrist, T.; Ramirez, A. P.

2018-03-01

An important challenge in magnetism is the unambiguous identification of a quantum spin liquid1,2, of potential importance for quantum computing. In such a material, the magnetic spins should be fluctuating in the quantum regime, instead of frozen in a classical long-range-ordered state. While this requirement dictates systems3,4 wherein classical order is suppressed by a frustrating lattice5, an ideal system would allow tuning of quantum fluctuations by an external parameter. Conventional three-dimensional antiferromagnets can be tuned through a quantum critical point—a region of highly fluctuating spins—by an applied magnetic field. Such systems suffer from a weak specific-heat peak at the quantum critical point, with little entropy available for quantum fluctuations6. Here we study a different type of antiferromagnet, comprised of weakly coupled antiferromagnetic spin-1/2 chains as realized in the molecular salt K2PbCu(NO2)6. Across the temperature-magnetic field boundary between three-dimensional order and the paramagnetic phase, the specific heat exhibits a large peak whose magnitude approaches a value suggestive of the spinon Sommerfeld coefficient of isolated quantum spin chains. These results demonstrate an alternative approach for producing quantum matter via a magnetic-field-induced shift of entropy from one-dimensional short-range order to a three-dimensional quantum critical point.

The quantum defect: Early history and recent developments

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

Rau, A.R.; Inokuti, M.

1997-03-01

The notion of the quantum defect is important in atomic and molecular spectroscopy and also in unifying spectroscopy with collision theory. In the latter context, the quantum defect may be viewed as an ancestor of the phase shift. However, the origin of the term {open_quotes}quantum defect{close_quotes} does not seem to be explained in standard textbooks. It occurred in a 1921 paper by Schr{umlt o}dinger, preceding quantum mechanics, yet giving the correct meaning as an index of the short-range interactions with the core of an atom. We present the early history of the quantum-defect idea, and sketch its recent developments. {copyright}more » {ital 1997 American Association of Physics Teachers.}« less

Hydrogenic molecular transitions in double concentric quantum donuts by changing geometrical parameters

NASA Astrophysics Data System (ADS)

Ospina-Londoño, D. A.; Fulla, M. R.; Marín, J. H.

2013-03-01

In this work it is considered a versatile model to study two different ionization processes starting from a D20 homonuclear hydrogenic molecule confined in double concentric quantum donuts. Very narrow quantum donut circular cross sections are considered to separate the radial and angular variables in the D20 Hamiltonian by using the well-known adiabatic approximation D20 total energy as a function of the inter donor spacing and the outer donut center line radius is calculated. The salient features of an artificial D20 hydrogenic molecule such as the dissociation energy and the equilibrium length are strongly dependent on the quantum donut geometrical parameters. By increasing systematically the quantum donut outer center line radius, it is possible to understand a first ionization process: D20→D2++e-. A second ionization process D20→D-+D+ can be carried out by fixing the first donor position and gradually moving away the second one. The results obtained in this study are in good agreement with those previously obtained in the limiting cases of very large inter donor separation. The model proposed here is computationally economical and provides a realistic description of both ionization processes and the few-particle system confined in double concentric quantum donuts.

Enhanced Photoluminescence from Long Wavelength InAs Quantum Dots Embedded in a Graded (In,Ga)As Quantum Well

DTIC Science & Technology

2002-01-01

emitting lasers operating from 1.0 to 1.3 gim with very low threshold currents have been reported [2,3,9]; in addition, vertical - cavity surface - emitting ...grown by solid source molecular beam epitaxy ( MBE ). By modifying Indium composition profile within quantum well (QW) region, it’s found the... lasers ( VCSELs ) have also been successfully demonstrated [4]. There are currently several approaches to grow 1.3 jim (In,Ga)As quantum dots by MBE

Quantum Spectra and Dynamics

NASA Astrophysics Data System (ADS)

Arce, Julio Cesar

1992-01-01

This work focuses on time-dependent quantum theory and methods for the study of the spectra and dynamics of atomic and molecular systems. Specifically, we have addressed the following two problems: (i) Development of a time-dependent spectral method for the construction of spectra of simple quantum systems--This includes the calculation of eigenenergies, the construction of bound and continuum eigenfunctions, and the calculation of photo cross-sections. Computational applications include the quadrupole photoabsorption spectra and dissociation cross-sections of molecular hydrogen from various vibrational states in its ground electronic potential -energy curve. This method is seen to provide an advantageous alternative, both from the computational and conceptual point of view, to existing standard methods. (ii) Explicit time-dependent formulation of photoabsorption processes --Analytical solutions of the time-dependent Schrodinger equation are constructed and employed for the calculation of probability densities, momentum distributions, fluxes, transition rates, expectation values and correlation functions. These quantities are seen to establish the link between the dynamics and the calculated, or measured, spectra and cross-sections, and to clarify the dynamical nature of the excitation, transition and ejection processes. Numerical calculations on atomic and molecular hydrogen corroborate and complement the previous results, allowing the identification of different regimes during the photoabsorption process.

QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS

NASA Astrophysics Data System (ADS)

Ma, Changru; Martin-Samos, Layla; Fabris, Stefano; Laio, Alessandro; Piccinin, Simone

2015-10-01

We present QMMMW, a new program aimed at performing Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics. The package operates as a wrapper that patches PWscf code included in the QUANTUM ESPRESSO distribution and LAMMPS Molecular Dynamics Simulator. It is designed with a paradigm based on three guidelines: (i) minimal amount of modifications on the parent codes, (ii) flexibility and computational efficiency of the communication layer and (iii) accuracy of the Hamiltonian describing the interaction between the QM and MM subsystems. These three features are seldom present simultaneously in other implementations of QMMM. The QMMMW project is hosted by qe-forge at

A generalized any particle propagator theory: Assessment of nuclear quantum effects on electron propagator calculations

NASA Astrophysics Data System (ADS)

Romero, Jonathan; Posada, Edwin; Flores-Moreno, Roberto; Reyes, Andrés

2012-08-01

In this work we propose an extended propagator theory for electrons and other types of quantum particles. This new approach has been implemented in the LOWDIN package and applied to sample calculations of atomic and small molecular systems to determine its accuracy and performance. As a first application of the method we have studied the nuclear quantum effects on electron ionization energies. We have observed that ionization energies of atoms are similar to those obtained with the electron propagator approach. However, for molecular systems containing hydrogen atoms there are improvements in the quality of the results with the inclusion of nuclear quantum effects. An energy term analysis has allowed us to conclude that nuclear quantum effects are important for zero order energies whereas propagator results correct the electron and electron-nuclear correlation terms. Results presented for a series of n-alkanes have revealed the potential of this method for the accurate calculation of ionization energies of a wide variety of molecular systems containing hydrogen nuclei. The proposed methodology will also be applicable to exotic molecular systems containing positrons or muons.

Structure of cold nuclear matter at subnuclear densities by quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

2003-09-01

Structure of cold nuclear matter at subnuclear densities for the proton fraction x=0.5, 0.3, and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases with slablike and rodlike nuclei, etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape, and also systematically analyze the structure of cold matter using two-point correlation functions and Minkowski functionals. In our simulations, we also observe intermediate phases, which have complicated nuclear shapes. It has been found out that these phases can be characterized as those with negative Euler characteristic. Our result implies the existence of these kinds of phases in addition to the simple “pasta” phases in neutron star crusts and supernova inner cores. In addition, we investigate the properties of the effective QMD interaction used in the present work to examine the validity of our results. The resultant energy per nucleon ɛn of the pure neutron matter, the proton chemical μ(0)p in pure neutron matter and the nuclear surface tension Esurf are generally reasonable in comparison with other nuclear interactions.

Andreev molecules in semiconductor nanowire double quantum dots.

PubMed

Su, Zhaoen; Tacla, Alexandre B; Hocevar, Moïra; Car, Diana; Plissard, Sébastien R; Bakkers, Erik P A M; Daley, Andrew J; Pekker, David; Frolov, Sergey M

2017-09-19

Chains of quantum dots coupled to superconductors are promising for the realization of the Kitaev model of a topological superconductor. While individual superconducting quantum dots have been explored, control of longer chains requires understanding of interdot coupling. Here, double quantum dots are defined by gate voltages in indium antimonide nanowires. High transparency superconducting niobium titanium nitride contacts are made to each of the dots in order to induce superconductivity, as well as probe electron transport. Andreev bound states induced on each of dots hybridize to define Andreev molecular states. The evolution of these states is studied as a function of charge parity on the dots, and in magnetic field. The experiments are found in agreement with a numerical model.Quantum dots in a nanowire are one possible approach to creating a solid-state quantum simulator. Here, the authors demonstrate the coupling of electronic states in a double quantum dot to form Andreev molecule states; a potential building block for longer chains suitable for quantum simulation.

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

PubMed

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

2014-06-10

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

[The photoluminescence characteristics of organic multilayer quantum wells].

PubMed

Zhao, De-Wei; Song, Shu-Fang; Zhao, Su-Ling; Xu, Zheng; Wang, Yong-Sheng; Xu, Xu-Rong

2007-04-01

By the use of multi-source high-vaccum organic beam deposition system, the authors prepared organic multilayer quantum well structures, which consist of alternate organic small molecule materials PBD and Alq3. Based on 4-period organic quantum wells, different samples with different thickness barriers and wells were prepared. The authors measured the lowest unoccupied molecular orbit (LUMO) and the highest occupied molecular orbit (HOMO) by electrochemistry cyclic voltammetry and optical absorption. From the energy diagrams, it seems like type-I quantum well structures of the inorganic semiconductor, in which PBD is used as a barrier layer and Alq3 as a well layer and emitter. From small angle X-ray diffraction measurements, the results indicate that these structures have high interface quality and uniformity. The photoluminescence characteristics of organic multilayer quantum wells were investigated. The PL peak has a blue-shift with the decrease of the well layer thickness. Meanwhile as the barrier thickness decreases the PL peaks of PBD disappear gradually. And the energy may be effectively transferred from PBD to Alq3, inducing an enhancement of the luminescence of Alq3.

