熵与生命和肿瘤的关系

热力学是研究能量转换规律的科学 ,本文针对热力学第二定律即熵与生命的关系提出一些见解和分析 ,来作以下讨论。1.熵与生命代谢的关系在克劳修斯的热力学第二定律中指出 :一个孤立系统不管其初始状态如何 ,最终将演化为最无序 ,最混乱的状态。而且满足热力学平衡的状态 ,简言之就是一个孤立系统的熵随时间增高 ,熵增加原理告诉我们自发过程是由比较有序向比较无序的方向进行的 ,自发过程总是伴随着熵的增加 ,或者说熵增加过程是自发过程。根据原理 ,熵的改变值 (△Ｓ)只由始态和终态确定 ,而与过程和途径无关。以人体为例 ,就生命的新陈代…     

等熵方程与生物熵限方程

本文分析了等熵方程;推导出核酸序列的熵限方程,率先提出了生物进化过程中核酸序列选择的熵原则;绘制了分析核酸序列熵变的等熵图．     

一个基于熵的指数精细定位人类复杂性状位点

近来,一个基于熵的指数被提出用来对人类复杂性状位点进行连锁不平衡定位．这个熵指数比较了患病个体与正常个体或极端样本之间标记基因频率的熵和条件熵．本文基于熵理论,提出了另一个备选指数．这个新的指数比较患病个体与正常个体之间标记基因型频率的熵和条件熵．计算机模拟结果表明本文提出的新指数平行于之前的熵指数．而基于遗传性血色病（hereditary haemochromatosis,HH）数据的分析表明了这个新指数能有效对人类复杂性状位点进行精细定位．     

生命现象与熵

自然界的演变不外乎包括了从有序到无序和无序到有序两种演变方式。从有序到无序的演化,正是热力学第二定律所概括的本质,即在封闭系统及与其相对应的环境所组成的孤立系统中,任何自发过程总是朝着使体系越来越混乱、越来越无序的方向演化,也就是熵只增不减,但对生命物质来说,其演化过程恰好与上述情况相反。以这一矛盾现象为起点,根据耗散结构理论,阐述用熵的概念来解释生命现象,是研究生命的一条重要途径。     

细胞寒害的热力学熵理论(Ⅱ)──超熵产生作为寒害稳定性判据的理论研究

本文从物质和能量交换的角度,运用非平衡态热力学超熵产生理论,分析了寒害定态的稳定性,并建立了超熵产生判据．理论分析所得的结论与实验结果基本相符．     

一种改进的近似熵——样品熵及其在颞叶癫痫患者脑电信号分析中的应用

采用了近似熵(approximately entropy,ApEn)和它的改进算法,即样品熵(sample entropy,SampEn)分析了8位颞叶癫痫患者和10位健康人员的短程脑电信号。在计算过程中使用了两种滑动窗口和5个不同的过滤标准r。结果显示颞叶癫痫患者组脑电信号的熵值显著低于健康组,而且患者癫痫病灶所在的脑半球的复杂度远远小于非癫痫病灶的脑半球。小的滑动窗口能更多地反映与癫痫发作相关的细节。对于1秒的滑动窗口,过滤标准r不能小于时间序列标准差的0．15％;而对于4秒的滑动窗口,则过滤标准r不能小于时间序列标准差的10％。研究结果表明,在短程脑电信号的非线性分析中,样品熵是一种比近似熵更为可靠的非线性分析方法。颞叶癫痫患者脑电信号的熵值低于健康人员,这可能表明脑电活动的非线性程度的降低是由于神经信号在大脑内的传递受到了阻碍或者损坏,使得神经信号成了相对孤立的信息源。     

