Receptor-based models with hysteresis for pattern formation in hydra

In this paper, we propose a new receptor-based model for pattern formation and regulation in a fresh-water polyp, namely hydra. The model is defined in the form of a system of reaction-diffusion equations with zero-flux boundary conditions coupled with a system of ordinary differential equations. The production of diffusible biochemical molecules has a hysteretic dependence on the density of these molecules and is modeled by additional ordinary differential equations. We study the hysteresis-driven mechanism of pattern formation and we demonstrate the advantages and constraints of its ability to explain different aspects of pattern formation and regulation in hydra. The properties of the model demonstrate a range of stationary and oscillatory spatially heterogeneous patterns, arising from multiple spatially homogeneous steady states and switches in the production rates.     

The thermodynamics of water-protein interactions

Information about the effects of water on protein structure and function can be obtained from studies on freeze dried protein powders of varying water content. Sorption isotherms of water on proteins can be used to obtain thermodynamic quantities for water-protein interactions. Since such isotherms show hysteresis, there is doubt in regard to their interpretation.General expressions for the thermodynamic quantities of sorption are derived. If isotherms represent data at equilibrium, it is possible to calculate these thermodynamic quantities.There are two types of hysteresis, non-equilibrium hysteresis and equilibrium hysteresis. Absorption and desorption isotherms can show equilibrium hysteresis if different protein conformations, which are only slowly interconvertible, can be present. In this case valid thermodynamic quantities can be obtained. Experimental tests for equilibrium hysteresis are presented. More experiments are needed before definite conclusions can be drawn in regard to isotherms in the literature.If the protein conformation in a protein powder is similar to the protein conformation in aqueous solution, equilibrium data obtained from sorption isotherms can be used to approximate thermodynamic quantities for the interaction of water with proteins in aqueous solution. Examination of what experimental evidence is available indicates that the protein in powders prepared by desorption of water should have a conformation similar to that in solution. Further study of such samples will help to clarify the thermodynamics of water-protein interactions in aqueous solution.     

Study of water-protein interaction by high resolution NMR

The interaction between carbonic anhydrase B in the molten globule state and water molecules was studied by high-resolution NMR spectroscopy. NMR spin diffusion experiments revealed spin diffusion propagation from the protein to waters. This is a process of complex bioexponential kinetics presented in spin diffusion spectra as a change in water signal intensity dependent on the post-excitation time of protein molecules. Its reverse, spin diffusion propagation from waters to the protein, was also found. These phenomena are protein concentration- and temperature-dependent and shown to be possibly explained with the assumption that there exist water-protein complexes provoking the formation of large branched associations. At a temperature above 309 K, a stepwise increase in the interaction between waters and proteins occurs in these complexes. The formation of water-protein associations is induced by increasing temperature and/or protein concentration. In these associations, at normal temperature, the protein mobility is close to that of carbonic anhydrase B dimers.     

Thermodynamic analysis of nonelectrolyte sorption in plant cuticles: The effects of concentration and temperature on sorption of 4-nitrophenol

The sorption of 4-nitrophenol (4-NP) in enzymatically isolated cuticles ofLycopersicon esculentum fruits andFicus elastica leaves was studied as a function of temperature and solute concentration. Plots of the concentrations of 4-NP sorbed in the cuticle versus the equilibrium concentrations in the aqueous phase gave linear isotherms at low concentrations that tended to approach plateaus at higher sorbate concentrations ( 10 mmol·kg^-1). At low concentrations of sorbed 4-NP, cuticles have sorptive properties similar to those of organic solvents which are able to form intermolecular hydrogen bonds, while at higher concentrations their solid nature becomes apparent. During sorption of 4-NP the cutin matrix swells and new sorption sites are successively formed. The partition coefficients of 4-NP in the system cuticle/buffer are functions of temperature and concentration. At high sorbate concentrations (approx. 1 mol·kg^-1) they approach a value of 1. Different sorptive properties were observed for the cutin regions normally encrusted with soluble cuticular lipids (SCL) and those without SCL. Increasing temperature augmented the number of sorption sites in the cutin ofLycopersicon while no effect was observed withFicus. The changes of partial molar free energy (G ^o _tr), enthalpy (H ^o _tr), and entropy (S ^o _tr) for the phase transfer of 4-NP also depended on sorbate concentration: H ^o _tr and S ^o _tr were negative and steeply decreased at high sorbate concentrations. This is due to solute-solute interactions replacing solute-cutin interactions at high concentrations resulting in solid precipitates of solute within the cutin matrix. This formation of ordered solid domaines starting from a small number of nonelectrolyte molecules interacting with the cutin is proposed as a model for the intracuticular deposition of SCL.Abbreviations CM cuticular membrane - MX polymer matrix membrane - 4-NP 4-nitrophenol - SCL soluble cuticular lipids     

