Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “quantum computing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,063 records · Page 59Linked to original sources
PubMed2001

Quantum solution to the Byzantine agreement problem.

We present a solution to an old problem in distributed computing. In its simplest form, a sender has to broadcast some information to two receivers, but they have access only to pairwise communication channels. Unlike quantum key distribution, here the goal is not secrecy but agreement, and the adversary (one of the receivers or the sender himself) is not outside but inside the game. Using only classical channels this problem is provably impossible. The solution uses pairwise quantum channels and entangled qutrits.

Journal Article↗
PubMed2002

Quantum dynamics of hydride transfer catalyzed by bimetallic electrophilic catalysis: synchronous motion of Mg(2+) and H(-) in xylose isomerase.

Xylose isomerase exhibits a bridged-bimetallic active-site motif in which the substrate is bound to two metals connected by a glutamate bridge, and X-ray crystallographic studies suggest that metal movement is involved in the hydride transfer rate-controlling catalytic step. Here we report classical/quantal dynamical simulations of this step that provide new insight into the metal motion. The potential energy surface is calculated by treating xylose with semiempirical molecular orbital theory augmented by a simple valence bond potential and the rest of the system by molecular mechanics. The rate constant for the hydride-transfer step was calculated by ensemble-averaged dynamical simulations including both variational transition-state theory for determination of the statistically averaged dynamical bottleneck and optimized multidimensional tunneling calculations. The dynamics calculations include 25 317 atoms, with quantized vibrational free energy in 89 active-site degrees of freedom, and with 32 atoms moving through static secondary zone transition-state configurations in the quantum tunneling simulation. Our simulations show that the average Mg-Mg distance R increases monotonically as a function of the hydride-transfer progress variable z. The range of the average R along the reaction path is consistent with the X-ray structure, thus providing a dynamical demonstration of the postulated role of Mg in catalysis. We also predicted the primary deuterium kinetic isotope effect (KIE) for the chemical step. We calculated a KIE of 3.8 for xylose at 298 K, which is consistent with somewhat smaller experimentally observed KIEs for glucose substrate at higher temperatures. More than half of our KIE is due to tunneling; neglecting quantum effects on the reaction coordinate reduces the calculated KIE to 1.8.

Aldose-Ketose Isomerases↗
PubMed2003

Ureases: quantum chemical calculations on cluster models.

Herein, we present results from a computational study of dinickel complexes that are relevant to the catalytic hydrolysis of urea exerted by the urease enzymes. The B3LYP density functional is used to characterize the equilibrium geometry, electronic and magnetic properties, and energies for a series of realistic complexes modeling the active site of ureases. The analysis of the theoretical results gives new insight into the structure, substrate binding, and catalytic mechanism. The water bridge between the two Ni(II) ions observed in the crystallographic structures of the ureases was assigned to a hydroxide bridge in agreement with the observed small antiferromagnetic coupling. Both monodentate and bidentate urea-bound complexes, in which urea had favorable orientations for catalysis, were characterized. Finally, two reaction mechanisms were investigated starting from the monodentate and bidentate urea-bound complexes, respectively. Both a Ni1...Ni2 bridging hydroxide and a Ni2-bound water molecule play crucial roles in the two mechanisms.

Bacillus↗
PubMed1993

Molecular modeling methods. Basic techniques and challenging problems.

An overview is presented of computer modeling and simulation methods that play an increasing role in drug design: quantum chemical methods, molecular mechanics, molecular dynamics and Brownian dynamics. The application of molecular dynamics for the prediction of thermodynamic properties like free energy differences and binding constants is discussed. The Brownian dynamics method is presented in connection with the calculation of effective electrostatic forces using the Poisson-Boltzmann equation, which allows one to sample ligand-binding geometries and to predict the kinetics of diffusion-limited enzyme reactions. New techniques that have recently been extensively developed, such as the global energy minimization and quantum-classical dynamics methods, are also introduced. The molecular modeling methods are illustrated with selected examples.

