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At least 811 records · Page 45Linked to original sources
PubMed2002

23Na NMR study of the interaction between hyaluronan and the bications Ca(++), Mg(++) and Cu(++).

The relaxation rate R = pi Delta nu(1/2) of the quadrupolar (23)Na nucleus was measured at pH approximately 7 using a 200 MHz NMR spectrometer with a view to observe the interaction between hyaluronan and its natural counterion Na(+) and the bications Ca(++), Mg(++) and Cu(++). An interpretation of our results, by means of the "entropy of fluctuations" concept of Na(+), is presented. We show that Cu(++) ions are more effective than Ca(++) and Mg(++). A possible model of complexation of Cu(++) in a cage formed by the 1-4 glycosidic bond, the carboxylate side-chain and the acetoamide side-chain is proposed, according to electrostatic potential computations using the ZINDO1 quantum semi empirical method.

Calcium↗
PubMed1981

Theoretical approach for radiosensitizers. Correlation between calculated electroaffinity and sensitization factors of nitro-compounds.

The electron affinity of eight well-known nitroaromatic and nitroheterocyclic radiosensitizers is computed resorting to a quantum mechanical approach. Four of the compounds studied were nitroimidazoles; but p-nitroacetophenone and some 5-nitrofuran derivatives were also investigated for comparison. A good correlation between the theoretical electroaffinity values and the radiosensitization efficiencies is found in the case of the nitroimidazoles, in which the pi-electron system appears to be limited to the aromatic ring, except for small side groups. In the case of molecules where the pi-electron system spreads out on the side-chain the theoretical procedure seems to fail.

Acetophenones↗
PubMed2004

Density matrix perturbation theory.

An orbital-free quantum perturbation theory is proposed. It gives the response of the density matrix upon variation of the Hamiltonian by quadratically convergent recursions based on perturbed projections. The technique allows treatment of embedded quantum subsystems with a computational cost scaling linearly with the size of the perturbed region, O(N(pert.)), and as O(1) with the total system size. The method allows efficient high order perturbation expansions, as demonstrated with an example involving a 10th order expansion. Density matrix analogs of Wigner's 2n+1 rule are also presented.

Journal Article↗
PubMed2005

Physical characterization of a prototype selenium-based full field digital mammography detector.

The purpose of this study was to measure experimentally the physical performance of a prototype mammographic imager based on a direct detection, flat-panel array design employing an amorphous selenium converter with 70 microm pixels. The system was characterized for two different anode types, a molybdenum target with molybdenum filtration (Mo/Mo) and a tungsten target with rhodium filtration (W/Rh), at two different energies, 28 and 35 kVp, with approximately 2 mm added aluminum filtration. To measure the resolution, the presampled modulation transfer function (MTF) was measured using an edge method. The normalized noise power spectrum (NNPS) was measured by two-dimensional Fourier analysis of uniformly exposed mammograms. The detective quantum efficiencies (DQEs) were computed from the MTFs, the NNPSs, and theoretical ideal signal to noise ratios. The MTF was found to be close to its ideal limit and reached 0.2 at 11.8 mm(-1) and 0.1 at 14.1 mm(-1) for images acquired at an RQA-M2 technique (Mo/Mo anode, 28 kVp, 2 mm Al). Using a tungsten technique (MW2; W/Rh anode, 28 kVp, 2 mm Al), the MTF went to 0.2 at 11.2 mm(-1) and to 0.1 at 13.3 mm(-1). The DQE reached a maximum value of 54% at 1.35 mm(-1) for the RQA-M2 technique at 1.6 microC/kg and achieved a peak value of 64% at 1.75 mm(-1) for the tungsten technique (MW2) at 1.9 microC/kg. Nevertheless, the DQE showed strong exposure and frequency dependencies. The results indicated that the detector offered high MTFs and DQEs, but structured noise effects may require improved calibration before clinical implementation.

Equipment Design↗
PubMed2002

Efficacy of proton pump inhibitor drugs against Plasmodium falciparum in vitro and their probable pharmacophores.