微生物生长稳定性超熵产生判据

运用非平衡热力学超熵产生理论和微生物生长动力学理论,以细胞、营养物和产物为参量,求得了微生物生长的超熵产生及稳定性判据,理论分析与实验计算结果基本一致．     

异质性干细胞增殖过程中的熵变化

干细胞在多细胞生物体内广泛存在,其增殖过程在生命体的生长、发育、衰老、组织修复过程中起着重要作用。正常组织中的细胞增殖过程受到严格的控制,干细胞的异常增殖与恶性肿瘤、肥胖症、再生障碍性贫血等疾病有密切关系。生命体内异质性细胞的增殖过程是复杂的动力系统行为,干细胞异常增殖过程伴随细胞的可塑性变化和细胞间相互作用的再平衡过程,如何对这一过程进行定量描述是重要的研究课题。本文构建包含细胞的增殖分化指标和异常增殖性指标异质性的干细胞增殖模型,通过所建立的模型研究由于微环境变化引起的细胞异常增殖过程的熵变化,建立不同增殖条件下的系统熵变化与宏观动力学和系统参数之间的关系。结果表明,在细胞微环境变化引起异常增殖和恢复的过程中,系统的熵与细胞数量之间存在对应关系,而与微环境变化的路径无关。 此外,熵对细胞数量的依赖关系在异常增殖和恢复阶段表现出不同的行为,显示了生物过程的微观不可逆性。本文从物理学的角度对细胞异常增殖过程中熵变化与细胞数量变化的动力学给出定量刻画,为定量描述异质性干细胞增殖过程给出新的研究思路。     

使用极端样本构建一个基于熵的对数量性状位点关联研究的统计量

基于熵理论,Zhao等提出了一个对复杂疾病易感基因进行关联研究的统计量．本文拓展了这一理论到数量性状,利用熵理论。获得了一个对数量性状位点进行关联研究的采用群体极端样本及稠密标记的统计量．     

基于Agent模型的生态公平指数构建与模拟

伴随着社会经济的发展,社会公平逐渐成为热点话题。社会公平问题不但体现在社会现象上,还对生态系统起着重要的影响。通过构建资本交换自主体模型,模拟社会财富分配动态过程,可观测资本交换熵指数变化情况,从而解释熵增原理。除此以外,不同系统的最终状态能达到的最大熵指数不同,用熵增原理与本文构建的最大熵指数模型可以对系统的生态公平进行纵向或横向评价。构建的资本交换熵模型也可以证明最大熵原理,同时,财富集中的现象将会使生态环境的选择权完全交予富人群体,影响可持续发展。     

Entropic elastic processes in protein mechanisms. II. Simple (passive) and coupled (active) development of elastic forces

The first part of this review on entropic elastic processes in protein mechanisms (Urry, 1988) demonstrated with the polypentapeptide of elastin (Val¹-Pro²-Gly³-Val⁴-Gly⁵)_n that elastic structure develops as the result of an inverse temperature transition and that entropic elasticity is due to internal chain dynamics in a regular nonrandom structure. This demonstration is contrary to the pervasive perspective of entropic protein elasticity of the past three decades wherein a network of random chains has been considered the necessary structural consequence of the occurrence of dominantly entropic elastomeric force. That this is not the case provides a new opportunity for understanding the occurrence and role of entropic elastic processes in protein mechanisms. Entropic elastic processes are considered in two classes: passive and active. The development of elastomeric force on deformation is class I (passive) and the development of elastomeric force as the result of a chemical process shifting the temperature of a transition is class II (active). Examples of class I are elastin, the elastic filament of muscle, elastic force changes in enzyme catalysis resulting from binding processes and resulting in the straining of a scissile bond, and in the turning on and off of channels due to changes in transmembrane potential. Demonstration of the consequences of elastomeric force developing as the result of an inverse temperature transition are seen in elastin, where elastic recoil is lost on oxidation, i.e., on decreasing the hydrophobicity of the chain and shifting the temperature for the development of elastomeric force to temperatures greater than physiological. This is relevant in general to loss of elasticity on aging and more specifically to the development of pulmonary emphysema. Since random chain networks are not the products of inverse temperature transitions and the temperature at which an inverse temperature transition occurs depends on the hydrophobicity of the polypeptide chain, it now becomes possible to consider chemical processes for turning elastomeric force on and off by reversibly changing the hydrophobicity of the polypeptide chain. This is herein called mechanochemical coupling of the first kind; this is the chemical modulation of the temperature for the transition from a less-ordered less elastic state to a more-ordered more elastic state. In the usual considerations to date, development of elastomeric force is the result of a standard transition from a more-ordered less elastic state to a less-ordered more elastic state. When this is chemically modulated, it is herein called mechanochemical coupling of the second kind. For elastin and the polypentapeptide of elastin, since entropic elastomeric force results on formation of a regular nonrandom structure and thermal randomization of chains results in loss of elastic modulus to levels of limited use in protein mechanisms, consideration of regular spiral-like structures rather than ramdom chain networks or random coils are proposed for mechanochemical coupling of the second kind. Chemical processes to effect mechanochemical coupling in biological systems are most obviously phosphorylation-dephosphorylation and changes in calcium ion activity but also changes in pH. These issues are considered in the events attending parturition in muscle contraction and in cell motility.     

