Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm

We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of rapidly determining multiple pathways between known states. Monotonic progress toward the target state is not required. The soft-ratcheting algorithm is applied to an all-atom model of alanine dipeptide, whose unbiased trajectories are assumed to follow overdamped Langevin dynamics. All possible pathways on the two-dimensional dihedral surface are determined. The associated probability scores, though not optimally distributed at present, may provide a mechanism for estimating reaction rates

Deactivation of TEM-1 beta-Lactamase investigated by isothermal batch and non-isothermal continuous enzyme membrane reactor methods

The thermal deactivation of TEM-1 β-lactamase was examined using two experimental techniques: a series of isothermal batch assays and a single, continuous, non-isothermal assay in an enzyme membrane reactor (EMR). The isothermal batch-mode technique was coupled with the three-state Equilibrium Model of enzyme deactivation, while the results of the EMR experiment were fitted to a four-state molten globule model . The two methods both led to the conclusions that the thermal deactivation of TEM-1 β -lactamase does not follow the Lumry-Eyring model and that the Teq of the enzyme (the point at which active and inactive states are present in equal amounts due to thermodynamic equilibrium) is at least 10 °C from the Tm (melting temperature), contrary to the idea that the true temperature optimum of a biocatalyst is necessarily close to the melting temperature

Rural Land-Use Trends in the Conterminous United States, 1950-2000.

In order to understand the magnitude, direction, and geographic distribution of land-use changes, we evaluated land-use trends in U.S. counties during the latter half of the 20th century. Our paper synthesizes the dominant spatial and temporal trends in population, agriculture, and urbanized land uses, using a variety of data sources and an ecoregion classification as a frame of reference. A combination of increasing attractiveness of nonmetropolitan areas in the period 1970–2000, decreasing household size, and decreasing density of settlement has resulted in important trends in the patterns of developed land. By 2000, the area of low-density, exurban development beyond the urban fringe occupied nearly 15 times the area of higher density urbanized development. Efficiency gains, mechanization, and agglomeration of agricultural concerns has resulted in data that show cropland area to be stable throughout the Corn Belt and parts of the West between 1950 and 2000, but decreasing by about 22% east of the Mississippi River. We use a regional case study of the Mid-Atlantic and Southeastern regions to focus in more detail on the land-cover changes resulting from these dynamics. Dominating were land-cover changes associated with the timber practices in the forested plains ecoregions and urbanization in the piedmont ecoregions. Appalachian ecoregions show the slowest rates of landcover change. The dominant trends of tremendous exurban growth, throughout the United States, and conversion and abandonment of agricultural lands, especially in the eastern United States, have important implications because they affect large areas of the country, the functioning of ecological systems, and the potential for restoratio