Thermodynamic models of binding ligands to nucleic acids

Models of adsorption were considered, which describe the binding of biologically active ligands on DNA templates. The binding is described most comprehensively and in greatest detail by the distribution function, which determines the probability of detecting the preset number of adsorbed ligands on the template. In the case of noncooperative binding, this function corresponds to the Gaussian distribution and is characterized by two quantities: the mean value of the occupation of the template by ligands and the dispersion of occupation. The accuracy of the occupation of the template by ligands is inversely proportional to dispersion. As the length of the template and the number of reaction sites covered by one ligand upon binding increase, the accuracy of the occupation of the template by ligands increases. An important characteristic of binding is the degree of coverage of the template by ligands. This characteristic represents the portion of template reaction sites covered by all ligands adsorbed on the template. If polycations are bound to nucleic acid molecules, the coverage of the template determines the transition of nucleic acids to a compact state. The degree of template coverage for extended ligands depends only slightly on the binding constant in a wide range of concentrations of a free ligand in solution. Different adsorption models are considered from the unified point of view. The classification of cooperative interactions for a wide class of systems is given, from situations when several ligands are bound on nucleic acid templates to a situation when templates change by the action of ligands and begin to interact with each other.     

Thermodynamic and breakthrough column studies for the selective sorption of chromium from industrial effluent on activated eucalyptus bark

Studies were carried out on adsorption of Cr(VI) on an adsorbent made from eucalyptus bark. Results revealed that sorption of chromium on activated eucalyptus bark (AEB) was endothermic in nature. Thermodynamic parameters such as the entropy change, enthalpy change and Gibb's free energy change were found out to be 100.97 J mol(-1)K(-1), 33 kJ mol(-1) and -0.737 kJ mol(-1), respectively. Industrial chrome effluent of different chromium concentration at different pH was used as feedstock for the fixed bed adsorption studies. When effluent was fed to the column at low pH of 2, the breakthrough volume increased significantly compared to effluent at higher pH of 4.85. The surface properties of sorbent were characterized by the Scanning electron microscopy, X-ray diffraction technique and Infrared techniques. It was concluded that AEB sorbent column could be used effectively for removal of chromium from industrial effluents by reducing the pH of chrome effluent to two and at optimal column conditions.     

Designing biological models of hysteresis live systems of osseous tissue and periosteum

Biological models of osseous tissue and periosteum have been developed. Biocompatible materials of titaniumnickel as an integral part of implant-tissue composites have been already functioning for five years, substituting for damaged bone fragments. The defects of skeletal kinematic sections of the mandible of experimental animals were replaced by biomechanical models of implant-tissue composites of the osseous tissue and periosteum. The composites were formed by joining the models of extracellular matrixes of osseous tissue and periosteum and the natural tissues. The validity of methodological propositions and optimal technological solutions have been proved by the absence of life-time signs of biochemical, biomechanical, hysteresis or thermodynamic incompatibility on tissue and skeletal levels.     

Observed hysteresis of virus capsid disassembly is implicit in kinetic models of assembly

For many protein multimers, association and dissociation reactions fail to reach the same end point; there is hysteresis preventing one and/or the other reaction from equilibrating. We have studied in vitro assembly of dimeric hepatitis B virus (HBV) capsid protein and dissociation of the resulting T = 4 icosahedral capsids. Empty HBV capsids composed of 120 capsid protein dimers were more resistant to dissociation by dilution or denaturants than anticipated from assembly experiments. Using intrinsic fluorescence, circular dichroism, and size exclusion chromatography, we showed that denaturants dissociate the HBV capsids without unfolding the capsid protein; unfolding of dimer only occurred at higher denaturant concentrations. The apparent energy of interaction between dimers measured in dissociation experiments was much stronger than when measured in assembly studies. Unlike assembly, capsid dissociation did not have the concentration dependence expected for a 120-subunit complex; consequently the apparent association energy systematically varied with reactant concentration. These data are evidence of hysteresis for HBV capsid dissociation. Simulations of capsid assembly and dissociation reactions recapitulate and provide an explanation for the observed behavior; these results are also applicable to oligomeric and multidomain proteins. In our calculations, we find that dissociation is impeded by temporally elevated concentrations of intermediates; this has the paradoxical effect of favoring re-assembly of those intermediates despite the global trend toward dissociation. Hysteresis masks all but the most dramatic decreases in contact energy. In contrast, assembly reactions rapidly approach equilibrium. These results provide the first rigorous explanation of how virus capsids can remain intact under extreme conditions but are still capable of "breathing." A biological implication of enhanced stability is that a triggering event may be required to initiate virus uncoating.     

