Interacting solitary waves in a damped driven Lennard-Jones chain

It is shown analytically that pulse solitary waves in a chain with Lennard-Jones type nearest neighbor interaction are strongly localized and marginally stable in the high energy limit.\ud \ud In a damped and periodically driven chain we obtain numerically families of states whose behavior is similar to that of equally many oscillators. We observe a period doubling sequence in a one-solitary wave family and bifurcation to (quasi-) periodic motion in a family of two solitary waves. We conclude that the damped and driven chain admits asymptotically stable states living on a low-dimensional manifold in phase space. These results depend sensitively on the shape of the driving term

Period-doubling density waves in a chain

The authors consider a one-dimensional chain of N+2 identical particles with nearest-neighbour Lennard-Jones interaction and uniform friction. The chain is driven by a prescribed periodic motion of one end particle, with frequency v and 'strength' parameter alpha . The other end particle is held fixed. They demonstrate numerically that there is a region in the alpha -v plane where the chain has a stable state in which a density wave runs to and fro between the two ends of the chain, similarly to a ball bouncing between two walls. More importantly, they observe a period-doubling transition to chaos, for fixed v and increasing alpha , while the localised (solitary wave) character of the motion is preserve

Specificity and Kinetics of Haloalkane Dehalogenase

Haloalkane dehalogenase converts halogenated alkanes to their corresponding alcohols. The active site is buried inside the protein and lined with hydrophobic residues. The reaction proceeds via a covalent substrate-enzyme complex. This paper describes a steady-state and pre-steady-state kinetic analysis of the conversion of a number of substrates of the dehalogenase. The kinetic mechanism for the “natural” substrate 1,2-dichloroethane and for the brominated analog and nematocide 1,2-dibromoethane are given. In general, brominated substrates had a lower Km, but a similar kcat than the chlorinated analogs. The rate of C-Br bond cleavage was higher than the rate of C-Cl bond cleavage, which is in agreement with the leaving group abilities of these halogens. The lower Km for brominated compounds therefore originates both from the higher rate of C-Br bond cleavage and from a lower Ks for bromo-compounds. However, the rate-determining step in the conversion (kcat) of 1,2-dibromoethane and 1,2-dichloroethane was found to be release of the charged halide ion out of the active site cavity, explaining the different Km but similar kcat values for these compounds. The study provides a basis for the analysis of rate-determining steps in the hydrolysis of various environmentally important substrates.

Ultra-sharp soliton switching in a directional coupler

By a numerical investigation it is shown that a directional coupler, described by two linearly coupled non-linear Schro¨dinger equations, can be used to construct a soliton switch with an extremely narrow transition region

Influence of mutations of Val226 on the catalytic rate of haloalkane dehalogenase

Haloalkane dehalogenase converts haloalkanes to their corresponding alcohols. The 3D structure, reaction mechanism and kinetic mechanism have been studied. The steady state kcat with 1,2-dichloroethane and 1,2-dibromoethane is limited mainly by the rate of release of the halide ion from the buried active-site cavity. During catalysis, the halogen that is cleaved off (Clα) from 1,2-dichloroethane interacts with Trp125 and the Clβ interacts with Phe172. Both these residues have van der Waals contacts with Val226. To establish the effect of these interactions on catalysis, and in an attempt to change enzyme activity without directly mutating residues involved in catalysis, we mutated Val226 to Gly, Ala and Leu. The Val226Ala and Val226Leu mutants had a 2.5-fold higher catalytic rate for 1,2-dibromoethane than the wild-type enzyme. A pre-steady state kinetic analysis of the Val226Ala mutant enzyme showed that the increase in kcat could be attributed to an increase in the rate of a conformational change that precedes halide release, causing a faster overall rate of halide dissociation. The kcat for 1,2-dichloroethane conversion was not elevated, although the rate of chloride release was also faster than in the wild-type enzyme. This was caused by a 3-fold decrease in the rate of formation of the alkyl-enzyme intermediate for 1,2-dichloroethane. Val226 seems to contribute to leaving group (Clα or Brα) stabilization via Trp125, and can influence halide release and substrate binding via an interaction with Phe172. These studies indicate that wild-type haloalkane dehalogenase is optimized for 1,2-dichloroethane, although 1,2-dibromoethane is a better substrate.