Single string based global optimizer for geometry optimization in strongly coupled finite clusters: An adaptive mutation-driven strategy.

We propose and implement a simple adaptive heuristic to optimize the geometries of clusters of point charges or ions with the ability to find the global minimum energy configurations. The approach uses random mutations of a single string encoding the geometry and accepts moves that decrease the energy. Mutation probability and mutation intensity are allowed to evolve adaptively on the basis of continuous evaluation of past explorations. The resulting algorithm has been called Completely Adaptive Random Mutation Hill Climbing method. We have implemented this method to search through the complex potential energy landscapes of parabolically confined 3D classical Coulomb clusters of hundreds or thousands of charges--usually found in high frequency discharge plasmas. The energy per particle (EN∕N) and its first and second differences, structural features, distribution of the oscillation frequencies of normal modes, etc., are analyzed as functions of confinement strength and the number of charges in the system. Certain magic numbers are identified. In order to test the feasibility of the algorithm in cluster geometry optimization on more complex energy landscapes, we have applied the algorithm for optimizing the geometries of MgO clusters, described by Coulomb-Born-Mayer potential and finding global minimum of some Lennard-Jones clusters. The convergence behavior of the algorithm compares favorably with those of other existing global optimizers.

Coulomb explosion in dicationic noble gas clusters: a genetic algorithm-based approach to critical size estimation for the suppression of Coulomb explosion and prediction of dissociation channels.

We present a genetic algorithm based investigation of structural fragmentation in dicationic noble gas clusters, Ar(n)(+2), Kr(n)(+2), and Xe(n)(+2), where n denotes the size of the cluster. Dications are predicted to be stable above a threshold size of the cluster when positive charges are assumed to remain localized on two noble gas atoms and the Lennard-Jones potential along with bare Coulomb and ion-induced dipole interactions are taken into account for describing the potential energy surface. Our cutoff values are close to those obtained experimentally [P. Scheier and T. D. Mark, J. Chem. Phys. 11, 3056 (1987)] and theoretically [J. G. Gay and B. J. Berne, Phys. Rev. Lett. 49, 194 (1982)]. When the charges are allowed to be equally distributed over four noble gas atoms in the cluster and the nonpolarization interaction terms are allowed to remain unchanged, our method successfully identifies the size threshold for stability as well as the nature of the channels of dissociation as function of cluster size. In Ar(n)(2+), for example, fissionlike fragmentation is predicted for n=55 while for n=43, the predicted outcome is nonfission fragmentation in complete agreement with earlier work [Golberg et al., J. Chem. Phys. 100, 8277 (1994)].

Spectral signatures of intramolecular charge transfer process in beta-enaminones: a combined experimental and theoretical analysis.

In this paper, we present spectroscopic signatures of intramolecular charge transfer (ICT) and effects of solvent on the ICT process in 3-(phenylamino)-2-cyclohexen-1-one (PACO), a member of the well-known molecular family, the beta-enaminones. The dual fluorescence in the steady state emission spectra of the molecule in polar solvents indicates the occurrence of ICT, which is further supported by time-resolved studies, using time correlated single photon counting technique with picosecond resolution. To understand the nature of the charge transfer, pH dependent studies of the probe in water were performed, where a quenching of fluorescence was observed even in the presence of very low concentrations of acids. Solvent induced fluorescence quenching was observed in ethanol and methanol. The ICT process was also investigated by quantum chemical calculations. To understand the role of solvents in the ICT process, we have theoretically studied the macroscopic and microscopic solvation of the probe in water. The absorption spectra of the molecule in the gas phase as well as in water were simulated using time dependent density functional theory with cc-pVTZ basis set and self-consistent reaction field theory that models macroscopic solvation. The possibility of microscopic solvation in water was probed theoretically and the formation of 1:3 molecular clusters by PACO with water molecules has been confirmed. Our findings could have a bearing on pH sensing applications of the probe.

A search for lowest energy structures of ZnS quantum dots: Genetic algorithm tight-binding study.

The lowest energy structures of ZnS quantum dots of different sizes have been determined by an unbiased search using genetic algorithm (GA) coupled with the density-functional tight-binding method. The GA search converges to a rather new ringlike configurations of ZnS quantum dots. We have studied the structural, electronic, and optical properties of these ringlike clusters and compared these properties with those of other reported structures of ZnS quantum dots, namely, hollow, zinc-blende, wurtzite, and rocksalt structures.

