CHROMOPHORE ROTATION IN 124-kD ALTON A vena sativa PHYTOCHROME AS MEASURED BY LIGHT-INDUCED CHANGES IN LINEAR DICHROISM

Abstract— From light-induced changes in linear dichroism, we have calculated the rotation of the long-wavelength-absorbing transition moment that occurs during phototransformation of 124-kilodalton Avena sativa phytochrome. Phytochrome was purified to homogeneity and immobilized onto Sepharose beads covalently coated with antibodies against A. sativa phytochrome. Changes in linear dichroism were induced by plane-polarized red or far-red light and measured by the absorbance differences at 660 and 730 nm using a dual-wavelength spectrophotometer equipped with polarizing filters in the measuring beams. From such measurements, we calculate a rotation angle of 31^o (or 149^o) during photoconversion of Pr to Pfr and 30^o (or 150^o) during photoconversion of Pfr to Pr. These values are similar to the value of 32^o (or 148^o) reported earlier for the rotation of the transition moment of "large" A. sativa phytochrome (∽ 120 kilodalton) isolated under conditions that did not preclude post homogenization proteolysis of the 124 kilodalton molecule.     

Four levels of pattern recognition

Problems of pattern recognition in chemistry and other subjects can be divided conveniently into four different types depending on the level of scope of the problem.(1) Classification into one of a number of defined classes. As an example blood samples taken from persons known to be either controls or welders are considered. The problem is whether trace element concentrations in these samples contain information on whether or not a person is a welder.(2) Level 1 plus the possibility that an object is an outlier, i.e. does not belong to any of the defined classes. As an example, the üse of ¹³C-n.m.r. data to decide whether 2-substituted norbornanes have the exo or endo structure is discussed. (2A) Level 2, asymmetric. This situation occurs when one class does not have a systematic structure, but another class is homogeneous and can be described by a level 2 model. This occurs in the classification of materials or compounds as good or bad, active or inactive, and in binary classifications. As an example the use of trace element data to classify steel samples as having good or poor properties of strength is discussed.(3) Level 2 plus the ability to relate the variables measured to external properties of continuous character. As an example, the classification of a series of chemical compounds as β -receptor blockers, β -receptor stimulants, or neither, on the basis of their structural variables is discussed. In addition, relations between these structural variables and the measured biological activity are sought within each of the two classes.(4) Level 3 with the difference that several external property variables in the objects are measured. It may be desirable to use variables of the objects both for classification and for relations to several property variables: such examples are numerous in analytical chemistry.     

Fourier transform infrared reflection-absorption spectroscopy of amino acids adsorbed on metal surfaces

Fourier transform infrared reflection-absorption spectroscopy (FT-IRAS) has been used to study the orientation and coordination of glycine, L-phenylalanine and L-histidine on gold and copper surfaces. It was found that glycine and L-histidine were weakly adsorbed (physisorbed) in the zwitterionic form on gold. The surface chemical bonding of L-histidine and L-phenylalanine to copper were chemical rather than physical by nature. Conclusive evidence was obtained for coordination to copper through both the amino-nitrogen and carboxylate-oxygen atoms.     

Shear softening and structure in a simulated three-dimensional binary glass

Three-dimensional model binary glasses produced by quenching from a range of liquid temperatures were tested in shear over a range of strain rates using molecular-dynamics techniques. Tests were performed under constant volume and constant pressure constraints. The simulations revealed a systematic change in short-range order as a function of the thermal and strain history of the glass. While subtle signs of differences in short-range order were evident in the pair distribution function, three-body correlations were observed to be markedly more sensitive to the changes in structure. One particular structural parameter, the number of aligned three-atom clusters, was analyzed as a function of the degree of supercooling, the strain and the strain rate. The glasses quenched from the supercooled liquid regime were observed to contain an initially higher number of such clusters, and this number decreased under shear. Those quenched from high-temperature equilibrium liquids contained lower numbers of such clusters and these increased or remained constant under shear. The glasses quenched from the supercooled liquid regime showed higher strength, more marked shear softening, and an increased propensity toward shear localization. The evolution of this structural parameter depended both on its initial value and on the imposed shear rate. These results were observed to hold for simulations performed under both constant density and constant pressure boundary conditions.     

Damage spreading in a single-component irreversible reaction process: Dependence of the system's immunity on the Euclidean dimension

The spreading of a globally distributed damage, created in the stationary regime, is studied in a single-component irreversible reaction process, i.e., the BK model [Browne and Kleban,Phys. Rev. A 40, 1615 (1989)]. The BK model describes one variant of the A+AA₂ reaction process on a lattice in contact with a reservoir of A species. The BK model has a single parameter, namely the rate of arrival of A species to the lattice (Y). The model, exhibits an irreversible phase transition between a stationary reactive state with production of A₂ species and a poisoned state with the lattice fully covered by A species. The transition takes place at critical points (Y _C ) which solely depend on the Euclidean dimensiond. It is found that the system is immune ford=1 andd=2, in the sense that even 100% of initial damage is healed within a finite healing period (T _H ). Within the reactive regime,T _H diverges when approachingY _C according toT _H (Y _C –Y)^–, with 1.62 and 1.08 ford=1 andd=2, respectively. Ford=3 a frozen-chaotic transition is found close toY _s 0.4125, i.e., well inside the reactive regime 0YY _C 0.4985. Just atY _S the damageD(t) heals according toD(t) t ^–, with 0.71. For the frozen-chaotic transition atd=3 the order parameter critical exponent 0.997 is determined.     

A general Brownian dynamics simulation program for biopolymer dynamics and its implementation on a vector computer

A Brownian dynamics simulation program for the computation of transport properties of charged polarizable macromolecules is presented. The program contains routines for simulating polymer dynamics in a gel network as well as in a quiescent fluid or in a shear field. An electric field can also be included to simulate e.g., gel electrophoresis or electric dichroism. Vector algorithms have been used where possible to obtain maximum efficiency on a vector processor. The length of the vector registers and the effect of computer memory organization have also been considered. On an IBM 3090-150S VF, more than 1.5 · 10⁶ steps are executed in one cpu hour for a chain with 128 subunits diffusing in a rigid gel consisting of 8828 beads.     

Hydrogen-bonding contributions to the lattice energy of salts for second harmonic generation

The lattice energies of a series of organic dihydrogenphosphate salts capable of second harmonic generation (SHG) have been calculated. These calculations, coupled with empirical data, indicate that a minimum of 20–25% of the lattice energy arises from hydrogen-bond interactions. Hydrogen bonding is shown to be a strong enough force to have a profound effect on the overall packing and crystal geometry of such ionic materials, and is thus an important factor to consider for crystal engineering.     

Nonadiabatic alignment of asymmetric top molecules: rotational revivals

The rotational revival structure of asymmetric top molecules, following irradiation by an intense picosecond laser pulse, is explored theoretically and experimentally. Numerically we solve nonperturbatively for the rotational dynamics of a general asymmetric top subject to a linearly polarized intense pulse, and analyze the dependence of the dynamical alignment on the field and system parameters. Experimentally we use time-resolved photofragment imaging to measure the alignment of two molecules with different asymmetry, iodobenzene, and iodopentafluorobenzene. Our numerical results explain the experimental observations and generalize them to other molecules. The rotational revival structure of asymmetric tops differs qualitatively from the intensively studied linear top case. Potentially it provides valuable structural information about molecules.