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 793 records · Page 44Linked to original sources
PubMed2005

SIMQUADNMR: a program for simulation and interpretation of multiple quantum-filtered NMR spectra of quadrupolar nuclei.

In this paper, we present a computer program which simulates NMR multiple quantum-filtered spectra of quadrupolar nuclei as a function of physical parameters, of the type of experiment and experimental conditions. The program works by solving relaxation theory equations for the given system, and it can be useful in order to plan the ideal conditions to set up specific experiments or to give a physical interpretation of experimental results. The program allows to independently follow the dependence of individual coherences and relaxation rates as a function of up to 50 parameters regarding the physical properties of the system under investigation, sample conditions and instrumental setup making it an helpful tool also for teaching purposes.

Algorithms↗
PubMed1997

Computer simulation study on the conversion of spirolactone to enones over H-Y zeolite.

We report here the results of computer modeling studies and quantum chemical calculations on the spirolactone-to-enone conversion reaction over the zeolite catalysts, especially H-Y zeolite. We studied the adsorption mode of the molecules inside the supercage of H-Y and the mechanism of electron transfer between organic molecules and the framework of zeolite H-Y by density functional theory (DFT) calculations. Because the organic molecules considered in the present study are less symmetrical we docked the molecule inside the supercage of H-Y and energy minimization was then applied to these docked structures to yield representative low-energy binding sites for the molecules within the host structure. The interaction energy results show that the major interaction is between the methylene hydrogen of the molecule and the oxygen of the framework. The molecular electrostatic potential maps show that the ketonic oxygen of the reactant molecules abstract proton from Brönsted acid site. Thus the mechanism proposed by DFT calculation matches well with the experimental observations.

Computer Simulation↗
PubMed2003

Prediction of blood-brain barrier permeation using quantum chemically derived information.

A model for the prediction of the blood-brain distribution (logBB) is obtained by multiple regression analysis of molecular descriptors for a training set of 90 compounds. The majority of the descriptors are derived from quantum chemical information using semi-empirical AM1 calculations to compute fundamental properties of the molecules investigated. The polar surface area of the compounds can be described appropriately by six descriptors derived from the molecular electrostatic potential. This set shows a strong correlation with the observed logBB. Additional quantum chemically computed properties that contribute to the final model comprise the ionization potential and the covalent hydrogen-bond basicity. Complementary descriptors account for the presence of certain chemical groups, the number of hydrogen-bond donors, and the number of rotatable bonds of the compounds. The quality of the fit is further improved by including variables derived from principal component analysis of the molecular geometry.

Biological Transport↗
PubMed2006

Be(II) in aqueous solution--an extended ab initio QM/MM MD study.

An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation at double-zeta restricted Hartree-Fock (RHF) level was performed at 293.15 K, including first and second hydration shell in the QM region to study the structural and dynamical properties of the Be(II)-hydrate in aqueous solution. The first tetrahedrally arranged hydration shell, with the four water molecules located at a mean Be-O distance of 1.61 A, is highly inert with respect to ligand exchange processes. The second shell, however, consisting in average of approximately 9.2 water ligands at a mean Be-O distance of 3.7 A and the third shell at a mean Be-O distance of 5.4 A with approximately 19 ligands rapidly exchange water molecules between them and with the bulk, respectively. Other structural parameters such as radial and angular distribution functions (RDF and ADF) and tilt- and theta-angle distributions were also evaluated. The dynamics of the hydrate were studied in terms of ligand mean residence times (MRTs) and librational and vibrational frequencies. The mean residence times for second shell and third shell ligands were determined as 4.8 and 3.2 ps, respectively. The Be-O stretching frequency of 658 cm(-1), associated with a force constant of 147 N m(-1) could be overestimated but it certainly reflects the exceptional stability of the ion-ligand bond in the first hydration shell.

Beryllium↗
PubMed2026

Electromagnetic Radiation Stimulated Learning in Perovskite Nickelates.

Biological plasticity refers to the ability of synapses to strengthen or weaken over time. These adaptive properties play a fundamental role in learning and memory, spanning many orders of magnitude in timescales. Short-term plasticity (STP) arises from rapid correlative activity, while long-term plasticity (LTP) is governed by slower biochemical processes. Here, we investigate electromagnetically driven relaxation dynamics in perovskite nickelate thin films as an analogue of biological learning behaviors. By comparing radio frequency (RF), infrared (IR), visible, and ultraviolet (UV) radiation as stimuli, we find that RF excitation primarily induces STP, while visible and IR illumination lead to reversible relaxation on behavioral timescales. In contrast, UV illumination results in persistent, non-thermal changes in conductivity over extended timescales. Notably, UV-exposed nickelate films exhibit glass-like dynamics, characterized by stretched exponential relaxation and aging phenomena. The films display habituation to repeated stimuli, along with sensitization and spontaneous recovery under controlled environments. A minimal dynamical systems model captures key qualitative features of the UV-induced resistance changes. Our results demonstrate that electromagnetic frequency enables multi-timescale relaxation spanning nearly nine orders of magnitude, suggesting perovskite nickelates as promising platforms for adaptive optoelectronic hardware and for linking computational neuroscience with emerging quantum technologies.

electromagnetic radiation↗
PubMed1995

Microscopic computation in human brain evolution.

