A fragment multipole approach to long-range Coulomb interactions in Hartree–Fock calculations on large systems

An efficient ab initio method for electronic structure calculations on extended molecular systems is presented, along with some illustrative applications. A division of the system into subunits allows the interactions to be separated into short- and long-range contributions, leading to a reduction of the computational effort from the original fourth-power size-dependence to one that is approximately quadratic. The short-range contributions to the Fock matrix are obtained in an essentially conventional fashion, while the long-range interactions are evaluated using a two-center multipole expansion formalism. The number of short-range contributions grows only linearly with the number of subunits, while the long-range contributions grow as N². Systematic studies of the computational efforts for systems of up to 99 water molecules organized as one-stranded chains, three-stranded chains, and three-dimensional clusters, as well as alkane chains with up to 69 carbon atoms, have been performed. In these model systems, the overall computational effort grows as N^K where 1 < K < 2.     

Optimum spray congealing conditions for masking the bitter taste of clarithromycin in wax matrix

The effects of operating conditions in the spray-congealing process on the release and the micromeritic properties of clarithromycin (CAM) wax matrix were evaluated. CAM wax matrix with 30% CAM, 60% glyceryl monostearate (GM) and 10% aminoalkyl methacrylate copolymer E (AMCE) was manufactured at various atomizer wheel speeds and liquid feed rates with a spray dryer. Release of CAM from the matrix exhibited a two-phase pattern, probably due to the dissolution of the fine portions broken on the surface of the matrix. The slope and the extrapolated y-intercept of the subsequent release pattern were defined as the release rate and the initial amount of release of CAM from the matrix, respectively. These release parameters, as well as the volume median diameter and the specific surface area of matrix, were selected as response variables, and multiple regression analysis was performed. For specific surface area and initial amount of release, a minimum point was observed on the contour curve when the atomizer wheel speed was constant and the liquid feed rate was varied. For the release rate, a maximum point was observed on the contour curve under the same conditions. These points were considered preferable for masking the bitter taste of CAM preparation. Microscopic observation revealed that a small spherical matrix with a smooth surface could be obtained with a high atomizer wheel speed and optimum liquid feed rate. This matrix also possessed excellent properties for taste masking, with small initial amount of release and subsequent high rate of release. In conclusion, the congealing speed of melt droplets was the dominant factor in masking the bitter taste of CAM.     

Charge-transfer biexciton annihilation in a donor–acceptor co-crystal yields high-energy long-lived charge carriers

Organic donor–acceptor (D–A) co-crystals have attracted much interest due to their important optical and electronic properties. Co-crystals having ⋯DADA⋯ π-stacked morphologies are especially interesting because photoexcitation produces a charge-transfer (CT) exciton, D˙⁺–A˙⁻, between adjacent D–A molecules. Although several studies have reported on the steady-state optical properties of this type of CT exciton, very few have measured the dynamics of its formation and decay in a single D–A co-crystal. We have co-crystallized a peri-xanthenoxanthene (PXX) donor with a N,N-bis(3-pentyl)-2,5,8,11-tetraphenylperylene-3,4:9,10-bis(dicarboximide) (Ph4PDI) acceptor to give an orthorhombic PXX–Ph4PDI ⋯DADA⋯ π-stacked co-crystal with a CT transition dipole moment that is perpendicular to the transition moments for S_n ← S₀ excitation of PXX and Ph4PDI. Using polarized, broadband, femtosecond pump–probe microscopy, we have determined that selective photoexcitation of Ph4PDI in the single co-crystal results in CT exciton formation within the 300 fs instrument response time. At early times (0.3 ≤ t ≤ 500 ps), the CT excitons decay with a t^−1/2 dependence, which is attributed to CT biexciton annihilation within the one-dimensional ⋯DADA⋯ π-stacks producing high-energy, long-lived (>8 ns) electron–hole pairs in the crystal. These energetic charge carriers may prove useful in applications ranging from photovoltaics and opto-electronics to photocatalysis.

Femtosecond transient absorption microscopy of donor–acceptor single co-crystals shows that photogenerated charge transfer excitons in one-dimensional donor–acceptor π stacks annihilate to produce high-energy, long-lived electrons and holes.     

