Structurally constrained protein evolution: results from a lattice simulation

We simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We use a cubic lattice model of the protein structure and test the neutrality conditions by extensive Monte Carlo simulations. We observe that sequence space is traversed by neutral networks, i.e. sets of sequences with the same fold connected by point mutations. Typical pairs of sequences on a neutral network are nearly as different as randomly chosen sequences. The fraction of neutral neighbors has strong sequence to sequence variations, which influence the rate of neutral evolution. In this paper we study the thermodynamic stability of different protein sequences. We relate the high variability of the fraction of neutral mutations to the complex energy landscape within a neutral network, arguing that valleys in this landscape are associated to high values of the neutral mutation rate. We find that when a point mutation produces a sequence with a new ground state, this is likely to have a low stability. Thus we tentatively conjecture that neutral networks of different structures are typically well separated in sequence space. This result indicates that changing significantly a protein structure through a biologically acceptable chain of point mutations is a rare, although possible, event. Received 8 July 1999     

Ploidy,sex and crossing over in an evolutionary aging model

Nowadays, many forms of reproduction coexist in nature: Asexual, sexual, apomictic and meiotic parthenogenesis, hermaphroditism and parasex. The mechanisms of their evolution and what made them successful reproductive alternatives are very challenging and debated questions. Here, using a simple evolutionary aging model, we give a possible scenario. By studying the performance of populations where individuals may have diverse characteristics—different ploidies, sex with or without crossing over, as well as the absence of sex—we find an evolution sequence that may explain why there are actually two major or leading groups: Sexual and asexual. We also investigate the dependence of these characteristics on different conditions of fertility and deleterious mutations. Finally, if the primeval organisms on Earth were, in fact, asexual individuals we conjecture that the sexual form of reproduction could have more easily been set and found its niche during a period of low-intensity mutations.     

老化丝织品的红外光谱分析研究

古代丝织品老化程度的检测有助于了解丝织品的保存状况及保护方法的选择与改进,通过红外光谱分析对丝织品老化原因及程度进行了研究。样品为经光老化、热老化和水解老化的白色丝织品和出土于湖北、内蒙古、青海的古代丝织品。对这些样品进行了显微红外分析,结果表明,红外光谱分析虽然只是提供半定量分析,但是对于发生了水解老化的丝织品来说,由于羧基含量的增加,红外分析能很容易提供定性及较好的半定量的分析结果,因此对于出土古代丝织品保存状况及老化机理的研究来说很有实用价值。     

TG and DSC studies of natural and artificial aging of polypropylene

We study the evolution of thermal degradation of samples of polypropylene (PP), during their aging for two periods of 60 and 80 days. The study, using thermogravimetric analysis (TG) and differential scanning calorimetric (DSC) analyses, focused on two types of aging: the natural one under the impact of the solar environment and the artificial one which was carried out by exposing the sample to radiations of a 100 W commercial lamp.The comparative study of these two types of aging shows that the thermal degradation of the PP increases as a function of time of aging. Indeed, for a same duration, this thermal degradation is more important in the artificial aging case than it is in the natural one and is an increasing function of aging. The prolonged and continuous thermal effect produced by the lamp, in the case of the artificial aging, weakened the polymer and implies very important acceleration of the process of degradation.The results obtained during heating and cooling of the samples, using the DSC, show an evolution of the phase transition temperatures and the corresponding enthalpies of melting and crystallization.     

An introduction to physical theory of molecular evolution

This work is a tutorial in Molecular Evolution from the point of view of Physics. We discuss Eigen's model, a link between evolutionary theory and physics. We will begin by assuming the existence of (marco) molecules or replicators with the template property, that is, the capacity to self-replicate. According to this assumption, information will be randomly generated and destroyed by mutations in the code (i.e., errors in the copying process) and new bits of information will be fixed (made stable) by the existence of an external pressure on the system (i.e., selection), and the ability of the molecules to replicate themselves. Our aim is to build a model in order to describe molecular evolution from as general a standpoint as possible. As we will see, even very simple models from the theoretical point of view will have surprisingly deep consequences.     

