On isomorphic factorizations of circulant graphs

We investigate the conjecture that every circulant graph X admits a k‐isofactorization for every k dividing |E(X)|. We obtain partial results with an emphasis on small values of k. © 2006 Wiley Periodicals, Inc. J Combin Designs 14: 406–414, 2006     

Corn stover fractions and bioenergy

Information is presented on structure, composition, and response to enzymes of corn stover related to barriers for bioconversion to ethanol. Aromatic compounds occurred in most tissue cell walls. Ferulic acid esterase treatment before cellulase treatment significantly improved dry weight loss and release of phenolic acids and sugars in most fractions over cellulase alone. Leaf fractions were considerably higher in dry weight loss and released sugars with esterase treatment, but stem pith cells gave up the most phenolic acids. Results help identify plant fractions more appropriate for coproducts and bioconversion and those more suitable as residues for soil erosion control.     

Importance of the Debye interaction in organic solutions: Henry's law constants for polar liquids in nonpolar solvents and vice versa

Henry's law constants have been determined for -butyrolactone (BL), ethyl acetate (EA), and 2-methyl-3-pentanol (MEP) in mixtures of iso-octane (ISO) and toluene (TOL), for BL, EA, TOL, and ISO in cinnamaldehyde (CIN) and for TOL and ISO in each other and in BL. From these data and published vapor pressures, the activity coefficients at infinite dilution and the standard molar Gibbs free energy of transfer, G ₂ ⁰ of the solutes from dilute solution in ISO to dilute solution in each solvent medium have been calculated. The different behavior patterns of BL and EA are attributed to differences in their abilities to exist in different conformations possessing different dipole moments. For polar solutes, G ₂ ⁰ decreases with increasing polarizability of the solvent and with increasing dipole moment of the solute, suggesting increased contributions from dipole-induced dipole (Debye) interactions. The sigmoidal plot of G ₂ ⁰ against the change in pair potential energy calculated from the classical expressions suggests that G ₂ ⁰ seriously underestimates the strength of the Debye interactions in comparison with the London interactions.     

A Branched Pore Model Analysis for the Adsorption of Acid Dyes on Activated Carbon

A new branched-pore adsorption model has been developed using an external mass transfer coefficient, K _f, an effective diffusivity, D _eff, a lumped micropore diffusion rate parameter, K _b, and the fraction of macropores, f, to describe sorption kinetic data from initial adsorbent-adsorbate contact to the long-term adsorption phase. This model has been applied to an environmental pollution problem—the removal of two dyes, Acid Blue 80 (AB80) and Acid Red 114 (AR114), by sorption on activated carbon. A computer program has been used to generate theoretical concentration-time curves and the four mass transfer kinetic parameters adjusted so that the model achieves a close fit to the experimental data. The best fit values of the parameters have been determined for different initial dye concentrations and carbon masses. Since the model is specifically applicable to fixed constant values of these four parameters, a further and key application of this project is to see if single constant values of these parameters can be used to describe all the experimental concentration-time decay curves for one dye-carbon system.The error analysis and best fit approach to modeling the decay curves for both dye systems show that the correlation between experimental and theoretical data is good for the fixed values of the four fitted parameters. A significantly better fit of the model predictions is obtained when K _f, K _b and f are maintained constant but D _eff is varied. This indicates that the surface diffusivity may vary as a function of surface coverage.     

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms

Multiple time step (MTS) algorithms present an effective integration approach to reduce the computational cost of dynamics simulations. By using force splitting to allow larger time steps for the more slowly varying force components, computational savings can be realized. The Particle-Mesh-Ewald (PME) method has been independently devised to provide an effective and efficient treatment of the long-range electrostatics interactions. Here we examine the performance of a combined MTS/PME algorithm previously developed for AMBER on a large polymerase beta/DNA complex containing 40,673 atoms. Our goal is to carefully combine the robust features of the Langevin/MTS (LN) methodology implemented in CHARMM-which uses position rather than velocity Verlet with stochasticity to make possible outer time steps of 150 fs-with the PME formulation. The developed MTS/PME integrator removes fast terms from the reciprocal-space Ewald component by using switch functions. We analyze the advantages and limitations of the resulting scheme by comparing performance to the single time step leapfrog Verlet integrator currently used in AMBER by evaluating different time-step protocols using three assessors for accuracy, speedup, and stability, all applied to long (i.e., nanosecond) simulations to ensure proper energy conservation. We also examine the performance of the algorithm on a parallel, distributed shared-memory computer (SGI Origin 2000 with 8 300-MHz R12000 processors). Good energy conservation and stability behavior can be demonstrated, for Newtonian protocols with outer time steps of up to 8 fs and Langevin protocols with outer time steps of up to 16 fs. Still, we emphasize the inherent limitations imposed by the incorporation of MTS methods into the PME formulation that may not be widely appreciated. Namely, the limiting factor on the largest outer time-step size, and hence speedup, is an intramolecular cancellation error inherent to PME. This error stems from the excluded-nonbonded correction term contained in the reciprocal-space component. This cancellation error varies in time and introduces artificial frequencies to the governing dynamics motion. Unfortunately, we find that this numerical PME error cannot be easily eliminated by refining the PME parameters (grid resolution and/or order of interpolating polynomial). We suggest that methods other than PME for fast electrostatics may allow users to reap the full advantages from MTS algorithms.     

Ab initio calculation of the effective valence shell hamiltonian of carbon: Simultaneous treatment of neutral and ion states

The n = 2 effective valence shell hamiltonian, $\text{H}$^v, of carbon is evaluated through second order using ³P Hartree—Fock orbitals (5s4p) with added d functions to provide results within a few percent of the spd convergence limits. The calculated $\text{H}$^v is employed to evaluate the n = 2 valence states of C, C^?, C⁺, C²⁺ and C³⁺ with an average deviation of the 21 excitation energies, ionization potentials and electron affinity from experimental values of 0.32 eV. Three-electron parts of $\text{H}$^v contribute substantially to a number of these excitation energies.     

Engineering reactions in crystalline solids: predicting photochemical decarbonylation from calculated thermochemical parameters

A detailed thermochemical analysis of the alpha-cleavage and decarbonylation reactions of acetone and several ketodiesters was carried out with the B3LYP/6-31G* density functional method. The heats of formation of several ground-state ketones and radicals were calculated at 298 K to determine bond dissociation energies (BDE) and radical stabilization energies (RSE) as a function of substituents. Results show that the radical-stabilizing abilities of the ketone substituents play a very important role on the thermodynamics of the alpha-cleavage and decarbonylation steps. An excellent correlation between calculated values and previous experimental observations suggests that photochemical alpha-cleavage and decarbonylation in crystals should be predictable from knowledge of excitation energies and the RSE of the substituent.     

Pyridinium p-toluenesulfonylmethylide as a formyl anion equivalent

Pyridinium $\text{p}$-toluenesulfonylmethylide serves as a formyl anion equivalent and, in the presence of an alcohol, undergoes 1,4-addition to $\text{N}$-substituted maleimides to give alkoxy- (or aryloxy)-methylene-succinimides. The protected aldehyde group can be liberated readily.