A Lanczos-powered implementation of the Faber polynomial quantum time propagator for reaction probabilities

Complementing our recent work on subspace wavepacket propagation [Chem. Phys. Lett. 336 (2001) 149], we introduce a Lanczos-based implementation of the Faber polynomial quantum long-time propagator. The original version [J. Chem. Phys. 101 (1994) 10493] implicitly handles non-Hermitian Hamiltonians, that is, those perturbed by imaginary absorbing potentials to handle unwanted reflection effects. However, like many wavepacket propagation schemes, it encounters a bottleneck associated with dense matrix-vector multiplications. Our implementation seeks to reduce the quantity of such costly operations without sacrificing numerical accuracy. For some benchmark scattering problems, our approach compares favourably with the original. (C) 2004 Elsevier B.V. All rights reserved.

Converged quantum calculations of HO2 bound states and resonances for J=6 and 10

Bound and resonance states of HO2 are calculated quantum mechanically using both the Lanczos homogeneous filter diagonalization method and the real Chebyshev filter diagonalization method for nonzero total angular momentum J=6 and 10, using a parallel computing strategy. For bound states, agreement between the two methods is quite satisfactory; for resonances, while the energies are in good agreement, the widths are in general agreement. The quantum nonzero-J specific unimolecular dissociation rates for HO2 are also calculated. (C) 2004 American Institute of Physics.

Iterative quantum computations of HO2 bound states and resonances for J=4 and 5

Bound and resonance states of HO2 have been calculated by both the complex Lanczos homogeneous filter diagonalisation (LHFD) method(1,2) and the real Chebyshev filter diagonalisation method(3,4) for non-zero total angular momentum J = 4 and 5. For bound states, the agreement between the two methods is quite satisfactory; for resonances while the energies are in good agreement, the widths are only in general agreement. The relative performances of the two iterative FD methods have also been discussed in terms of efficiency as well as convergence behaviour for such a computationally challenging problem. A helicity quantum number Ohm assignment (within the helicity conserving approximation) is performed and the results indicate that Coriolis coupling becomes more important as J increases and the helicity conserving approximation is not a good one for the HO2 resonance states.

Unimolecular Rovibrational Bound and Resonance States for Large Angular Momentum: J=20 Calculations for HO2

We explore the calculation of unimolecular bound states and resonances for deep-well species at large angular momentum using a Chebychev filter diagonalization scheme incorporating doubling of the autocorrelation function as presented recently by Neumaier and Mandelshtam [Phys. Rev. Lett. 86, 5031 (2001)]. The method has been employed to compute the challenging J=20 bound and resonance states for the HO2 system. The methodology has firstly been tested for J=2 in comparison with previous calculations, and then extended to J=20 using a parallel computing strategy. The quantum J-specific unimolecular dissociation rates for HO2-> H+O-2 in the energy range from 2.114 to 2.596 eV have been reported for the first time, and comparisons with the results of Troe and co-workers [J. Chem. Phys. 113, 11019 (2000) Phys. Chem. Chem. Phys. 2, 631 (2000)] from statistical adiabatic channel method/classical trajectory calculations have been made. For most of the energies, the reported statistical adiabatic channel method/classical trajectory rate constants agree well with the average of the fluctuating quantum-mechanical rates. Near the dissociation threshold, quantum rates fluctuate more severely, but their average is still in agreement with the statistical adiabatic channel method/classical trajectory results.

Symmetry contaminations in reactive scattering through long-lived collision complexes

We extend our Lanczos subspace time-independent wave packet method [J. Chem. Phys. 116 (2002) 2354] to investigate the issue of symmetry contaminations for the challenging deep-well H + O-2 reaction. Our central objective is to address the issue of whether significant symmetry contamination can occur if a wavepacket initially possessing the correct O-O exchange symmetry is propagated over tens of thousands of recursive steps using a basis which does not explicitly enforce the correct symmetry, and if so how seriously this affects the results. We find that symmetry contamination does exist where the symmetry constraint is not explicitly enforced in the basis. While it affects individual resonances and the associated peak amplitudes, the overall shape of the more averaged quantities such as total reaction probabilities and vibrational branching ratios are not seriously affected. (C) 2004 Elsevier B.V. All rights reserved.

