Global optimization for molecular conformation problems

A primal-relaxed dual global optimization algorithm is presented along with an extensive review for finding the global minimum energy configurations of microclusters composed by particles interacting with any type of two-body central forces. First, the original nonconvex expression for the total potential energy is transformed to the difference of two convex functions (DC transformation) via an eigenvalue analysis performed for each pair potential that constitutes the total potential energy function. Then, a decomposition strategy based on the GOP algorithm [1–4] is designed to provide tight upper and lower bounds on the global minimum through the solutions of a sequence of relaxed dual subproblems. A number of theoretical results are included which expedite the computational effort by exploiting the special mathematical structure of the problem. The proposed approach attains-convergence to the global minimum in a finite number of iterations. Based on this procedure global optimum solutions are generated for small Lennard-Jones and Morse (a=3) microclustersn7. For larger clusters (8N24 for Lennard-Jones and 8N30 for Morse), tight lower and upper bounds on the global solution are provided which serve as excellent initial points for local optimization approaches.     

Loss compensated negative index material at optical wavelengths

We present a computational approach, allowing for a self-consistent treatment of three-dimensional (3D) fishnet metamaterial operating at 710 nm wavelength coupled to a gain material incorporated into the nanostructure. We show numerically that loss-free negative index material is achievable by incorporating gain material inside the fishnet structure. The effective gain coefficient of the combined fishnet-gain system is much larger than its bulk counterpart and the figure-of-merit (FOM = | Re(n)/Im(n) |) increases dramatically with gain. Transmission, reflection, and absorption data, as well as the retrieved effective parameters, are presented for the fishnet structure with and without gain.     

Tissue-specific and neural activity-regulated expression of human BDNF gene in BAC transgenic mice

Background  

Brain-derived neurotrophic factor (BDNF) is a small secreted protein that has important roles in the developing and adult nervous system. Altered expression or changes in the regulation of the BDNF gene have been implicated in a variety of human nervous system disorders. Although regulation of the rodent BDNF gene has been extensively investigated, in vivo studies regarding the human BDNF gene are largely limited to postmortem analysis. Bacterial artificial chromosome (BAC) transgenic mice harboring the human BDNF gene and its regulatory flanking sequences constitute a useful tool for studying human BDNF gene regulation and for identification of therapeutic compounds modulating BDNF expression.     

Spontaneous emission in the near field of two-dimensional photonic crystals

We show theoretically that photonic crystal membranes cause large variations in the spontaneous emission rate of dipole emitters, not only inside but also in the near field above the membranes. Our three-dimensional finite-difference time-domain calculations reveal an inhibition of more than five times and an enhancement of more than ten times for the spontaneous emission rate of emitters with select dipole orientations and frequencies. Furthermore, we demonstrate theoretically the potential of a nanoscopic emitter attached to the end of a glass fiber tip as a local probe for mapping the large spatial variations of the photonic crystal local radiative density of states. This arrangement is promising for on-command modification of the coupling between an emitter and the photonic crystal in quantum optical experiments.     

Experimental determination of human erythrocyte membrane permeability coefficients for a series of amides

Erythrocyte membrane permeability coefficients have been determined for a series of amides by a method based on the physical and mathematical modelling of hypotonic haemolysis process. The results show that penetration of the substances occurs by two alternative ways through aqueous pores formed by proteins and by the direct dissolving of the molecules in membrane lipids. This conclusion can be confirmed by the correlation analysis between permeability coefficients of native erythrocytes and those pre-incubated with the monosodium salt of p-chloromercuribenzenesulfonic acid (pCMBS), and the partition coefficients of the substances in hydrophilic-hydrophobic phases. Penetration of substances through hydrophilic channels is limited by the sterical factor and diameter in particular. Permeability coefficients for erythrocytes pre-incubated with pCMBS increase in an accordance with the rise of the partition coefficients with correlation coefficient of 0.94, thereby indicating a lipid route of permeation of molecules through erythrocyte membranes.     

Radiocaesium pollution of fly agaric Amanita muscaria in fruiting bodies decreases with developmental stage

Amanita muscaria collected from a forested area in northern Poland in 2015 were analysed for activity concentrations of ¹³⁷Cs and ⁴⁰K. Total K concentration values were calculated from ⁴⁰K data. Mushrooms were grouped in six fruiting bodies size classes regarding to their developmental stage. The ¹³⁷Cs activity concentrations declined in A. muscaria as the fruiting bodies maturated. The contents of ⁴⁰K/K activity remained constant in caps at different developmental stage, while for stipes an increase was around twofold (⁴⁰K from 925?±?55 Bq kg^?1 dry biomass in the baby individuals and 1600?±?63–1700?±?53 Bq kg^?1 dry biomass in two oldest classes). A. muscaria is a weak accumulator of ¹³⁷Cs, while a steep drop in activity concentrations of this nuclide in the fruiting bodies as they maturate has not been reported earlier for mushrooms. Clearly, a fate of ¹³⁷Cs in A. muscaria is highly different from that of ⁴⁰K/K that is an essential element to fungi. In parallel, an observed increase in the content of ⁴⁰K/K in stipes of fruiting bodies with developmental state can be related to its ‘hardening’ and more fibrous nature with age and basic function to support the cap, but this has not been studied.     

Diffusional coagulation of superparamagnetic particles in the presence of an external magnetic field

In this paper, we investigate the diffusional coagulation of colloidal superparamagnetic (SP) latex particles that are under the influence of an external magnetic field. The cluster size distributions (CSDs) that evolve with time were determined using an optical set-up that permits the direct visualization of particle clusters. Following the dynamic scaling analysis of van Dongen and Ernst (Phys. Rev. Lett. 54 (1985) 1396), we find that the CSDs all collapse onto a master curve when properly scaled. The bell-shape of this master curve indicates that large clusters preferentially scavenge small clusters in our system. From the time evolution of the average cluster size we infer that the reactivity between large clusters diminishes with increasing cluster size. These results are consistent with a simple mathematical formulation of the coagulation rate constant, or kernel, for the Brownian coagulation of magnetic particles. Moreover, our results support a growing body of evidence that the dynamic scaling theory developed by van Dongen and Ernst is a useful framework with which to study the microscale processes governing particle coagulation.     

Generation of single-crystalline domain in nano-scale silicon pillars by near-field short pulsed laser

We observe laser-induced grain morphology change in silicon nanopillars under a transmission electron microscopy (TEM) environment. We couple the TEM with a near-field scanning optical microscopy pulsed laser processing system. This novel combination enables immediate scrutiny on the grain morphologies that the pulsed laser irradiation produces. We find unusual transformation of the tip of the amorphous or polycrystalline silicon pillar into a single crystalline domain via melt-mediated crystallization. On the basis of the three-dimensional finite difference simulation result and the dark field TEM data, we propose that the creation of the distinct single crystalline tip originates from the dominant grain growth initiated at the apex of the non-planar liquid–solid interface. Our microscopic observation provides a fundamental basis for laser-induced conversion of amorphous nanostructures into coarse-grained crystals.     

Fluorescence in alkali-metal salts of some acyclic,resonance-stabilized carbanions

While fluorescence can be clearly observed in resonance-stabilized acyclic anions, its occurrence is insufficient for unambiguous assignment of either ion-pairing type or anion geometry. As in cyclic, aromatic anions, the requirement for contact ion-pairing is less severe in the excited state than in the ground state. The fluorescence lifetimes of acyclic anions are affected more by the associated cation than by the type of ion-pairing.