Cladribine↗
PubMed1990

Quantum mechanics and cellular information processing: the self-assembly paradigm.

Biological cells have greater information processing efficiency than the programmable computers used to model them. In part this is due to the larger number of interactions that can contribute to function. General arguments suggest that systems in which quantum features play a prominent role are more powerful than classical physical-dynamical analogs. A hypothetical model, involving macromolecular self-assembly, is used to illustrate how the parallelism inherent in the quantum mechanical wave function could play a role in cellular pattern processing. Signals impinging on the external membrane of the cell trigger the release of specifically shaped macromolecules. These aggregate into a mosaic shape features that reflect different groupings of the signal input patterns. The shape features are in turn read out and connected to effector actions by adaptor molecules. The self-assembly model fits into a more general hierarchical scheme of biological information processing in which macroscopic signals are transduced to mesoscopic and then microphysical representations, processed largely at the microphysical level, and then amplified for macroscopic action. The physical dynamics are controlled by proteins and other macromolecules that are molded through the evolutionary process of variation and selection. The organizational requirements for evolutionary moldability and for efficient information processing function are completely consistent. They include high dimensionality, multiplicity of weak interactions, and hierarchical-compartmental structure.

Biological Evolution↗
PubMed2005

Glycolaldehyde + OH gas phase reaction: a quantum chemistry + CVT/SCT approach.

We present a theoretical study of the mechanism and kinetics of the OH hydrogen abstraction from glycolaldehyde. Optimum geometries, frequencies, and gradients have been computed at the BHandHLYP/6-311++G(d,p) level of theory for all stationary points, as well as for additional points along the minimum energy path (MEP). Energies are obtained by single-point calculations at the above geometries using CCSD(T)/6-311++G(d,p) to produce the potential energy surface. The rate coefficients are calculated for the temperature range 200-500 K by using canonical variational theory (CVT) with small-curvature tunneling (SCT) corrections. Our analysis suggests a stepwise mechanism involving the formation of a reactant complex in the entrance channel and a product complex in the exit channel, for all the modeled paths. The overall agreement between the calculated and experimental kinetic data that are available at 298 K is very good. This agreement supports the reliability of the parameters obtained for the temperature dependence of the glycolaldehyde + OH reaction. The expressions that best describe the studied reaction are k(overall) = 7.76 x 10(-13) e(1328/)(RT) cm(3).molecule(-1).s(-1) and k(overall) = 1.09 x 10(-21)T(3.03) e(3187/)(RT) cm(3) molecule(-1) s(-1), for the Arrhenius and Kooij approaches, respectively. The predicted activation energy is (-1.36 +/- 0.03) kcal/mol, at about 298 K. The agreement between the calculated and experimental branching ratios is better than 10%. The intramolecular hydrogen bond in OO-s-cis glycolaldehyde is found to be responsible for the discrepancies between SAR and experimental rate coefficients.

Acetaldehyde↗
PubMed2002

The Hydrogen-Bond: computational approaches and applications to drug design.

This mini-review begins with a presentation of the hydrogen-bond in the context of other intermolecular recognition forces of significance in molecular biology and molecular pharmacology. This is followed by a survey of the various computational methods available to calculate the hydrogen-bonding capacity of compounds. Such methods use quantum mechanics, molecular mechanics, or algorithms based on experimental fragmental values. A recent and promising advance in the computation of H-bonding capacity is the development of specific molecular interaction fields (MIFs) known as molecular hydrogen-bonding potentials (MHBPs). Their interest in relating molecular properties to pharmacokinetic behaviour is highlighted with two examples, namely oral drug absorption and blood-brain barrier permeation.

Computational Biology↗
PubMed2006

Development, validation, and applications of anisotropic polarizable molecular mechanics to study ligand and drug-receptor interactions.