Simultaneous deterministic control of distant qubits in two semiconductor quantum dots.

PubMed

Gamouras, A; Mathew, R; Freisem, S; Deppe, D G; Hall, K C

2013-10-09

In optimal quantum control (OQC), a target quantum state of matter is achieved by tailoring the phase and amplitude of the control Hamiltonian through femtosecond pulse-shaping techniques and powerful adaptive feedback algorithms. Motivated by recent applications of OQC in quantum information science as an approach to optimizing quantum gates in atomic and molecular systems, here we report the experimental implementation of OQC in a solid-state system consisting of distinguishable semiconductor quantum dots. We demonstrate simultaneous high-fidelity π and 2π single qubit gates in two different quantum dots using a single engineered infrared femtosecond pulse. These experiments enhance the scalability of semiconductor-based quantum hardware and lay the foundation for applications of pulse shaping to optimize quantum gates in other solid-state systems.

Molecular recognition using receptor-free nanomechanical infrared spectroscopy based on a quantum cascade laser

PubMed Central

Kim, Seonghwan; Lee, Dongkyu; Liu, Xunchen; Van Neste, Charles; Jeon, Sangmin; Thundat, Thomas

2013-01-01

Speciation of complex mixtures of trace explosives presents a formidable challenge for sensors that rely on chemoselective interfaces due to the unspecific nature of weak intermolecular interactions. Nanomechanical infrared (IR) spectroscopy provides higher selectivity in molecular detection without using chemoselective interfaces by measuring the photothermal effect of adsorbed molecules on a thermally sensitive microcantilever. In addition, unlike conventional IR spectroscopy, the detection sensitivity is drastically enhanced by increasing the IR laser power, since the photothermal signal comes from the absorption of IR photons and nonradiative decay processes. By using a broadly tunable quantum cascade laser for the resonant excitation of molecules, we increased the detection sensitivity by one order of magnitude compared to the use of a conventional IR monochromator. Here, we demonstrate the successful speciation and quantification of picogram levels of ternary mixtures of similar explosives (trinitrotoluene (TNT), cyclotrimethylene trinitramine (RDX), and pentaerythritol tetranitrate (PETN)) using nanomechanical IR spectroscopy. PMID:23346368

Spin fine structure of optically excited quantum dot molecules

NASA Astrophysics Data System (ADS)

Scheibner, M.; Doty, M. F.; Ponomarev, I. V.; Bracker, A. S.; Stinaff, E. A.; Korenev, V. L.; Reinecke, T. L.; Gammon, D.

2007-06-01

The interaction between spins in coupled quantum dots is revealed in distinct fine structure patterns in the measured optical spectra of InAs/GaAs double quantum dot molecules containing zero, one, or two excess holes. The fine structure is explained well in terms of a uniquely molecular interplay of spin-exchange interactions, Pauli exclusion, and orbital tunneling. This knowledge is critical for converting quantum dot molecule tunneling into a means of optically coupling not just orbitals but also spins.

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

PubMed

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

2016-05-12

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

The Molecular Structure of Phenetole Studied by Microwave Spectroscopy and Quantum Chemical Calculations

NASA Astrophysics Data System (ADS)

Ferres, Lynn; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

2016-06-01

A pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2 - 26.5 GHz was used to measure the spectrum of phenetole (ethyl phenyl ether or ethoxybenzene, C6H5OC2H5). The conformational landscape is completely determined by the orientations of the phenyl ring and the ethyl group. A two-dimensional potential energy surface was calculated at the MP2/6-311++G(d,p) level of theory. Two conformers were found: The trans conformer has a Cs symmetry, and the gauche conformer has the ethyl group tilted out of the phenyl plane by about 70°. Totally 186 rotational transitions were assigned to the more stable planar trans conformer, and fitted using a semi-rigid rotor model to measurement accuracy of 2 kHz. Highly accurate rotational and centrifugal distortion constants were determined. Several method and basis set combinations were applied to check for convergence and to compare with the experimentally deduced molecular parameters. The inertial defect of the observed conformer Δc = (Ic - Ia - Ib) = -6.718 uÅ2 confirms that the heavy atom skeleton is planar with two pairs of hydrogen atoms out of plane. All lines in the spectrum could be assigned to the trans conformer, which confirms that the gauche conformer cannot be observed under our measurement conditions. In agreement with the rather high torsional barrier of the methyl group (V3 = 1168 wn) calculated by quantum chemical methods, all assigned lines appeared sharp and no signs of splittings were observed for the methyl internal rotation.

Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

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

Thomas, Robert E.; Overy, Catherine; Opalka, Daniel

Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, themore » present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.« less

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

PubMed Central

2015-01-01

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

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

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

PubMed

Sturniolo, Simone

2018-05-01

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

Quantum mechanical tunneling in the automerization of cyclobutadiene

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Quantum dot-based molecular beacon to monitor intracellular microRNAs.