The substituted benzimidazoles omeprazole, lansoprazole, rabeprazole, and pantoprazole were found to have in vitro activity against three different isolates of Plasmodium falciparum: D6 (which is chloroquine and pyrimethamine sensitive), W2 (chloroquine and pyrimethamine resistant), and TM91C235 (multidrug resistant). Lansoprazole and rabeprazole were the most effective against all three isolates, with a 50% inhibitory concentration (IC(50)) range of 7 to 11 microM. Omeprazole showed intermediate activity against D6 and W2 isolates, with IC(50)s of 27 to 28 microM, but had poor activity against TM91C235, with an IC(50) of 76 microM. Pantoprazole was the least effective, with IC(50)s of 73 microM against D6, 53 microM against W2, and 39 microM against TM91C235. A pharmacophore model describing the important features responsible for potent activity of the drugs was developed using computational techniques of semiempirical quantum chemical methods and the three-dimensional QSAR procedure of the CATALYST software. The important features of the pharmacophore, according to the findings based on the CATALYST procedures, are the hydrogen bond acceptor and donor sites at the benzimidine nitrogen atoms and the two aromatic hydrophobic sites in the molecules. AM1 quantum chemical calculations identified the electrostatic potential surface surrounding the sulfoxide atom as crucial for potent activity.

Animals↗
PubMed1989

Determination of electron density, mass density and calcium fraction by mass of soft and osseous tissues by dual energy CT.

Techniques of CT analysis of trabecular regions are concerned with bone mineral assessment, with considerable attention being paid to the effect of unknown fat content. Information concerning mass density and electron density might provide a more complete picture but is not normally obtained. A method for the calculation of mass and electron density, as well as the fraction of calcium by mass, is described and requires only a measurement of effective beam energy on the skin in addition to the CT numbers from a dual energy scan. The method uses the six major elements, H, C, N, O, P and Ca as compartments for the analysis and can also be applied to soft tissue by using only the first four. The calculated mass fraction of Ca is found to be sensitive to fat content and difference between surface and internal energies which can lead to serious underestimates below a fraction of about 0.04. Mass and electron density results are independent of fat content and only marginally affected by energy differences. Results were obtained with simple materials confirming mass density can be calculated to the order of 3% and electron density to considerably better than 1%.

Body Composition↗
PubMedDate not supplied

A two-stage shift register for clocked Quantum-Dot Cellular Automata.

Quantum-Dot Cellular Automata (QCA) is a computational scheme utilizing the position of interacting single electrons within arrays of quantum dots ("cells") to encode and process binary information. Clocked QCA architectures can provide power gain, logic level restoration, and memory features. Using arrays of micron-sized metal dots, we experimentally demonstrate operation of a QCA latch-inverter and a two-stage shift register.

Aluminum↗
PubMed2006

Performance evaluation of a computed radiography imaging device using a typical "front side" and novel "dual side" readout storage phosphors.

The Fourier-space modulation transfer function (MTF), normalized noise power spectrum (nNPS), and detective quantum efficiency (DQE) of a computed radiography (CR) x-ray imaging device were measured. Two different storage phosphor screens were used in conjunction with a single CR reader (Fuji, Clearview, CS). One of the storage phosphor plates (ST-BD) had a clear backing material which allowed "dual side read" of the latent image from both the "front" and "back" sides of the phosphor. The other phosphor plate had a light occluding backing material, limiting the readout to front side only (ST-VI). The standard RQA-5 beam quality was used. The MTF was measured using a 1 mm thick tungsten edge device. Compared to the ST-55BD phosphor, the ST-VI phosphor was found to have modestly higher MTF at all spatial frequencies. The nNPS(f) and DQE(f) were measured for nominal incident exposure levels ranging from 0.1 to 10 mR. The dual side read phosphor demonstrated superior DQE, especially at low spatial frequencies. At the frequency 0.5 cycles/mm, the DQE values for the 1 mR exposure were 0.36 and 0.21 for the ST-55BD and ST-VI phosphor plates, respectively. The differences between the spatial-frequency dependent DQE of the two plates can be attributed to the increased signal collection efficiency of the dual side read plates and differences in storage phosphor structure noise.

Humans↗
PubMed2006

Population size bias in descendant-weighted diffusion quantum Monte Carlo simulations.

