Parallel Smoothed Aggregation Multilevel Schwarz Preconditioned Newton-Krylov Algorithms for Poisson-Boltzmann Problems

We study a multilevel Schwarz preconditioned Newton-Krylov algorithm to solve the Poisson-Boltzmann equation with applications in multi-particle colloidal simulation. The smoothed aggregation-type coarse mesh space is introduced in collaboration with the one-level Schwarz method as a composite preconditioner for accelerating the convergence of a Krylov subspace method for solving the Jacobian system at each Newton step. The important feature of the proposed solution algorithm is that the geometric mesh information needed for constructing the multilevel preconditioner is the same as the one-level Schwarz method on the fine mesh. Other components, such as the definition of the coarse mesh, all the mesh transfer operators, and the coarse mesh problem, are taken care of by the Trillinos/ML packages of the Sandia National Laboratories in the United States. After algorithmic parameter tuning, we show that the proposed smoothed aggregation multilevel Newton-Krylov-Schwarz (NKS) algorithm numerically outperforms than smoothed aggregation multigrid method and one-level version of the NKS algorithm with satisfactory parallel performances up to a few thousand cores. Besides, we investigate how the electrostatic forces between particles for the separation distance depend on the radius of spherical colloidal particles and valence ratios of cation and anion in a cubic system.     

Approximate analytical expressions for the electrical potential between two planar, cylindrical, and spherical surfaces

Approximate analytical expressions for the electrical potential of planar, cylindrical, and spherical surfaces are derived for the case in which the dispersion medium contains counterions only. On the basis of the results for single surfaces, those for two identical surfaces can be derived. The curvature effect of a surface on the electrical potential distribution can be neglected when the order of its radius exceeds approximately 100 times the thickness of the corresponding double layer. If this effect needs to be considered, it can be taken into account by multiplying a correction function by the electrical potential of a planar surface. The electrical potential at the center between two derived surfaces is readily applicable to the evaluation of the electrostatic force per unit area between two surfaces, or the osmotic pressure. For the same set of parameters, the magnitudes of the osmotic pressure for various types of surfaces rank as follows: planar surface > cylindrical surfaces > spherical surfaces.     

Enumerative meaning of mirror maps for toric Calabi–Yau manifolds

We prove that the inverse of a mirror map for a toric Calabi–Yau manifold of the form _KY$K_Y$, where Y$Y$ is a compact toric Fano manifold, can be expressed in terms of generating functions of genus 0 open Gromov–Witten invariants defined by Fukaya–Oh–Ohta–Ono (2010)  [15]. Such a relation between mirror maps and disk counting invariants was first conjectured by Gross and Siebert (2011)  [24, Conjecture 0.2 and Remark 5.1] as part of their program, and was later formulated in terms of Fukaya–Oh–Ohta–Ono’s invariants in the toric Calabi–Yau case in Chan et al. (2012)  [8, Conjecture 1.1].     

Efficient algorithms for the longest common subsequence problem with sequential substring constraints

In this paper, we generalize the inclusion constrained longest common subsequence (CLCS) problem to the hybrid CLCS problem which is the combination of the sequence inclusion CLCS and the string inclusion CLCS, called the sequential substring constrained longest common subsequence   (SSCLCS) problem. In the SSCLCS problem, we are given two strings A$A$ and B$B$ of lengths m$m$ and n$n$, respectively, formed by alphabet Σ$\Sigma$ and a constraint sequence C$C$ formed by ordered strings (C¹,C²,C³,…,C^l)$(C^1,C^2,C^3,\dots ,C^l)$ with total length r$r$. The problem is that of finding the longest common subsequence D$D$ of A$A$ and B$B$ containing C¹,C²,C³,…,C^l$C^1,C^2,C^3,\dots ,C^l$ as substrings and with the order of the C$C$’s retained. This problem has two variants, depending on whether the strings in C$C$ cannot overlap or may overlap. We propose algorithms with O(mnl+(m+n)(|Σ|+r))$O(mnl+(m+n)(\left|\Sigma \right|+r))$ and O(mnr+(m+n)|Σ|)$O(mnr+(m+n)\left|\Sigma \right|)$ time for the two variants. For the special case with one or two constraints, our algorithm runs in O(mn+(m+n)(|Σ|+r))$O(mn+(m+n)(\left|\Sigma \right|+r))$ or O(mnr+(m+n)|Σ|)$O(mnr+(m+n)\left|\Sigma \right|)$ time, respectively—an order faster than the algorithm proposed by Chen and Chao.     

