Arithmetic coding as a non-linear dynamical system

In order to perform source coding (data compression), we treat messages emitted by independent and identically distributed sources as imprecise measurements (symbolic sequence) of a chaotic, ergodic, Lebesgue measure preserving, non-linear dynamical system known as Generalized Luröth Series (GLS). GLS achieves Shannon’s entropy bound and turns out to be a generalization of arithmetic coding, a popular source coding algorithm, used in international compression standards such as JPEG2000 and H.264. We further generalize GLS to piecewise non-linear maps (Skewed-nGLS). We motivate the use of Skewed-nGLS as a framework for joint source coding and encryption.     

Polar networks control oligomeric assembly in membranes

Polar interactions have a profound influence on membrane stability and structure. A membrane-solubilized GCN4 peptide, MS-1, is used to study the impact of polar networks. Amide functionalities from amino acid side chains have been shown to promote peptide oligomerization, but lacked specificity. Herein, the hydrogen bonding interactions of an Asn side chain are coupled with the hydroxyl of Ser or Thr to generate a polar network. Analytical ultracentrifugation and fluorescence resonance energy transfer studies indicate that a trimer assembly is established where each membrane-embedded hydrogen bond contributes 1 kcal mol-1.     

Arraying of intact liposomes into chemically functionalized microwells

Here, we describe a protocol to bind individual, intact phospholipid bilayer liposomes, which are on the order of 1 microm in diameter, in microwells etched in a regular array on a silicon oxide substrate. The diameter of the wells is on the order of the liposome diameter, so only one liposome is located in each well. The background of the silicon oxide surface is functionalized with a PEG oligomer using the contact printing of a PEG silane to present a surface that resists the adsorption of proteins, lipid material, and liposomes. The interiors of the wells are functionalized with an aminosilane to facilitate the conjugation of biotin, which is then bound to Neutravidin. The avidin-coated well interiors bind the liposomes whose surfaces contain biotinylated lipids. The specific binding of the liposomes to the surface using the biotin-avidin linkage, together with the resistant nature of the background and the physical confinement of the wells, allows the liposomes to remain intact and to not unravel, rupture, and fuse onto the surface. We demonstrate this intact arraying using confocal laser scanning microscopy of fluorophores specifically tagging the microwells, the lipid bilayer, and the aqueous interior of the liposome.     

Computational design of heterochiral peptides against a helical target

Polypeptides incorporating D-amino acids occasionally occur in nature and are an important class of pharmaceutical molecules. With the use of heterochiral Monte Carlo (HCMC), a method inspired by the de novo design of proteins, we develop peptide scaffolds for interacting with a molecular target, a left-handed alpha-helix. The HCMC approach concurrently seeks to optimize a peptide sequence, its internal conformation, and its docked conformation with a target surface. Several major classes of interactions are observed: (1) homochiral interactions between two alphaL helices, (2) heterochiral interactions between an alphaL and an alphaR helix, and (3) heterochiral interactions between the alphaL target and novel nonhelical structures. We explore the application of HCMC to simulating the preferential enantioselectivity of heterochiral complexes. Implications for biomimetic design in molecular recognition are discussed.     

DNA interaction,anticancer, cytotoxicity and genotoxicity studies with potential pyrazine-bipyrazole dinuclear µ-oxo bridged Au(III) complexes

Molecular Diversity - Pyrazine-bipyrazole-based µ-oxo bridged dinuclear Au(III) complexes were synthesized and characterized by various spectrometric (1H-NMR, 13C (APT) NMR, FT-IR, Mass...     

Exploring aromatic chemical space with NEAT: novel and electronically equivalent aromatic template

In this paper, we describe a lead transformation tool, NEAT (Novel and Electronically equivalent Aromatic Template), which can help identify novel aromatic rings that are estimated to have similar electrostatic potentials, dipoles, and hydrogen bonding capabilities to a query template; hence, they may offer similar bioactivity profiles. In this work, we built a comprehensive heteroaryl database, and precalculated high-level quantum mechanical (QM) properties, including electrostatic potential charges, hydrogen bonding ability, dipole moments, chemical reactivity, and othe properties. NEAT bioisosteric similarities are based on the electrostatic potential surface calculated by Brood, using the precalculated QM ESP charges and other QM properties. Compared with existing commercial lead transformation software, (1) NEAT is the only one that covers the comprehensive heteroaryl chemical space, and (2) NEAT offers a better characterization of novel aryl cores by using high-evel QM properties that are relevant to molecular interactions. NEAT provides unique value to medicinal chemists quickly exploring the largely uncharted aromatic chemical space, and one successful example of its application is discussed herein.     

