A statistical model for unwarping of 1-D electrophoresis gels

A statistical model is proposed which relates density profiles in 1-D electrophoresis gels, such as those produced by pulsed-field gel electrophoresis (PFGE), to databases of profiles of known genotypes. The warp in each gel lane is described by a trend that is linear in its parameters plus a first-order autoregressive process, and density differences are modelled by a mixture of two normal distributions. Maximum likelihood estimates are computed efficiently by a recursive algorithm that alternates between dynamic time warping to align individual lanes and generalised-least-squares regression to ensure that the warp is smooth between lanes. The method, illustrated using PFGE of Escherichia coli O157 strains, automatically unwarps and classifies gel lanes, and facilitates manual identification of new genotypes.     

Properties of a mixed-valence (Fe(II))2(Fe(III))2 square cell for utilization in the quantum cellular automata paradigm for molecular electronics

The di-mixed-valence complex [{(eta(5)-C5H5)Fe(eta(5)-C5H4)}4(eta(4)-C4)Co(eta(5)-C5H5)]2+, 1(2+), has been evaluated as a molecular four-dot cell for the quantum cellular automata paradigm for electronic devices. The cations 1(1+) and 1(2+) are prepared in good yield by selective chemical oxidation of 1(0) and are isolated as pure crystalline materials. The solid-state structures of 1(0) and 1(1+) and the midrange- and near-IR spectra of 1(0), 1(1+), 1(2+), and 1(3+) have been determined. Further, the variable-temperature EPR spectra of 1(1+) and 1(2+), magnetic susceptibility of 1(1+) and 1(2+), M?ssbauer spectra of 1(0), 1(1+), and 1(2+), NMR spectra of 1(0), and paramagnetic NMR spectra of 1(1+) and 1(2+) have been measured. The X-ray structure determination reveals four ferrocene "dots" arranged in a square by C-C bonds to the corners of a cyclobutadiene linker. The four ferrocene units project from alternating sides of the cyclobutadiene ring and are twisted to minimize steric interactions both with the Co(eta(5)-C5H5) fragment and with each other. In the solid state 1(2+) is a valence-trapped Robin and Day class II compound on the 10(-12) s infrared time scale, the fastest technique used herein, and unambiguous evidence for two Fe(II) and two Fe(III) sites is observed in both the infrared and M?ssbauer spectra. Both EPR and magnetic susceptibility measurements show no measurable spin-spin interaction in the solid state. In solution, the NMR spectra show that free rotation around the C-C bonds connecting the ferrocene units to the cyclobutadiene ring becomes increasingly hindered with decreasing temperature, leading to spectra at the lowest temperature that are consistent with the solid-state structure. Localization of the charges in the cations, which is observed in the paramagnetic NMR spectra as a function of temperature, correlates with the fluxional behavior. Hence, the alignment between the pi systems of the central linker and the ferrocene moieties most likely controls the rate of electron exchange between the dots.     

On the Energetics of Ions in Carbon and Gold Nanotubes

We investigate the insertion of halide and alkali atoms into narrow single‐walled carbon nanotubes with diameters <9 Å by density functional theory; both chiral and non‐chiral tubes are considered. The atoms are stored in the form of ions; the concomitant charge transfer affects the band structure and makes originally semiconducting tubes conducting. The electrostatic interaction between a charge and the walls of the tube is explicitly calculated. The insertion energies and the positions of the ions are determined by a competition between electrostatic energy and Pauli repulsion. For comparison, we consider ions in gold nanotubes. Alkali ions follow the same principles in gold as in carbon tubes, but chloride is specifically adsorbed inside gold tubes.     

Action of Lawesson's reagent on substituted 2‐amino‐1,4‐naphthoquinones: Novel synthesis of benzodiphenoquinone‐bis‐1,3,2‐thiazaphospholine‐2‐sulfide derivatives

1,3,2,4‐Dithiadiphosphetane‐2,4‐disulfide 1 reacts with substituted 2‐amino‐1,4‐naphthoquinons 2a–d to give 4,5,4′,5′‐benzodiphenoquinone‐bis‐1,3,2‐thiazaphospholine‐2‐sulfide derivatives of type 3. Compatible analytical and spectroscopic results were obtained for all the new compounds. A mechanism is proposed to explain the formation of compounds 3. © 1999 John Wiley & Sons, Inc. Heteroatom Chem 10: 488–491, 1999     

Dielectric and thermal characterization of low density ethylene/10‐undecen‐1‐ol copolymers prepared with nickel catalysts

Ethylene and 10‐undecen‐1‐ol copolymers, prepared using a nickel complex as catalyst, were studied using differential scanning calorimetry (DSC), X‐ray diffraction, and dielectric relaxation spectroscopy. The behavior exhibited by copolymers containing incorporated 10‐undecen‐1‐ol amounts within 0.5 and 4.6 mol % was compared with neat polyethylene. DSC revealed that a new crystalline region with lower thickness lamellae emerges in copolymers due to the side‐chains crystallization. Nevertheless, the global crystallization degree decreases due to the loss of crystallinity that occurs in a greater extent in PE‐like regions. Dielectric relaxation spectroscopy detected two processes, a low activation energy process below ?20 °C related with localized mobility increasing in intensity and deviating to higher temperatures with the increase in 10‐undecen‐1‐ol amount, and a high activation energy process ascribed to the glass transition, located at higher temperatures for the different copolymers relatively to neat polyethylene. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2802–2812, 2007     

Synthesis,characterization and thermal behaviour of solid-state compounds of yttrium and lanthanide benzoates

Solid-state Ln(Bz)₃·H₂O compounds where Ln stands for trivalent yttrium or lanthanides and Bz is benzoate have been synthesized. Simultaneous thermogravimetry-differential thermal analysis (TG-DTA), X-ray powder diffractometry, infrared spectroscopy and chemical analysis were used to characterize and to study the thermal behaviour of these compounds. The results led to information about the composition, dehydration, thermal stability and thermal decomposition of the isolated compounds.     

Port space allocation with a time dimension

In the Port of Singapore, as in many other ports, space has to be allocated in yards for inbound and transit cargo. Requests for container space occur at different times during the planning period, and are made for different quantities and sizes of containers. In this paper, we study space allocation under these conditions. We reduce the problem to a two-dimensional packing problem with a time dimension. Since the problem is NP-hard, we develop heuristic algorithms, using tabu search, simulated annealing, a genetic algorithm and ‘squeaky wheel’ optimization, as solution approaches. Extensive computational experiments compare the algorithms, which are shown to be effective for the problem.     

A new Monte Carlo code for absorption simulation of laser-skin tissue interaction

In laser clinical applications, the process of photon absorption and thermal energy diffusion in the target tissue and its surrounding tissue during laser irradiation are crucial. Such information allows the selection of proper operating parameters such as laser power, and exposure time for optimal therapeutic. The Monte Carlo method is a useful tool for studying laser-tissue interaction and simulation of energy absorption in tissue during laser irradiation. We use the principles of this technique and write a new code with MATLAB 6.5, and then validate it against Monte Carlo multi layer (MCML) code. The new code is proved to be with good accuracy. It can be used to calculate the total power bsorbed in the region of interest. This can be combined for heat modelling with other computerized programs.