Adjacent Boxes Research Articles

Molecular interactions in the control region of the carAB operon encoding Escherichia coli carbamoylphosphate synthetase

The control region of the carAB operon, encoding carbamoylphosphate synthetase, comprises two tandem promoters (P1, upstream and P2, downstream) located 67 base-pairs apart and repressed respectively by pyrimidines and arginine. RNA polymerase and pure arginine repressor bind to the P2 region in mutually exclusive ways. Repressor protects the two adjacent palindromic ARG boxes overlapping P2 against DNase I. Binding of RNA polymerase to P1 is abnormal; the region protected against DNase I is shifted upstream by about 20 nucleotides with respect to the position expected from the transcription startpoint. This pattern is not due to interference with polymerase binding at P2, since it is observed also in the presence of repressor and on an isolated P1 region. Binding of RNA polymerase is relatively weak and heparin-sensitive suggesting that, in vivo, an ancillary factor is required to promote the formation of an open complex. S 1 nuclease mapping experiments show that the simultaneous presence of pyrimidines and arginine represses the downstream arginine-specific promoter (P2) more efficiently than arginine alone. This effect is not due to a direct regulatory interaction between pyrimidines and P2, since it is not observed when P1 is inactivated by insertion mutations or partial deletion. It has been shown that transcription initiated at P1 can proceed even when arginine represses P2. We therefore suggest that P2 operator-arginine repressor complex is destabilized by RNA polymerase binding at P1 or transcription from P1. We describe a novel technique to select for expression-down mutants in a lac fusion context.

Efficient algorithm for estimating the correlation dimension from a set of discrete points.

We present an algorithm which computes the standard Grassberger-Procaccia correlation dimension of a strange attractor from a finite sample of N points on the attractor. The usual algorithm involves measuring the distances between all pairs of points on the attractor, but then discarding those distances greater than some cutoff ${r}_{0}$. Our idea is to avoid computing those larger distances altogether. This is done with a spatial grid of boxes (each of size ${r}_{0}$) into which the points are organized. By computing distances between pairs of points only if those points are in the same or in adjacent boxes, we get all the distances less than ${r}_{0}$ and avoid computing many of the larger distances. The execution time for the algorithm depends on the choice of ${r}_{0}$, the smaller ${r}_{0}$, the fewer distances to calculate, and in general the shorter the run time. The minimum time scales as O(NlogN); this compares with the O(${N}^{2}$) time that is usually required. Using this algorithm, we have obtained speedup factors of up to a thousand over the usual method.

Independent particle model for nucleon transfer in heavy ion collisions

We formulate a three-dimensional quantum-mechanical model for the study of nucleon transfer in heavy ion collisions. This model describes the independent particle motion of nucleons initially separated in two adjacent cubic boxes and brought into contact through a window created in the separating wall. We calculate the one-sided flux and the spread of the mass distribution and compare them with results derived from other models.

Wigner function and the one-sided flux

We calculate the Wigner function of the one-body density of a system of 32 independent particles moving in two adjacent cubic boxes communicating through a window. We discuss the applicability of the currently used definition of the classical analog of the one-sided flux obtained from the Wigner function.[NUCLEAR REACTIONS Wigner function for a simple quantum mechanical model, nucleon exchange, static one-sided flux.]

Quantum mechanical model for the one-sided flux in heavy ion collisions

We construct a three-dimensional quantum mechanical model relevant for nucleon transfer in heavy ion collisions. It consists of two adjacent cubic boxes with a rectangular window in the wall which separates them. We calculate the one-sided flux as a function of the window size and compare it with previous results.

Electrophoresis of interacting proteins II. A simple method of simulation

Goad's method for the numerical solution of the conservation-of-mass equation of a system of migrating and simultaneously interacting macromolecules is simplified by taking into account the velocity fluxes between adjacent boxes only. The error introduced in this way is used to advantage to simulate the effect of the diffusional flux. It is shown that this procedure is essentially the same as the counter-current analog method developed by Bethune and Kegeles to account for the effect of diffusion on transport patterns of interacting proteins. The adjustment of the simulated diffusion coefficients to their actual values is discussed and the results of different calculations are compared. It is shown that diffusional spreading has only a secondary influence on the development of a reaction boundary.