Competitive processes. II. Stability of random systems

In this work, by employing the concept of vector Lyapunov functions and the theory of random differential inequalities, the stability analysis of random competitive systems is initiated in a systematic and unified way. Furthermore, an attempt has been made to formulate and partially resolve the “deterministic vs. stochastic”, and the “complexity vs. stability” problems in stochastic competitive processes. Finally, the usefulness of the stability analysis of the competitive systems has been demonstrated by exhibiting several well-known examples of competitive processes in biological, medical, physical and social sciences in a coherent way.     

A low temperature investigation of the intermediates of the photocycle of light-adapted bacteriorhodopsin. Optical absorption and fluorescence measurements.

Optical absorption and emission measurements have been made on samples of light-adapted purple membrane of Halobacterium halobium at temperatures ranging from 77 K to room temperature. As a result of these experiments a set of equations is given which described thermal and photochemical reactions interrelating various intermediates of the reaction cycle of the chromophore of light-adapted bacteriorhodopsin (BR). Further some specific problems connected to these intermediates have been investigated. Thus the room temperature emission spectrum of bacteriorhodopsin has been found to exhibit a Stokes shift of 3430 cm-1 only, if low excitation intensities are used. The recently detected intermiediate P-BR can be shown to convert thermally into bacteriorhodopsin following a first-order decay with the activation energy delta E = 2.4 +/- 0.2 kcal/mol. The thermal decay of K-BR consists of two exponentials if measured on purple membrane suspensions in a mixture of H2O and glycerol (1 : 1, v/v). A simple procedure is given for trapping the intermediate L-BR at 170 K in a very pure form. M-BR is shown to consist of two species, MI-BR and MII-BR. They are characterized by similar optical absorption spectra but different thermal stability. Further the oscillator strengths corresponding to the long wavelength absorption bands of the intermediates bacteriorhodopsin, K-, L, MI- and MII-BR have been calculated. They have been discussed with respect to the question which of the corresponding absorption spectra show the characteristics of isomerism of the chromophore or simply solvatochromism.     

Transport processes in a sound of a large lake

There are some problems in modelling the water exchange between a bay and the main body of a large lake. The objective of this study was to clarify which processes are important in the water exchange and must be taken into account in modelling. The study was mainly based on current measurements in the outlet of a bay system (Tiirinselkä-Lehesselkä) of lake Päijänne with an acoustic current profiler and recordings of temperature profile. High currents in the hypolimnion were observed during periods of high stratification, when the flow in the hypolimnion is caused by the horizontal pressure gradient associated with the thermocline slope in the sound. In some cases the large water exchange was due to the seiches in main body of the lake. Water exchange and current velocity in the sound were clearly smaller when the water was homogeneous. This paper gives quantitative results of water exchange and its dependence on different factors for summer 1989.     

Combined nitrification-denitrification processes

Abstract: Nitrification and denitrification have traditionally been regarded as essentially separate phenomena, carried out by different bacteria in segregated areas of soil, sediments, water or reactors. However, research in the 1980s and 1990s has established that nitrifiers and denitrifiers are not as metabolically fastidious as previously thought, and strict segregation is not necessary. Moreover, some bacteria are able to convert NH⁴₄ and other reduced nitrogen compounds to nitrogen gas and the gaseous nitrogen oxides in combined nitrification/denitrification processes. Such organisms are of interest for wastewater treatment for two opposing reasons. Firstly, the idea of single-stage nitrogen removal has obvious attractions for system design. Secondly, N₂O is a serious pollutant, implicated in virtually all current environmental problems (e.g. acid rain, greenhouse effect, ozone depletion).     

沼泽湿地垦殖前后土壤温度变化及其对土壤热状况的影响

沼泽湿地具有重要的生态与环境功能,其对全球气候变化较为敏感,土壤温度变化能够很好地指示气候的波动.沼泽湿地土壤温度呈明显的"正弦曲线"型年、季动态,不同深度土壤年均温度呈"U"型特征.5～9月份沼泽湿地10 cm土壤平均温度为11.69±3.04℃,垦殖后农田土壤为1.80±3.41℃.沼泽湿地土壤8、9月份土壤呼吸分别为156.41±76.91 mg·m^-2·h^-1和116.75±57.43 m^-2·h^-1,是同时期农田土壤呼吸通量的14.6%和13.1%,土壤温度与土壤呼吸通量呈显著正相关关系.     

Interacting processes in protein coagulation.

