Optimization for pattern classification using biased random search techniques

We demonstrate how optimization problems arise in the field of pattern classification, in particular in using piecewise-linear classification and classification based on an optimal linear separator. We motivate the need in this area for a general purpose optimization approach. We discuss ALOPEX, a biased random search approach, from the point of view of this need. While ALOPEX itself failed to fulfil our need, a newly-introduced generalization of it (iterated ALOPEX) was found to be appropriate for the optimization problems of our particular concern. We conclude the paper with a brief critical evaluation of this approach as compared to our original aims.     

Photoinduced axial ligation and deligation dynamics of nonplanar nickel dodecaarylporphyrins

The ground- and excited-state metal-ligand dynamics of nonplanar nickel(II) 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (NiDPP) and two fluorinated analogues (NiF(20)DPP and NiF(28)DPP) have been investigated using static and time-resolved absorption spectroscopy in toluene and in ligating media that differ in basicity, aromaticity, and steric encumbrance. Because of the electronic and steric consequences of nonplanarity, NiDPP does not bind axial ligands in the ground state, but metal coordination does occur after photoexcitation with multistep dynamics that depend on the properties of the ligand. Following the structural relaxations that occur in all nickel porphyrins within approximately 10 ps, ligand binding to photoexcited NiDPP is progressively longer in pyridine, piperidine, and 3,5-lutidine (25-100 ps) but does not occur at all in 2,6-lutidine in which the ligating nitrogen is sterically encumbered. The transient intermediate that is formed, which nominally could be either a five- or six-coordinate species, also has a ligand-dependent lifetime (200-550 ps). Decay of this intermediate occurs partially via ligand release to re-form the uncoordinated species, in competition with binding of the second axial ligand and/or conformational/electronic relaxations (of a six-coordinate intermediate) to give the ground state of the bis-ligated photoproduct. The finding that the photoproduct channel principally depends on ligand characteristics along with the time-evolving spectra suggests that the transient intermediate may involve a five-coordinate species. In contrast to NiDPP, the fluorinated analogues NiF(20)DPP and NiF(28)DPP do coordinate axial ligands in the ground state but eject them after photoexcitation. Collectively, these results demonstrate the sensitivity with which the electronic and structural characteristics of the macrocycle, substituents, and solvent (ligands) can govern the photophysical and photochemical properties of nonplanar porphyrins and open new avenues for exploring photoinduced ligand association and dissociation behavior.     

Probing the contribution of electronic coupling to the directionality of electron transfer in photosynthetic reaction centers

Subpicosecond transient absorption studies are reported for a set of Rhodobacter (R.) capsulatus bacterial photosynthetic reaction centers (RCs) designed to probe the origins of the unidirectionality of charge separation via one of two electron transport chains in the native pigment-protein complex. All of the RCs have been engineered to contain a heterodimeric primary electron donor (D) consisting of a bacteriochlorophyll (BChl) and a bacteriopheophytin (BPh). The BPh component of the M heterodimer (Mhd) or L heterodimer (Lhd) is introduced by substituting a Leu for His M200 or His L173, respectively. Previous work on primary charge separation in heterodimer mutants has not included the Lhd RC from R. capsulatus, which we report for the first time. The Lhd and Mhd RCs are used as controls against which we assess RCs that combine the heterodimer mutations with a second mutation (His substituted for Leu at M212) that results in replacement of the native L-side BPh acceptor with a BChl (beta). The transient absorption spectra reveal clear evidence for charge separation to the normally inactive M-side BPh acceptor (H(M)) in Lhd-beta RCs to form D+H(M)- with a yield of approximately 6%. This state also forms in Mhd-beta RCs but with about one-quarter the yield. In both RCs, deactivation to the ground state is the predominant pathway of D decay, as it is in the Mhd and Lhd single mutants. Analysis of the results indicates an upper limit ofV2L/V2m < or = 4 for the contribution of the electronic coupling elements to the relative rates of electron transfer to the L versus M sides of the wild-type RC. In comparison to the L/M rate ratio (kL/kM) approximately 30 for wild-type RCs, our findings indicate that electronic factors contribute approximately 35% at most to directionality with the other 65% deriving from energetic considerations, which includes differences in free energies, reorganization energies, and contributions of one- and two-step mechanisms on the two sides of the RC.     

Phosphorus-based SAHA analogues as histone deacetylase inhibitors

[structure: see text] Three analogues of suberoyl anilide hydroxamic acid (SAHA) with phosphorus metal-chelating functionalities were synthesized as inhibitors of histone deacetylases (HDACs). The compounds showed weak activity for HeLa nuclear extracts (IC(50) = 0.57-6.1 mM), HDAC8 (IC(50) = 0.28-0.41 mM), and histone-deacetylase-like protein (HDLP, IC(50) = 0.33-1.9 mM), suggesting that the transition state of HDAC is not analogous to zinc proteases. Antiproliferative activity against A2780 cancer cells (IC(50) = 0.11-0.12 mM), comparable to SAHA (0.15 mM), was observed.     

