Long timestep dynamics of peptides by the dynamics driver approach

Previous experience with the Langevin/implicit-Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high-frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13-residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small-time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time-dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all-atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full α_R-helix starting structure, and a high-temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA-generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two-state model for helix–coil transition. The good, near-Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley-Liss, Inc.     

Mutant hemoglobin stability depends upon location and nature of single point mutation

The temperature dependence of the rates of heme release from the beta subunits of methemoglobin A and 5 beta mutant methemoglobins has been determined. The rates were largest for two hemoglobins with mutations distal to heme, previously known to be unstable. The other 3 mutants also released heme faster than A. These hemoglobins, with single point mutations at the alpha 1/beta 2 interface, were previously thought to be stable. The low reported yields of the 5 mutant proteins covaries with the relative rates of heme release from the met species.     

On the optimal harvesting of persistent age-structured populations

Summary This paper discusses optimal harvesting policies for age-structured populations harvested with effort independent of age.     

The effect of turbulent motion on the diffusion of microorganisms

The effect of turbulent fluid motion on the diffusion of simple organisms is discussed. The net reproduction rate and the turbulent flow are assumed to be Gaussian-correlated random variables. For homogeneous istropic turbulence, simple equations for the average concentration of the organisms are derived in terms of the energy density of the fluid. It is shown that the effective diffusivity generated by the motion is positive-definite, and is independent of the helicity of the flow.     

Dynamics of distribution in animal communities: Theory and analysis

Theoretical and analytical problems of the dynamics of distribution and abundance in animal communities were examined. In many communities, species with low abundance and of limited spatial occurrence (i.e., rare species) typically form a conspicuous peak when a frequency distribution of the number of species is constructed with respect to the proportion of sites occupied within an area of distribution. Models of distribution dynamics, including a new model proposed here, were compared with a range of animal community data using a new procedure to assess single- and bi-modal patterns in frequency distributions of spatial occurrence. Data reveal that single-modality with an excess of rare species occurs more frequently than bimodality. Even when bimodality is detected, the mode representing wide-spread species is in the majority of cases smaller than that for rare species. Thus, a new model in which the rate of local extinctions is assumed to be negatively related to patch occupancy (or population abundance) is in better agreement with observed data than earlier models. Some problems of analysis, in particular model assumptions and testing, are discussed.     

Analysis of cellular interactions in density-dependent inhibition of 3T3 Cell proliferation

Subpopulations of different proliferative status are determined during cell-density dependent proliferation of 3T3 cells. From these data the probability of conversion of proliferative to quiescent cells is derived and found to correlate well with published data on binding of growth-inhibiting factors secreted from growth-inhibited cells.Based on material presented at the Symposium Intercellular Communication Stuttgart, September 16–17, 1982     

A regression analysis of the summer population dynamics of Polyarthra vulgaris in a northern Michigan bog lake

The population dynamics of a planktonic rotifer (Polyarthra vulgaris) were examined in a brown water, acid lake in northern Michigan, U.S.A. Predation by Chaoborus punctipennis and low food (Navicula spp. and Cyclotella spp.) concentrations were the main factors limiting P. vulgaris populations of all factors examined. The data presented here support a hypothesis for zooplankton limitation by an invertebrate predator.     

Correlation of rotifer associations in a chain of lakes fed by reclaimed sewage

The quantitative composition of the rotifer fauna of seven interconnected lakes located in southern California was studied in a preliminary investigation. The lakes are fed by reclaimed sewage, and the water quality increases rapidly from the first lake, barely able to support life, to a series of lovely lakes stocked with fish and utilized for recreation. The Shannon index of rotifer population diversity showed an appropriate increase. Up to 24 – 28 different rotifer taxa in each lake provided a rich community dominated by Brachionids, Keratella and Trichocerca. The diversity and quantity of the rotifer association then declined again in the last lake. Comparison of the lakes using the Bray and Curtis index of similarity and cluster analysis supported the picture of a lake-chain evolution, a biotic development showing a maximum curve.     

基于SD的生态安全指标阈值的确定及应用——以上海崇明岛为例

结合区域复合生态系统的特点,建立由经济、人口、资源、环境和生态5个子系统71个参数构成的上海崇明岛区域生态安全的系统动力学模型,并以变量"净GDP"为参考依据,通过情景仿真进行生态安全趋势分析和方案比较,确定生态安全的指标阈值;通过系统模拟对阈值进行验证,认为阈值在反映系统动态发展趋势上,是一定发展模式下的生态安全的特征参照系。这一尝试克服了目前生态安全指标阈值的研究中以参照法为主的静态性缺憾。将确定的阈值应用于崇明岛生态安全的评价和因子分析中,发现由于崇明岛生态岛的定位和生态保障措施的实施,近几年生态安全综合得分呈现逐步提高的特点,但目前(2007年)得分为0.523,仍处于中等水平;并以阈值为标准的因子检验发现各主要安全因子差异较大,主要的制约因子主要体现为环境治污水平和能源利用等方面。