Graph spectra as a systematic tool in computational biology

We present the spectrum of the (normalized) graph Laplacian as a systematic tool for the investigation of networks, and we describe basic properties of eigenvalues and eigenfunctions. Processes of graph formation like motif joining or duplication leave characteristic traces in the spectrum. This can suggest hypotheses about the evolution of a graph representing biological data.     

Altered Membrane Mechanics Provides a Receptor-Independent Pathway for Serotonin Action

Serotonin, an important signaling molecule in humans, has an unexpectedly high lipid membrane affinity. The significance of this finding has evoked considerable speculation. Here we show that membrane binding by serotonin can directly modulate membrane properties and cellular function, providing an activity pathway completely independent of serotonin receptors. Atomic force microscopy shows that serotonin makes artificial lipid bilayers softer, and induces nucleation of liquid disordered domains inside the raft-like liquid-ordered domains. Solid-state NMR spectroscopy corroborates this data at the atomic level, revealing a homogeneous decrease in the order parameter of the lipid chains in the presence of serotonin. In the RN46A immortalized serotonergic neuronal cell line, extracellular serotonin enhances transferrin receptor endocytosis, even in the presence of broad-spectrum serotonin receptor and transporter inhibitors. Similarly, it increases the membrane binding and internalization of oligomeric peptides. Our results uncover a mode of serotonin–membrane interaction that can potentiate key cellular processes in a receptor-independent fashion.     

Unique rate expression for glucose production in C(4) plants

A physicochemical interpretation of a recently formulated temperature-dependent, steady-state rate expression for the production of glucose equivalent in C(4) plants is given here. We show that the rate equation is applicable to a wide range of C(4) plants.     

Unique bonding pattern and resulting bond stretch isomerism in

The bond‐stretch isomers are characterized by a principal change in the bond‐length with the rest of the molecule being unaltered. The electronic structure regulates the bond stretch isomerism phenomenon in which has been investigated with density functional theory, ab initio CASSCF, highly efficient n‐electron valence state perturbation theory and multireference configuration interaction calculations. Two isomers are distinguished on different potential energy surfaces and the corresponding avoided crossing is also studied in details. The bonding pattern in two isomers are analysed through adaptive natural density partitioning analysis and quantum theory of atoms in molecules analysis. The bonds in both the isomers primarily involve the 2p orbitals, which overlap face‐to‐face in long‐bond isomer. Whereas, in‐plane π‐bonding occurs at the short‐bond isomer leading to unusual bent bond. © 2015 Wiley Periodicals, Inc.     

Magic sized ZnS quantum dots as a highly sensitive and selective fluorescence sensor probe for Ag+ ions

A green and simple chemical synthesis of magic sized water soluble blue-emitting ZnS quantum dots (QDs) has been accomplished by reacting anhydrous Zn acetate, sodium sulfide and thiolactic acid (TLA) at room temperature in aqueous solution. Refluxing of this mixture in open air yielded ZnS clusters of about 3.5 nm in diameter showing very strong and narrow photoluminescence properties with long stability. Refluxing did not cause any noticeable size increment of the clusters. As a result, the QDs obtained after different refluxing conditions showed similar absorption and photoluminescence (PL) features. Use of TLA as a capping agent effectively yielded such stable and magic sized QDs. The as-synthesized and 0.5 h refluxed ZnS QDs were used as a fluorescence sensor for Ag(+) ions. It has been observed that after addition of Ag(+) ions of concentration 0.5-1 μM the strong fluorescence of ZnS QDs was almost quenched. The quenched fluorescence can be recovered by adding ethylenediamine to form a complex with Ag(+) ions. The other metal ions (K(+), Ca(2+), Au(3+), Cu(2+), Fe(3+), Mn(2+), Mg(2+), Co(2+)) showed little or no effect on the fluorescence of ZnS QDs when tested individually or as a mixture. In the presence of all these ions, Ag(+) responded well and therefore ZnS QDs reported in this work can be used as a Ag(+) ion fluorescence sensor.     

N-[2-(4-Methoxy-phenyl)-ethyl]-2-(quinolin-8-yloxy)acetamide: a receptor for acid binding

Different hydrates of the receptor, N-[2-(4-methoxy-phenyl)-ethyl]-2-(quinolin-8-yloxy)acetamide (I), and its co-crystals with acetic acid and l(+)α-hydroxy-phenylacetic acid are synthesised and their structures are studied. The acids such as acetic acid, l(+)α-hydroxy-phenylacetic acid quench fluorescence of I. The receptor I shows a fluorescence quenching on interaction with perchloric acid in benzene, whereas in methanol the solution of I results in the generation of a new fluorescence emission at higher wavelengths. The crystal structure of the perchlorate salt is determined to explain the protonation behaviour of the receptor I and the perchlorate salt in methanol leads to fluorescence emission at a place different from that of the parent compound.     

Interaction between coherent structures and surface temperature and its effect on ground heat flux in an unstably stratified boundary layer

Surface layer plumes, thermals, downdrafts and roll vortices are the most prominent coherent structures in an unstably stratified boundary layer. They contribute most of the temperature and vertical velocity variance, and their time scales increase with height. The effects of these multi-scale structures (surface layer plumes scale with surface layer depth, thermals scale with boundary layer height and the resulting roll vortices scale with convective time scale) on the surface temperature and ground heat flux were studied using turbulence measurements throughout the atmospheric boundary layer and the surface temperature measurements from an infrared camera. Plumes and thermals imprint on the surface temperature as warm structures and downdrafts imprint as cold structures. The air temperature trace shows a ramp-like pattern, with small ramps overlaid on a large ramp very close to the surface; on the other hand, surface temperature gradually increases and decreases. Turbulent heat flux and ground heat flux show similar patterns, with the former lagging the latter. The maximum values of turbulent heat flux and ground heat flux are 4 and 1.2 times the respective mean values during the ejection event. Surface temperature fluctuations follow a similar power-law exponent relationship with stability as suggested by surface layer similarity theory.     

Ionic liquid catalysed reaction of thiols with α,β-unsaturated carbonyl compounds--remarkable influence of the C-2 hydrogen and the anion

Hydrogen bond induced reactivity and selectivity control in the 1-butyl-3-methylimidazolium based ionic liquid catalysed reaction of thiols with α,β-unsaturated carbonyl compounds is reported with remarkable influence of the anion and the C-2 hydrogen in catalytic activity and reversal of selectivity.     

NOR and NAND gates using two photon absorption in silicon wire waveguide

Ultrafast all-optical NOR gate based on two photon absorption (2PA) process in SOI waveguide is already established. We have designed NAND gate also based on this process with a novel waveguide coupler structure. Power attenuation due to 2PA process and the working of these gates is developed with FDTD simulation. Dominant 2PA process is incorporated in FDTD update equations and it is shown that the influence of high intensity pump pulses on a different frequency continuous probe beam can be utilized to form NOR as well as NAND gates.