We consider the influence of population size on the accuracy of diffusion quantum Monte Carlo simulations that employ descendant weighting or forward walking techniques to compute expectation values of observables that do not commute with the Hamiltonian. We show that for a simple model system, the d-dimensional isotropic harmonic oscillator, the population size must increase rapidly with d in order to ensure that the simulations produce accurate results. When the population size is too small, expectation values computed using descendant-weighted diffusion quantum Monte Carlo simulations exhibit significant systematic biases.

Journal Article↗
PubMed2005

Bounds for the scattering length of spin-polarized helium from high-accuracy electronic structure calculations.

We developed a series of correlation-consistent, polarized multiple zeta basis sets optimized specifically for the energy of the 2 3S state of helium atom. These basis sets were subsequently augmented with diffuse functions optimized for the van der Waals constants C6 through C14 which determine the asymptotic behavior of the second-order dispersion interaction between 2 3S helium atoms at large interatomic separation R. The resulting bases were applied to compute the Born-Oppenheimer (BO) potential for the lowest 5Sigmag+ state of the helium dimer. The coupled cluster and the full configuration-interaction techniques were employed to account for the electron correlation effects. The cardinal number extrapolation technique was used to obtain the complete-basis-set limit V(R) for the interaction potential and to find its lower VL(R) and upper VU(R) bounds. The resulting potentials were fitted to an analytical function containing accurate van der Waals constants C6 through C12 (including C11). We found that the complete-basis-set BO potential has a well depth De=1048.24+/-0.36 cm-1. The highest rotationless vibrational level is bound by D14=90.2+/-4.7 MHz, much stronger than the previous most accurate estimation of 15.2 MHz. The error bounds for De and D14 were obtained using the VL(R) and VU(R) potentials. The S-wave scattering length computed using the VL(R), V(R), and VU(R) potentials (assuming atomic masses) is aL=7.41 nm, a=7.54 nm, and aU=7.69 nm, respectively. We also computed the adiabatic, relativistic, and quantum electrodynamics (QED) corrections to the BO potential. When these corrections are taken into account the values of D14 and of a (both computed assuming nuclear masses) are 87.4+/-6.7 MHz and 7.64+/-0.20 nm; the error bounds reflect now also the uncertainty of the included adiabatic, relativistic, and QED corrections. The value of the scattering length resulting from our investigation lies outside the error bounds of all experimental determinations based on the properties of Bose-Einstein condensate of spin-polarized helium atoms.

Journal Article↗
PubMed2006

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

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

Binding Sites↗
PubMed2005

Particle scattering in loop quantum gravity.

We devise a technique for defining and computing -point functions in the context of a background-independent gravitational quantum field theory. We construct a tentative implementation of this technique in a perturbatively finite model defined using spin foam techniques in the context of loop quantum gravity.

Journal Article↗
PubMed2006

Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase.

Nuclear quantum mechanical effects have been examined for the proton transfer reaction catalyzed by triosephosphate isomerase, with the normal mode centroid path integral molecular dynamics based on the potential energy surface from the recently developed reaction path potential method. In the simulation, the primary and secondary hydrogens and the C and O atoms involving bond forming and bond breaking were treated quantum mechanically, while all other atoms were dealt classical mechanically. The quantum mechanical activation free energy and the primary kinetic isotope effects were examined. Because of the quantum mechanical effects in the proton transfer, the activation free energy was reduced by 2.3 kcal/mol in comparison with the classical one, which accelerates the rate of proton transfer by a factor of 47.5. The primary kinetic isotope effects of kH/kD and kH/kT were estimated to be 4.65 and 9.97, respectively, which are in agreement with the experimental value of 4+/-0.3 and 9. The corresponding Swain-Schadd exponent was predicted to be 3.01, less than the semiclassical limit value of 3.34, indicating that the quantum mechanical effects mainly arise from quantum vibrational motion rather than tunneling. The reaction path potential, in conjunction with the normal mode centroid molecular dynamics, is shown to be an efficient computational tool for investigating the quantum effects on enzymatic reactions involving proton transfer.

Carbon↗
PubMed2004

Quantum statistical mechanics with Gaussians: equilibrium properties of van der Waals clusters.