Chemical-to-mechanical energy conversion in biomacromolecular machines: a plasmon and optimum control theory for directional work. 1. General considerations

To rationalize coherence and mechanochemical aspects of proteins acting as molecular machines, a plasmon concept for dealing with protein nonequilibrium dynamics is introduced and tested with respect to thermodynamic consistency. A stochastic optimum-control theory for protein conformational diffusion is developed and the corresponding stochastic Newton's second law derived for optimum-controlled conformational diffusion in proteins. The plasmon concept is shown to be consistent with this theory, in that optical plasmons can pump entropy out of (or into) the protein, decreasing (or increasing) its conformational diffusion and, at the same time, help decrease intra- and intermolecular friction, as well as (potentially) break the symmetry of the latter. Instead, acoustic plasmons may break the spatial symmetry of a protein's "potential of mean force", thus converting it into an effective Brownian ratchet potential by applying quasistatic deformational corrections to the former. These concepts seem to be of rather general applicability and might also be useful when studying, for example, intercalation of cationic dyes into DNA duplexes, positively charged oligopeptide transduction through cell membranes, or even DNA translocation through nanopores.     

On a singular perturbation problem involving a ``circular-well' potential

We study the asymptotic behavior, as a small parameter goes to 0, of the minimizers for a variational problem which involves a ``circular-well' potential, i.e., a potential vanishing on a closed smooth curve in . We thus generalize previous results obtained for the special case of the Ginzburg-Landau potential.

     

A phase transition for the metric distortion of percolation on the hypercube

Let H _n be the hypercube {0, 1} ⁿ , and denote by H _n,p Bernoulli bond percolation on H _n , with parameter p = n ^−α . It is shown that at α = 1/2 there is a phase transition for the metric distortion between H _n and H _n,p . For α < 1/2, the giant component of H _n,p is likely to be quasi-isometric to H _n with constant distortion (depending only on α). For 1/2 < α < 1 the minimal distortion tends to infinity as a power of n. We argue that the phase 1/2 < α < 1 is an analogue of the non-uniqueness phase appearing in percolation on non-amenable graphs.     

Integrating proteomics with electrochemistry for identifying kinase biomarkers

We present an integrated approach for highly sensitive identification and validation of substrate-specific kinases as cancer biomarkers. Our approach combines phosphoproteomics for high throughput cancer-related biomarker discovery from patient tissues and an impedimetric kinase activity biosensor for sensitive validation. Using non-small-cell lung cancer (NSCLC) as a proof-of-concept study, label-free quantitative phosphoproteomic analysis of a pair of cancerous and its adjacent normal tissues revealed 198 phosphoproteins that are over-phosphorylated in NSCLC. Among the differentially regulated phosphorylation sites, the most significant alteration was in residue S165 in the Hepatoma Derived Growth Factor (HDGF) protein. Hence, HDGF was selected as a model system for the electrochemical studies. Further motif-based analysis of this altered phosphorylation site revealed that extracellular-signal-regulated kinase 1/2 (ERK1/2) are most likely to be the corresponding kinases. For validation of the kinase–substrate pair, densely packed peptide monolayers corresponding to the HDGF phosphorylation site were coupled to a gold electrode. Phosphorylation of the monolayer by ERK2 and dephosphorylation by alkaline phosphatase (AP) were detected by electrochemical impedance spectroscopy (EIS) and surface roughness analysis. Compared to other methods for quantification of kinase concentration, this label-free electrochemical assay offers the advantages of ultra-sensitivity as well as higher specificity for the detection of cancer-related kinase–substrate pair. With implementation of multiple kinase–substrate biomarker pairs, we expect this integrated approach to become a high throughput platform for discovery and validation of phosphorylation-mediated biomarkers.     

Spectral and instantaneous flow field characteristics of the laminar to turbulent transition in a cone and plate apparatus

Fluid-surface interaction, is very much influenced by the flow distribution and the flow spectra. For biological surfaces, cell functions such as mytosis and cell turnover, can be triggered by the instantaneous flow fluctuations which induce augmented shear stress levels inside the wall surface boundary layer. The objective of this work is to study the flow field along a cellular surface and to understand the interaction process. For that purpose, a cone and plate apparatus was built in which the transitional and turbulent instantaneous flow field characteristics, especially near the plate surface, were investigated using spatial hot wire anemometry, concentrating on time domain and spectral analysis. The frequency spectrum of velocity fluctuations near the plate is influenced by the plate roughness. We found that there is a linear relation between wall roughness and the preferred frequencies of the spectra. In addition a universal law exists for mean velocities, similar to the logarithmic law of the wall, when normalized by R˜ ^1/2, the apparatus Reynolds number. Received: 31 March 1998/Accepted: 11 January 1999     

Upper bounds on the height difference of the Gaussian random field and the range of random graph homomorphisms into ℤ

Bounds on the range of random graph homomorphism into ℤ, and the maximal height difference of the Gaussian random field, are presented. © 2000 John Wiley & Sons, Inc. Random Struct. Alg., 17: 20–25, 2000