Structures and energetics of electrosprayed uracil(n)Ca2+ clusters (n = 14-4) in the gas phase

Clusters of uracil (U) about a calcium dication, U(n)Ca(2+) (n = 14-4), have been studied in the gas phase by both experimental and theoretical methods. Temperature dependent blackbody infrared radiative dissociation (BIRD) experiments were performed on U(n)Ca(2+) clusters with n = 14-5 and the observed Arrhenius parameters are reported here. Master equation modeling of the BIRD kinetics data was carried out to determine threshold dissociation energies. Initial geometry calculations were performed using the B3LYP density functional and 3-21G(d) basis set. A sample of ten conformations per cluster was obtained through a simulated annealing study. These structures were optimized using B3LYP/6-31G(d) level of theory. Fragment-based hybrid many body interaction (HMBI) MP2/6-311++G(2df,2p)/Amoeba calculations were performed on representative conformations to determine theoretical binding energies. Results were examined in relation to cluster size (n). A significant increase in the energy required to remove uracil from U(6)Ca(2+) when compared to larger clusters supports previous reports that the calcium ion is coordinated by six uracil molecules in the formation of an inner shell. For clusters larger than n = 6, an odd-even alternation in threshold dissociation energies was observed, suggesting that the outer shell uracil molecules bind as dimers to the inner core. Proposed binding schemes are presented. Multiple structures of U(5)Ca(2+) are suggested as being present in the gas phase where the fifth uracil may be either part of the first or second solvation shell.     

Structural, dielectric relaxation and piezoelectric characterization of Sr substituted modified PMS-PZT ceramic

Pyrochlore phase free [Pb_0.94Sr_0.06] [(Mn_1/3Sb_2/3)_0.05(Zr_0.53Ti_0.47)_0.95] O₃ ceramics has been synthesized with pure Perovskite phase by semi-wet route using the columbite precursor method. The field dependences of the dielectric response and the conductivity have been measured in a frequency range from 50 Hz to 1 MHz and in a temperature range from 303 K to 773 K. An analysis of the real and imaginary parts of the dielectric permittivity with frequency has been performed, assuming a distribution of relaxation times. The scaling behavior of the dielectric loss spectra suggests that the distribution of the relaxation times is temperature independent. The SEM photographs of the sintered specimens present the homogenous structures and well-grown grains with a sharp grain boundary. The material exhibits tetragonal structure. When measured at frequency (100 Hz), the polarization shows a strong field dependence. Different piezoelectric figures of merit (k_p, d₃₃ and Q_m) of the material have also been measured obtaining their values as 0.53, 271 pC/N and 1115, respectively, which are even higher than those of pure PZT with morphotropic phase boundary (MPB) composition. Thus the present ceramics have the optimal overall performance and are promising candidates for the various high power piezoelectric applications.     

Synthesis of zinc oxide porous structures by anodization with water as an electrolyte

We report a simple, reliable and one-step method of synthesizing ZnO porous structures at room temperature by anodization of zinc (Zn) sheet with water as an electrolyte and graphite as a counter electrode. We observed that the de-ionized (DI) water used in the experiment is slightly acidic (pH=5.8), which is due to the dissolution of carbon dioxide from the atmosphere forming carbonic acid. Porous ZnO is characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy and photoluminescence (PL) studies. The current-transient measurement is carried out using a Gamry Instruments Reference 3000 and the thickness of the deposited films is measured using a Dektak surface profilometer. The PL, Raman and X-ray photoelectron spectroscopy are used to confirm the presence of ZnO phase. We have demonstrated that the hybrid structures of ZnO and poly (3,4-ethylenedioxythiophene):poly (styrene sulfonate) (PEDOT:PSS) exhibit good rectifying characteristics. The evaluated barrier height and the ideality factor are 0.45 eV and 3.6, respectively.     

The Hazard Rate and the Reversed Hazard Rate Orders, with Applications to Order Statistics

In this paper we first point out a simple observation that can be used successfully in order to translate results about the hazard rate order into results about the reversed hazard rate order. Using it, we derive some interesting new results which compare order statistics in the hazard and in the reversed hazard rate orders; as well as in the usual stochastic order. We also simplify proofs of some known results involving the reversed hazard rate order. Finally, a few further applications of the observation are given.