Effect of surfactant-perturbed nanocaging on the ground and excited state proton transfer reaction.

The effect of mixed cyclodextrin-surfactant systems on the ground and excited state proton transfer reactions of 4-methyl-2,6-diformylphenol (MFOH) in aqueous solution has been investigated by steady state and time-resolved fluorescence spectroscopy. It has been found that micellar media perturbs the solvation of MFOH and facilitates nanocaging. In the presence of micelle, MFOH preferentially resides in the interfacial region. Depending on the local pH due to compartmentalization of reaction media, normal or anionic form of MFOH dominates. Encapsulation of the probe within the cyclodextrin nanocavity enhances the shorter lifetime component of MFOH unexpectedly, which has been explained on the basis of reduced solvation and reduced dipolar effect due to confinement.

Activated T lymphocytes induce degranulation and cytokine production by human mast cells following cell-to-cell contact.

Activated mast cells reside in close apposition to T cells in some inflammatory processes. In this study, we analyzed whether this close physical proximity affects human mast cell degranulation and cytokine release. Thus HMC-1 human mast cells or primary bone marrow-derived human mast cells were cocultured with activated and with resting T cells. Mast cells cocultured with activated T cells released histamine and beta-hexosaminidase and produced tumor necrosis factor alpha (TNF-alpha), an effect that peaked at 20 h. Kinetics of histamine release paralleled the formation of heterotypic aggregates. Separation of the two cell populations with a porous membrane prevented mediator release and TNF-alpha production. Addition of the PI3-kinase inhibitor, wortmannin, inhibited the heterotypic adhesion-associated degranulation but not TNF-alpha production. These data thus indicate a novel pathway through which human mast cells are activated to both release granule-associated mediators and to produce cytokines in association with heterotypic adhesion to activated human T cells.

Structural analysis of DNA cleaved in vivo by bacteriophage T4 terminase.

Phage terminases are protein complexes that cleave concatemeric phage DNA and generate termini of the packaged DNA molecule. In phage T4, the DNA packaging proteins gp16 and gp17 are supposed to function as terminases. The recombinant T4 terminase proteins, upon expression in vivo from strong promoters, cleaved plasmid DNA in a sequence-independent manner. Resolution of the cleaved DNA by agarose-gel electrophoresis showed a smear throughout the lane including a fraction that was retained in the well [Bhattacharyya and Rao, Virology 196 (1993) 34-44]. The appearance of a smear in the high-M(r) region could not be explained solely on the basis of a simple random-cutting mechanism. Various hypotheses were tested to elucidate the structure of the high-M(r) DNA. The data show that the high-M(r) DNA did not arise either by attachment of protein(s) to DNA, or by covalent linkage of cleaved DNA molecules by a recombinational mechanism. It appears that the high-M(r) DNA arose as a result of non-covalent linkage of plasmid DNA through single strands. A working model for the action of T4 terminase is presented.

Ubiquitination of Lyn-kinase in rat basophilic leukemia RBL-2H3 cells.

Receptor-mediated signal transduction pathways of cells involved in allergy and inflammations are extremely significant. Lyn is a member of the Src family of non-receptor protein tyrosine kinases and is associated with a number of cell surface receptors, including the B-cell antigen receptor and immunoglobulin E receptor (FcepsilonRI). Lyn is necessary for FcepsilonRI-mediated mast cell activation. To investigate how the level of Lyn is maintained in mast cell activation, it was studied whether Lyn binds to ubiquitin and is ubiquitinated for proteasomal degradation in cells. In the yeast two hybrid system, Lyn specifically interacted with ubiquitin in vivo. Furthermore, Lyn bound to ubiquitin-conjugated Sepharose beads in vitro and was efficiently competed by soluble ubiquitin. Pulse-chase experiments indicated intracellular degradation of Lyn was associated with the generation of a high molecular weight complex in the presence of proteasome-specific inhibitor, lactacystin. This high molecular weight complex cross-reacted with anti-Lyn and anti-ubiquitin demonstrating the ubiquitination Lyn. Overexpression of Lyn and ubiquitin in COS 7.2 cells also resulted in the ubiquitination of Lyn in the presence of lactacystin, supporting the ubiquitination of Lyn by a proteasome specific pathway.

Interaction between methyl glyoxal and ascorbic acid: experimental and theoretical aspects.