When human psychological performance is viewed in terms of cognitive modules, our species displays remarkable differences in computational power. Algorithmically simple computations are generally difficult to perform, whereas optimal routing or "Traveling Salesman" Problems (TSP) of far greater complexity are solved on an everyday basis. It is argued that even "simple" instances of TSP are not purely Euclidian problems in human computations, but involve emotional, autonomic, and cognitive constraints. They therefore require a level of parallel processing not possible in a macroscopic system to complete the algorithm within a brief period of time. A microscopic neurobiological model emphasizing the computational power of excited atoms within the neuronal membrane is presented as an alternative to classical connectionist approaches. The evolution of the system is viewed in terms of specific natural selection pressures driving satisfying computations toward global optimization. The relationship of microscopic computation to the nature of consciousness is examined, and possible mathematical models as a basis for simulation studies are briefly discussed.

Algorithms↗
PubMed1995

Potential energy functions.

When energy is a critical quantity, accurate biomolecular simulations rest in substantial part on accurate potential energy functions (force fields). Improvements in methodology for determining parameters--particularly, in the systematic use of computational data obtained from quantum chemical calculations--and enhancements in functional form are leading to better potential energy functions. New calculations have been developed for water (including calculations that incorporate electronic polarizability to take account of the degree to which a molecule can be polarized), proteins, nucleic acids, carbohydrates, lipids, and general organic molecules. Most notably, two new biomolecular force fields have recently been derived and significant redeterminations of the parameters of two existing biomolecular force fields have been carried out. Some progress has also been made in incorporating polarizability into potential energy functions for molecules in general and in improving the treatment of metal-ligand interactions in systems of biomolecular interest.

Electrochemistry↗
PubMed2005

Influence of the anisotropic hyperfine interaction on the 14N ENDOR and the ESEEM orientation-disordered spectra.

The influence of the anisotropic hyperfine interaction on the 14N electron-nuclear double resonance/electron spin echo envelope modulation spectra is studied by approximate analytical and graphical methods for the case of the isotropic g-factor. The suggested determination of the modified characteristic directions of the magnetic field due to anisotropy enhances the insight in the structural details of the system and analytical solutions of the secular equation for these conditions are derived. The graphical method, previously used for the analysis of the orientation dependence of the 14N nuclear-transition frequencies in orientation-disordered samples for isotropic hyperfine interaction is extended to the case of arbitrary anisotropic hyperfine tensor. The above analytical and graphical methods are illustrated and tested against exact simulations in two practically important cases: (i) isotropic hyperfine interaction (hfi) exceeding other nuclear interactions in nuclear spin Hamiltonian. (ii) Cancellation of the isotropic part of the hfi.

Algorithms↗
PubMed2005

Density functional theory study of the FT-IR spectra of phthalimide and N-bromophthalimide.

Fourier transform infrared (FT-IR) spectra of phthalimide and N-bromophthalimide have been recorded in the range of 4000-400 cm-1. With the hope of providing more and effective information on the fundamental vibrations, a normal coordinate analysis has been performed on phthalimide and N-bromophthalimide, by assuming C2v symmetry. Density functional theory (DFT)-Beck3-Lee-Yang-Parr (B3LYP) levels with 6-31G* and 6-311+G** basis sets have been employed in quantum chemical analysis. The computational frequencies are in good agreement with the observed results. The theoretical spectra obtained along with intensity data agree well with the observed spectra.

Models, Chemical↗
PubMed2002

Passive water transport in biological pores.

Three kinds of membrane proteins have been shown to have water channels properties: the aquaporins, the cotransporters, and the uniports. A molecular-kinetic description of water transport in pores is compared to analytical models based on macroscopic parameters such as pore diameter and length. The use and limitations of irreversible thermodynamics is discussed. Experimental data on water and solute permeability in aquaporins are reviewed. No unifying transport model based on macroscopic parameters can be set up; for example, there is no correlation between solute diameter and permeability. Instead, the influence of hydrogen bonds between solute and pore, and the pH dependence of permeability, point toward a model based upon chemical interactions. The atomic model for AQP1 based on electron crystallographic data defines the dimensions and chemical nature of the aqueous pore. These structural data combined with quantum mechanical modeling and computer simulation might result in a realistic description of water transport. Data on water and solute permeability in cotransporters and uniports are reviewed. The function of these proteins as substrate transporters involves a series of conformational changes. The role of conformational equilibria on the water permeability will be discussed.