Development of biological models of hysteresis live systems of the osseous tissue and periosteum

Biological models of osseous tissue and periosteum have been developed. Biocompatible materials from titaniumnickel as an organic part of implant - tissue composites have been already functioning for five years, replacing injured osteal fragments. The defects of skeletal kinematic sections of the mandible of experiment animals were replaced by biomechanical models of implant - tissue composites of the osseous tissue and periosteum. The composites were formed by joining the models of extracellular matrices of osseous tissue and periosteum and natural tissues. The validity of methodological propositions and optimum technological solutions have been proved by the absence of life-time signs of biochemical, biomechanical, hysteresis, and thermodynamic incompatibility on tissue and skeletal levels.     

Thermal hysteresis proteins

Extreme environments present a wealth of biochemical adaptations. Thermal hysteresis proteins (THPs) have been found in vertebrates, invertebrates, plants, bacteria and fungi and are able to depress the freezing point of water (in the presence of ice crystals) in a non-colligative manner by binding to the surface of nascent ice crystals. The THPs comprise a disparate group of proteins with a variety of tertiary structures and often no common sequence similarities or structural motifs. Different THPs bind to different faces of the ice crystal, and no single mechanism has been proposed to account for THP ice binding affinity and specificity. Experimentally THPs have been used in the cryopreservation of tissues and cells and to induce cold tolerance in freeze susceptible organisms. THPs represent a remarkable example of parallel and convergent evolution with different proteins being adapted for an anti-freeze role.     

蛋白质折迭的不可逆热力学理论及蛋白质动态热力学结构(英)

在机械力学及热力学基础上阐述蛋白质的各种物理性质是从物理学角度理解生物学的基础性工作.详细讨论了蛋白质折迭的不可逆热力学理论,蛋白质动态热力学结构理论.理论推断蛋白质动态热力学变化是一切生物学状态变化的基本热力学状态单位并作为分子生物学变化的分子开关.利用此理论解释了蛋白质的物理学性质及麻醉药的生物物理学机制.     

Isotherm and kinetic models and cell surface analysis for determination of the mechanism of metal sorption by Aspergillus versicolor

The isolate Aspergillus versicolor was obtained from an estuary, which is exposed to metal contamination. It was found to have a good metal tolerance and sorption capacity. Further studies revealed that the rate of metal removal from solution is very rapid in the first 5-10 min, and is favoured by a pH of 6.0. The biosorption data obtained was explained by the Freundlich adsorption isotherm model and followed a pseudo-second order kinetics reaction. The fungus showed a higher accumulation of fatty acids when grown in presence of metals as compared to the mycelium grown in absence of the metal; there was also an increase in the saturation index of fatty acids in presence of Cu(2+) which serves as a protective mechanism for the fungus. Fourier Transform Infrared, scanning electron microscopy and EDAX analysis indicated that metal removal from solution by A. versicolor occurred by a passive adsorption to the fungal cell surface, involving an ion exchange mechanism.     

Pseudo-second order model for sorption processes

A literature review of the use of sorbents and biosorbents to treat polluted aqueous effluents containing dyes/organics or metal ions has been conducted. Over 70 systems have been reported since 1984 and over 43 of these reported the mechanism as being a pseudo-first order kinetic mechanism. Three sorption kinetic models are presented in this paper and have been used to test 11 of the literature systems previously reported as first order kinetics and one system previously reported as a second order process. In all 12 systems, the highest correlation coefficients were obtained for the pseudo-second order kinetic model.     

Correlation between Thermodynamic Efficiency and Ecological Cyclicity for Thermodynamic Power Cycles

A sustainable global community requires the successful integration of environment and engineering. In the public and private sectors, designing cyclical (“closed loop”) resource networks increasingly appears as a strategy employed to improve resource efficiency and reduce environmental impacts. Patterning industrial networks on ecological ones has been shown to provide significant improvements at multiple levels. Here, we apply the biological metric cyclicity to 28 familiar thermodynamic power cycles of increasing complexity. These cycles, composed of turbines and the like, are scientifically very different from natural ecosystems. Despite this difference, the application results in a positive correlation between the maximum thermal efficiency and the cyclic structure of the cycles. The immediate impact of these findings results in a simple method for comparing cycles to one another, higher cyclicity values pointing to those cycles which have the potential for a higher maximum thermal efficiency. Such a strong correlation has the promise of impacting both natural ecology and engineering thermodynamics and provides a clear motivation to look for more fundamental scientific connections between natural and engineered systems.