PubMed

Lee, Jonghwan; Moon, Sung Ung; Lee, Yong Seung; Ali, Bahy A; Al-Khedhairy, Abdulaziz A; Ali, Daoud; Ahmed, Javed; Al Salem, Abdullah M; Kim, Soonhag

2015-06-02

Fluorescence monitoring of endogenous microRNA (miRNA or miR) activity related to neuronal development using nano-sized materials provides crucial information on miRNA expression patterns in a noninvasive manner. In this study, we report a new method to monitor intracellular miRNA124a using quantum dot-based molecular beacon (R9-QD-miR124a beacon). The R9-QD-miR124a beacon was constructed using QDs and two probes, miR124a-targeting oligomer and arginine rich cell-penetrating peptide (R9 peptide). The miR124a-targeting oligomer contains a miR124a binging sequence and a black hole quencher 1 (BHQ1). In the absence of target miR124a, the R9-QD-miR124a beacon forms a partial duplex beacon and remained in quenched state because the BHQ1 quenches the fluorescence signal of the R9-QD-miR124a beacon. The binding of miR124a to the miR124a binding sequence of the miR124a-targeting oligomer triggered the separation of the BHQ1 quencher and subsequent signal-on of a red fluorescence signal. Moreover, enhanced cellular uptake was achieved by conjugation with the R9 peptide, which resulted in increased fluorescent signal of the R9-QD-miR124a beacons in P19 cells during neurogenesis due to the endogenous expression of miR124a.

Strained GaSb/AlAsSb Quantum Wells for p-Channel Field-Effect Transistors

DTIC Science & Technology

2008-01-01

Available online 18 October 2008 PACS: 72.80.Ey 73.61.Ey 81.05.Ea 85.30.Tv Keywords: A3. Molecular beam epitaxy A3. Quantum wells B2. Semiconducting III–V...were grown by molecular beam epitaxy on GaAs substrates. The buffer layer and barrier layers consisted of relaxed AlAsxSb1x. The composition of the...composition in order to control the strain in the GaSb quantum well. The heterostructures studied here are grown by molecular beam epitaxy (MBE) on semi

Mixed QM/MM molecular electrostatic potentials.

PubMed

Hernández, B; Luque, F J; Orozco, M

2000-05-01

A new method is presented for the calculation of the Molecular Electrostatic Potential (MEP) in large systems. Based on the mixed Quantum Mechanics/Molecular Mechanics (QM/MM) approach, the method assumes both a quantum and classical description for the molecule, and the calculation of the MEP in the space surrounding the molecule is made using this dual treatment. The MEP at points close to the molecule is computed using a full QM formalism, while a pure classical evaluation of the MEP is used for points located at large distances from the molecule. The algorithm allows the user to select the desired level of accuracy in the MEP, so that the definition of the regions where the MEP is computed at the classical or QM levels is adjusted automatically. The potential use of this QM/MM MEP in molecular modeling studies is discussed.

Quantum Chaos

NASA Astrophysics Data System (ADS)

Casati, Giulio; Chirikov, Boris

2006-11-01

Preface; Acknowledgments; Introduction: 1. The legacy of chaos in quantum mechanics G. Casati and B. V. Chirikov; Part I. Classical Chaos and Quantum Localization: 2. Stochastic behaviour of a quantum pendulum under a periodic perturbation G. Casati, B. V. Chirikov, F. M. Izrailev and J. Ford; 3. Quantum dynamics of a nonintegrable system D. R. Grempel, R. E. Prange and S. E. Fishman; 4. Excitation of molecular rotation by periodic microwave pulses. A testing ground for Anderson localization R. Blümel, S. Fishman and U. Smilansky; 5. Localization of diffusive excitation in multi-level systems D. K. Shepelyansky; 6. Classical and quantum chaos for a kicked top F. Haake, M. Kus and R. Scharf; 7. Self-similarity in quantum dynamics L. E. Reichl and L. Haoming; 8. Time irreversibility of classically chaotic quantum dynamics K. Ikeda; 9. Effect of noise on time-dependent quantum chaos E. Ott, T. M. Antonsen Jr and J. D. Hanson; 10. Dynamical localization, dissipation and noise R. F. Graham; 11. Maximum entropy models and quantum transmission in disordered systems J.-L. Pichard and M. Sanquer; 12. Solid state 'atoms' in intense oscillating fields M. S. Sherwin; Part II. Atoms in Strong Fields: 13. Localization of classically chaotic diffusion for hydrogen atoms in microwave fields J. E. Bayfield, G. Casati, I. Guarneri and D. W. Sokol; 14. Inhibition of quantum transport due to 'scars' of unstable periodic orbits R. V. Jensen, M. M. Sanders, M. Saraceno and B. Sundaram; 15. Rubidium Rydberg atoms in strong fields G. Benson, G. Raithel and H. Walther; 16. Diamagnetic Rydberg atom: confrontation of calculated and observed spectra C.-H. Iu, G. R. Welch, M. M. Kash, D. Kleppner, D. Delande and J. C. Gay; 17. Semiclassical approximation for the quantum states of a hydrogen atom in a magnetic field near the ionization limit M. Y. Kuchiev and O. P. Sushkov; 18. The semiclassical helium atom D. Wintgen, K. Richter and G. Tanner; 19. Stretched helium: a model for quantum chaos