A strong interest is currently focused on protein self-association and deposit. This usually involves conformational changes of the entire protein or of a fragment. It can occur even at low concentrations and is responsible for pathologies such as systemic amyloidosis, Alzheimer's and Prion diseases, and other neurodegenerative pathologies. Readily available proteins, exhibiting at low concentration self-association properties related to conformational changes, offer very convenient model systems capable of providing insight into this class of problems. Here we report experiments on bovine serum albumin, showing that the process of conformational change of this protein towards an intermediate form required for coagulation occurs simultaneously and interacts with two more processes: mesoscopic demixing of the solution and protein cross-linking. This pathway of three interacting processes allows coagulation even at very low concentrations, and it has been recently observed also in the case of a nonpeptidic polymer. It could therefore be a fairly common feature in polymer coagulation/gelation. Proteins 1999;37:116-120.     

Stochastic processes in nano-biomachines revealed by single molecule detection

Proteins and their assemblies are in the size of nanometers and are exposed to thermal disturbances. Many molecular processes in these nano-biomachines are stochastic, reflecting the fact that the input energy level is comparable to that of thermal energy. These stochastic properties have been revealed by recently developed single molecule detection techniques. The movement of molecular motors, myosin, and kinesin, has been suggested to be thermally driven. Random thermal movement is biased using the energy of the ATP hydrolysis. Thus, the molecular motors may harness thermal energy. This unique mechanism may be important in understanding the operation of the biosystems.     

Principles of optimization and scaling of certain processes in the vaccine production technology. 3. Method of determination of the optimal method of thermal sterilization of sugar solutions

One of the most widespread methods of thermal sugar sterilization is the use of saturated water vapour under pressure in the capacity of heat source. Guaranteed sterility of solutions should be reached under conditions providing the least sugar splitting. However, in practice the integral effect of the thermal field on the solution is as a rule not taken into consideration. A new calculation method permitting to determine the amount of sugar split in the varying thermal field.     

Biological applications of the theory of birth-and-death processes

In this review, we discuss applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described. Birth-and-death processes, with some straightforward additions such as innovation, are a simple, natural and formal framework for modeling a vast variety of biological processes such as population dynamics, speciation, genome evolution, including growth of paralogous gene families and horizontal gene transfer and somatic evolution of cancers. We further describe how empirical data, e.g. distributions of paralogous gene family size, can be used to choose the model that best reflects the actual course of evolution among different versions of birth-death-and-innovation models. We conclude that birth-and-death processes, thanks to their mathematical transparency, flexibility and relevance to fundamental biological processes, are going to be an indispensable mathematical tool for the burgeoning field of systems biology.     

Calcium regulation in neurons: transport processes.

The ionic stoichiometry of the major Ca2+ transport mechanisms in neurons is still a matter for debate. The past year has seen some particularly interesting developments in this field, not least the finding that the neuronal Na(+)-Ca2+ exchange may be able to transport K+.     

Controlled freezing of nonideal solutions with application to cryosurgical processes.

Success of a cryosurgical procedure, i.e., maximal cell destruction, requires that the cooling rate be controlled during the freezing process. Standard cryosurgical devices are not usually designed to perform the required controlled process. In this study, a new cryosurgical device was developed which facilitates the achievement of a specified cooling rate during freezing by accurately controlling the probe temperature variation with time. The new device has been experimentally tested by applying it to an aqueous solution of mashed potatoes. The temperature field in the freezing medium, whose thermal properties are similar to those of biological tissue, was measured. The cryoprobe temperature was controlled according to a desired time varying profile which was assumed to maximize necrosis. The tracking accuracy and the stability of the closed loop control system were investigated. It was found that for most of the time the tracking accuracy was excellent and the error between the measured probe temperature and the desired set point is within +/- 0.4 degrees C. However, noticeable deviations from the set point occurred due to the supercooling phenomenon or due to the instability of the liquid nitrogen boiling regime in the cryoprobe. The experimental results were compared to those obtained by a finite elements program and very good agreement was obtained. The deviation between the two data sets seems to be mainly due to errors in positioning of the thermocouple junctions in the medium.     

Permeability of lipid membranes revised in relation to freeze-thaw processes.

Water and solute activity gradients created during freeze-thaw processes produce water and solute fluxes across the cell membrane resulting in volume changes. Under these conditions, osmotic and thermal stresses affect the curvature, the phase behavior, and the surface properties of the lipid bilayer. These structural changes are not considered by the classical formalisms describing permeability of lipid membranes to water and nonelectrolytes such as the Nernst-Planck equation, Eyring's absolute rate theory, and Kedem-Katchalsky's thermodynamic of irreversible processes approach. In this paper, the influence of such changes on the glycerol permeation kinetics are reported. The results indicate that osmotic and chemical effects of the cryoprotectant on the membrane properties affect the rate of volume swelling depending on whether the membrane is in the gel or in the liquid crystalline state.     

