Dynamical aspects of P systems

A dynamical analysis of P systems is given that is focused on basic phenomena of biological relevance. After a short presentation of a new kind of P systems (PB systems), membrane systems with environment, called PBE systems, are introduced that are more suitable for modeling complex membrane interactions. Some types of periodicity and non-periodicity are considered for PBE systems by showing some "minimal" examples of systems that exhibit these properties. In particular, a discrete formulation of the Belousov-Zhabotinsky (BZ) reaction is given in terms of PBE systems. Some questions and open problems for future research are indicated.     

Qualitative theory of compartmental systems with lags

Dynamic models of many processes in the biological and physical sciences give systems of ordinary differential equations called compartmental systems. Often, these systems include time lags; in this context, continuous probability density functions (pdfs) of lags are far more important than discrete lags. There is a relatively complete theory of compartmental systems without lags, both linear and non-linear [SIAM Rev. 35 (1993) 43]. The authors extend their previous work on compartmental systems without lags to show that, for discrete lags and for a very large class of pdfs of continuous lags, compartmental systems with lags are equivalent to larger compartmental systems without lags. Consequently, the properties of compartmental systems with lags are the same as those of compartmental systems without lags. For a very large class of compartmental systems with time lags, one can show that the time lags themselves can be generated by compartmental systems without lags. Thus, such systems can be partitioned into a main system, which is the original system without the lags, plus compartmental subsystems without lags that generate the lags. The latter may be linear or non-linear and may be inserted into main systems that are linear or non-linear. The state variables of the compartmental lag subsystems are hidden variables in the formulation with explicit lags.     

固体载体支承的双层膜系统

固态载体支承的双层膜的各种制备过程都简便易行,较脂质体等系统有重复性好、其物化性质可严格控制等优越性,并可将膜蛋白质分子镶嵌其中,是研究生物膜的良好模型．由于其研究方法日益成熟,固态载体支承的双层膜系统越来越成为研究生物膜与膜蛋白的有利工具之一．对固态载体支承的双层膜的制备技术和研究方法进行了系统的综述,并列举了一些在膜生物物理化学领域的应用．     

Entity grammar systems: A grammatical tool for studying the hierarchal structures of biological systems

The hierarchal structures of biological systems are the typical complex hierarchal dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical toolmainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed.     

反相胶束体系中的酶学研究

反胶束是新的酶学研究体系,酶在反胶束体系中的性质与在水溶液中相比有较大区别.评述了反胶束体系的性质及酶在其中的催化活性及构象变化,讨论了影响酶活性及构象变化的各种因素,并简单介绍了反胶束酶学研究及应用的最新进展.     

Adsorption Behavior of Polydisperse Polymeric Systems

Adsorption behavior of polydisperse polymers at interfaces is studied by the Monte Carlo simulation method based on a lattice model. Effects of temperature and adsorption energies on the polymer density profile, cluster distributions and adsorption layer thickness are evaluated in two different polydisperse systems. It is found that adsorption properties are greatly different in these two systems. In normal distribution polydisperse systems, polymers are more sensitive to the excluded volume effects while in average distribution polymers are more inclined to adsorb on adsorbing interfaces. As higher temperature and lower attraction constrain the polymer adsorption, more clusters are found under these conditions. When temperature approaches the critical temperature of monodisperse systems, stable and large clusters exist in these two polydisperse systems. These results suggest that micro phase transition may exist in polydisperse systems. Polydisperse systems take little change of phase transition temperatures but altered the clusters morphology to some extent. The adsorption layer thickness changes are more sensitive to both temperature and polymer–interface interactions in average distribution systems when the whole polymer concentration increases slightly. This work also suggests significant differences between the polydisperse and the monodisperse systems in adsorption behavior. Therefore, quantitative system errors may exist when the monodisperse system models are used in simulation to evaluate polymer adsorption properties.     

The semiotics of control and modeling relations in complex systems

We provide a conceptual analysis of ideas and principles from the systems theory discourse which underlie Pattee's semantic or semiotic closure, which is itself foundational for a school of theoretical biology derived from systems theory and cybernetics, and is now being related to biological semiotics and explicated in the relational biological school of Rashevsky and Rosen. Atomic control systems and models are described as the canonical forms of semiotic organization, sharing measurement relations, but differing topologically in that control systems are circularly and models linearly related to their environments. Computation in control systems is introduced, motivating hierarchical decomposition, hybrid modeling and control systems, and anticipatory or model-based control. The semiotic relations in complex control systems are described in terms of relational constraints, and rules and laws are distinguished as contingent and necessary functional entailments, respectively. Finally, selection as a meta-level of constraint is introduced as the necessary condition for semantic relations in control systems and models.     