Quantum Chaos

NASA Astrophysics Data System (ADS)

Casati, Giulio; Chirikov, Boris

1995-04-01

Preface; Acknowledgments; Introduction: 1. The legacy of chaos in quantum mechanics G. Casati and B. V. Chirikov; Part I. Classical Chaos and Quantum Localization: 2. Stochastic behaviour of a quantum pendulum under a periodic perturbation G. Casati, B. V. Chirikov, F. M. Izrailev and J. Ford; 3. Quantum dynamics of a nonintegrable system D. R. Grempel, R. E. Prange and S. E. Fishman; 4. Excitation of molecular rotation by periodic microwave pulses. A testing ground for Anderson localization R. Blümel, S. Fishman and U. Smilansky; 5. Localization of diffusive excitation in multi-level systems D. K. Shepelyansky; 6. Classical and quantum chaos for a kicked top F. Haake, M. Kus and R. Scharf; 7. Self-similarity in quantum dynamics L. E. Reichl and L. Haoming; 8. Time irreversibility of classically chaotic quantum dynamics K. Ikeda; 9. Effect of noise on time-dependent quantum chaos E. Ott, T. M. Antonsen Jr and J. D. Hanson; 10. Dynamical localization, dissipation and noise R. F. Graham; 11. Maximum entropy models and quantum transmission in disordered systems J.-L. Pichard and M. Sanquer; 12. Solid state 'atoms' in intense oscillating fields M. S. Sherwin; Part II. Atoms in Strong Fields: 13. Localization of classically chaotic diffusion for hydrogen atoms in microwave fields J. E. Bayfield, G. Casati, I. Guarneri and D. W. Sokol; 14. Inhibition of quantum transport due to 'scars' of unstable periodic orbits R. V. Jensen, M. M. Sanders, M. Saraceno and B. Sundaram; 15. Rubidium Rydberg atoms in strong fields G. Benson, G. Raithel and H. Walther; 16. Diamagnetic Rydberg atom: confrontation of calculated and observed spectra C.-H. Iu, G. R. Welch, M. M. Kash, D. Kleppner, D. Delande and J. C. Gay; 17. Semiclassical approximation for the quantum states of a hydrogen atom in a magnetic field near the ionization limit M. Y. Kuchiev and O. P. Sushkov; 18. The semiclassical helium atom D. Wintgen, K. Richter and G. Tanner; 19. Stretched helium: a model for quantum chaos

Hot-hole extraction from quantum dot to molecular adsorbate.

PubMed

Singhal, Pallavi; Ghosh, Hirendra N

2015-03-09

Ultrafast thermalized and hot-hole-transfer processes have been investigated in CdSe quantum dot (QD)/catechol composite systems in which hole transfer from photoexcited QDs to the catechols is thermodynamically favorable. A series of catechol derivatives were selected with different electron-donating and -withdrawing groups, and the effect of these groups on hole transfer and charge recombination (CR) dynamics has been investigated. The hole-transfer time was determined using the fluorescence upconversion technique and found to be 2-10 ps depending on the molecular structure of the catechol derivatives. The hot-hole-transfer process was followed after monitoring 2S luminescence of CdSe QDs. Interestingly, hot-hole extraction was observed only in the CdSe/3-methoxycatechol (3-OCH3) composite system owing to the higher electron-donating property of the 3-methoxy group. To confirm the extraction of the hot hole and to monitor the CR reaction in CdSe QD/catechol composite systems, ultrafast transient absorption studies have been carried out. Ultrafast transient-absorption studies show that the bleach recovery kinetics of CdSe QD at the 2S excitonic position is much faster in the presence of 3-OCH3. This faster bleach recovery at the 2S position in CdSe/3-OCH3 suggests hot-hole transfer from CdSe QD to 3-OCH3. CR dynamics in CdSe QD/catechol composite systems was followed by monitoring the excitonic bleach at the 1S position and was found to decrease with free energy of the CR reaction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of magnetic and diamagnetic interactions in molecular optics and scattering

NASA Astrophysics Data System (ADS)

Forbes, Kayn A.

2018-05-01

This paper aims to explicitly clarify the role and interpretation of diamagnetic interactions between molecules and light in quantum electrodynamics. In contrast to their electric and magnetic counterparts, the diamagnetic couplings between light and matter have received relatively little interest in the field of molecular optics. This intriguing disregard of an interaction term is puzzling. The diamagnetic couplings possess unique physical properties that warrant their inclusion in any multiphoton process, and the lack of gauge invariance for paramagnetic and diamagnetic susceptibilities necessitates their inclusion. Their role and importance within nonrelativistic molecular quantum electrodynamics in the Coulomb gauge is illuminated, and it is highlighted how for any multiphoton process their inclusion should be implicit. As an indicative example of the theory presented, the diamagnetic contributions to both forward and nonforward Rayleigh scattering are derived and put into context alongside the electric and magnetic molecular responses. The work represents clarification of diamagnetic couplings in molecular quantum electrodynamics, which subsequently should proffer the study of diamagnetic interactions in molecular optics due to their unique physical attributes and necessary inclusion in multiphoton processes.