The absorption spectral change of methyl glyoxal (MG) due to the interaction with ascorbic acid (AA or Vitamin C) has been investigated using steady-state spectroscopic technique. A plausible explanation for the spectral change has been discussed on the basis of hydrogen bonding interaction between the two interacting species. The equilibrium constant for the complex formation due to hydrogen bonding interaction between MG and AA has been obtained from absorption spectral changes. Ab inito calculations with DFT B3LYP/6/31G (d,p) basis sets have been used to find out the molecular structure of the hydrogen bonded complex. The O...H distance found in the O-H...O hydrogen bond turns out to be quite short (1.974 A) which is in conformity with the large value of the equilibrium constant determined experimentally.

Influence of fowl uropygial gland and its secretory lipid components on growth of skin surface bacteria of fowl.

Bacterial species, which occur on the breast skin surface of adult (1 year old) white leghorn fowl with intact uropygial gland, were identified as : Staphylococcus epidermidis, Sarcina lutea, Streptomyces sp. and a facultative diphtheroid belonging to the genus Corynebacterium; S. epidermidis being the most predominant one. Two species of bacteria, namely, Staphylococcus aureus and Proteus sp. were shown to colonize the skin surface after 60 days of captivity. Extirpation of uropygial gland caused severe depletion of population of S. epidermidis, Streptomyces sp. and diphtheroid. The effect was more conspicuous after 60 days compared to that after 30 days of the gland removal. On the skin surface of glandless fowls the population of S. aureus increased significantly and a new form identified as anthracoid bacillus became the most predominant species after 60 days. Addition of total lipids from the free-flowing fowl uropygial secretion, as 0.2% suspension, to trypticase soya broth cultures of individual bacteria of fowl skin surface encouraged strongly the growth of S. epidermidis, Streptomyces sp. and Proteus sp. but suppressed the population of the anthracoid. When identical amount of diester wax or wax alcohol of the secretion was supplemented to the culture, more or less similar result was obtained. Wax alcohol also had a mild inhibitory effect on Streptomyces sp. Wax acids, added to the culture (0.2%) suppressed population of all the bacterial forms except Proteus sp., while the hydrocarbon fraction, which also contained some amount of squalene, produce an opposite effect.

Influence of fowl uropygial gland and its secretory lipid components on the growth of skin surface fungi of fowl.

Fungal species, which were shown to colonize consistently on the skin surface of the breast region of adult (1 year old) white leghorn fowl, were identified as Aspergillus sydowii, A. tamarii, A. rugulosus and Absidia corymbifera. Of these, A. sydowii and A. tamarii were the dominant forms. Two species of fungi, namely, Aspergillus niger and Scopulariopsis brevicaulis were shown to be present in the cultures of the scrubbings from breast skin surface after 60 days of captivity of the fowls. Extirpation of the uropygial gland resulted in encouragement of the in vitro population growth of all species of fungi except that of A. rugulosus. The effect was found to be very conspicuous for A. sydowii and A. tamarii, particularly after 60 days of gland removal. Addition of total lipids and the wax diester component of free-flowing uropygial secretion as 0.2% suspension in Sabouraud's agar medium of individual fungal isolates caused marked suppression of the population growth of A. sydowii, A. tamarii, Absidia corymbifera and to some extent of S. brevicaulis. Other components of secretory lipids, such as wax alcohols (2,3-alkane-diols), wax acids, triglycerides and hydrocarbons (including squalene) when supplemented separately to culture medium of individual fungi at identical concentration, were also shown to cause inhibition of the growth of most of fungal species at different degrees.

Adrenocortical influence on histokinetics and lipid components of uropygial gland of immature chick.

Adrenocortical influence on uropygial gland of 10-day old male white leghorn chicken was assessed by suppressing glucocorticoid level with metyrapone and following corticosterone and deoxycorticosterone acetate (DOC) treatments (im), 100 micrograms each on alternate day for a period of 15 days. Metyrapone treatment resulted in significant atrophy of the uropygial gland with a severe regression of the glandular alveoli due to cytopycnosis, cellular disintegration and drastic cell loss. Concomitantly, there was a depletion of glandular lipid and its diester wax fraction. Corticosterone, administered simultaneously with metyrapone, counteracted severe adverse effects of the latter on the uropygial gland. In the normal chicken also corticosterone alone caused glandular hypertrophy with increased rate of cell renewal and cell growth within the alveoli and, to a lesser extent, augmented output of the glandular lipids. Simultaneous administration of corticosterone and testosterone propionate (TP), on the other hand, caused a moderate suppressive influence on this gland. DOC treatment alone or with metyrapone and TP failed to exert any noteworthy change in the uropygial gland excepting a moderate reduction of gland weight and a rise of glandular lipids observed after combined injections of DOC with TP and with metyrapone respectively.

