Thermodynamics of the disproportionation of adenosine 5'-diphosphate to adenosine 5'-triphosphate and adenosine 5'-monophosphate. I. Equilibrium model

The thermodynamic treatment of the disproportionation reaction of adenosine 5′-diphosphate to adenosine 5′-triphosphate and adenosine 5′-monophosphate is discussed in terms of an equilibrium model which includes the effects of the multiplicity of ionic and metal bound species and the presence of long range electrostatic and short range repulsive interactions. Calculated quantities include equilibrium constants, enthalpies, heat capacities, entropies, and the stoichiometry of the overall reaction. The matter of how these calculations can be made self-consistent with respect to both calculated values of the ionic strength and the molality of the free magnesium ion is discussed. The thermodynamic data involving proton and magnesium-ion binding data for the nucleotides involved in this reaction have been evaluated.     

Entropy in evolution

Daniel R. Brooks and E. O. Wiley have proposed a theory of evolution in which fitness is merely a rate determining factor. Evolution is driven by non-equilibrium processes which increase the entropy and information content of species together. Evolution can occur without environmental selection, since increased complexity and organization result from the likely capture at the species level of random variations produced at the chemical level. Speciation can occur as the result of variation within the species which decreases the probability of sharing genetic information. Critics of the Brooks-Wiley theory argue that they have abused terminology from information theory and t thermodynamics. In this paper I review the essentials of the theory, and give an account of hierarchical physical information systems within which the theory can be interpreted. I then show how the major conceptual objections can be answered.     

Entropy effects on the ion-diffusion rate in transmembrane protein channels

We treat the transport of univalent cations through pore-like protein channels in biological membranes analytically, using two models (A + B) for the channel and the ion-channel interaction. A Lennard-Jones-type repulsion between the ions and the pore wall is introduced. We also include Van der Waals- and coulomb-type interactions between polar ligands of the pore-forming protein (e.g., carbonyl groups directed towards the axis of the channel) and the migrating particles. In model A, the polar groups are assumed to occur in pairs of dipoles pointing in opposite directions (as in the gramicidin A channel), while in model B the channel is treated as a pore with a radially isotropic charge distribution. In both models the ion-channel interaction leads to the occurrence of periodic potentials, corresponding to quasi-equilibrium and transition state sites of the ion in the pore. The diffusion rate can be calculated employing rate-theoretical concepts on the basis of microscopic parameters. It is demonstrated that the anomaly (inversion of the normal mass effect) for the transport rates of different ions can be related to differences in the activation entropy. The latter quantity is estimated analytically for both models. As a test, we performed numerical calculations with parameters based on the gramicidin A model. The results are in good agreement with experimental data and data from computer simulations. This shows that simple analytic expressions are well suited for predicting trends in the ionic conductivity of protein channels on the basis of microscopic interactions.     

Selenium nanovirus and its cytotoxicity in selenite-exposed higher living organisms

Selenium (Se) is an essential micronutrient in living organisms, having a narrow margin between essential and potentially toxic intake/exposure. Thus, the biochemistry of Se in living organisms must be studied in-depth to determine the underlying mechanism of Se cytotoxicity. In this study, we report the emergence of selenium nanovirus (SeNVs) in selenite-exposed fish (freshwater and saltwater) and plants (dryland) and its toxicity in them. SeNVs were found in both the abdomen and tail of Oryzias melastigma and saltwater Rhodeus ocellatus, which led to their death. The occurrence of the intracellular assembly of SeNVs was observed in the roots and leaves of corn Zea mays, but not in those of Limnobium laevigatum. SeNVs led to the death of Z. mays but caused chronic toxicity in L. laevigatum. SeNVs should be a system or structure that dissipates the intracellular redox gradients of the host cells, with simple information consisting Se–O, Se–N, or Se–S bond, that would ensure elemental Se ligand binding with nearly specific biomolecules in host cells, thereby maintaining their composition and stabilizing their structure. The multiple toxic effects of Se, therefore, could be the consequence of increase of entropy in the host cells caused by the intracellular assembly of SeNVs. This study may provide an insight into the underlying mechanism of Se in environmental toxicology and its applications in human health.     

Thermodynamic view on decision-making process: emotions as a potential power vector of realization of the choice

This research is devoted to possible mechanisms of decision-making in frames of thermodynamic principles. It is also shown that the decision-making system in reply to emotion includes vector component which seems to be often a necessary condition to transfer system from one state to another. The phases of decision-making system can be described as supposed to be nonequilibrium and irreversible to which thermodynamics laws are applied. The mathematical model of a decision choice, proceeding from principles of the nonlinear dynamics considering instability of movement and bifurcation is offered. The thermodynamic component of decision-making process on the basis of vector transfer of energy induced by emotion at the given time is surveyed. It is proposed a three-modular model of decision making based on principles of thermodynamics. Here it is suggested that at entropy impact due to effect of emotion, on the closed system—the human brain,—initially arises chaos, then after fluctuations of possible alternatives which were going on—reactions of brain zones in reply to external influence, an order is forming and there is choice of alternatives, according to primary entrance conditions and a state of the closed system. Entropy calculation of a choice expectation of negative and positive emotion shows judgment possibility of existence of “the law of emotion conservation” in accordance with several experimental data.     