The variational Gaussian wave-packet method for computation of equilibrium density matrices of quantum many-body systems is further developed. The density matrix is expressed in terms of Gaussian resolution, in which each Gaussian is propagated independently in imaginary time beta=(k(B)T)(-1) starting at the classical limit beta=0. For an N-particle system a Gaussian exp[(r-q)(T)G(r-q)+gamma] is represented by its center qinR(3N), the width matrix GinR(3Nx3N), and the scale gammainR, all treated as dynamical variables. Evaluation of observables is done by Monte Carlo sampling of the initial Gaussian positions. As demonstrated previously at not-very-low temperatures the method is surprisingly accurate for a range of model systems including the case of double-well potential. Ideally, a single Gaussian propagation requires numerical effort comparable to the propagation of a single classical trajectory for a system with 9(N(2)+N)/2 degrees of freedom. Furthermore, an approximation based on a direct product of single-particle Gaussians, rather than a fully coupled Gaussian, reduces the number of dynamical variables to 9N. The success of the methodology depends on whether various Gaussian integrals needed for calculation of, e.g., the potential matrix elements or pair correlation functions could be evaluated efficiently. We present techniques to accomplish these goals and apply the method to compute the heat capacity and radial pair correlation function of Ne(13) Lennard-Jones cluster. Our results agree very well with the available path-integral Monte Carlo calculations.

Journal Article↗
PubMed2005

Atomistic simulation of a nematogen using a force field derived from quantum chemical calculations.

Bulk phase atomistic computer simulations of 4-n-pentyl-4'-cyanobiphenyl (5CB) were performed with a specific force field obtained from ab initio and DFT calculations. The intermolecular potential was previously derived through the fragmentation reconstruction method (FRM), developed in our group. The description of some intramolecular interactions, like the torsional potential between the phenyl rings and at the aryl-alkyl linkage, is achieved through accurate DFT studies. Lengthy ( approximately 40 ns) molecular dynamics (MD) simulations were then carried out at constant atmospheric pressure and different temperatures. The system was stable in the experimental crystalline structure up to 285 K, where the early stage of the melting process appears with the loss of positional order. At higher temperatures (between 290 and 305 K) a kinetically stable, orientationally ordered phase is obtained. This nematic phase was reached starting with three initial configurations, differing in their orientational order parameter. The calculated values of thermodynamic and structural properties of each phase were in fairly good agreement with the relevant experimental data.

Journal Article↗
PubMed1999

Test of semiclassical amplitudes for quantum ray-splitting systems.

We compute semiclassically and numerically the weights of ray-splitting orbits in the density of states of a rectangular and an annular ray-splitting billiard. The agreement between the semiclassical and the numerical results is very good, confirming the necessity of including reflection and transmission coefficients of non-Newtonian ray-splitting orbits in semiclassical expressions for the density of states of ray-splitting systems.

Journal Article↗
PubMed2006

Quantum catalysis in B12-dependent methylmalonyl-CoA mutase: experimental and computational insights.

B12-dependent methylmalonyl-CoA mutase catalyses the interchange of a hydrogen atom and the carbonyl-CoA group on adjacent carbons of methylmalonyl-CoA to give the rearranged product, succinyl-CoA. The first step in this reaction involves the transient generation of cofactor radicals by homolytic rupture of the cobalt-carbon bond to generate the deoxyadenosyl radical and cob(II)alamin. This step exhibits a curious sensitivity to isotopic substitution in the substrate, methylmalonyl-CoA, which has been interpreted as evidence for kinetic coupling. The magnitude of the isotopic discrimination is large and a deuterium isotope effect ranging from 35.6 at 20 degrees C to 49.9 at 5 degrees C has been recorded. Arrhenius analysis of the temperature dependence of this isotope effect provides evidence for quantum tunnelling in this hydrogen transfer step. The mechanistic complexity of the observed rate constant for cobalt-carbon bond homolysis together with the spectroscopically silent nature of many of the component steps limits the insights that can be derived by experimental approaches alone. Computational studies using a newly developed geometry optimization scheme that allows determination of the transition state in the full quantum mechanical/molecular mechanical coordinate space have yielded novel insights into the strategy deployed for labilizing the cobalt-carbon bond and poising the resulting deoxyadenosyl radical for subsequent hydrogen atom abstraction.

Carbon↗