Animals↗
PubMed2002

A theoretical analysis of the thermodynamic contributions for the adsorption of individual protein residues on functionalized surfaces.

Although the denaturing of adsorbed proteins on biomaterials surfaces is believed to lead to adverse tissue reactions to implanted materials, very little is currently known of the actual mechanisms involved. These mechanisms must be understood if surfaces are to be proactively designed to control protein adsorption behavior. Concepts widely employed in rational drug design and in protein and RNA folding predictions provide a means to approach this problem. Accordingly, a theoretical analysis has been conducted to estimate the thermodynamic contributions (changes in enthalpy, entropy, and Gibbs free energy) for the adsorption of selected individual mid-chain protein residues to functionalized surfaces. Enthalpic contributions from residue-surface interactions were calculated using semi-empirical quantum mechanical-based computational chemistry methods in a simulated aqueous environment (MOPAC/COSMO), and enthalpic and entropic contributions due to water restructuring effects assumed to occur during adsorption were estimated from experimental data for functional group wetting and calculated changes in solvent accessible surface area as each protein residue approached each surface. When combined with intraprotein residue-residue interactions, the understanding of residue-surface adsorption energy relationships provides a means to begin to predict protein adsorption behavior as a function of biomaterials surface chemistry. It is recognized that several assumptions have been made in this approach that could be challenged, and that truncations necessary due to programming limitations have been applied that may neglect potentially important interactions. Therefore, it must be understood that the modeling predictions may not be directly applicable to biomaterials for surface design under actual physiologic conditions at this stage. However, this attempt at modeling fundamental components of protein adsorption is presented as an initial approach to understanding these complex events.

Adsorption↗
PubMed1999

The Galton-Watson branching process as a quantitative tool in parasitology.

Stochastic growth processes abound in the biology of parasitism, and one mathematical tool that is particularly well suited for describing such phenomena is the Galton-Watson branching process. Introduced more than a century ago to settle a debate over the rate of disappearance of surnames in the British peerage, branching processes are applied today in fields as diverse as quantum physics and theoretical computer science. In this article, Dale Taneyhill, Alison Dunn and Melanie Hatcher provide a simple introduction to branching processes, and demonstrate their uses in quantitative parasitology.

Animals↗
PubMed2006

Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis.

Glycine N-methyltransferase (GNMT) is an S-adenosyl-l-methionine dependent enzyme that catalyzes glycine transformation to sarcosine. Here, we present a hybrid quantum mechanics/molecular mechanics (QM/MM) computational study of the reaction compared to the counterpart process in water. The process takes place through an SN2 mechanism in both media with a transition state in which the transferring methyl group is placed in between the donor (SAM) and the acceptor (the amine group of glycine). Comparative analysis of structural, electrostatic, and electronic characteristics of the in-solution and enzymatic transition states allows us to get a deeper insight into the origins of the enzyme's catalytic power. We found that the enzyme is able to stabilize the substrate in its more active basic form by means of a positively charged residue (Arg175) placed in the active site. However, the maximum stabilization is attained for the transition state. In this case, the enzyme is able to form stronger hydrogen bonds with the positively charged amine group. Finally, we show that in agreement with previous computational studies on other methyltransferases, there is no computational evidence for the compression hypothesis, as was formulated by Schowen (Hegazi, M. F., Borchardt, R. T., and Schowen, R. L. (1979) J. Am. Chem. Soc. 101, 4359-4365).

Catalysis↗
PubMed2006

In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions.

Recently, researchers have used acetylcholinesterase (AChE) as a reaction vessel to synthesize its own inhibitors. Thus, 1 (syn-TZ2PA6), a femtomolar AChE inhibitor, which is formed in a 1:1 mixture with its anti-isomer by solution phase reaction from 3 (TZ2) and 4 (PA6), can be synthesized exclusively inside the AChE gorge. Our computational approach based on quantum mechanical/molecular mechanical (QM/MM) calculations, molecular dynamics (MD), and targeted molecular dynamics (TMD) studies answers why 1 is the sole product in the AChE environment. Ab initio QM/MM results show that the reaction in the AChE gorge occurs when 3/azide and 4/acetylene are extended in a parallel orientation. An MD simulation started from the final structure of QM/MM calculations keeps the azide's and acetylene's parallel orientations intact for 10 ns of simulation time. A TMD simulation applied on an antiparallel azide-acetylene conformation flips the acetylene easily to bring it to a position that is parallel to azide. A second set of QM/MM calculations performed on this flipped structure generates a similar minimum-energy path as obtained previously. Even a TMD simulation carried out on a parallel azide-acetylene conformation could not deform their parallel arrangement. All of these results, thus, imply that inside the AChE gorge, the azide group of 3 and the acetylene group of 4 always remain parallel, with the consequence that 1 is the only product. The architecture of the gorge plays an important role in this selective formation of 1.