Voice disorders assessed by (cross-) Sample Entropy of electroglottogram and microphone signals

The quantitative analysis of vocal disorders by nonlinear signal processing methods has been extensively used in the last two decades. In this work, two algorithms for nonlinear time-series analysis, Sample Entropy and cross-Sample Entropy, are used on electroglottogram (EGG) and microphone (MIC) signals recorded from 51 normal and 80 dysphonic subjects, to obtain summary measures of voice disorders through SampEn and cross-SampEn indices. Such parameters quantify, respectively, the degree of irregularity (in the sense of self-dissimilarity) within a time-series and of asynchrony (in the sense of cross-dissimilarity) between two distinct time-series. The aims of this work are: to determine if statistically significant differences in terms of signal irregularity quantified by SampEn occur between normal and pathological subjects, investigating whether or not such differences can be equally seen in EGG and MIC; to assess if cross-SampEn reveals different degrees of asynchrony between EGG and MIC signals in the two groups. Results show that SampEn in pathological subjects is higher than in normal subjects for both EGG and MIC time-series, with a statistically significant difference detectable from both signals (Pe < 10^?4 for EGG and Pe < 10^?7 for MIC). Cross-SampEn exhibits a statistically significant difference too, showing a higher degree of cross-dissimilarity between EGG and MIC time-series for pathological subjects (Pe < 10^?4). In conclusion, SampEn and cross-SampEn well quantify the increase of complexity of both EGG and MIC signals and the decrease of their cross-similarity in presence of vocal disorders. Thanks to the complementarity of nonlinear indicators to the traditionally considered linear ones, SampEn and cross-SampEn appear as suitable candidates to enter the pool of approaches to investigate speech pathologies and to obtain potentially new insights on their nature.     

中国植物分布模拟研究现状

在过去的20年里, 物种分布模型已广泛应用于动植物地理分布的模拟研究。该文以植物物种分布模拟为例, 利用中国知网、维普网以及Web of Science文献数据库的检索与统计, 分析了2000-2018年间, 中国研究人员利用各种物种分布模型对植物物种分布模拟研究的发文量、模拟模型、物种类型、数据来源、研究目的等信息。最终共收集到366篇有效文献, 分析表明2011年以来中国的物种分布模型应用发展迅速, 且以最近5年最为迅猛, 在生态学、中草药业、农业和林业等行业部门应用广泛。在使用的33种模型中, 应用最广的为最大熵模型(MaxEnt)。有一半研究的环境数据仅包含气候数据, 另一半研究不仅包含气候数据还包括地形与土壤等数据; 环境及物种数据的来源多样, 国际及本土数据库均得到使用。模拟涉及有明确清单的562个植物种, 既有木本植物(52.7%), 也有草本植物(41.8%), 其中中草药、果树、园林植物、农作物等占比较高。研究目的主要集中在过去、现在和未来气候变化对植物种分布的影响及预测, 以及物种分布评估与生物多样性评价(包括入侵植物风险评估)两大方面。预测物种潜在分布范围与气候变化影响等基础研究, 与模拟物种适生区与推广种植等应用研究并重, 物种分布模型在生态学与农业、林业和中草药业等多学科、多行业开展多种应用, 多物种、多模型和多来源数据共同参与模拟与比较, 开发新的机理性物种分布模型, 拓展新的物种分布模拟应用领域, 是今后研究的重点发展方向。     

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。     

Double-exponential kinetics of binding and redistribution of the fluorescent dyes in cell membranes witness for the existence of lipid microdomains

New technique of detecting lateral heterogeneity of the plasma membrane of living cells by means of membrane-binding fluorescent dyes is proposed. The kinetics of dye incorporation into the membrane or its lateral diffusion inside the membrane is measured and decomposed into exponential components by means of the Maximum Entropy Method. Two distinct exponential components are obtained consistently in all cases for several fluorescent dyes, two different cell lines and in different types of experiments including spectroscopy, flow cytometry and fluorescence recovery after photobleaching. These components are attributed to the liquid-ordered and disordered phases in the plasma membrane of studied cells in their dynamic equilibrium.     

Enthalpy/entropy compensation phenomena in the reduction thermodynamics of electron transport metalloproteins

Compensation phenomena between the enthalpy and entropy changes of the reduction reaction for all classes of electron transport metalloproteins, namely cytochromes, iron-sulfur, and blue copper proteins, are brought to light. This is the first comprehensive report on such effects for biological redox reactions. Following Grunwalds approach for the interpretation of H/S compensation for solution reactions, it is concluded that reduction-induced solvent reorganization effects involving the hydration shell of the molecule dominate the reduction thermodynamics in these species, although they have no net effect on the E° values, owing to exact compensation. Thus the reduction potentials of these species are primarily determined by the selective enthalpic stabilization of one of the two oxidation states due to ligand binding interactions and electrostatics at the metal site and by the entropic effects of reduction-induced changes in protein flexibility.