Increases in environmental entropy demand evolution

An application of the entropic theory of perception to evolutionary systems indicates that environmental entropy increases will exert pressures on an organism to adapt. We speculate that the instability caused by such environmental changes will also cause an increase in the mutation rate of organisms leading to an eventual increase in their complexity. Such complexity generation allows organisms to adapt to the more entropic environment. Although we conclude that increases in environmental entropy cause an organism to evolve into a more complex organism, increases in entropy may not be necessary for complexity generationper se.     

Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways

The role of disulfide bonds in directing protein folding is studied using lattice models. We find that the stability and the specificity of the disulfide bond interactions play quite different roles in the folding process: Under some conditions, the stability decreases the overall rate of folding; the specificity, however, by yielding a simpler connectivity of intermediates, always increases the rate of folding. This conclusion is intimately related to the selection mechanism entailed by entropic driving forces, such as the loop formation probability, and entropic barriers separating the native and the many native-like metastable states. The folding time is found to be a minimum for a certain range of the effective disulfide bond interaction. Examination of a model, which allows for the formation of disulfide bonded intermediates, suggests that folding proceeds via a threestage multiple pathways kinetics. We show that there are pathways to the native state involving only native-like intermediates, as well as those that are mediated by nonnative intermediates. These findings are interpreted in terms of the appropriate energy landscape describing the barriers connecting low energy conformations. The consistency of our conclusions with several experimental studies is also discussed. © 1995 Wiley-Liss, Inc.     

Entropy-driven motility of Sinorhizobium meliloti on a semi-solid surface

Sinorhizobium meliloti growing on soft agar can exhibit an unusual surface spreading behaviour that differs from other bacterial surface motilities. Bacteria in the colony secrete an exopolysaccharide-rich mucoid fluid that expands outward on the surface, carrying within it a suspension of actively dividing cells. The moving slime disperses the cells in complex and dynamic patterns indicative of simultaneous bacterial growth, swimming and aggregation. We find that while flagellar swimming is required to maintain the cells in suspension, the spreading and the associated pattern formation are primarily driven by the secreted exopolysaccharide EPS II, which creates two entropy-increasing effects: an osmotic flow of water from the agar to the mucoid fluid and a crowding or depletion attraction between the cells. Activation of these physical/chemical phenomena may be a useful function for the high molecular weight EPS II, a galactoglucan whose biosynthesis is tightly regulated by the ExpR/SinI/SinR quorum-sensing system: unlike bacterial colonies that spread via bacterium-generated, physical propulsive forces, S. meliloti under quorum conditions may use EPS II to activate purely entropic forces within its environment, so that it can disperse by passively ‘surfing’ on those forces.     