On the microscopic mechanism of carbon gasification: A theoretical study

In this paper we report the results of ab initio calculations on the energetics and kinetics of oxygen-driven carbon gasification reactions using a small model cluster, with full characterisation of the stationary points on the reaction paths. We show that previously unconsidered pathways present significantly reduced barriers to reaction and must be considered as alternative viable paths. At least two electronic spin states of the model cluster must be considered for a complete description. (C) 2004 Elsevier Ltd. All rights reserved.

Photodissociation of benzene under collision-free conditions: An ab initio/Rice-Ramsperger-Kassel-Marcus study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of benzene at various wavelengths upon absorption of one or two UV photons followed by internal conversion into the ground electronic state. Reaction pathways leading to various decomposition products have been mapped out at the G2M level and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for C6H5+H, C6H4+H-2, C4H4+C2H2, C4H2+C2H4, C3H3+C3H3, C5H3+CH3, and C4H3+C2H3 have been calculated subsequently using both numerical integration of kinetic master equations and the steady-state approach. The results show that upon absorption of a 248 nm photon dissociation is too slow to be observable in molecular beam experiments. In photodissociation at 193 nm, the dominant dissociation channel is H atom elimination (99.6%) and the minor reaction channel is H-2 elimination, with the branching ratio of only 0.4%. The calculated lifetime of benzene at 193 nm is about 11 mus, in excellent agreement with the experimental value of 10 mus. At 157 nm, the H loss remains the dominant channel but its branching ratio decreases to 97.5%, while that for H-2 elimination increases to 2.1%. The other channels leading to C3H3+C3H3, C5H3+CH3, C4H4+C2H2, and C4H3+C2H3 play insignificant role but might be observed. For photodissociation upon absorption of two UV photons occurring through the neutral hot benzene mechanism excluding dissociative ionization, we predict that the C6H5+H channel should be less dominant, while the contribution of C6H4+H-2 and the C3H3+C3H3, CH3+C5H3, and C4H3+C2H3 radical channels should significantly increase. (C) 2004 American Institute of Physics.

Full S matrix calculation via a single real-symmetric Lanczos recursion: The Lanczos artificial boundary inhomogeneity method

We present an efficient and robust method for the calculation of all S matrix elements (elastic, inelastic, and reactive) over an arbitrary energy range from a single real-symmetric Lanczos recursion. Our new method transforms the fundamental equations associated with Light's artificial boundary inhomogeneity approach [J. Chem. Phys. 102, 3262 (1995)] from the primary representation (original grid or basis representation of the Hamiltonian or its function) into a single tridiagonal Lanczos representation, thereby affording an iterative version of the original algorithm with greatly superior scaling properties. The method has important advantages over existing iterative quantum dynamical scattering methods: (a) the numerically intensive matrix propagation proceeds with real symmetric algebra, which is inherently more stable than its complex symmetric counterpart; (b) no complex absorbing potential or real damping operator is required, saving much of the exterior grid space which is commonly needed to support these operators and also removing the associated parameter dependence. Test calculations are presented for the collinear H+H-2 reaction, revealing excellent performance characteristics. (C) 2004 American Institute of Physics.

Recent developments in the quantum dynamical characterization of unimolecular resonances

We give a selective review of quantum mechanical methods for calculating and characterizing resonances in small molecular systems, with an emphasis on recent progress in Chebyshev and Lanczos iterative methods. Two archetypal molecular systems are discussed: isolated resonances in HCO, which exhibit regular mode and state specificity, and overlapping resonances in strongly bound HO2, which exhibit irregular and chaotic behavior. Recent progresses for non-zero total angular momentum J calculations of resonances including parallel computing models are also included and future directions in this field are discussed.

