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At least 955 records · Page 53Linked to original sources
PubMed1993

Theoretical conformational analyses of endothelin-1 in vacuum, aqueous, and lipid environments.

Endothelin-1 (ET-1) is a flexible molecule capable of existing in multiple shapes (conformations) depending on the surrounding molecular solvation. The conformational diversity of ET-1 was studied in three solvation spheres (gas phase, aqueous, and membrane lipid) with the new evolving biotechnology of computational biomolecular simulation. Simulations were performed using a combination of molecular mechanics, molecular dynamics, and semiempirical quantum mechanics calculations in a RISC architecture large-scale computing environment. Marked differences between the gas phase "folded" conformation and the membrane lipid "extended" conformation were identified.

Chemical Phenomena↗
PubMed2003

Substituting a qubit for an arbitrarily large number of classical bits.

We show that a qubit can be used to substitute for a classical analog system requiring an arbitrarily large number of classical bits to represent digitally. Let a physical system S interact locally with a classical field varphi(x) as S travels directly from point A to point B. Our task is to use S to answer a simple yes/no question about varphi(x). If S is a qubit, the task can be done perfectly. We show that any classical system S must encode an arbitrarily large number of classical bits to solve the same task. This result implies a large quantum advantage in the memory size necessary for some computations. We also show that no finite amount of one-way classical communication can perfectly simulate the effect of quantum entanglement.

Journal Article↗
PubMed2001

Quantum chemical modeling of Co--C bond activation in B(12)-dependent enzymes.

Recent progress in computational modeling of the catalytic activation of cobalt-carbon bond cleavage shows that quantum chemical calculations could be an important part of coenzyme B(12) research. Particular emphasis has been placed on density functional theory, which is now emerging as a powerful tool to elucidate the electronic structure and spectroscopic properties of the active sites of metalloenzymes.

Cobalt↗
PubMed1999

Quality of preimplant low-dose tomography.

OBJECTIVES: The aim of this study was to test the influence of radiation dose on image quality in mandibular preimplant computed tomographic examinations and to compare the quality of computed and conventional spiral tomographic images. STUDY DESIGN: Cross-sectional images were obtained on 17 patients with conventional spiral tomography (Scanora technique) and reformatted computed tomography at 40 and 80 mAs. Observers graded the acceptability of images for implant planning and traced the contour of the mandibular body and canal. RESULTS: Conventional spiral tomographic images scored significantly higher than computed tomographic images whereas mean score differences between computed tomographic techniques were not statistically significant. Anatomic structures, in particular the mandibular canal, were more frequently untraceable in high-dose than in low-dose computed tomography but always traceable in conventional tomograms. CONCLUSION: Conventional spiral tomograms were subjectively preferred over computed tomographic images. For mandibular implant planning, computed tomography examinations can be performed with lower-than-standard mAs. Quantum noise seems to contribute to the visibility of anatomic structures in reformatted computed tomographic images.

Adult↗
PubMed2000

Ultimate physical limits to computation

Computers are physical systems: the laws of physics dictate what they can and cannot do. In particular, the speed with which a physical device can process information is limited by its energy and the amount of information that it can process is limited by the number of degrees of freedom it possesses. Here I explore the physical limits of computation as determined by the speed of light c, the quantum scale h and the gravitational constant G. As an example, I put quantitative bounds to the computational power of an 'ultimate laptop' with a mass of one kilogram confined to a volume of one litre.

Journal Article↗
PubMed2007

Finite group theory for large systems. 3. Symmetry-generation of reduced matrix elements for icosahedral C(20) and C(60) molecules.

This paper uses symmetry-generation to simplify the determination of Hamiltonian reduced matrix elements. It is part of a series on using computers to apply finite group theory to quantum mechanical calculations on large systems. Symmetry-generation is an expression of the whole molecule as a sum of symmetry transformations on a smaller reference structure. Then on a suitably-conditioned symmetry-adapted basis, the reduced matrix elements of the Hamiltonian are averages of certain elements of the simpler reference structure matrix. The smaller the reference structure, the greater is the computational savings. Single atom reference structures are used here for the Hückel treatment of icosahedral C(20) and C(60) fullerenes. The analytical power of this approach is illustrated by determining the two bond lengths of C(60) from spectral data.

