UPON THE OPTIMAL GRAPHICAL REPRESENTATION OF FLASH DATA FROM PHOTOCHEMICAL SYSTEMS OBEYING FIRST ORDER KINETICS

Abstract— It is recommended that plots of absorbance change vs. log time be considered as a way to represent many decades of flash spectroscopy data when several separate decays are present. The values of the rate constants k , for the decays are easily revealed by nearly linear portions of the plots centered near t _j= k ⁻¹_j, which are inflection points in the graphs. The amplitudes of the decays are easily seen because they are proportional to the slopes of the linear portions of the plots. Such plots introduce no spurious singularities and they are easy to construct using semi-log paper. Examples, including one from bacteriorhodopsin, are presented. A simple mathematical proof of these features is provided.     

Orientation of tie-lines in the phase diagram of DOPC/DPPC/cholesterol model biomembranes

We report the direction of tie-lines of coexisting phases in a ternary diagram of DOPC/DPPC/cholesterol lipid bilayers, which has been a system of interest in the discussion of biological rafts. For coexisting Ld and Lo phases, we find that the orientation angle α of the tie-lines increases as the cholesterol concentration increases and it also increases as temperature increases from T = 15 °C to T = 30 °C. Results at lower cholesterol concentrations support the existence of a different two-phase coexistence region of Ld and So phases and the existence of a three-phase region separating the two two-phase regions. Our method uses the X-ray lamellar D-spacings observed in oriented bilayers as a function of varying hydration. Although this method does not obtain the ends of the tie-lines, it gives precise values (±1°) of their angles α in the ternary phase diagram.     

The notion of motion: covariational reasoning and the limit concept

This paper investigates outcomes of building students’ intuitive understanding of a limit as a function's predicted value by examining introductory calculus students’ conceptions of limit both before and after instruction. Students’ responses suggest that while this approach is successful at reducing the common limit equals function value misconception of a limit, new misconceptions emerged in students’ responses. Analysis of students’ reasoning indicates a lack of covariational reasoning that coordinates changes in both x and y may be at the root of the emerging limit reached near x = c misconception. These results suggest that although dynamic interpretations of limit may be intuitive for many students, care must be taken to foster a dynamic conception that is both useful at the introductory calculus level and is in line with the formal notion of limit learned in advanced mathematics. In light of the findings, suggestions for adapting the pedagogical approach used in this study are provided.     

Proof of gridlock in a polymer model

It has been suggested that some lattice models of polymers, especially ones that incorporate more realistic excluded volume interactions extending to further neighbors, may be subject to gridlock. A model is defined to have the property of gridlock if it cannot melt at any temperature unless a density decrease is allowed. Classical theories of polymer melting are incompatible with the property of gridlock. This paper proves rigorously that a two-dimensional square-lattice model of polymer chains that have nearest-neighbor excluded volume interactions (called the X1S model) has the gridlock property. The proof uses elementary concepts from graph theory. Also, different interpretations of the X1S model are given in terms of real polymers. This leads to a discussion of a number of different classes of melting depending upon whether the intramolecular rotameric energies and the attractive intermolecular energies are antagonistic to or supportive of the melting transition.     

Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

A general strategy for creating "inactive-conformation" abl inhibitors

Kinase inhibitors that bind to the ATP cleft can be broadly classified into two groups: those that bind exclusively to the ATP site with the kinase assuming a conformation otherwise conducive to phosphotransfer (type I), and those that exploit a hydrophobic site immediately adjacent to the ATP pocket made accessible by a conformational rearrangement of the activation loop (type II). To date, all type II inhibitors were discovered by using structure-activity-guided optimization strategies. Here, we describe a general pharmacophore model of type II inhibition that enables a rational "hybrid-design" approach whereby a 3-trifluoromethylbenzamide functionality is appended to four distinct type I scaffolds in order to convert them into their corresponding type II counterparts. We demonstrate that the designed compounds function as type II inhibitors by using biochemical and cellular kinase assays and by cocrystallography with Abl.     

On the protonated state of amidinium-like diaromatic derivatives: X-ray and UV studies

We present the crystal structures of the chloride salts of the mono-guanidinium 1 (–CH₂CH₂– linker) and the bis-isouronium 2 (–O– linker) that have been resolved by us indicating that these compounds are diprotonated in the solid state as informed by the counterions positions. To determine the pK _a values of these compounds as well as those of their analogues 3 (mono-2-aminoimidazolinium with a –CH₂CH₂– linker) and 4 (mono-guanidinium with a –O– linker), the corresponding UV–Vis titrations were carried out. Thus, in aqueous solution compounds 1, 3 and 4 were present as mono-cationic species while derivative 2 was a bis-cation.     

Analytical performance characteristics of thin and thick film amperometric microcells

The analytical performance of amperometric microcells with different electrode geometries is compared for enzyme activity measurements. The microcells were fabricated with thin film photolithography or thick film screen-printing in four different designs. The cells made with the thin film process used flexible substrate with microelectrode array or a circular, disk-shaped working electrode. The screen-printed working electrodes had semicircle or disk shape on ceramic chips. Putrescine oxidase (PUO) activity measurement was used as a model. The determination of PUO activity is important in the clinical diagnosis of premature rupture of the amniotic membrane. An electropolymerized m-phenylenediamine size-exclusion layer was used to eliminate common interferences. The size exclusion layer revealed also to be advantageous in protecting the electrodes from fouling by putrescine (enzyme substrate). The electrode fouling of bare electrodes was insignificant for screen-printed electrodes, but very severe for electroplated platinum working electrodes. The microelectrode array electrodes demonstrated smaller RSD and higher normalized sensitivities for hydrogen peroxide and PUO activity. All the other electrodes were demonstrating comparable analytical performances.     

Infrared microspectroscopic study of the thermo-oxidative degradation of hydroxy-terminated polybutadiene/isophorone diisocyanate polyurethane rubber

Hydroxy-terminated polybutadiene/isophorone diisocyanate (HTPB/IPDI) polyurethane rubber which was aged in air at elevated temperatures has been studied by infrared microspectroscopy. Spectra were collected in transmission mode on microtomed samples. Analysis of sets of spectra taken across the sectioned material showed that most of the degradation occurred in the polybutadiene part of the polymer and that the urethane linkage was essentially unchanged. The trans isomer of the polybutadiene appears to be preferentially degraded compared with the vinyl isomer. The IR technique does not provide significant information about the cis isomer. The IR spectra indicated that likely degradation products included acids, esters, alcohols, and small amounts of other products containing a carbonyl functional group. Band area ratios, supported by a principal components analysis, were used to derive degradation profiles for the material. These profiles were steep-sided indicating an oxygen diffusion limited process.     

Onsager,ice, biomembranes,dimer models and the F-model

Personal recollections give a sampling of some of Onsager's later interests in ice and biomembranes. The author's involvement in these topics led to modeling a particular biomembrane phase transition using dimer models. Recent work is described for a particularly rich dimer model which is isomorphic to the F-model in three kinds of fields (direct, staggered, and quarter). New results for the full three-dimensional phase diagram show (1) how the anomalous OK multicritical point is destroyed by a direct field, and (2) how a new line of critical points must be added to the phase diagram in direct and staggered fields obtained previously by Baxter, due to diverging susceptibilities in the quarter field.