Liapunov functions: Geometry and stability

Summary Several geometrical interpretations of Liapunov functions for non-linear ecological models are examined and their limitations pointed out. In particular the geometrical nonuniqueness of Liapunov functions is illustrated by displaying explicitly and comparing four different Liapunov functions for the symmetric competition model for two species. The main point is that considerable care must be taken in using the geometrical properties of an arbitrary Liapunov function as a guide to stability under perturbations.     

Lotka-Volterra equations: Decomposition,stability, and structure

Summary The major objective of this paper is to propose a new decomposition-aggregation framework for stability analysis of Lotka-Volterra equations employing the concept of vector Liapunov functions. Both the disjoint and the overlapping decompositions are introduced to increase flexibility in constructing Liapunov functions for the overall system. Our second objective is to consider the Lotka-Volterra equations under structural perturbations, and derive conditions under which a positive equilibrium is connectively stable. Both objectives of this paper are directed towards a better understanding of the intricate interplay between stability and complexity in the context of robustness of model ecosystems represented by Lotka-Volterra equations. Only stability of equilibria in models with constant parameters is considered here. Nonequilibrium analysis of models with nonlinear time-varying parameters is the subject of a companion paper.Research supported by U.S. Department of Energy under the Contract EC-77-S-03-1493.On leave from Kobe University, Kobe, Japan.     

具有脉冲效应的非自治Lotka-Valterra竞争系统的持久性和渐近行为

本文考虑了两种群具有脉冲效应的非自治Lotka-Valterra竞争系统．运用比较定理和李雅普诺夫函数法,建立了系统的持久性和渐近行为的充分条件．     

On global stability of discrete population models

A necessary and sufficient condition for the global stability of a large class of discrete population models is provided which does not require the construction of a Liapunov function. The general result is applied to difference equations defined in terms of “two hump” functions and to an example of frequency dependent selection.     

一类病毒自身发生变异的传染病模型的全局分析

针对病毒变异前和变异后传染病患者具有不同的传染率情形,建立了一类分阶段传播的SIS模型,通过构造Liapunov函数和定性分析,得到病毒变异前和变异后传染病患者平衡点的存在条件以及它们的全局渐近稳定性。     

A contact energy function considering residue hydrophobic environment and its application in protein fold recognition

The three-dimensional （3D） structure prediction of proteins ：is an important task in bioinformatics. Finding energy functions that can better represent residue-residue and residue-solvent interactions is a crucial way to improve the prediction accu- racy. The widely used contact energy functions mostly only consider the contact frequency between different types of residues; however, we find that the contact frequency also relates to the residue hydrophobic environment. Accordingly, we present an improved contact energy function to integrate the two factors, which can reflect the influence of hydrophobic interaction on the stabilization of protein 3D structure more effectively. Furthermore, a fold recognition （threading） approach based on this energy function is developed. The testing results obtained with 20 randomly selected proteins demonstrate that, compared with common contact energy functions, the proposed energy function can improve the accuracy of the fold template prediction from 20% to 50%, and can also improve the accuracy of the sequence-template alignment from 35% to 65%.     

Discrimination of the native from misfolded protein models with an energy function including implicit solvation.

An essential requirement for theoretical protein structure prediction is an energy function that can discriminate the native from non-native protein conformations. To date most of the energy functions used for this purpose have been extracted from a statistical analysis of the protein structure database, without explicit reference to the physical interactions responsible for protein stability. The use of the statistical functions has been supported by the widespread belief that they are superior for such discrimination to physics-based energy functions. An effective energy function which combined the CHARMM vacuum potential with a Gaussian model for the solvation free energy is tested for its ability to discriminate the native structure of a protein from misfolded conformations; the results are compared with those obtained with the vacuum CHARMM potential. The test is performed on several sets of misfolded structures prepared by others, including sets of about 650 good decoys for six proteins, as well as on misfolded structures of chymotrypsin inhibitor 2. The vacuum CHARMM potential is successful in most cases when energy minimized conformations are considered, but fails when applied to structures relaxed by molecular dynamics. With the effective energy function the native state is always more stable than grossly misfolded conformations both in energy minimized and molecular dynamics-relaxed structures. The present results suggest that molecular mechanics (physics-based) energy functions, complemented by a simple model for the solvation free energy, should be tested for use in the inverse folding problem, and supports their use in studies of the effective energy surface of proteins in solution. Moreover, the study suggests that the belief in the superiority of statistical functions for these purposes may be ill founded.     