Journal Article↗
PubMed2005

Feedforward neural network models for handling class overlap and class imbalance.

This paper proposes a framework for training feedforward neural network models capable of handling class overlap and imbalance by minimizing an error function that compensates for such imperfections of the training set. A special case of the proposed error function can be used for training variance-controlled neural networks (VCNNs), which are developed to handle class overlap by minimizing an error function involving the class-specific variance (CSV) computed at their outputs. Another special case of the proposed error function can be used for training class-balancing neural networks (CBNNs), which are developed to handle class imbalance by relying on class-specific correction (CSC). VCNNs and CBNNs are compared with conventional feedforward neural networks (FFNNs), quantum neural networks (QNNs), and resampling techniques. The properties of VCNNs and CBNNs are illustrated by experiments on artificial data. Various experiments involving real-world data reveal the advantages offered by VCNNs and CBNNs in the presence of class overlap and class imbalance.

Artifacts↗
PubMed2002

Understanding the role of stereoelectronic effects in determining collagen stability. 2. A quantum mechanical/molecular mechanical study of (Proline-Proline-Glycine)(n) polypeptides.

The importance of vicinal and long-range interresidue effects in determining the stability of the collagen triple helix has been investigated by quantum mechanical (QM) and molecular mechanical (MM) computations on suitable model polypeptides, taking into account solvent effects by the polarizable continuum model (PCM). At the QM level, the PII conformation corresponds to an energy minimum for pentapeptide analogues incorporating the sequence Gly-Pro-Pro-Gly, irrespective of the down or up puckering of the pyrrolidine ring. However, our computations indicate that the alternation of down and up prolines characterizing collagen and collagen-like peptides is not due to an intrinsic preference of the Pro-Pro-Gly sequence. This result is confirmed by MM computations of longer polypeptides. Next, MM computations on model triple helices show that a better packing is obtained for specific values of backbone dihedrals, which, in turn, favor the alternation of down and up prolines along each chain.

Collagen↗
PubMed2004

Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide.

The purpose of this work is, first, to present a fast and accurate technique to compute Boltzmann-averaged values of the quantum-chemical 13C chemical shifts for each amino acid in oligopeptides, demonstrated here by an application to the peptide Ac-XXAAAAAAAOO-NH2 (where X denotes diaminobutyric acid, A is alanine, and O is ornithine) [XAO] and, second, to discuss the capability of the 13Calpha and 13Cbeta chemical shifts to distinguish the PP(II) conformation from the alpha-helix and statistical-coil conformations. Use is made of a combination of approaches, summarized as follows: (1) derivation of an ensemble of conformations by using a molecular mechanics technique; (2) use of a clustering procedure to form families and build a reduced set of conformations consisting of the lowest-energy conformations of each family, and (3) computation of the 13C chemical shifts for the lowest-energy conformations of each family, using a quantum-chemical approach that treats a selected residue, or group of residues, with a 6-311+G(2d,p) locally-dense basis set, while the remaining residues in the sequence are treated with a 3-21G basis set. The whole procedure is quite accurate and speeds up the computation of the Boltzmann-averaged values of the 13C-chemical shifts by several orders of magnitude. The present application sheds some light on the conformational preference for alanine and non-alanine residues to occupy the PP(II) helical region of the Ramachandran map.

Alanine↗
PubMed2006

Toward an integrated computational approach to CW-ESR spectra of free radicals.