The development of a portable line-shaping optical system for silicon surface treatment

This study proposes a beam shaper for converting a circle beam profile generated with a Gaussian intensity distribution by an 808 nm diode laser into a line beam profile for silicon surface treatment applications. To produce a hand-held and low-cost device with a large spot-size laser, this study uses a portable optical system consisting of a diode laser source, a collimator, a cylindrical lens, and a plano-convex lens to generate an approximately 40 × 3:5mm² line beam profile at a working distance of 200 mm. The silicon surface treated by the line-shaped laser beam has significantly reduced reflectance spectra. The proposed system is also suitable for the surface cleaning of materials.     

Note on Characterization of Projective Spaces

We prove a numerical characterization of ?ⁿ for varieties with at worst isolated local complete intersection quotient singularities. In dimension 3, we prove such a numerical characterization of ?³ for normal ?-Gorenstein projective varieties.     

Additive‐dependent iptycene incorporation in polyanilines: Insights into the pentiptycene clipping effect and the polymerization mechanism

Despite the long history of polyaniline chemistry, backbone‐substituted polyanilines are limited. Here, we report the synthesis of pentiptycene‐incorporated polyanilines through acidic aniline oxidative polymerization with three pentiptycene derivatives, TA, DA, and TP, as nucleate additives. The reactivity of TA > DA ? TP, as evidenced by structural and property analysis of the corresponding polyaniline products, demonstrates a radical coupling mechanism and the formation of Dewar π‐complex intermediates for the chain propagation. In addition, the iptycene substituent effect on enhancing the electrochemical stability and charge storage capability of polyaniline are discussed with a clip model, namely, the threading of neighboring polyaniline chains through the U‐ and V‐shaped cavities of pentiptycene restricts lateral motions of the polymer chains and promotes interchain conductivity. Density function theory (DFT) calculations suggest a larger clipping effect for the U versus V cavities. Both the conclusion of a terminal planar p‐phenylenediamine (ppda) group being the key component of an effective nucleate and the concept of interchain clipping for enhanced electrochemical performance should facilitate the design and synthesis of novel polyanilines for electronic applications.     

Quantum chemical investigation of the detection properties of alternariol and alternariol monomethyl ether

Structural Chemistry - Alternariol and alternariol monomethyl ether are mycotoxins occasionally found in food and beverages that have been contaminated by certain fungi of the Alternaria genus....     

Energy limits imposed by two-photon absorption for pulse amplification in high-power semiconductor optical amplifiers

We study the combined effects of dynamic gain saturation and two-photon absorption on the amplification of short pulses in semiconductor optical amplifiers and show that two-photon absorption can saturate the amplifier gain and limit the output pulse energies even for amplifiers with large gain saturation energies. We discuss the upper limits for the pulse energies obtainable from semiconductor optical amplifiers in the presence of two-photon absorption and show that for single transverse mode waveguide amplifiers these upper limits can range from values as small as a few picojoules to several hundred picojoules for pulse widths in the 0.5 ps to 20 ps range, respectively.     

Long range correlation and possible electron conduction through DNA sequences

Long range correlation analysis and charge conductivity investigation are applied to sequences in 16 chromosomes in the Saccharomyces cerevisiae genome. DNA sequence data are analyzed via Hurst’s analysis and Detrended Fluctuation Analysis (DFA) analysis. Super diffusive nature of mapping sequences are evident with the measured Hurst exponent H to be around the value of 0.60 for all sequences in the 16 chromosomes. The DFA result is consistent with the result from the Hurst analysis. Tight binding models are applied for the investigation of charge conduction through DNA sequences. The overall averaged transmission coefficients, 〈T_N〉_av, calculated from sixteen chromosomes are shown to be significantly different from values calculated from random as well as periodic sequences. Sequences from the S. cerevisiae genome promise better charge conduction ability than random sequences. Finally, delocalized electronic wave function patterns are also shown through calculations using the tight binging model. Slightly delocalized electronic wavefunctions are seen on sequences in sixteen chromosomes, as compared with those obtained from random sequences on the same eigenenergies.