The computation of chromatic polynomials

AbstractThe planar graph representing the truncated icosahedron is a cubic graph with 60 vertices and 90 edges. The computation of the chromatic polynomial of this graph is computed by enhancing the algorithm based on the classical Delete-Contract theorem as well as finding approaches for substantially modifying a computation tree during computation. The result itself is an interesting example of the time/space tradeoffs that are important in large computations

Structure of the retinal chromophore in sensory rhodopsin I from resonance Raman spectroscopy

Bio-organic Synthesi

Characterizing organic particle impacts on inert metal surfaces: Foundations for capturing organic molecules during hypervelocity transits of Enceladus plumes

The presence and accessibility of a sub‐ice‐surface saline ocean at Enceladus, together with geothermal activity and a rocky core, make it a compelling location to conduct further, in‐depth, astrobiological investigations to probe for organic molecules indicative of extraterrestrial life. Cryovolcanic plumes in the south polar region of Enceladus enable the use of remote in situ sampling and analysis techniques. However, efficient plume sampling and the transportation of captured organic materials to an organic analyzer present unique challenges for an Enceladus mission. A systematic study, accelerating organic ice‐particle simulants into soft inert metal targets at velocities ranging 0.5–3.0 km s−1, was carried out using a light gas gun to explore the efficacy of a plume capture instrument. Capture efficiency varied for different metal targets as a function of impact velocity and particle size. Importantly, organic chemical compounds remained chemically intact in particles captured at speeds up to ~2 km s−1. Calibration plots relating the velocity, crater, and particle diameter were established to facilitate future ice‐particle impact experiments where the size of individual ice particles is unknown

Probing structural evolution along multidimensional reaction coordinates with femtosecond stimulated Raman spectroscopy

Mapping out multidimensional potential energy surfaces has been a goal of physical chemistry for decades in the quest to both predict and control chemical reactivity. Recently a new spectroscopic approach called Femtosecond Stimulated Raman Spectroscopy or FSRS was introduced that can structurally interrogate multiple dimensions of a reactive potential energy surface. FSRS is an ultrafast laser technique which provides complete time-resolved, background-free Raman spectra in a few laser shots. The FSRS technique provides simultaneous ultrafast time (~50 fs) and spectral (~8 cm⁻¹) resolution, thus enabling one to follow reactive structural evolutions as they occur. In this perspective we summarize how FSRS has been used to follow structural dynamics and provide mechanistic detail on three classical chemical reactions: a structural isomerization, an electron transfer reaction, and a proton transfer reaction.This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the Royal Society of Chemistry and can be found at: http://pubs.rsc.org/en/journals/journalissues/cp

Infrared spectroscopy of phytochrome and model pigments

Fourier-transform infrared difference spectra between the red-absorbing and far-red-absorbing forms of oat phytochrome have been measured in H2O and 2H2O. The difference spectra are compared with infrared spectra of model compounds, i.e. the (5Z,10Z,15Z)- and (5Z,10Z,15E)-isomers of 2,3,7,8,12,13,17,18-octaethyl-bilindion (Et8-bilindion), 2,3-dihydro-2,3,7,8,12,13,17,18-octaethyl-bilindion (H2Et8-bilindion), and protonated H2Et8-bilindion in various solvents. The spectra of the model compounds show that only for the protonated forms can clear differences between the two isomers be detected. Since considerable differences are present between the spectra of Et8-bilindion and H2Et8-bilindion, it is concluded that only the latter compound can serve as a model system of phytochrome. The 2H2O effect on the difference spectrum of phytochrome supports the view that the chromophore in red-absorbing phytochrome is protonated and suggests, in addition, that it is also protonated in far-red-absorbing phytochrome. The spectra show that protonated carboxyl groups are influenced. The small amplitudes in the difference spectra exclude major changes of protein secondary structure

Simultaneous quantification of 12 different nucleotides and nucleosides released from renal epithelium and in human urine samples using ion-pair reversed-phase HPLC

Nucleotides and nucleosides are not only involved in cellular metabolism but also act extracellularly via P1 and P2 receptors, to elicit a wide variety of physiological and pathophysiological responses through paracrine and autocrine signalling pathways. For the first time, we have used an ion-pair reversed-phase high-performance liquid chromatography ultraviolet (UV)-coupled method to rapidly and simultaneously quantify 12 different nucleotides and nucleosides (adenosine triphosphate, adenosine diphosphate, adenosine monophosphate, adenosine, uridine triphosphate, uridine diphosphate, uridine monophosphate, uridine, guanosine triphosphate, guanosine diphosphate, guanosine monophosphate, guanosine): (1) released from a mouse renal cell line (M1 cortical collecting duct) and (2) in human biological samples (i.e., urine). To facilitate analysis of urine samples, a solid-phase extraction step was incorporated (overall recovery rate ? 98 %). All samples were analyzed following injection (100 ?l) into a Synergi Polar-RP 80 Å (250 × 4.6 mm) reversed-phase column with a particle size of 10 ?m, protected with a guard column. A gradient elution profile was run with a mobile phase (phosphate buffer plus ion-pairing agent tetrabutylammonium hydrogen sulfate; pH 6) in 2-30 % acetonitrile (v/v) for 35 min (including equilibration time) at 1 ml min(-1) flow rate. Eluted compounds were detected by UV absorbance at 254 nm and quantified using standard curves for nucleotide and nucleoside mixtures of known concentration. Following validation (specificity, linearity, limits of detection and quantitation, system precision, accuracy, and intermediate precision parameters), this protocol was successfully and reproducibly used to quantify picomolar to nanomolar concentrations of nucleosides and nucleotides in isotonic and hypotonic cell buffers that transiently bathed M1 cells, and urine samples from normal subjects and overactive bladder patients

pH and rate of ‘dark’ events in toad retinal rods : test of a hypothesis on the molecular origin of photoreceptor noise

Thermal activation of the visual pigment constitutes a fundamental constraint on visual sensitivity. Its electrical correlate in the membrane current of dark-adapted rods are randomly occurring discrete ‘dark events’ indistinguishable from responses to single photons. It has been proposed that thermal activation occurs in a small subpopulation of rhodopsin molecules where the Schiff base linking the chromophore to the protein part is unprotonated. On this hypothesis, rates of thermal activation should increase strongly with rising pH. The hypothesis has been tested by measuring the effect of pH changes on the frequency of discrete dark events in red rods of the common toad Bufo bufo. Dark noise was recorded from isolated rods using the suction pipette technique. Changes in cytoplasmic pH upon manipulations of extracellular pH were quantified by measuring, using fast single-cell microspectrophotometry, the pH-dependent metarhodopsin I–metarhodopsin II equilibrium and subsequent metarhodopsin III formation. These measurements show that, in the conditions of the electrophysiological experiments, changing perfusion pH from 6.5 to 9.3 resulted in a cytoplasmic pH shift from 7.6 to 8.5 that was readily sensed by the rhodopsin. This shift, which implies an 8-fold decrease in cytoplasmic [H+], did not increase the rate of dark events. The results contradict the hypothesis that thermal pigment activation depends on prior deprotonation of the Schiff base