Interpretation of structural properties and dynamic behaviour of molecules in solution is of fundamental importance to understand their stability, chemical reactivity and catalytic action. Information can be gained, in principle, by a variety of spectroscopic techniques, magnetic as well as optical. In particular, continuous wave electron spin resonance (CW-ESR) measurements are highly informative. However, the wealth of structural and dynamic information which can be extracted from ESR spectroscopy is, at present, limited by the necessity of employing computationally efficient models, which are increasingly complex as they need to take into account diverse relaxation processes affecting the spectrum. In this paper, we address the basic theoretical tools needed to predict, essentially ab initio, CW-ESR spectra observables according to the stochastic Liouville equation (SLE) approach, combined with quantum mechanical and hybrid methods for the accurate and efficient computation of structural, spectroscopic and magnetic properties of molecular systems. We shall discuss, on one hand, the quantum mechanical calculation of magnetic observables, via density functional theory (DFT), time-dependent DFT (TD-DFT) and application of the polarizable continuum model (PCM) for the description of environmental effects, including anisotropic environments and systems where different regions are characterized by different dielectric constants. One the other hand, the explicit evaluation of dynamical effects will be discussed based on the numerically exact treatment of the SLE in the presence of several relaxation processes, which has been proven to be a challenging task.

Biomechanical Phenomena↗
PubMed2001

Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution.

How do enzymes achieve very large rate enhancements compared to corresponding uncatalyzed reactions in solution? We present a computational approach which combines high-level ab initio quantum mechanical calculations with classical free energy calculations to address this question. Our calculations lead to accurate estimates of DeltaG for both trypsin and catechol O-methyltransferase-catalyzed and reference uncatalyzed reactions and give new insights into the nature of enzyme catalysis. The same methodology applied to steps in the catalytic mechanism of citrate synthase further supports the conclusion that one need not invoke special concepts such as "low-barrier hydrogen bonds" or "pK(a) matching" to explain enzyme catalysis.

Catalysis↗
PubMed2005

Quantum chemical topology (QCT) descriptors as substitutes for appropriate Hammett constants.

A technique called quantum topological molecular similarity (QTMS) was recently proposed [J. Chem. Inf. Comput. Sci., 2001, 41, 764] in order to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs, based on modern ab initio wave functions of geometry optimised molecules, in combination with quantum chemical topology (QCT). The current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In previous work [J. Chem. Soc., Perkin Trans. 2, 2002, 1231] it was proven that a set of Hammett constants (sigma(p), sigma(m), sigma(I) and sigma(p)0) for a sizeable set of mono- and polysubstituted carboxylic acids can be replaced by QCT bond descriptors. Using QTMS and proper statistical validation we examined seven data sets in total. The first three sets (para-substituted phenols (sigma-), substituted toluenes (sigma+) and bromophenethylamines (sigma+)) corroborate that a wider class of Hammett constants can also be replaced by QCT descriptors. A fourth set (benzyl radicals) focuses on non-Hammett behaviour being superimposed on Hammett behaviour. QCT descriptors selectively correlate with Hammett behaviour. The QTMS analysis of the last three sets (toxicity of benzyl alcohols, chromatographic capacity factors of chalcones and herbicidal activity of 5-chloro-2,3-dicyanopyrazines) screens for false positives. This test is successfully passed in that QCT descriptors fail when lipophilicity/hydrophobicity is in charge. Hence, overall, the discriminatory capacity of QCT descriptors is established, in detecting Hammett behaviour and specifically replacing the Hammett constants by more modern and non-empirical descriptors.

Journal Article↗
PubMed2003

The Military Health System Computer-based Patient Record.

The Composite Health Care System II (CHCS II) is the Military's electronic Computer-based Patient Record, a clinical information system that will generate, maintain, and provide secure online access to a comprehensive and legible health record. In moving to CHCS II, the Department of Defense (DoD) is making the quantum leap from paper based medical records to computer based patient record (CPR). The CPR will enable DoD health care to meet its strategic goals for the 21st century and is paramount to providing comprehensive patient-focused information.

Humans↗
PubMed2003

A study of homonuclear dipolar recoupling pulse sequences in solid-state nuclear magnetic resonance.