The relationship between two different mechanical cost functions and muscle oxygen consumption

Inverse-dynamic models often use cost functions to solve the load-sharing problem. Although it is often assumed that energy is minimised, most cost functions are based on mechanically related measures like muscle force or stress. The aim of this study was to analyse the relationships of two cost functions with experimentally determined data on muscle energy consumption. Four subjects performed isometric contractions generating combinations of elbow flexion/extension and pro/supination moments. Muscle oxygen consumption (VO2) of the m. biceps breve, m. biceps longum, m. brachioradialis and m. triceps laterale was measured with near infrared spectroscopy. Both cost functions were implemented into an existing inverse-dynamic shoulder and elbow model and the individual cost values per muscle were calculated, normalised and subsequently compared to experimental VO2 values. The minimum stress cost function led to a good correspondence between VO2 and cost for the m. triceps laterale but for the flexor muscles cost was significantly lower. A newly proposed energy-related cost function showed, however, a far better correspondence. The inclusion of a linear term and muscle mass in the new criterion led model results to correspond better to experimental results. The energy-related cost function appeared to be a better measure for muscle energy consumption than the stress cost function and led to more realistic predictions of muscle activation.     

具有时滞再生养分竞争模型的全局稳定性

考虑具有再生养分的两个微生物种群竞争一个有限食物营养液的数学模型．利用构造李雅普诺夫函数得到模型内部平衡点全局稳定的充分条件．     

具有三个年龄阶段的单种群自食模型

建立并研究了两个具有三个年龄阶段的单种群自食模型．这篇文章的主要目的是研究时滞对种群生长的作用,对于没有时滞的的模型,我们利用Liapunov函数,得到了系统平衡点全局渐近稳定的充分条件;而具有时滞的的模型,我们得到,随着时滞T增加,当系数满足一定条件时,正平衡点的稳定性可以改变有限次,最后变成不稳定;否则,时滞模型的正平衡点的稳定性不改变。     

一类具有广义Logistic增长的比率型捕食模型的定性分析

对具有广义Logistic增长的比率型捕食模型进行了分析,得到了系统永久持续生存的充分条件．通过对系统进行无量纲代换和应用Liapunov函数的方法,进一步得到了正平衡点全局渐近稳定的充分条件．     

Willis环状脑动脉瘤模型的概周期解

运用构造Liapunov函数的方法，证明了一类非线性系统+(μ+f(x))x+αx-βx2+γx3+g(x)=Fcosωt+e(t)(其中α，β，γ，μ均为正数)，在一定条件下存在唯一的一致渐近稳定的概周期解     

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

One of the common methods for assessing energy functions of proteins is selection of native or near-native structures from decoys. This is an efficient but indirect test of the energy functions because decoy structures are typically generated either by sampling procedures or by a separate energy function. As a result, these decoys may not contain the global minimum structure that reflects the true folding accuracy of the energy functions. This paper proposes to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native conformations. Global energy minimization of these short unfolded segments, a challenging yet tractable problem, is a direct test of the energy functions. As an illustrative example, refolding terminal segments is employed to assess two closely related all-atom statistical energy functions, DFIRE (distance-scaled, finite, ideal-gas reference state) and DOPE (discrete optimized protein energy). We found that a simple sequence-position dependence contained in the DOPE energy function leads to an intrinsic bias toward the formation of helical structures. Meanwhile, a finer statistical treatment of short-range interactions yields a significant improvement in the accuracy of segment refolding by DFIRE. The updated DFIRE energy function yields success rates of 100% and 67%, respectively, for its ability to sample and fold fully unfolded terminal segments of 15 proteins to within 3.5 A global root-mean-squared distance from the corresponding native structures. The updated DFIRE energy function is available as DFIRE 2.0 upon request.     