Swallowtail porphyrins: synthesis, characterization and incorporation into porphyrin dyads

The incorporation of symmetrically branched tridecyl ("swallowtail") substituents at the meso positions of porphyrins results in highly soluble building blocks. Synthetic routes have been investigated to obtain porphyrin building blocks bearing 1-4 swallowtail groups. Porphyrin dyads have been synthesized in which the zinc or free base (Fb) porphyrins are joined by a 4,4'-diphenylethyne linker and bear swallowtail (or n-pentyl) groups at the nonlinking meso positions. The swallowtail-substituted Zn(2)- and ZnFb-dyads are readily soluble in common organic solvents. Static absorption and fluorescence spectra and electrochemical data show that the presence of the swallowtail groups slightly raises the energy level of the filled a(2u)(pi) HOMO. EPR studies of the pi-cation radicals of the swallowtail porphyrins indicate that the torsional angle between the proton on the alkyl carbon and p-orbital on the meso carbon of the porphyrin is different from that of a porphyrin bearing linear pentyl groups. Regardless, the swallowtail substituents do not significantly affect the photophysical properties of the porphyrins or the electronic interactions between the porphyrins in the dyads. In particular, time-resolved spectroscopic studies indicate that facile excited-state energy transfer occurs in the ZnFb dyad, and EPR studies of the monocation radical of the Zn(2)-dyad show that interporphyrin ground-state hole transfer is rapid.     

Longitudinal dispersion in flows that are homogeneous in the streamwise direction

The longitudinal dispersion of a pulse of passive scalar contaminant within a flow that is unchanging in the downstream direction is established to be a function of the mean-velocity-history of molecules from a uniform distribution on the flow cross-section. The specific case of laminar flow between parallel plates is investigated in detail, wherein it is found that $$\frac{1}{2}\frac{{\overline {d\eta (t)^2 } }}{{dt}} = \frac{9}{{2\pi ^6 }}\frac{{\bar U^2 d^2 }}{k}\sum\limits_{n = 1}^\infty {\frac{1}{{n^6 }}} \left( {1 - \exp \left( {\frac{{ - (2n\pi )^2 tK}}{{d^2 }}} \right)} \right),$$ where η(t) is the displacement relative to an axis located byūt whenū is the discharge velocity,K is the molecular diffusivity andd is the plate separation. This flow is used to show that the molecule mean velocity-histories can be approximated by a function that does not directly depend on the release position of the molecule on the flow cross-section. The results of a numerical simulation of the dispersion in this flow are presented for comparison.     

Analysis of carbenoxolone by ultra‐high‐performance liquid chromatography tandem mass spectrometry in mouse brain and blood after systemic administration

Carbenoxolone is a derivative of glycyrrhetinic acid found in the root of Glycyrrhiza glabra, colloquially known as licorice. It has been used as a treatment for peptic and oral ulcers. In recent years, carbenoxolone has been utilized in basic research for its ability to block gap junctional communication. Better understanding the distribution of carbenoxolone after systemic administration can lead to a better understanding of its potential sites of action. Presented is an ultra high‐performance liquid chromatography tandem mass spectrometer (UHPLC–MS/MS) method for the identification and quantification of carbenoxolone in mouse blood and brain tissue. Twenty mice were injected intraperitoneally with 25 mg/kg carbenoxolone and brain tissue and blood were collected for analysis. Blood concentrations (mean ± SD) at 15, 30, 60 and 120 min were determined to be (n = 5) 5394 ± 778, 2636 ± 836, 1564 ± 541 and 846 ± 252 ng/mL, respectively. Brain concentrations (mean ± SD) at 15, 30, 60 and 120 mins were determined to be (n = 5) 171 ± 62, 102 ± 35, 55 ± 10 and 27 ± 9 ng/g, respectively. The analysis of these specimens at the four different time points resulted in blood and brain half‐lives in mice of ~43 and 41 min, respectively. The UHPLC–MS/MS method was determined to be sensitive and robust for quantification of carbenoxolone.     

Light-induced helix formation

This study shows that incorporation of [Rub2m-OH]2+ at the N-terminus of the Fs peptide enhances its stability by approximately 0.15 kcal/mol through the mechanism of dipole-dipole coupling at the excited state, suggesting that photoinduced charge generation at a well-controlled and specific location provides a convenient means to trigger helix-coil transition on nanosecond or even faster time scales.     

Quantum theory of a massless spinning particle

The classical and quantum mechanics of a free massless point-like fermion is presented. The action is invariant under local 1-dimensional reparametrizations and supersymmetry, as well as a large set of rigid symmetries, including conformal and chiral symmetries. An infinite set of rigid symmetries is derived starting from the chiral invariance, but only a finite subset does not vanish on shell. The BRST-transformations corresponding to thed=1 local symmetries are constructed and the quantization is performed. Finally, the BRST-cohomology is investigated and the conditions producing the physical states are derived.     

A suppression strategy for antibiotic discovery

High-throughput phenotype screening and target identification have been combined in an effort to isolate antimicrobial, small-molecule therapeutics. This approach, developed by Brown and colleagues and reported in this issue, is a major technological advance for antimicrobial drug discovery.