Adaptation of asexual populations in correlated environments

We introduce two computational models of subdivided populations of asexual organisms which present variability in selection pressure. In both models one can handle the level of environmental correlation among the subpopulations (demes), which is dependent on the length of the shortest path between the demes. This work mainly addresses how environmental heterogeneity can affect the rate at beneficial mutations fixes in a structured population, and the conditions under which clonal interference becomes significant. Although the fixation probability of beneficial mutations is roughly the same as in a panmitic population and so does not depend on the level of correlation among the demes, the simulation results show that fixation rates may be strongly influenced by environmental variability. Based on our simulations we conclude that an increased variability in selection leads to a smaller fixation rate. The effect of environmental heterogeneity on the adaptive process is enhanced as the flow of organisms between subpopulations is reduced. In extreme scenarios, the fixation rate decreases as the rate of beneficial mutations rises.     

一种尼龙老化评价的新方法

作为一种广泛使用的工程塑料,尼龙的老化备受关注。当作为电力系统芯片的封装材料时,尼龙在自然环境下的老化有可能会导致封装失效,从而影响芯片使用的可靠性,严重时甚至导致芯片的失效,给电力行业带来巨大损失。常规的自然老化和人工加速老化评价周期非常漫长,不同因素对尼龙老化的影响机理十分复杂,且这种影响难以研究,使得评价尼龙的老化稳定性成为一大难题。采用自主开发的原位老化评价系统,对尼龙6（PA6）和尼龙66（PA66）的老化稳定性及湿度对老化的影响进行了研究。该系统可以实现光照/温度/湿度/氧气等环境因素的加载,通过高灵敏度地测定材料在综合环境因素作用下产生的气相降解产物来评价材料的老化稳定性,评价时间缩短到几小时。实验表明,PA6和PA66的气相降解产物以H₂O和CO₂为主,由于H₂O在气相中的浓度不稳定,因此以CO₂的产生量作为老化评价指标。通过对不同自然老化时间PA6和PA66的原位老化评价,并与其ATR-FTIR红外光谱图进行对照,证明了原位老化评价方法能够较好地反映尼龙的老化程度,自然老化时间越长,PA6和PA66的稳定性越低,CO₂的产生量越大。进一步,采用该方法研究了湿度对PA6和PA66老化反应的影响,证明增大湿度对尼龙老化存在促进作用,而且升高温度会进一步促进湿度对老化的促进作用。研究表明,原位老化评价方法是一种快速评价尼龙老化稳定性及环境因素影响的有力手段。     

基于高维拉曼光谱数据的变压器油纸绝缘老化评估方法研究

采用激光拉曼光谱技术对变压器油纸绝缘老化状态检测是一种有效的方法。随着样本量的扩充,亟待处理的数据集维度逐渐增大,研究适用于高维拉曼光谱数据的变压器油纸绝缘老化评估方法具有重要的意义。设计与现场变压器内部绝缘结构相似的油纸绝缘环境,进行加速热老化实验并定期采样,获取到10类老化程度依次递增的油样本,采用激光拉曼光谱技术对样本进行检测。选用复合稀疏导数建模法对样本原始拉曼光谱数据预处理,可以一步完成去噪与基线校正;引入差异特征选取方法筛选不同老化程度下光谱中变化显著的特征,计算同一拉曼频移下不同老化程度的特征点数据集方差,选择差异较大的数据序列所对应的拉曼特征变量,设定方差阈值为0.5进行特征选择,每个样本都从1 023个光谱特征点抽取出304个特征点进行后续分析;针对变压器油纸绝缘老化拉曼光谱高维样本数据集,引入多种不同类型的算法对其处理。分别运用K-means聚类算法、Fisher算法与随机森林算法对获取到的样本预处理后的数据建立模型,引入评估准确度、提升度以及Kappa系数对各算法建立的模型判别效果进行评估。结果表明：有监督学习的Fisher算法与随机森林算法效果较好,相对于无监督学习的K-means聚类算法,模型判别能力分别提升了1.166 6和1.95,论证了有监督学习模型在变压器油纸绝缘老化的评估中具有判别优势;从模型判别准确度和Kappa系数来看,强分类器随机森林算法建立的判别模型均高于Fisher判别模型,其准确度提升了10%,且Kappa系数上升了0.111 5,论证了随机森林算法作为由多个单一分类器组成的强分类器,相对单一分类器来说,在变压器油纸绝缘老化的评估中模型的泛化能力较好,且模型较为稳定可靠。通过对三种不同类型的算法对比,确定了在变压器油纸绝缘老化评估中,有监督学习强分类器随机森林算法的判别优势,为变压器油纸绝缘老化的有效评估打下了基础。     