Dipolar recoupling pulse sequences are of great importance in magic angle spinning solid-state NMR. Recoupling sequences are used for excitation of double-quantum coherence, which, in turn, is employed in experiments to estimate internuclear distances and molecular torsion angles. Much effort is spent on the design of recoupling sequences that are able to produce double-quantum coherence with high efficiency in demanding spin systems, i.e., spin systems with small dipole-dipole couplings and large chemical-shift anisotropies (CSAs). The sequence should perform robustly under a variety of experimental conditions. This paper presents experiments and computer calculations that extend the theory of double-quantum coherence preparation from the strong coupling/small CSA limit to the weak coupling limit. The performance of several popular dipole-dipole recoupling sequences-DRAWS, POST-C7, SPC-5, R1, and R2-are compared. It is found that the optimum performance for several of these sequences, in the weak coupling/large CSA limit, varies dramatically, with respect to the sample spinning speed, the magnitude and orientation of the CSAs, and the magnitude of dipole-dipole couplings. It is found that the efficiency of double-quantum coherence preparation by gamma-encoded sequences departs from the predictions of first-order theory. The discussion is supported by density-matrix calculations.

Alanine↗
PubMed2006

A QUICKSTEP-based quantum mechanics/molecular mechanics approach for silica.

Quantum mechanics/molecular mechanics (QM/MM) approaches are currently used to describe several properties of silica-based systems, which are local in nature and require a quantum description of only a small number of atoms around the site of interest, e.g., local chemical reactivity or spectroscopic properties of point defects. We present a QM/MM scheme for silica suitable to be implemented in the general QM/MM framework recently developed for large scale molecular dynamics simulations, within the QUICKSTEP approach to the description of the quantum region. Our scheme has been validated by computing the structural and dynamical properties of an oxygen vacancy in alpha-quartz, a prototypical defect in silica. We have found that good convergence in the Si-Si bond length and formation energy is achieved by using a quantum cluster of only eight atoms in size. We check the suitability of the method for molecular dynamics and evaluate the Si-Si bond frequency from the velocity-velocity correlation function.

Journal Article↗
PubMed1988

Future in biomolecular computation.

Large-scale computations for biomolecules are dominated by three levels of theory: rigorous quantum mechanical calculations for molecules with up to about 30 atoms, semi-empirical quantum mechanical calculations for systems with up to several hundred atoms, and force-field molecular dynamics studies of biomacromolecules with 10,000 atoms and more including surrounding solvent molecules. It can be anticipated that increased computational power will allow the treatment of larger systems of ever growing complexity. Due to the scaling of the computational requirements with increasing number of atoms, the force-field approaches will benefit the most from increased computational power. On the other hand, progress in methodologies such as density functional theory will enable us to treat larger systems on a fully quantum mechanical level and a combination of molecular dynamics and quantum mechanics can be envisioned. One of the greatest challenges in biomolecular computation is the protein folding problem. It is unclear at this point, if an approach with current methodologies will lead to a satisfactory answer or if unconventional, new approaches will be necessary. In any event, due to the complexity of biomolecular systems, a hierarchy of approaches will have to be established and used in order to capture the wide ranges of length-scales and time-scales involved in biological processes. In terms of hardware development, speed and power of computers will increase while the price/performance ratio will become more and more favorable. Parallelism can be anticipated to become an integral architectural feature in a range of computers.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical Phenomena↗
PubMed2005

Entanglement in quantum spin chains, symmetry classes of random matrices, and conformal field theory.

We compute the entropy of entanglement between the first N spins and the rest of the system in the ground states of a general class of quantum spin chains. We show that under certain conditions the entropy can be expressed in terms of averages over ensembles of random matrices. These averages can be evaluated, allowing us to prove that at critical points the entropy grows like kappalog(2N+kappa as N-->infinity, where kappa and kappa are determined explicitly. In an important class of systems, kappa is equal to one-third of the central charge of an associated Virasoro algebra. Our expression for kappa therefore provides an explicit formula for the central charge.

Journal Article↗