Effect of glucose on the activity of feeding centres before and after parasagittal cuts between medial and lateral hypothalamus.

Intracarotid administration of isotonic glucose (0.5 ml of 5.4%) in the starving albino rats produced an increase in the multiunit activity (MUA) of ventromedial hypothalamus (satiety centre) and a decrease in the MUA of the lateral hypothalamic area (feeding centre). Intracarotid infusion of normal saline did not change the MUA of any of these centres. Parasagittal knife cuts placed in between the satiety and feeding centres did not affect the responsiveness of these centres to glucose administration as indicated by the recorded multiunit activity.

Composition of lipids from the glands of the external ear canal of the adult chicken.

Six classes of neutral lipids, i.e. triacylglycerol (TG), free fatty acids (FFA), monoester waxes (MW), free- and esterified sterols (FST and SE), and squalene (SQ) were identified by thin layer chromatography of the lipid materials extracted separately from the secretion as well as from the isolated whole glands present in the skin of the floor of the external ear canal of the domestic fowl. Secretory lipids contained considerable proportions of MW fractions (17.03%), TG (22.23%), and SQ (14.66%), while TG was the major component (41.10%) in the lipids from the isolated glands. Polar lipids, which comprised about 16-20% of total glandular lipids, were shown to be composed primarily of sphingomyelin.

Spectral response of 4-methyl-2,6-dicarbomethoxyphenol, an excited-state intramolecular proton-transfer probe in cyclohexane-ethanol mixtures: signatures of medium microheterogeneity.

In this paper, we explore the role of microscopic heterogeneity of the medium on the spectral response of an excited-state proton-transfer (ESIPT) probe, namely, 4-methyl-2,6-dicarbomethoxyphenol (CMOH) using steady-state and time-resolved emission spectroscopy. The mixtures of two solvents with widely different properties, viz., cyclohexane, a nonpolar, and ethanol, a polar protic solvent, were used as microheterogeneous media for spectroscopic studies. Dual fluorescence (normal and tautomer fluorescence) is observed in the nonpolar solvent (cyclohexane), while only a single peak is observed in the protic solvent, ethanol. The spectral responses of CMOH in the binary mixtures have been found to be dependent on the solvent composition and excitation wavelength. The emission spectral properties of CMOH in the cyclohexane-ethanol mixture have been seen to be superposition of spectral properties in their bulk counterparts, indicating the presence of microscopic heterogeneity in the system. A zwitterionic species of CMOH appears to have been detected in binary solvent mixtures with higher ethanol content only through low-energy excitations. The species is converted into an anionic species as excitation energy increases. Density functional theory calculations indicate that two intramolecularly hydrogen bonded rotamers of CMOH have a small energy difference. The formation of a hydrogen bonded 1:1 molecular cluster of CMOH with ethanol has been investigated in the ground state at the same level of theory. Our findings are expected to shed light on the mechanism of many acid-base reactions occurring in microscopically inhomogeneous media that often mimic many biologically relevant processes.

Blending Determinism with Evolutionary Computing: Applications to the Calculation of the Molecular Electronic Structure of Polythiophene.

A density matrix based soft-computing solution to the quantum mechanical problem of computing the molecular electronic structure of fairly long polythiophene (PT) chains is proposed. The soft-computing solution is based on a "random mutation hill climbing" scheme which is modified by blending it with a deterministic method based on a trial single-particle density matrix [P((0))(R)] for the guessed structural parameters (R), which is allowed to evolve under a unitary transformation generated by the Hamiltonian H(R). The Hamiltonian itself changes as the geometrical parameters (R) defining the polythiophene chain undergo mutation. The scale (λ) of the transformation is optimized by making the energy [E(λ)] stationary with respect to λ. The robustness and the performance levels of variants of the algorithm are analyzed and compared with those of other derivative free methods. The method is further tested successfully with optimization of the geometry of bipolaron-doped long PT chains.