Properties and applications of quantum dot heterostructures grown by molecular beam epitaxy

PubMed Central

2006-01-01

One of the main directions of contemporary semiconductor physics is the production and study of structures with a dimension less than two: quantum wires and quantum dots, in order to realize novel devices that make use of low-dimensional confinement effects. One of the promising fabrication methods is to use self-organized three-dimensional (3D) structures, such as 3D coherent islands, which are often formed during the initial stage of heteroepitaxial growth in lattice-mismatched systems. This article is intended to convey the flavour of the subject by focussing on the structural, optical and electronic properties and device applications of self-assembled quantum dots and to give an elementary introduction to some of the essential characteristics.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis.

PubMed

Stauch, Tim; Dreuw, Andreas

2016-11-23

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

NASA Astrophysics Data System (ADS)

Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

2009-02-01

The problem of quantum-like representation in economy cognitive science, and genetics / L. Accardi, A. Khrennikov and M. Ohya -- Chaotic behavior observed in linea dynamics / M. Asano, T. Yamamoto and Y. Togawa -- Complete m-level quantum teleportation based on Kossakowski-Ohya scheme / M. Asano, M. Ohya and Y. Tanaka -- Towards quantum cybernetics: optimal feedback control in quantum bio informatics / V. P. Belavkin -- Quantum entanglement and circulant states / D. Chruściński -- The compound Fock space and its application in brain models / K. -H. Fichtner and W. Freudenberg -- Characterisation of beam splitters / L. Fichtner and M. Gäbler -- Application of entropic chaos degree to a combined quantum baker's map / K. Inoue, M. Ohya and I. V. Volovich -- On quantum algorithm for multiple alignment of amino acid sequences / S. Iriyama and M. Ohya --Quantum-like models for decision making in psychology and cognitive science / A. Khrennikov -- On completely positive non-Markovian evolution of a d-level system / A. Kossakowski and R. Rebolledo -- Measures of entanglement - a Hilbert space approach / W. A. Majewski -- Some characterizations of PPT states and their relation / T. Matsuoka -- On the dynamics of entanglement and characterization ofentangling properties of quantum evolutions / M. Michalski -- Perspective from micro-macro duality - towards non-perturbative renormalization scheme / I. Ojima -- A simple symmetric algorithm using a likeness with Introns behavior in RNA sequences / M. Regoli -- Some aspects of quadratic generalized white noise functionals / Si Si and T. Hida -- Analysis of several social mobility data using measure of departure from symmetry / K. Tahata ... [et al.] -- Time in physics and life science / I. V. Volovich -- Note on entropies in quantum processes / N. Watanabe -- Basics of molecular simulation and its application to biomolecules / T. Ando and I. Yamato -- Theory of proton-induced superionic conduction in hydrogen-bonded systems

Quantum-SAR Extension of the Spectral-SAR Algorithm. Application to Polyphenolic Anticancer Bioactivity

PubMed Central

Putz, Mihai V.; Putz, Ana-Maria; Lazea, Marius; Ienciu, Luciana; Chiriac, Adrian

2009-01-01

Aiming to assess the role of individual molecular structures in the molecular mechanism of ligand-receptor interaction correlation analysis, the recent Spectral-SAR approach is employed to introduce the Quantum-SAR (QuaSAR) “wave” and “conversion factor” in terms of difference between inter-endpoint inter-molecular activities for a given set of compounds; this may account for inter-conversion (metabolization) of molecular (concentration) effects while indicating the structural (quantum) based influential/detrimental role on bio-/eco- effect in a causal manner rather than by simple inspection of measured values; the introduced QuaSAR method is then illustrated for a study of the activity of a series of flavonoids on breast cancer resistance protein. PMID:19399244

Photodissociation of quantum state-selected diatomic molecules yields new insight into ultracold chemistry

NASA Astrophysics Data System (ADS)

McDonald, Mickey; McGuyer, Bart H.; Lee, Chih-Hsi; Apfelbeck, Florian; Zelevinsky, Tanya

2016-05-01

When a molecule is subjected to a sufficiently energetic photon it can break apart into fragments through a process called ``photodissociation''. For over 70 years this simple chemical reaction has served as a vital experimental tool for acquiring information about molecular structure, since the character of the photodissociative transition can be inferred by measuring the 3D photofragment angular distribution (PAD). While theoretical understanding of this process has gradually evolved from classical considerations to a fully quantum approach, experiments to date have not yet revealed the full quantum nature of this process. In my talk I will describe recent experiments involving the photodissociation of ultracold, optical lattice-trapped, and fully quantum state-resolved 88Sr2 molecules. Optical absorption images of the PADs produced in these experiments reveal features which are inherently quantum mechanical in nature, such as matter-wave interference between output channels, and are sensitive to the quantum statistics of the molecular wavefunctions. The results of these experiments cannot be predicted using quasiclassical methods. Instead, we describe our results with a fully quantum mechanical model yielding new intuition about ultracold chemistry.