Acetylcholinesterase↗
PubMed2002

Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and (15)N NMR.

The acid/base character of nucleobases affects phenomena such as self-association, interaction with metal ions, molecular recognition by proteins, and nucleic acid base-pairing. Therefore, the investigation of proton-transfer equilibria of natural and synthetic nucleos(t)ides is of great importance to obtain a deeper understanding of these phenomena. For this purpose, a set of ATP prototypes was investigated using (15)N NMR spectroscopy, and the corresponding adenine bases were investigated by theoretical calculations. (15)N NMR measurements provided not only acidity constants but also information on the protonation site(s) on the adenine ring and regarding the ratio of the singly protonated species in equilibrium. Substituents of different nature and position on the adenine ring did not change the preferred protonation site, which remained N1. However, for 2-thioether-ATP derivatives a mixed population of N1 and N7 singly protonated species was observed. Reduction of basicity of 0.4-1 pK(a) units relative to ATP was also observed for all evaluated ATP derivatives, except for 2-Cl-ATP, for which K(a) was ca. 10,000-fold lower. To explain the substitution-dependent variations in the experimental pK(a) values of the ATP analogues, gas-phase proton affinities (PA), Delta Delta G(hyd), and pK(a) values of the corresponding adenine bases were calculated using quantum mechanical methods. The computed PA and Delta Delta G(hyd) values successfully explained the experimental pK(a) values. A computational procedure for the prediction of accurate pK(a) values was developed using density functional theory and polarizable continuum model calculations. In this procedure, we developed a set of parameters for the polarizable continuum model that was fitted to reproduce experimental pK(a) values of nitrogen heterocycles. This method is proposed for the prediction of pK(a) values and protonation site(s) of purine analogues that have not been synthesized or analyzed.

Adenine↗
PubMed2006

Novel seco-dibenzopyrrocoline alkaloid from Cryptocarya oubatchensis.

[structure: see text] A novel seco-dibenzopyrrocoline alkaloid, named oubatchensine 6, and five phenanthroindolizidines (1-5) were isolated from Cryptocarya oubatchensis, and their structures were elucidated. Displacement centrifugal partition chromatography was used to purify compounds 1 and 6. Structure determination of the latter was carried out by mass spectrometry, NMR spectroscopy, quantum chemistry, and computer-assisted structure determination. Cytotoxic activity against KB cells was then investigated.

Alkaloids↗
PubMed2004

All-forward semiclassical simulations of nonlinear response functions.

We propose a quantum trajectory algorithm for computing nonlinear response functions of condensed phase molecular systems based on a time-ordered expansion of the density matrix. The nth-order response function is expressed as a sum of 2(n) impulsive response pathways representing trajectories involving zero, one, and up to n interactions with short external pulses. These are evaluated using a forward propagation algorithm based upon a Liouville space extension of the Bohmian propagation method.

Journal Article↗
PubMed2006

Rotational spectrum of cyanoacetylene solvated with helium atoms.

The high resolution microwave spectra of He(N)-HCCCN clusters were studied in the size ranges of 1-18 and 25-31. In the absence of an accompanying infrared study, rotational excitation energies were computed by the reptation quantum Monte Carlo method and used to facilitate the search and assignment of R(0) transitions from N > 6, as well as R(1) transitions with N > 1. The assignments in the range of 25-31 are accurate to +/-2 cluster size units, with an essentially certain relative ordering. The rotational transition frequencies decrease with N = 1-6 and then show oscillatory behavior for larger cluster sizes, which is now recognized to be a manifestation of the onset and microscopic evolution of superfluidity. For cluster sizes beyond completion of the first solvation shell the rotational frequencies increase significantly above the large-droplet limit. This behavior, common to other linear molecules whose interaction with He features a strong nearly equatorial minimum, is analyzed using path integral Monte Carlo simulations. The He density in the incipient second solvation shell is shown to open a new channel for long permutation cycles, thus increasing the decoupling of the quantum solvent from the rotation of the dopant molecule.

Journal Article↗