Transition-state-theory calculations for reactions of O(3P) with halogenated olefins

The potential energy surfaces for the reactions of atomic oxygen in its ground electronic state, O(P-3), with the olefins: CF2=CCl2 and CF2=CF - CF3, have been characterized using ab initio molecular orbital calculations. Geometry optimization and vibrational frequency calculations were performed for reactants, transition states and products at the MP2 and QCISD levels of theory using the 6-31G(d) basis set. This database was then used to calculate the rate constants by means of Transition-State-Theory. To obtain a better reference and to test the reliability of the activation barriers we have also carried out computations using the CCSD(T)(fc)/6-311Gdagger, MP4(SDQ)(fc)/CBSB4 and MP2(fc)/CBSB3 single point energy calculations at both of the above levels of theory, as well as with the composite CBS-RAD procedure ( P. M. Mayer, C. J. Parkinson, D. M. Smith and L. Radom, J. Chem. Phys., 1998, 108, 604) and a modi. cation of this approach, called: CBS-RAD( MP2, MP2). It was found that the kinetic parameters obtained in this work particularly with the CBS-RAD ( MP2, MP2) procedure are in reasonable agreement with the experimental values. For both reactions it is found that the channels leading to the olefin double-bond addition predominates with respect to any other reaction pathway. However, on account of the different substituents in the alkenes we have located, at all levels of theory, two transition states for each reaction. Moreover, we have found that, for the reactions studied, a correlation exists between the activation energies and the electronic structure of the transition states which can explain the influence of the substituent effect on the reactivity of the halo-olefins.

Walking performance, oxygen uptake kinetics and resting muscle pyruvate dehydrogenase complex activity in peripheral arterial disease

In the present study, we tested the hypothesis that walking intolerance in intermittent claudication (IC) is related to both slowed whole body oxygen uptake (Vo(2)) kinetics and altered activity of the active fraction of the pyruvate dehydrogenase complex (PDCa) in skeletal muscle. Ten patients with IC and peripheral arterial disease [ankle/brachial index (ABI) = 0.73 +/- 0.13] and eight healthy controls (ABI = 1. 17 +/- 0.13) completed three maximal walking tests. From these tests, averaged estimates of walking time, peak Vo(2) and the time constant of Vo(2) (tau) during submaximal walking were obtained. A muscle sample was taken from the gastrocnemius medialis muscle at rest and analysed for PDCa and several other biochemical variables. Walking time and peak Vo(2) were approx. 50 % lower in patients with IC than controls, and tau was 2-fold higher (P < 0.05). r was significantly correlated with walking time (r = -0.72) and peak Vo(2) (r = -0.66) in patients with IC, but not in controls. PDCa was not significantly lower in patients with IC than controls; however, PDCa tended to be correlated with tau (r = -0.56, P = 0.09) in patients with IC, but not in controls (r = -0.14). A similar correlation was observed between resting ABI and tau (r = -0.63, P = 0.05) in patients with IC. These data suggest that the impaired Vo(2) kinetics contributes to walking intolerance in IC and that, within a group of patients with IC, differences in Vo(2) kinetics might be partly linked to differences in muscle carbohydrate oxidation.

A genetic investigation of the covariation among Inspection Time, Choice Reaction Time, and IQ subtest scores

Information processing speed, as measured by elementary cognitive tasks, is correlated with higher order cognitive ability so that increased speed relates to improved cognitive performance. The question of whether the genetic variation in Inspection Time (IT) and Choice Reaction Time (CRT) is associated with IQ through a unitary factor was addressed in this multivariate genetic study of IT, CRT, and IQ subtest scores. The sample included 184 MZ and 206 DZ twin pairs with a mean age of 16.2 years (range 15-18 years). They were administered a visual (pi-figure) IT task, a two-choice RT task, five computerized subtests of the Multidimensional Aptitude Battery, and the digit symbol substitution subtest from the WAIS-R. The data supported a factor model comprising a general, three group (verbal ability, visuospatial ability, broad speediness), and specific genetic factor structure, a shared environmental factor influencing all tests but IT, plus unique environmental factors that were largely specific to individual measures. The general genetic factor displayed factor loadings ranging between 0.35 and 0.66 for the IQ subtests, with IT and CRT loadings of -0.47 and -0.24, respectively. Results indicate that a unitary factor is insufficient to describe the entire relationship between cognitive speed measures and all IQ subtests, with independent genetic effects explaining further covariation between processing speed (especially CRT) and Digit Symbol.