Exciton shelves for charge and energy transport in third-generation quantum-dot devices

NASA Astrophysics Data System (ADS)

Goodman, Samuel; Singh, Vivek; Noh, Hyunwoo; Casamada, Josep; Chatterjee, Anushree; Cha, Jennifer; Nagpal, Prashant

2014-03-01

Quantum dots are semiconductor nanocrystallites with size-dependent quantum-confined energy levels. While they have been intensively investigated to utilize hot-carriers for photovoltaic applications, to bridge the mismatch between incident solar photons and finite bandgap of semiconductor photocells, efficient charge or exciton transport in quantum-dot films has proven challenging. Here we show development of new coupled conjugated molecular wires with ``exciton shelves'', or different energy levels, matched with the multiple energy levels of quantum dots. Using single nanoparticle and ensemble device measurements we show successful extraction and transport of both bandedge and high-energy charge carriers, and energy transport of excitons. We demonstrate using measurements of electronic density of states, that careful matching of energy states of quantum-dot with molecular wires is important, and any mismatch can generate midgap states leading to charge recombination and reduced efficiency. Therefore, these exciton-shelves and quantum dots can lead to development of next-generation photovoltaic and photodetection devices using simultaneous transport of bandedge and hot-carriers or energy transport of excitons in these nanostructured solution-processed films.

Multiphase Equation of State and Strength Properties of Beryllium from AB INITIO and Quantum Molecular Dynamics Calculations.

NASA Astrophysics Data System (ADS)

Robert, G.; Sollier, A.; Legrand, Ph.

2007-12-01

In the framework of density functional theory, static properties and phonon spectra of beryllium have been calculated under high compression (for pressures up to 4 Mbar) for two solid phases: hexagonal compact (hcp) and body-centered cubic (bcc). The melting curve and some isotherms in the liquid phase have been calculated using quantum molecular dynamics. The coupling of these theoretical data to a quasi-harmonic approach (phonon moments) allows us to suggest a new theoretical phase diagram and to build a multiphase equation of state (EOS) valid in a large range of pressure and temperature. The resulting Hugoniot curves as well as the evolution of the longitudinal sound speed with both pressure and temperature are in good agreement with available experimental data.

An ultrasensitive SiO2-encapsulated alloyed CdZnSeS quantum dot-molecular beacon nanobiosensor for norovirus.

PubMed

Adegoke, Oluwasesan; Seo, Min-Woong; Kato, Tatsuya; Kawahito, Shoji; Park, Enoch Y

2016-12-15

Ultrasensitive, rapid and selective diagnostic probes are urgently needed to overcome the limitations of traditional probes for norovirus (NV). Here, we report the detection of NV genogroup II via nucleic acid hybridization technology using a quantum dot (QD)-conjugated molecular beacon (MB) probe. To boost the sensitivity of the MB assay system, an ultrasensitive QD fluorophore with unique optical properties was synthesized, characterized and exploited as a fluorescence signal generator. Alloyed thioglycolic (TGA)-capped CdZnSeS QDs with a high photoluminescence (PL) quantum yield (QY) value of 92% were synthesized, and a modified silanization method was employed to encapsulate the thiol-capped QDs in a silica layer. The resulting highly luminescent alloyed SiO2-coated CdZnSeS QDs had a remarkable PL QY value of 98%. Transmission electron microscopy and dynamic light scattering confirmed the monodispersity of the alloyed nanocrystals, and zeta potential analysis confirmed their colloidal stability. Powder X-ray diffraction and PL lifetime measurements confirmed the surface modification of the QDs. The alloyed TGA-capped and SiO2-coated CdZnSeS QD-conjugated MB bioprobes detected extremely low concentrations of NV RNA. Ultrasensitive detection of low concentrations of NV RNA with a limit of detection (LOD) of 8.2copies/mL in human serum and a LOD of 9.3 copies/mL in buffer was achieved using the SiO2-coated CdZnSeS QD-MB probes, an increase in sensitivity of 3-fold compared with the detection limit for NV RNA using TGA-capped CdZnSeS QD-MBs. The additional merits of our detection system are rapidity, specificity and improved sensitivity over conventional molecular test probes. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Quantum-chemical Calculations in the Study of Antitumour Compounds

NASA Astrophysics Data System (ADS)

Luzhkov, V. B.; Bogdanov, G. N.

1986-01-01

The results of quantum-chemical calculations on antitumour preparations concerning the mechanism of their action at the electronic and molecular levels and structure-activity correlations are discussed in this review. Preparations whose action involves alkylating and free-radial mechanisms, complex-forming agents, and antimetabolites are considered. Modern quantum-chemical methods for calculations on biologically active substances are described. The bibliography includes 106 references.