A correct representation of intermolecular interaction energies is necessary for reliable drug-receptor docking studies. While ab initio quantum chemistry with extended basis sets is the most accurate tool for that purpose, its use is precluded for very large molecular complexes. This constitutes the incentive for the development of accurate molecular mechanics potentials, in which the first-order electrostatic, and the second-order polarization energy contributions, are of essential importance. In this paper, we review the most important steps in the development of anisotropic, polarizable molecular mechanics (APMM) procedures. Among these, we illustrate validation tests of the ab initio-grounded, polarizable molecular mechanics potential, SIBFA (Sum of Interactions Between Fragments Ab initio computed). These are done by comparisons with parallel quantum-chemical (QC) results on representative multiply hydrogen-bonded complexes and polycoordinated complexes of one, or of two, divalent metal cations. For both kinds of complexes, the need to reproduce the non-additivity of the QC interaction energies is emphasized. One difficulty arises upon handling flexible molecules, due to the need to account simultaneously and consistently for the onset of inter- and intra-molecular polarization and charge-transfer effects. A new approach in the context of SIBFA was recently developed towards this aim, and tested in two cases of conformation-dependent cation-ligand interaction energies. The first relates to the complexes formed between the mecapto-carboxamide anion, an essential building-block of several Zn-metalloenzyme inhibitors, and Zn(II). The second relates to the complexes of the tetra-anionic pyrophosphate anion, a key building-block of ATP and GTP, with one or two divalent Zn(II) cations used as a probe. In the domain of applications, two recent studies are then presented. The first is the docking of the captopril drug to the active site of the binuclear Zn(II)- beta-lactamase enzyme. The second is the complex of a non-hydrolyzable analog of ATP with the active site of a binuclear Mg(II)-dependent kinase. An extension to an open-shell cation, Cu(II), is finally presented. The encouraging results presented in this review show that APMM procedures could be used in large-scale studies of ligand and drug-receptor interactions.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2002

Derivation of semiconductor laser mean-field and Swift-Hohenberg equations.

Bulk and quantum well semiconductor lasers by nature display fundamentally different physical characteristics relative to multilevel gas and solid state lasers. In particular, the refractive index is nonzero at peak gain and the peak gain can shift strongly with varying carrier density or temperature. Moreover, a quantum well laser gain may be strongly asymmetric if more than the lowest subband is populated. Rigorously computed and experimentally validated, gain and refractive index spectra are now available for a variety of quantum well structures emitting from the infrared to the visible. Active devices can be designed and grown such that the gain spectrum remains approximately parabolic for carrier density variations typically encountered in above threshold pumped broad area edge-emitting semiconductor lasers. Under this assumption, we derive a robust optical propagation model that tracks the important peak gain shifts and broadening as long as the gain remains approximately parabolic over the relevant energy range in a running laser. We next derive a multimode model where the longitudinal modes are projected out of the total field. The next stage is to derive a mean-field single longitudinal mode model for a wide aperture semiconductor laser. The mean-field model allows for significant cavity losses and widely different facet reflectivities such as occurs with antireflection- and high-reflectivity-coated facets. The single mode mean-field model is further reduced using an asymptotic expansion of the relevant physical fields with respect to a small parameter. The end result is a complex semiconductor Swift-Hohenberg description of a single longitudinal mode wide aperture laser. The latter should provide a useful model for studying scientifically and technologically important lasers such as vertical cavity surface emitting semiconductor lasers.

Journal Article↗
PubMed2001

New developments in applying quantum mechanics to proteins.

Algorithmic improvements of quantum mechanical methodologies have increased our ability to study the electronic structure of fragments of a biomolecule (e.g. an enzyme active site) or entire biomolecules. Three main strategies have emerged as ways in which quantum mechanics can be applied to biomolecules. The supermolecule approach continues to be utilized, but it is slowly being replaced by the so-called coupled quantum mechanical/molecular mechanical methodologies. An exciting new direction is the continued development and application of linear-scaling quantum mechanical approaches to biomolecular systems.

Algorithms↗
PubMed2006

Controlled flow of spin-entangled electrons via adiabatic quantum pumping.