Energy model for contrast detection: spatiotemporal characteristics of threshold vision

A model for contrast detection of spatiotemporal stimuli is proposed which consists of a spatiotemporal linear filter, an energy device and a threshold device. Assuming the existence of independent intrinsic noise, the probability of stimulus detection was approximated by a Weibull function of the response energy. With this assumption, the stimulus energy is a constant at fixed detection probability. This energy model for contrast detection satisfactorily accounted for the elliptical threshold contours of line pairs at stimulus separations within the range 2–30 min and at stimulus onset asynchronies within the range 20–140 ms. The threshold contour at a large stimulus onset asynchrony (300 ms) was in the form of a rounded square. This finding was explained by assuming that the probability of seeing the line pair was determined by the joint probability that at least one stimulus had been detected. With the energy model, the temporal and spatial autocorrelation functions of the response to a flashed line were evaluated. The autocorrelation functions thus determined were used to predict the temporal contrast sensitivity function to a flickering line stimulus and the spatial contrast sensitivity function to flashed gratings, which were in agreement with the experimental data. The data obtained were fitted adequately by an impulse response approximated by a spatiotemporal Gabor-like function. Received: 08 December 1997 / Accepted in revised form: 26 January 1999     

一个带有自扩散和交差扩散的年龄结构模型

主要考虑了一个带有自扩散和交差扩散的空间分布非均匀的年龄结构模型.基于相应的常微分模型利用Liapunov方法得到了一致稳态的全局稳定性,进而也讨论了扩散效应对于稳定态的作用.     

具有扩散的非自治两种群Lotka-Volterra模型的概周期问题

研究非自治两种群竞争系统,其中一种群可以在两个斑块之间扩散。而另一种群在一个斑块中,不能扩散。本文结合运用Liapunov函数,得到该系统唯一存在全局渐近稳定的正概周期解的条件．     

Description of hydration free energy density as a function of molecular physical properties

A method to calculate the solvation free energy density (SFED) at any point in the cavity surface or solvent volume surrounding a solute is proposed. In the special case in which the solvent is water, the SFED is referred to as the hydration free energy density (HFED). The HFED is described as a function of some physical properties of the molecules. These properties are represented by simple basis functions. The hydration free energy of a solute was obtained by integrating the HFED over the solvent volume surrounding the solute, using a grid model. Of 34 basis functions that were introduced to describe the HFED, only six contribute significantly to the HFED. These functions are representations of the surface area and volume of the solute, of the polarization and dispersion of the solute, and of two types of electrostatic interactions between the solute and its environment. The HFED is described as a linear combination of these basis functions, evaluated by summing the interaction energy between each atom of the solute with a grid point in the solvent, where each grid point is a representation of a finite volume of the solvent. The linear combination coefficients were determined by minimizing the error between the calculated and experimental hydration free energies of 81 neutral organic molecules that have a variety of functional groups. The calculated hydration free energies agree well with the experimental results. The hydration free energy of any other solute molecule can then be calculated by summing the product of the linear combination coefficients and the basis functions for the solute.     

The energetic savings of sleep versus temperature in the Desert Iguana (Dipsosaurus dorsalis) at three ecologically relevant temperatures

One of the proposed ecological functions of sleep is to conserve energy. The majority of studies that support this theory have been done on endothermic animals whose body temperatures drop during sleep due to the reduced neurological control of thermoregulation. In the present study, we examined typical temperatures to which the Desert Iguana, Dipsosaurus dorsalis, is exposed to in the field and found that mean high temperatures ranged from 24-58 degrees C throughout the active portion of the year. We also examined the ecological savings that sleep could provide for this ectothermic iguana using a closed system respirometer. We found that laboratory-acclimated iguanas are able to save significantly more (27.6%) energy by sleeping than by being awake and that field iguanas also had significant savings of energy (69.1%) while asleep. However, iguanas could save more energy by remaining awake at cooler temperatures than by sleeping at warmer temperatures. In addition, we found no correlation for time of night with metabolic rate. Our study supports the hypothesis that one potential function of sleep is to conserve energy.     

When the feasibility of an ecosystem is sufficient for global stability?

We show via a Liapunov function that in every model ecosystem governed by generalized Lotka-Volterra equations, a feasible steady state is globally asymptotically stable if the number of interaction branches equals n-1, where n is the number of species. This means that the representative graph for which the theorem holds is a 'tree' and not only an alimentary chain. Our result is valid also in the case of non-homogeneous systems, which model situations in which input fluxes are present.