Effect of addition of maltodextrin on drying kinetics and stickiness of sugar and acid-rich foods during convective drying: experiments and modelling

The effect of addition of maltodextrin on drying kinetics of drops containing fructose, glucose, sucrose and citric acid individually and in mixtures was studied experimentally using single drop drying experiments and numerically by solving appropriate mass and heat transfer equations. The numerical predictions agreed with the experimental moisture and temperature histories within 5-6% average relative (absolute) errors and average differences of +/- 1degreesC, respectively. The stickiness of these drops was determined using the glass transition temperature (T-g) of the drops' surface layer as an indicator. The experimental stickiness histories followed the model predictions with reasonable accuracy. A safe drying (non-sticky) regime in a spray drying environment has been proposed, and used to estimate the optimum amount of addition of maltodextrin for successful spray drying of 120 micron diameter droplets of fruit juices. (C) 2003 Elsevier Ltd. All rights reserved.

Scaling and non-scaling of muscle activity, kinematics, and dynamics in sit-ups with different degrees of difficulty

The purpose of this study was to investigate how the CNS adjusts motor patterns for variants of a complex axial movement-the situp. Adjustments were induced by changing the support surface contact and mass distribution of the body. Healthy adults performed straight-legged sit-ups, 3 s in duration, with support added to or removed from the lumbar trunk, or with mass added to the head or to the legs. Each of these interventions either increased or decreased the difficulty of the task. The study addressed the extent to which changes in sit-up difficulty are compensated by scaling of muscle activity, kinematics, and dynamics versus the extent to which they are compensated by changing discretely the motor pattern. The analysis of muscle activity, kinematics, and dynamics focused on the first 30-40% of the sit-up-the trunk flexion phase-since this is the most critical part of the movement. Our results demonstrate that, in some respects, sit-up kinematics and dynamics scaled with difficulty, but in other respects, they did not. Muscle activity also scaled, in many respects, but in more difficult sit-ups, abdominal flexor activity decreased instead of increased. Non-scaling changes in these parameters suggest that complex movements, such as the sit-up, may require discrete changes in motor pattern in order to deal with large loads, which challenge the available leverage. (C) 2005 Elsevier Ltd. All rights reserved.

Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling

Pyrin domain (PYD)-containing proteins are key components of pathways that regulate inflammation, apoptosis, and cytokine processing. Their importance is further evidenced by the consequences of mutations in these proteins that give rise to autoimmune and hyperinflammatory syndromes. PYDs, like other members of the death domain ( DD) superfamily, are postulated to mediate homotypic interactions that assemble and regulate the activity of signaling complexes. However, PYDs are presently the least well characterized of all four DD subfamilies. Here we report the three-dimensional structure and dynamic properties of ASC2, a PYD-only protein that functions as a modulator of multidomain PYD-containing proteins involved in NF-KB and caspase-1 activation. ASC2 adopts a six-helix bundle structure with a prominent loop, comprising 13 amino acid residues, between helices two and three. This loop represents a divergent feature of PYDs from other domains with the DD fold. Detailed analysis of backbone N-15 NMR relaxation data using both the Lipari-Szabo model-free and reduced spectral density function formalisms revealed no evidence of contiguous stretches of polypeptide chain with dramatically increased internal motion, except at the extreme N and C termini. Some mobility in the fast, picosecond to nanosecond timescale, was seen in helix 3 and the preceding alpha 2-alpha 3 loop, in stark contrast to the complete disorder seen in the corresponding region of the NALP1 PYD. Our results suggest that extensive conformational flexibility in helix 3 and the alpha 2-alpha 3 loop is not a general feature of pyrin domains. Further, a transition from complete disorder to order of the alpha 2-alpha 3 loop upon binding, as suggested for NALP1, is unlikely to be a common attribute of pyrin domain interactions.