NMR relaxation and NMR imaging of elastomers in the course of thermal aging

A complex aging regime occurs in the course of thermal aging of elastomers. Depending on the type and the content of the rubber filler materials, temperature, chemical environment (normally air), and time, a different aging process can be observed also by nuclear magnetic resonance (NMR) [1–6]. The methods used are the common spin-echo ¹H-NMR, including variable echo times and parameter-selective NMR-¹H-imaging (material properties imaging). The decay of the echo-magnetization is discussed on the basis of a single-chain model with a distribution of dipolar interactions. This model is based on the influence of a very fast, but anisotropic, local motion, as well as larger and slower motions, which are able to diminish the residual dipolar interaction. Carbon-black-filled natural rubber, as well as silica and carbon-black-filled E-SBR (emulsion-polymerized styrene butadiene rubber) and S-SBR (solution-polymerized SBR) are the systems under investigation, with the results showing some characteristic features of the course of aging observable by NMR.     

The Dynamics of Power laws: Fitness and Aging in Preferential Attachment Trees

Continuous-time branching processes describe the evolution of a population whose individuals generate a random number of children according to a birth process. Such branching processes can be used to understand preferential attachment models in which the birth rates are linear functions. We are motivated by citation networks, where power-law citation counts are observed as well as aging in the citation patterns. To model this, we introduce fitness and age-dependence in these birth processes. The multiplicative fitness moderates the rate at which children are born, while the aging is integrable, so that individuals receives a finite number of children in their lifetime. We show the existence of a limiting degree distribution for such processes. In the preferential attachment case, where fitness and aging are absent, this limiting degree distribution is known to have power-law tails. We show that the limiting degree distribution has exponential tails for bounded fitnesses in the presence of integrable aging, while the power-law tail is restored when integrable aging is combined with fitness with unbounded support with at most exponential tails. In the absence of integrable aging, such processes are explosive.     

双复杂网络间的演化博弈

复杂网络的演化博弈是社会结构与稳定的重要模型. 基于单网络演化博弈模型, 提出了一种双复杂动态网络的演化博弈模型, 考虑双复杂网络在两个不同收益矩阵的囚徒困境博弈下增长, 当两个网络没有相互联系时, 发现增长网络中的空间互利性所导致的平均合作水平的突变, 推广了前人的结论. 在两个网络有相互联系时, 平均合作水平可以两者出现高度同步. 在网络的收益系数达到一定时, 才实现较高的合作水平. 增加网络内连接数量时, 自然选择不利于网络的合作, 而公平选择却有利于网络的合作, 说明了更新策略的影响. 当增加网络间连接数量时, 两个网络合作水平都下降. 当保持网络间和网络内的连接比例不变时, 网络的平均度越大, 平均合作水平越小. 本文发现了背叛领袖的存在, 并揭示了双网络模型下背叛领袖对平均合作水平的影响及其与合作领袖的互动机理, 这结果给出社会结构, 稳定和演化的重要信息和启示.     

Evolution of species from Darwin theory: A simple model

Evolution of species is a complex phenomenon. Some theoretical models take into account evolution of species, like the Bak–Sneppen model that obtain punctuated equilibrium from self-organized criticality and the Penna model for biological aging that consists in a bit-string model subjected to aging, reproduction and death. In this work we propose a simple model to study different scenarios used to simulate the evolution of species. This model is based on Darwin’s ideas of evolution. The present findings show that punctuated equilibria and stasis seem to be obtained directly from the mutation, selection of parents and the genetic crossover, and are very close to the fossil data analysis.     

小麦种子自然老化程度的近红外光谱无损识别

应用近红外光谱技术无损分析小麦种子短期自然老化过程中主要化学成分的变化趋势,并结合支持向量机建立快速判别小麦种子自然老化程度的分析模型。本实验应用VERTEX 70傅里叶变换红外光谱仪,以大样品杯旋转采样方式跟踪采集了45份小麦种子在自然老化初期、4个月、7个月、9个月的近红外光谱。标准差可以用来表征数据离散程度,因此本实验通过计算每份样本在4个自然老化阶段的光谱标准差来筛选与自然老化时间显著相关的谱区。为避免单个样本由于偶然因素导致的离散度值异常,实验统计了45份样本的光谱标准差均值,根据均值光谱得到如下谱峰：8 362,6 950,7 563,5 319,4 998和4 478 cm-1处。解析谱峰所在区域对应的化学基团归属可得：6 950 cm-1处对应的是液态水中O-H伸缩振动的一级倍频且该处离散度值较大,因此小麦种子在短期自然老化阶段中水分变化较为显著;5 319,4 998和4 478 cm-1处离散度值较6 950 cm-1处小,对应的是蛋白质仲酰胺、伯酰胺和酰胺的合频和倍频信息,因此蛋白质变化较水分而言相对平缓;8 362和7 563 cm-1处反映的主要是C-H振动的二级倍频信息且离散度值较大,而种子中蛋白质、淀粉等均具有C-H官能团,因此蛋白和淀粉等成分综合变化较为显著。在上述分析基础上,本文采用多分类支持向量机结合近红外光谱建立快速识别小麦种子四种自然老化程度的定性模型。将180份样本光谱按照3∶1随机抽取135个样本作为训练集,其余样本作为测试集。选择核函数为径向基函数,通过网格搜索法进行参数寻优得到惩罚参数为8,核参数为0.008 974 2时,训练集和测试集的识别正确率可达99.26％和99.78％。实验结果表明：近红外光谱技术结合支持向量机可快速判别小麦种子短期自然老化程度,为种子贮藏过程中生理特性变化的无损监测及开发利用提供便捷的检测手段。     