We propose a method to dynamically generate and control the flow of spin-entangled electrons, each belonging to a spin singlet, by means of adiabatic quantum pumping. The pumping cycle functions by periodic time variation of localized two-body interactions. We develop a generalized approach to adiabatic quantum pumping as traditional methods based on a scattering matrix in one dimension cannot be applied here. We specifically compute the flow of spin-entangled electrons within a Hubbard-like model of quantum dots, discuss possible implementations, and identify parameters that can be used to control the singlet flow.

Journal Article↗
PubMed2003

Alcohols, ethers, carbohydrates, and related compounds. IV. Carbohydrates.

Ab initio calculations [B3LYP/6-311++G(2d,2p)] have been carried out on 84 conformations of 12 different sugars (hexoses), in both pyranose and furanose forms, with the idea of generating a data base for carbohydrate structural energies that may be used for developing the predictive value of molecular mechanics calculations for carbohydrates. The average value for the apparent gas phase anomeric effect for a series of 31 pairs of pyranose conformations was found to be 1.83 kcal/mol (vs. 2.67 kcal/mol with a smaller basis set used in earlier calculations). In developing MM4 to reproduce these data, it was necessary first to have good energies for simple alcohols and ethers, together with an adequate treatment of hydrogen bonding, and then to include the anomeric effect, and the ethylene glycol type system, as was previously recognized. It was also found that the so-called delta-2 effect, long recognized in carbohydrates, must be explicitly included, in order to obtain acceptable results. When a force field that included all of these items as developed from the small molecules based on the MM4 hydrocarbon force field was applied without any parameter adjustment to the set of hexopyranose and furanose conformations mentioned earlier, the E(beta) - E(alpha) was found to have an average value of 1.88 kcal/mol, versus 1.74 for the quantum calculations. The signed average and RMS deviations of the MM4 from the QM results were +0.15 and 0.87 kcal/mol.

Alcohols↗
PubMedDate not supplied

Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches.

Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of residue types to be separated by a certain spatial distance or to have a given relative orientation. Several such potentials, describing different kinds of correlations between residue types, distances, and orientations, are derived and combined in a way that maximizes their information content and minimizes their redundancy. To test the ability of these potentials to describe cation-pi and amino-pi systems, we compare their energies with those computed with the CHARMM molecular mechanics force field and with quantum chemistry calculations at the Hartree-Fock level (HF) and at the second order of the Møller-Plesset perturbation theory (MP2). The latter calculations are performed in the gas phase and in acetone, in order to mimic the average dielectric constant of protein environments. The energies computed with the best of our statistical potentials and with gas-phase HF or MP2 show correlation coefficients up to 0.96 when considering one side-chain degree of freedom in the statistical potentials and up to 0.94 when using a totally simplified model excluding all side-chain degrees of freedom. These potentials perform as well as, or better than, the CHARMM molecular mechanics force field that uses a much more detailed protein representation. The good performance of our cation-pi statistical potentials suggests their utility in protein structure and stability prediction and in protein design.

Algorithms↗
PubMed2006

Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex.

Protein-protein interactions are very important in the function of a cell. Computational studies of these interactions have been of interest, but often they have utilized classical modelling techniques. In recent years, quantum mechanical (QM) treatment of entire proteins has emerged as a powerful approach to study biomolecular systems. Herein, we apply a semi-empirical divide and conquer (DC) methodology coupled with a dielectric continuum model for the solvent, to explore the contribution of electrostatics, polarization and charge transfer to the interaction energy between barnase and barstar in their complex form. Molecular dynamic (MD) simulation was performed to account for the dynamic behavior of the complex. The results show that electrostatics, charge transfer and polarization favor the formation of the complex. Our study shows that electrostatics dominates the interaction between barnase and barstar ( approximately 73%), while charge transfer and polarization are approximately 21% and approximately 6%, respectively. Close inspection of the polarization and charge-transfer effects on the charge distribution of the complex reveals the existence of two, well localized, regions in barstar. The first region includes the residues between P27 and Y47 and the second region is between N65 and D83. Since no such regions could be detected in barnase clearly suggests that barstar is well optimized for efficiently binding barnase. Furthermore, using our interaction energy decomposition scheme, we were able to identify all residues that have been experimentally determined to be important for the complex formation and to suggest other residues never have been investigated. This suggests that our approach will be useful as an aid in further understanding protein-protein contacts for the ultimate goal to produce successful inhibitors for protein complexes.