Individual-and population-based diversity in restriction-modification systems

Restriction-modification (RM) systems are cognate gene complexes that code for an endonuclease and a methylase. They are often thought to have developed in bacteria as protection against invading genetic material, e.g., phage DNA. The high diversity of RM systems, as observed in nature, is often ascribed to the coevolution of RM systems (which ‘invent’ novel types) and phages. However, the extent to which phages are insensitive to RM systems casts doubts on the effectiveness of RM systems as protection against infection and thereby on the reason for the diversity of RM systems. We present an eco-evolutionary model in order to study the evolution of the diversity of RM systems. The model predicts that in general diversity of RM systems is high. More importantly, the diversity of the RM systems is expressed either at the individual level or at the population level. In the first case all individuals carry RM systems of all sequence specificities, whereas in the second case they carry only one RM system or no RM systems at all. Nevertheless, in the second case the same number of sequence specificities are present in the population.     

Synchronous and asynchronous systems of threshold elements

The role of synchronism in systems of threshold elements (such as neural networks) is examined. Some important differences between synchronous and asynchronous systems are outlined. In particular, important restrictions on limit cycles are found in asynchronous systems along with multi-frequency oscillations which do not appear in synchronous systems. The possible role of deterministic chaos in these systems is discussed.     

Type IVB secretion by intracellular pathogens

A growing number of pathogens are being found to possess specialized secretion systems which they use in various ways to subvert host defenses. One class, called type IV, are defined as having homology to the conjugal transfer systems of naturally occurring plasmids. It has been proposed that pathogens with type IV secretion systems have acquired and adapted the conjugal transfer systems of plasmids and now use them to export toxins. Several well-characterized intracellular pathogens, including Legionella pneumophila , Coxiella burnetii , Brucella abortus , and Rickettsia prowazekii , contain type IV systems which are known or suspected to be of critical importance in their ability to cause disease. Specifically, these systems are believed to be the key factors determining intracellular fate, and thus the ability to replicate and cause disease.     

Learning to live in a global commons: socioeconomic challenges for a sustainable environment

Ecologists, economists and other social scientists have much incentive for interaction. First of all, ecological systems and socioeconomic systems are linked in their dynamics, and these linkages are key to coupling environmental protection and economic growth. Beyond this, however, are the obvious similarities in how ecological systems and socioeconomic systems function, and the common theoretical challenges in understanding their dynamics. This should not be surprising. Socioeconomic systems are in fact ecological systems, in which the familiar ecological phenomena of exploitation, cooperation and parasitism all can be identified as key features. Or, viewed from the opposite perspective, ecological systems are economic systems, in which competition for resources is key, and in which an evolutionary process shapes the individual agents to a distribution of specialization of function that leads to the emergence of flows and functionalities at higher levels of organization. Most fundamentally, ecological and socioeconomic systems alike are complex adaptive systems, in which patterns at the macroscopic level emerge from interactions and selection mechanisms mediated at many levels of organization, from individual agents to collectives to whole systems and even above. In such complex adaptive systems, robustness must be understood as emergent from selection processes operating at these many different levels, and the inherent nonlinearities can trigger sudden shifts in regimes that, in the case of the biosphere, can have major consequences for humanity. This lecture will explore the complex adaptive nature of ecosystems, and the implications for the robustness of ecosystem services on which we depend, and in particular examine the conditions under which cooperative behavior emerges. It will then turn attention to the socioeconomic systems in which environmental management is based, and ask what lessons can be learned from our examination of natural systems, and how we can modify social norms to achieve global cooperation in managing our common future. Of special interest will be issues of intragenerational and intergenerational equity, and the importance of various forms of discounting.     

Stability Investigations of Linearized Systems with Random Structure

The relationship between complexity and stability of linearized systems, being characterized by structural parameters like dimension and connectance and interaction strength are investigated by computing relative frequencies of stability. The results are compared with those of other authors. Additionally systems with a special cyclic subsystem structure are investigated. Comparing the stability properties for structured and unstructered systems no increase in stability can be stated if systems are structures in the supposed way.     

Toxin-Antitoxin Systems in the Mobile Genome of Acidithiobacillus ferrooxidans

Toxin-antitoxin (TA) systems are genetic modules composed of a pair of genes encoding a stable toxin and an unstable antitoxin that inhibits toxin activity. They are widespread among plasmids and chromosomes of bacteria and archaea. TA systems are known to be involved in the stabilization of plasmids but there is no consensus about the function of chromosomal TA systems. To shed light on the role of chromosomally encoded TA systems we analyzed the distribution and functionality of type II TA systems in the chromosome of two strains from Acidithiobacillus ferrooxidans (ATCC 23270 and 53993), a Gram-negative, acidophilic, environmental bacterium that participates in the bioleaching of minerals. As in other environmental microorganisms, A. ferrooxidans has a high content of TA systems (28-29) and in twenty of them the toxin is a putative ribonuclease. According to the genetic context, some of these systems are encoded near or within mobile genetic elements. Although most TA systems are shared by both strains, four of them, which are encoded in the active mobile element ICEAfe1, are exclusive to the type strain ATCC 23270. We demostrated that two TA systems from ICEAfe1 are functional in E. coli cells, since the toxins inhibit growth and the antitoxins counteract the effect of their cognate toxins. All the toxins from ICEAfe1, including a novel toxin, are RNases with different ion requirements. The data indicate that some of the chromosomally encoded TA systems are actually part of the A. ferrooxidans mobile genome and we propose that could be involved in the maintenance of these integrated mobile genetic elements.     