WavePacket: A Matlab package for numerical quantum dynamics.II: Open quantum systems, optimal control, and model reduction

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard; Hartmann, Carsten

2018-07-01

WavePacket is an open-source program package for numeric simulations in quantum dynamics. It can solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows, e.g., to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semi-classical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. Being highly versatile and offering visualization of quantum dynamics 'on the fly', WavePacket is well suited for teaching or research projects in atomic, molecular and optical physics as well as in physical or theoretical chemistry. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] which dealt with closed quantum systems and discrete variable representations, the present Part II focuses on the dynamics of open quantum systems, with Lindblad operators modeling dissipation and dephasing. This part also describes the WavePacket function for optimal control of quantum dynamics, building on rapid monotonically convergent iteration methods. Furthermore, two different approaches to dimension reduction implemented in WavePacket are documented here. In the first one, a balancing transformation based on the concepts of controllability and observability Gramians is used to identify states that are neither well controllable nor well observable. Those states are either truncated or averaged out. In the other approach, the H2-error for a given reduced dimensionality is minimized by H2 optimal model reduction techniques, utilizing a bilinear iterative rational Krylov algorithm. The present work describes the MATLAB version of WavePacket 5.3.0 which is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

PubMed

Sponer, Jiří; Sponer, Judit E; Mládek, Arnošt; Jurečka, Petr; Banáš, Pavel; Otyepka, Michal

2013-12-01

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. Copyright © 2013 Wiley Periodicals, Inc.

Strong coupling-like phenomenon in single metallic nanoparticle embedded in molecular J-aggregates

NASA Astrophysics Data System (ADS)

Feng, Xin; Wang, Chen; Ma, Hongjing; Chen, Yuanyuan; Duan, Gaoyan; Zhang, Pengfei; Song, Gang

2018-02-01

Strong coupling-like phenomenon between plasmonic cavities and emitters provides a new way to realize the quantum-like effect controlling at microscale/nanoscale. We investigate the strong coupling-like phenomenon in the structure of single metallic nanoparticle embedded in molecular J-aggregates by the classical simulation method and show that the size of the metallic nanoparticle and the oscillator strength of molecular J-aggregates impact the strong coupling-like phenomenon. The strong coupling-like phenomenon is induced by the interactions between two dipoles formed by the metallic nanoparticle and molecular J-aggregates or the interactions between the dipole generated from molecular J-aggregates and the quadrupole generated from the metallic nanoparticle. The strong coupling-like phenomenon appears evidently with the increase in oscillator strength of molecular J-aggregates. The detuning energy linearly decreases with the increase in radius of the metallic nanoparticle. Our structure has potential applications in quantum networks, quantum key distributions and so on.

Quantum Sensing for High Energy Physics

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

van Bibber, Karl; Boshier, Malcolm; Demarteau, Marcel

The Coordinating Panel for Advanced Detectors (CPAD) of the APS Division of Particles and Fields organized a first workshop on Quantum Sensing for High Energy Physics (HEP) in early December 2017 at Argonne National Laboratory. Participants from universities and national labs were drawn from the intersecting fields of Quantum Information Science (QIS), high energy physics, atomic, molecular and optical physics, condensed matter physics, nuclear physics and materials science. Quantum-enabled science and technology has seen rapid technical advances and growing national interest and investments over the last few years. The goal of the workshop was to bring the various communities togethermore » to investigate pathways to integrate the expertise of these two disciplines to accelerate the mutual advancement of scientific progress.« less

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

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

Chen, Jie; Yin, Hongyun; Wang, Dunyou

2013-02-20

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

A simple molecular orbital treatment of current distributions in quantum transport through molecular junctions

NASA Astrophysics Data System (ADS)

Jhan, Sin-Mu; Jin, Bih-Yaw

2017-11-01

A simple molecular orbital treatment of local current distributions inside single molecular junctions is developed in this paper. Using the first-order perturbation theory and nonequilibrium Green's function techniques in the framework of Hückel theory, we show that the leading contributions to local current distributions are directly proportional to the off-diagonal elements of transition density matrices. Under the orbital approximation, the major contributions to local currents come from a few dominant molecular orbital pairs which are mixed by the interactions between the molecule and electrodes. A few simple molecular junctions consisting of single- and multi-ring conjugated systems are used to demonstrate that local current distributions inside molecular junctions can be decomposed by partial sums of a few leading contributing transition density matrices.

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.

Numerical studies of acceleration of thorium ions by a laser pulse of ultra-relativistic intensity

NASA Astrophysics Data System (ADS)

Domanski, Jaroslaw; Badziak, Jan

2018-01-01

One of the key scientific projects of ELI-Nuclear Physics is to study the production of extremely neutron-rich nuclides by a new reaction mechanism called fission-fusion using laser-accelerated thorium (232Th) ions. This research is of crucial importance for understanding the nature of the creation of heavy elements in the Universe; however, they require Th ion beams of very high beam fluencies and intensities which are inaccessible in conventional accelerators. This contribution is a first attempt to investigate the possibility of the generation of intense Th ion beams by a fs laser pulse of ultra-relativistic intensity. The investigation was performed with the use of fully electromagnetic relativistic particle-in-cell code. A sub-μm thorium target was irradiated by a circularly polarized 20-fs laser pulse of intensity up to 1023 W/cm2, predicted to be attainable at ELI-NP. At the laser intensity 1023 W/cm2 and an optimum target thickness, the maximum energies of Th ions approach 9.3 GeV, the ion beam intensity is > 1020 W/cm2 and the total ion fluence reaches values 1019 ions/cm2. The last two values are much higher than attainable in conventional accelerators and are fairly promising for the planned ELI-NP experiment.

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