Bacterial Proteins↗
PubMed1996

Density resolution in quantitative computed tomography of foam and lung.

This study was performed to assess density resolution in quantitative computed tomography (CT) of foam and lung. Density resolution, a measure for the ability to discriminate materials of different density in a CT number histogram, is normally determined by quantum noise. In a cellular solid, variations in mass in the volumes sampled by CT cause an additional degradation of density resolution by the linear partial volume effect. The sample volume, which is directly related to spatial resolution, can be varied by choosing different section thicknesses and reconstruction filters. Several polyethene (PE) foams, as simple models of lung tissue, and five patients were investigated using various sample volumes. For the uniform PE foams, density resolution could be directly determined as the full width at half maximum of CT number histograms. Density resolution for foams with cell sizes of 0.8-1.5 mm was dominated by effects caused by the limited sample size, not by quantum noise. The relative magnitudes of density resolution could roughly be explained with a model for a hypothetic random cellular solid. Since lungs are not of uniform density, analysis of patient data was more complicated. A combined convolution least-squares fit procedure, together with information obtained in the studies of foam, were used to determine density resolution in lung studies. Density resolution, both for foams and lung, was strongly dependent on sample volume, and was quite poor for thin sections and sharp filters. Consequently, histogram-shape related parameters are sensitive to the spatial resolution chosen on CT. Thin section densitometry, using a 1-mm section with a standard or high resolution filter, is not recommended except in determining average density. When using thicker sections, an in-plane spatial resolution similar to section thickness is advised.

Humans↗
PubMed2001

Quantum trajectory analysis of multimode subsystem-bath dynamics.

The dynamics of a swarm of quantum trajectories is investigated for systems involving the interaction of an active mode (the subsystem) with an M-mode harmonic reservoir (the bath). Equations of motion for the position, velocity, and action function for elements of the probability fluid are integrated in the Lagrangian (moving with the fluid) picture of quantum hydrodynamics. These fluid elements are coupled through the Bohm quantum potential and as a result evolve as a correlated ensemble. Wave function synthesis along the trajectories permits an exact description of the quantum dynamics for the evolving probability fluid. The approach is fully quantum mechanical and does not involve classical or semiclassical approximations. Computational results are presented for three systems involving the interaction on an active mode with M=1, 10, and 15 bath modes. These results include configuration space trajectory evolution, flux analysis of the evolving ensemble, wave function synthesis along trajectories, and energy partitioning along specific trajectories. These results demonstrate the feasibility of using a small number of quantum trajectories to obtain accurate quantum results on some types of open quantum systems that are not amenable to standard quantum approaches involving basis set expansions or Eulerian space-fixed grids.

Journal Article↗
PubMed1999

CT reconstruction by using the MLS-ART technique and the KCD imaging system--I: low-energy X-ray studies.

We investigated the use of the kinestatic charge detector (KCD) combined with the multilevel scheme algebraic reconstruction technique (MLS-ART) for X-ray computer tomography (CT) reconstruction. The KCD offers excellent detective quantum efficiency and contrast resolution. These characteristics are especially helpful for applications in which a limited number of projections are used. In addition, the MLS-ART algorithm offers better contrast resolution than does the conventional convolution backprojection (CBP) technique when the number of projections is limited. Here we present images of a Rando-head phantom that was reconstructed by using the KCD and MLS-ART. We also present, for comparison, the images reconstructed by using the CBP technique. The combination of MLS-ART and the KCD yielded satisfactory images after just one or two iterations.

Algorithms↗