Mathematical modeling and parameters estimation of anaerobic fermentation processes

In the paper some problems of the mathematical modeling of anaerobic (methane) fermentation of animal waste in stirred tank bioreactors are considered. Laboratory experiments are carried out with highly concentrated organic pollutants and transient step responses of the control output for continuous methane fermentation are obtained. The dynamic behavior of this process is described by sets of deterministic nonlinear differential equations from 2nd order with different structures. Static characteristics are obtained with these models analytically. Investigations by computer simulation of the methane fermentation are performed with the aim to chose appropriate models for automatic control system design of this process.     

Entropy flow in cyclic biological processes

Biological processes are quantized, molecular, and often cyclical. Taken altogether, they comprise a heat engine working between an upper thermal reservoir at 6000 K and a lower thermal reservoir at 300 K. For optimum efficiency, such a heat engine would give out as much entropy at 300 K as it takes in at 6000 K. Yet the individual processes comprising this heat engine are quantized and molecular. What does entropy mean for them? Can we trace the entropy flow in the separate molecular cycles that are all we have when we look carefully at the overall heat engine? I think we can, and in doing so will learn why so many biological units are 5–10 μm in size.     

LCA in decision-making processes

Synthetic sulfuric acid is used in a wide range of applications in fine chemical industry. Despite an already performed optimization of input amounts, used sulfuric acid is still a quantitatively important waste by-product. As a result, different utilization technologies for used sulfuric acid exist:

1. production of gypsum
2. thermal reductive cracking
3. thermal cracking and oxidation

This makes an LCA study of this waste by-product quite interesting. In this paper:

? the starting point for a comparative LCA of the above mentioned utilization technologies at a concrete situation is explained, in a work of Ciba-Geigy Corp.

? a short summary of the comparative LCA is presented

? lessons learned from performing the LCA and using it in a decision process are described.

     

Abstract processes in texture discrimination.

In this study some experiments on texture segmentation are reported using the local Gabor power spectrum. The techniques applied are: (1) supervised pixel classification; (2) boundary detection by spectral dissimilarity estimation; (3) region-based segmentation based on Gaussian spectral estimation; and (4) the same as (3) but based on central moments of the local spectrum. It is shown that very-acceptable-to-excellent results can be obtained. It is argued, however, that the shortcomings of region-based and boundary-based approaches require that both processes should act in parallel, not only in digital image processing but also in the modelling of visual perception.     

Denatured increments of heat capacity in globular proteins and its connection with vitrification processes

Absolute values of heat capacity for some hydrated globular proteins have been studied by differential scanning calorimetry (DSC) method. It has been found that for the proteins with completely bound water, like in the case of protein solutions, the value of heat capacity of denatured proteins is higher than that prior to denaturation. Depending on temperature and humidity the denatured proteins can be either in high elastic or glass state. Specific heat capacities for these two states have the same values for all proteins and depend only on temperature with a characteristic increment of 0.55 J/g.K. at glass transition. The glass transitions were observed not only in denatured but also in native proteins. As it follows from our results, the main contribution to the heat capacity increment at denaturation is connected with the thermal motion in the protein globule which is in contrast with the commonly accepted ideas.     

Metabolic effects of furaldehydes and impacts on biotechnological processes

There is a growing awareness that lignocellulose will be a major raw material for production of both fuel and chemicals in the coming decades—most likely through various fermentation routes. Considerable attention has been given to the problem of finding efficient means of separating the major constituents in lignocellulose (i.e., lignin, hemicellulose, and cellulose) and to efficiently hydrolyze the carbohydrate parts into sugars. In these processes, by-products will inevitably form to some extent, and these will have to be dealt with in the ensuing microbial processes. One group of compounds in this category is the furaldehydes. 2-Furaldehyde (furfural) and substituted 2-furaldehydes—most importantly 5-hydroxymethyl-2-furaldehyde—are the dominant inhibitory compounds found in lignocellulosic hydrolyzates. The furaldehydes are known to have biological effects and act as inhibitors in fermentation processes. The effects of these compounds will therefore have to be considered in the design of biotechnological processes using lignocellulose. In this short review, we take a look at known metabolic effects, as well as strategies to overcome problems in biotechnological applications caused by furaldehydes.     

Alkaline serine proteinase from Thermomonospora fusca YX. Stability to heat and denaturants.

The serine proteinase isolated from Thermomonospora fusca YX shows considerable thermal stability up to 80 degrees C, and progressive inactivation occurs at higher temperatures. Lyotropic salts affected the thermal stability of the enzyme at 85 degrees C, suggesting that disruption of hydrophobic interactions play an important role in the decreased thermal stability of the enzyme above 80 degrees C. Thermal stability is highly pH-dependent; above pH 6.0-6.5 there is a sharp decrease in the stability of the enzyme, reflecting increased autolysis. Although some stabilization occurs upon increasing ionic strength, Ca2+ binding does not appear to play a role in thermal stability. Denaturants, i.e. 8 M-urea, 6 M-guanidinium chloride or 1% SDS, had no significant effect on the activity of the enzyme after 24 h at 25 degrees C.