Computer Dependence of An Improvement of The Cell Neighbour-Table Method For Short-Range Potentials

Abstract

A comparative test is presented for molecular dynamics, MD, computer simulation between the original Cell Neighbour-Table method, CNT, and a later development, the Link-Cell Neighbour-Table, LCNT. The test was simultaneously carried out on a vector Convex 210 computer and on a scalar Pentium 120. The comparison of the two methods for very large systems (up to 100000 particles) and for two short-range pair potentials (Weeks-Chandler-Andersen, WCA, and Lennard-Jones, LJ) showed that on the Convex, in vectorial mode, the LCNT method is about 25% more efficient in time than the CNT method for the shorter-range WCA potential, the difference being unnoticeable (less than 5%) for the LJ potential. However, when the scalar mode is on in the Convex, the difference disappears. In the Pentium, which was found to be systematically faster than the Convex even in vectorial mode, no significant difference of any kind between the both methods was found, with the either of the two potentials.     

Plant litter feedback and population dynamics in an annual plant,<Emphasis Type="Italic"> Cardamine pensylvanica</Emphasis>

The presence of litter has the potential to alter the population dynamics of plants. In this paper, we explore the effects of litter on population dynamics using a simple experimental laboratory system with populations of the annual crucifer, Cardamine pensylvanica. Using a factorial experiment with four densities and three litter levels, we determined the effect of litter on biomass and plant fecundity, and the life stages responsible for these changes in yield. Although litter had significant effects on seed germination and on seedling survivorship, we show, using a population dynamics model, that these effects were not demographically significant. Rather, the potential effect of litter on population dynamics resulted almost entirely from its effect on biomass. Persistent litter suppressed plant biomass and apparently removed the direct density effect present in the absence of litter. Thus, litter changed the shape of the recruitment curve from slightly humped to asymptotic. In addition to changing the shape of the recruitment curve, litter reduced the carrying capacity of the populations. Thus, the population dynamics model indicated that not all statistically significant responses were dynamically significant. Given the potential complexity of litter effects, simple population models provide a powerful tool for understanding the potential consequences of short-term responses. Received: 8 September 1999 / Accepted: 5 April 2000     

Protein degradation in aged nematodes (Turbatrix aceti).

The rates of degradation of total soluble proteins in the free-living nematode, $\text{Turbatrix aceti}$, have been estimated by following the loss of acid-insoluble insoluble radioactivity from protein during a nonradioactive chase period after initial labeling with [³⁵S]methionine. These proteins appear to lose label kinetically as a homogeneous class in age-synchronized nematode populations. However, proteins are degraded more slowly in senescent cultures than in young cultures. Protein degradation rates decline progressively during nematode aging. These findings suggest that the protein degradative system in T. aceti may become partially defective with advancing age which may result in the accumulation of aberrant protein molecules in senescent organisms.     

Influence of ionic strength and pH on the interaction between high-affinity heparin and antithrombin

Binding constants for the binding of high-affinity heparin to antithrombin at different ionic strengths were determined by fluorescence titrations and were also estimated from dissociation curves of the heparin-antithrombin complex. These curves were monitored by near-ultraviolet circular dichroism or fluorescence. The dependence of the binding constant on the activity of NaCl suggested that maximally 5–6 charged groups are directly involved in the interaction between the two macromolecules. Major pH-dependent changes of the interaction, as evident by changes of the spectroscopic properties of the complex between the molecules, were found to occur below pH 5.5 and above pH 8.5. The acid change, which was irreversible, was most likely caused by an irreversible conformational change of antithrombin. At alkaline pH, however, the gross conformation of antithrombin was stable up to pH 12, while the affinity of high-affinity heparin for antithrombin began to decrease markedly at pH 8.5. The dissociation curve, which was reversible, had a midpoint around pH 9.5. This is compatible with the loss of affinity being caused by either a local conformational change, by ionization of tyrosine or by titration of one or more amino groups.     

Prey: predator ratio dependence in the functional response of a freshwater amphipod

1. First known for their shredding activity, freshwater amphipods also behave as active predators with consequences for prey population regulation and amphipod coexistence in the context of biological invasions. 2. A way to quantify predation is to determine the average consumption rate per predator, also known as its functional response (FR). 3. Although amphipods are gregarious and can display social interactions that can alter per capita consumption rates, previous studies using the FR approach to investigate amphipod predation ignored such potential mutual interference because they did not consider variations in predator density. 4. We investigated the FR of Echinogammarus berilloni feeding on dipteran larvae with joint variations in prey and predator densities. This bivariate experimental design allowed us to estimate interference and to compare the fits of the three main classes of theoretical FR models, in which the predation rate is a function of prey density alone (prey‐dependent models), of both prey and predator densities (predator‐dependent models) or of the prey‐to‐predator ratio (ratio‐dependent models). 5. The Arditi–Ginzburg ratio‐dependent FR model provided the best representation of the FR of E. berilloni, whose predation rate showed a decelerating rise to a horizontal asymptote as prey abundance increased. 6. Ratio dependence means that mutual interference between amphipods leads to prey sharing. Mutual interference is likely to vary between amphipod species, depending on their level of aggressiveness.     

Electrophoretic profiles of cyanobacterial membrane polypeptides showing heme-dependent peroxidase activity

The photosynthetic membranes of Anacystis nidulans R2 were examined electrophoretically following solubilization with lithium dodecyl sulfate. Electrophoresis yielded six prominent chlorophyll-containing bands. In addition, five polypeptides were observed which possessed heme-dependent peroxidase activity, monitored by incubating gels with 3,3′,5,5′-tetramethylbenzidine plus hydrogen peroxide. One such polypeptide, at 105 kdaltons, was removed by repeated washing of the membranes. Four remaining peroxidase-active polypeptides were observed at 7.2, 13.5, 18.5 and 33 kdaltons. Further examination of these four polypeptides yielded the following results. (1) The mobility of the 33 kdalton polypeptide was altered from 29 to 33 kdaltons upon heating (70°C) during membrane solubilization. (2) All four polypeptides showed stable heme-protein associations in the presence of 8 M urea; however, in the presence of urea, alterations in protein mobility were observed for each poly-peptide and only two (at 13.5 and 33 kdaltons) showed peroxidase activity following heating (70°C) during membrane solubilization. (3) The presence of thiols during membrane solubilization at 0°C was required to observe peroxidase activity at 7.2 kdaltons. These results, when compared to known properties of isolated cytochromes, suggest that the four polypeptides characterized here correspond to the subunits of photosynthetic cytochromes. Electrophoretic assessment of maize mutants lacking cytochrome f and b₆ activity supports this suggestion.