Specific interactions by the N-terminal arm inhibit self-association of the AraC dimerization domain

Deletion of the regulatory N-terminal arms of the AraC protein from its dimerization domain fragments increases the susceptibility of the dimerization domain to form a series of higher order polymers by indefinite self-association. We investigated how the normal presence of the arm inhibits this self-association. One possibility is that arms can act as an entropic bristles to interfere with the approach of other macromolecules, thereby decreasing collision frequencies. We examined the repulsive effect of flexible arms by measuring the rate of trypsin cleavage of a specially constructed ubiquitin-arm protein. Adding an arm to ubiquitin or increasing its length produced only a modest repulsive effect. This suggests that arms such as the N-terminal arm of AraC do not reduce self-association by entropic exclusion. We consequently tested the hypothesis that the arm on AraC reduces self-association by binding to the core of the dimerization domain even in the absence of arabinose. The behaviors of dimerization domain mutants containing deletions or alterations in the N-terminal arms substantiate this hypothesis. Apparently, interactions between the N-terminal arm and the dimerization domain core position the arm to interfere with the protein-protein contacts necessary for self-association.     

The stability of Taq DNA polymerase results from a reduced entropic folding penalty; identification of other thermophilic proteins with similar folding thermodynamics

The thermal stability of Taq DNA polymerase is well known, and is the basis for its use in PCR. A comparative thermodynamic characterization of the large fragment domains of Taq (Klentaq) and E. coli (Klenow) DNA polymerases has been performed by obtaining full Gibbs‐Helmholtz stability curves of the free energy of folding (ΔG) versus temperature. This analysis provides the temperature dependencies of the folding enthalpy and entropy (ΔH and ΔS), and the heat capacity (ΔC_p) of folding. If increased or enhanced non‐covalent bonding in the native state is responsible for enhanced thermal stabilization of a protein, as is often proposed, then an enhanced favourable folding enthalpy should, in general, be observed for thermophilic proteins. However, for the Klenow–Klentaq homologous pair, the folding enthalpy (ΔH_fold) of Klentaq is considerably less favorable than that of Klenow at all temperatures. In contrast, it is found that Klentaq's extreme free energy of folding (ΔG_fold) originates from a significantly reduced entropic penalty of folding (ΔS_fold). Furthermore, the heat capacity changes upon folding are similar for Klenow and Klentaq. Along with this new data, comparable extended analysis of available thermodynamic data for 17 other mesophilic–thermophilic protein pairs (where enough applicable thermodynamic data exists) shows a similar pattern in seven of the 18 total systems. When analyzed with this approach, the more familiar “reduced ΔC_p mechanism” for protein thermal stabilization (observed in a different six of the 18 systems) frequently manifests as a temperature dependent shift from enthalpy driven stabilization to a reduced‐entropic‐penalty model. Proteins 2014; 82:785–793. © 2013 Wiley Periodicals, Inc.     

Coupling of global and local vibrational modes in dynamic allostery of proteins

It is now recognized that internal global protein dynamics play an important role in the allosteric function of many proteins. Alterations of protein flexibility on effector binding affect the entropic cost of binding at a distant site. We present a coarse-grained model for a potential amplification of such entropic allostery due to coupling of fast, localized modes to the slow, global modes. We show how such coupling can give rise to large compensating entropic and enthalpic terms. The model corresponds to the pattern of calorimetry and NMR data from experiments on the Met repressor.     

Calculating Stress: From Entropy to a Thermodynamic Concept of Health and Disease

To date, contemporary science has lacked a satisfactory tool for the objective expression of stress. This text thus introduces a new–thermodynamically derived–approach to stress measurement, based on entropy production in time and independent of the quality or modality of a given stressor or a combination thereof. Hereto, we propose a novel model of stress response based on thermodynamic modelling of entropy production, both in the tissues/organs and in regulatory feedbacks. Stress response is expressed in our model on the basis of stress entropic load (SEL), a variable we introduced previously; the mathematical expression of SEL, provided here for the first time, now allows us to describe the various states of a living system, including differentiating between states of health and disease. The resulting calculation of stress response regardless of the type of stressor(s) in question is thus poised to become an entirely new tool for predicting the development of a living system.