Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms

Several parallel algorithms for Fock matrix construction are described. The algorithms calculate only the unique integrals, distribute the Fock and density matrices over the processors of a massively parallel computer, use blocking techniques to construct the distributed data structures, and use clustering techniques on each processor to maximize data reuse. Algorithms based on both square and row-blocked distributions of the Fock and density matrices are described and evaluated. Variants of the algorithms are discussed that use either triple-sort or canonical ordering of integrals, and dynamic or static task clustering schemes. The algorithms are shown to adapt to screening, with communication volume scaling down with computation costs. Modeling techniques are used to characterize algorithm performance. Given the characteristics of existing massively parallel computers, all the algorithms are shown to be highly efficient for problems of moderate size. The algorithms using the row-blocked data distribution are the most efficient. © 1996 by John Wiley & Sons, Inc.     

A quantum-mechanical calculation of the dynamic structure factors of magnesium difluoride

Ab initio calculations of dynamic structure factors are performed with a methodology that requires the crystalline density matrix determined by the periodic Hartree-Fock CRYSTAL code. Amplitudes and orientations of the atomic vibrations are fixed by the mean-square displacements available in the literature. This method, which is here upgraded so as to satisfy normalization conditions, gives rise, for any temperature T, to a “dynamic” density matrix different from the static one. An application to the calculation of the dynamic structure factors of magnesium difluoride (MgF₂), which has anisotropic mean-square displacement tensors, is proposed and compared with experiments at 298 K. © 1996 John Wiley & Sons, Inc.     

Monte Carlo modelling of the polymer glass transition

We are proposing a lattice model with chemical input for the computer modelling of the polymer glass transition. The chemical input information is obtained by a coarse graining procedure applied to a microscopic model with full chemical detail. We use this information on Bisphenol-A-Polycarbonate to predict it's Vogel-Fulcher temperature out of a dynamic Monte Carlo Simulation. The microscopic structure of the lattice model is that of a genuine amorphous material, and the structural relaxation obeys the time temperature superposition.     

Segment orientation in topologically constrained networks

Using the continous Edwards–chain model the simultaneous influence of harmonic–like constraints and of a stochastic order parameter field on the segment orientation in polymer networks is investigated. The harmonic potential reduces the orientation order parameter in comparison to the value for an unconstrained freely jointed chain. This reference value is approached from below in the case of strong topological constraints. The introduction of a stochastic order parameter field enlarges the orientation but the reference value remains the upper boundary.     

Swelling and fractal heterogeneities in networks

In this paper we revisit old swelling data on polymer networks that have not been interpreted theoretically on a closed molecular basis. If the osmotic pressure of the swollen network is compared to the osmotic pressure of the corresponding uncrosslinked solution unsolved problems appear, when the relative osmotic pressure is plotted against the degree of swelling, i.e. the deformation due to swelling. A significant maximum appears which cannot be explained by any of the recently derived elastic models, such as junction constraint or other entanglement models. It is suggested in this paper that the maximum is a consequence of structural heterogeneities of fractal nature. If such fractal heterogeneities are assumed a strong maximum in the relative osmotic pressure can be reproduced. The physical reason is the different thermodynamic behavior of uncrosslinked linear chains and crosslinked self-similar (non-linear) polymers. The conclusion is supported by numerical (Monte Carlo) simulations.     

Discovery of an NAD+ analogue with enhanced specificity for PARP1

Among various protein posttranslational modifiers, poly-ADP-ribose polymerase 1 (PARP1) is a key player for regulating numerous cellular processes and events through enzymatic attachments of target proteins with ADP-ribose units donated by nicotinamide adenine dinucleotide (NAD⁺). Human PARP1 is involved in the pathogenesis and progression of many diseases. PARP1 inhibitors have received approvals for cancer treatment. Despite these successes, our understanding about PARP1 remains limited, partially due to the presence of various ADP-ribosylation reactions catalyzed by other PARPs and their overlapped cellular functions. Here we report a synthetic NAD⁺ featuring an adenosyl 3′-azido substitution. Acting as an ADP-ribose donor with high activity and specificity for human PARP1, this compound enables labelling and profiling of possible protein substrates of endogenous PARP1. It provides a unique and valuable tool for studying PARP1 in biology and pathology and may shed light on the development of PARP isoform-specific modulators.

An analogue of nicotinamide adenine dinucleotide (NAD⁺) featuring an azido group at 3′-OH of adenosine moiety is found to possess high specificity for human PARP1-catalyzed protein poly-ADP-ribosylation.     

Mixing-Limited Reactions in Porous Media

Transport in Porous Media - Acid mine drainage is generated when sulfide minerals are exposed to air and water through the porous subsurface, and it is significantly accelerated by the action of...