Slow dynamics due to entropic barriers in the one-dimensional ‘descent model’

We propose a novel one-dimensional simple model without disorder exhibiting slow dynamics and aging at the zero temperature limit. This slow dynamics is due to entropic barriers. We exactly solve the statics of the model. We derive an evolution equation for the slow modes of the dynamics which are responsible for the aging. This equation is equivalent to a random walker on the energetic landscape. This latter elementary model can be solved analytically up to some basic approximations and is shown to present aging by itself, as well as a slow logarithmic relaxation of the energy: at large t.Received: 22 July 2003, Published online: 2 April 2004PACS: 02.50.Ey Stochastic processes - 05.70.Ln Nonequilibrium thermodynamics, irreversible processes     

Speed of adaptation in structured populations

Adaptation of populations takes place with the occurrence and subsequent fixation of mutations that confer some selective advantage to the individuals which acquire it. For this reason, the study of the process of fixation of advantageous mutations has a long history in the population genetics literature. Particularly, the previous investigations aimed to find out the main evolutionary forces affecting the strength of natural selection in the populations. In the current work, we investigate the dynamics of fixation of beneficial mutations in a subdivided population. The subpopulations (demes) can exchange migrants among their neighbors, in a migration network which is assumed to have either a random graph or a scale-free topology. We have observed that the migration rate drastically affects the dynamics of mutation fixation, despite of the fact that the probability of fixation is invariant on the migration rate, accordingly to Maruyama's conjecture. In addition, we have noticed a topological dependence of the adaptive evolution of the population when clonal interference becomes effective.     

Adaptive walks and extreme value theory

We study biological evolution in a high-dimensional genotype space in the regime of rare mutations and strong selection. The population performs an uphill walk which terminates at local fitness maxima. Assigning fitness randomly to genotypes, we show that the mean walk length is logarithmic in the number of initially available beneficial mutations, with a prefactor determined by the tail of the fitness distribution. This result is derived analytically in a simplified setting where the mutational neighborhood is fixed during the adaptive process, and confirmed by numerical simulations.     

Evolutionary games in a generalized Moran process with arbitrary selection strength and mutation

By using a generalized fitness-dependent Moran process, an evolutionary model for symmetric 2×2 games in a well-mixed population with a finite size is investigated. In the model, the individuals' payoff accumulating from games is mapped into fitness using an exponent function. Both selection strength β and mutation rate ε are considered. The process is an ergodic birth-death process. Based on the limit distribution of the process, we give the analysis results for which strategy will be favoured when ε is small enough. The results depend on not only the payoff matrix of the game, but also on the population size. Especially, we prove that natural selection favours the strategy which is risk-dominant when the population size is large enough. For arbitrary β and ε values, the 'Hawk--Dove' game and the 'Coordinate' game are used to illustrate our model. We give the evolutionary stable strategy (ESS) of the games and compare the results with those of the replicator dynamics in the infinite population. The results are determined by simulation experiments.     

核磁共振氢谱法鉴定油性圆珠笔文书的书写时间

油性圆珠笔文书书写时间的鉴定是司法鉴定工作中的热点.该文采用核磁共振氢谱法(~1H NMR)对所购6种不同型号油性圆珠笔的油墨进行了表征,研究了圆珠笔油墨中的溶剂——苯氧基乙醇在文书老化过程中的变化,并建立了MG-115书写文书的自然老化标准曲线.该标准曲线能够准确鉴定MG-115圆珠笔4个月内的文书书写时间,重现性良好;同时,该文探究了人工老化与自然老化的关系,为文书书写时间的鉴定提供了依据.