非线性森林发展系统研究进展

就近年来国内外对非线性森林发展系统的研究进展做一综述，介绍了一些非线性森林发展系统模型，分析了非线性森林系统的研究结果。     

The numerical solution of stiff differential equations

This paper first discusses the conditions in which a set of differential equations should give stable solutions, starting with linear systems assuming that these do not differ greatly in this respect from non-linear systems. Methods of investigating the stability of particular systems are briefly discussed. Most real biochemical systems are known from observation to be stable, but little is known of the regions over which stability persists; moreover, models of biochemical systems may not be stable, because of inaccurate choice of parameter values.The separate problem of stability and accuracy in numerical methods of approximating the solution of systems of non-linear equations is then treated. Stress is laid on the consistently unsatisfactory results given by explicit methods for systems containing "stiff" equations, and implicit multistep methods are particularly recommended for this class of problem, which is likely to include many biochemical model systems. Finally, an iteration procedure likely to give convergence both in multistep methods and in the steady-state approach is recommended, and areas in which improvement in methods is likely to occur are outlined.     

Evaluation of the sustainability of contrasted pig farming systems: breeding programmes

The sustainability of breeding activities in 15 pig farming systems in five European countries was evaluated. One conventional and two differentiated systems per country were studied. The Conventional systems were the standard systems in their countries. The differentiated systems were of three categories: Adapted Conventional with focus on animal welfare, meat quality or environment (five systems); Traditional with local breeds in small-scale production (three systems) and Organic (two systems). Data were collected with a questionnaire from nine breeding organisations providing animals and semen to the studied farming systems and from, on average, five farmers per farming system. The sustainability assessment of breeding activities was performed in four dimensions. The first dimension described whether the market for the product was well defined, and whether the breeding goal reflected the farming system and the farmers’ demands. The second dimension described recording and selection procedures, together with genetic change in traits that were important in the system. The third dimension described genetic variation, both within and between pig breeds. The fourth dimension described the management of the breeding organisation, including communication, transparency, and technical and human resources. The results show substantial differences in the sustainability of breeding activities, both between farming systems within the same category and between different categories of farming systems. The breeding activities are assessed to be more sustainable for conventional systems than for differentiated systems in three of the four dimensions. In most differentiated farming systems, breeding goals are not related to the system, as these systems use the same genetic material as conventional systems. The breeds used in Traditional farming systems are important for genetic biodiversity, but the small scale of these systems renders them vulnerable. It is hoped that, by reflecting on different aspects of sustainability, this study will encourage sustainable developments in pig production.     

Bimolecular systems: I. Linear systems of complexes

A vast number of biologically important processes are based upon bimolecular systems. In these systems intermediate complexes are formed. Bimolecular systems in which no complex-complex interactions occur are called linear systems of complexes. A definition and some characteristic properties of these systems are given here. There may exist a contradiction of Onsager's principle of detailed balancing in these systems; however, no principal differences are found between the steady state behavior of an open system and that of a closed system. It is shown that the steady state behavior of a linear system of complexes of arbitrary complexity has some similarities with the steady state behavior of a simple bimolecular system, e.g., Michaelis-Menten enzymatic reaction. Multiplicity of action of the substances participating in biomolecular processes may produce some qualitative differences in the steady state behavior of the system.     

THE COORDINATION OF POTENTIAL PACEMAKERS IN THE HYDROID TUBULARIA

Sectioning experiments and electrical recording indicate thatthere are many potential pacemakers in polyps of the hydroidTubularia. Functionally the pacemakers are organized primarilyinto pacemaker systems, groups within which there is tight coupling.The different pacemaker systems of a polyp are loosely coupledto one another. There are two principal systems in Tubularia,one in the polyp neck (the NP system) and one in the hydranth(the HP system). In addition, there are pacemakers controllingactivities of individual tentacles. Activity in the NP systemis usually not associated with observable polyp behavior. HPsystem activity is correlated with behavioral responses termedconcerts. Concerts are probably digestive activities; they resultin the mixing of food being digested and the distribution ofthe products of this digestion. The NP systems of polyps ona colony are loosely coupled to one another through one of thethree conducting systems found in Tubularia stalks. The loosecoupling between NP systems of polyps on a colony and the loosecoupling between NP and HP systems within single polyps resultsin there being some coordination of concert activity throughouta colony.     

Autonomy and hypersets

This paper has two primary aims. The first is to provide an introductory discussion of hyperset theory and its usefulness for modeling complex systems. The second aim is to provide a hyperset analysis of several perspectives on autonomy: Robert Rosen's metabolism-repair systems and his claim that living things are closed to efficient cause, Maturana and Varela's autopoietic systems, and Kauffman's cataytically closed systems. Consequences of the hyperset models for Rosen's claim that autonomous systems have non-computable models are discussed.