A new model for thermal diffusion: kinetic approach

We present a new model for thermal diffusion, and we compare its results for both simple and real systems. This model is derived from a kinetic approach with explicit mass and chemical contributions. It involves self-diffusion activation free energies, following Prigogine's original approach. We performed, furthermore, both equilibrium and nonequilibrium molecular dynamics evaluations in order to compute respectively the self-diffusion activation free enthalpies and the Soret coefficient when no experimental data were available. Our model is in very good agreement with simulation data on Lennard-Jones mixtures, and a good behavior is noted for the water-ethanol mixture, where the composition dependence at which the Soret coefficient changes its sign is predicted very accurately. Finally, we propose a new water-ethanol experiment at higher temperature in order to check the validity of our model.     

Ice-surface adsorption enhanced colligative effect of antifreeze proteins in ice growth inhibition

This Communication describes a mechanism to explain antifreeze protein's function to inhibit the growth of ice crystals. We propose that the adsorption of antifreeze protein (AFP) molecules on an ice surface induces a dense AFP-water layer, which can significantly decrease the mole fraction of the interfacial water and, thus, lower the temperature for a seed ice crystal to grow in a super-cooled AFP solution. This mechanism can also explain the nearly unchanged melting point for the ice crystal due to the AFP's ice-surface adsorption. A mathematical model combining the Langmuir theory of adsorption and the colligative effect of thermodynamics has been proposed to find the equilibrium constants of the ice-surface adsorptions, and the interfacial concentrations of AFPs through fitting the theoretical curves to the experimental thermal hysteresis data. This model has been demonstrated by using the experimental data of serial size-mutated beetle Tenebrio molitor (Tm) AFPs. It was found that the AFP's ice-surface adsorptions could increase the interfacial AFP's concentrations by 3 to 4 orders compared with those in the bulk AFP solutions.     

Novel three-stage kinetic model for aqueous benzene adsorption on activated carbon

We propose a novel kinetic model for adsorption of aqueous benzene onto both granular activated carbon (GAC) and powdered activated carbon (PAC). The model is based on mass conservation of benzene coupled with three-stage adsorption: (1) the first portion for an instantaneous stage or external surface adsorption, (2) the second portion for a gradual stage with rate-limiting intraparticle diffusion, and (3) the third portion for a constant stage in which the aqueous phase no longer interacts with activated carbon. An analytical solution of the kinetic model was validated with the kinetic data obtained from aqueous benzene adsorption onto GAC and PAC in batch experiments with two different solution concentrations (C(0)=300 mg L(-1), 600 mg L(-1)). Experimental results revealed that benzene adsorption for the two concentrations followed three distinct stages for PAC but two stages for GAC. The analytical solution could successfully describe the kinetic adsorption of aqueous benzene in the batch reaction system, showing a fast instantaneous adsorption followed by a slow rate-limiting adsorption and a final long constant adsorption. Use of the two-stage model gave incorrect values of adsorption coefficients in the analytical solution due to inability to describe the third stage.     

Molecular basis for antifreeze activity difference of two insect antifreeze protein isoforms

The insect spruce budworm(Choristoneura fumiferana) produces antifreeze protein(AFP) to assist in the protection of the over-wintering larval stage and contains multiple isoforms. Structures for two isoforms,known as CfAFP-501 and CfAFP-337,show that both possess similar left-handed β-helical structure,although thermal hysteresis activity of the longer isoform CfAFP-501 is three times that of CfAFP-337. The markedly enhanced activity of CfAFP-501 is not proportional to,and cannot be simply accounted for,by the increased ice-binding site resulting from the two extra coils in CfAFP-501. In or-der to investigate the molecular basis for the activity difference and gain better understanding of AFPs in general,we have employed several different computational methods to systematically study the structural properties and ice interactions of the AFPs and their deletion models. In the context of intact AFPs,a majority of the coils in CfAFP-501 has better ice interaction and causes stronger ice lattice disruption than CfAFP-337,strongly suggesting a cooperative or synergistic effect among β-helical coils. The synergistic effect would play a critical role and make significant contributions to the anti-freeze activity β-helical antifreeze proteins. This is the first time that synergistic effect and its implica-tion for antifreeze activity are reported for β-helical antifreeze proteins.     

A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.     

Approximate critical conditions in thermal explosion theory for a two-step kinetic model

Approximate critical conditions for a thermal explosion problem is developed for a two-step reactions based on theories of Semenov and Frank-Kamenetskii. The aim is to examine the contributions of the radical termination step and the temperature dependent pre-exponential factor on the critical parameters within the framework of classical stationary and non-stationary theories. In the non-stationary case, a more general expression for the critical Semenov parameter (Ψ _cr ) and critical temperature (θ _cr ) were obtained by asymptotic procedure. In the stationary case, numerical estimates for the critical Frank-Kamenetskii parameter (δ _cr ) and the critical temperature (θ _cr ) were obtained by variational method technique. It was observed that the Semenov and Frank-Kamenetskii parameters are greatly influenced by the termination step and the variable pre-exponential factor. Apart from elucidating hitherto unknown features in the theory of thermal explosion, the results are more general as some known results are easily recovered.     

A kinetic model for limonene oxidation

The kinetic regularities of the autooxidation of R(+)−limonene (LH) were experimentally studied at various temperatures. A kinetic model including the main elementary reactions and the corresponding rate constants was developed. The degenerate chain branching during limonene oxidation proceeds via bimolecular reactions and involves hydroperoxide LOOH + LH → L· + LO· + H₂O and LOOH + LOOH → LO· + LO₂ · + H₂O. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 80–86, January, 2008.     

A kinetic model for predicting biodegradation

Biodegradation plays a key role in the environmental risk assessment of organic chemicals. The need to assess biodegradability of a chemical for regulatory purposes supports the development of a model for predicting the extent of biodegradation at different time frames, in particular the extent of ultimate biodegradation within a '10 day window' criterion as well as estimating biodegradation half-lives. Conceptually this implies expressing the rate of catabolic transformations as a function of time. An attempt to correlate the kinetics of biodegradation with molecular structure of chemicals is presented. A simplified biodegradation kinetic model was formulated by combining the probabilistic approach of the original formulation of the CATABOL model with the assumption of first order kinetics of catabolic transformations. Nonlinear regression analysis was used to fit the model parameters to OECD 301F biodegradation kinetic data for a set of 208 chemicals. The new model allows the prediction of biodegradation multi-pathways, primary and ultimate half-lives and simulation of related kinetic biodegradation parameters such as biological oxygen demand (BOD), carbon dioxide production, and the nature and amount of metabolites as a function of time. The model may also be used for evaluating the OECD ready biodegradability potential of a chemical within the '10-day window' criterion.     

A kinetic model for predicting biodegradation

Biodegradation plays a key role in the environmental risk assessment of organic chemicals. The need to assess biodegradability of a chemical for regulatory purposes supports the development of a model for predicting the extent of biodegradation at different time frames, in particular the extent of ultimate biodegradation within a ‘10?day window’ criterion as well as estimating biodegradation half-lives. Conceptually this implies expressing the rate of catabolic transformations as a function of time. An attempt to correlate the kinetics of biodegradation with molecular structure of chemicals is presented. A simplified biodegradation kinetic model was formulated by combining the probabilistic approach of the original formulation of the CATABOL model with the assumption of first order kinetics of catabolic transformations. Nonlinear regression analysis was used to fit the model parameters to OECD 301F biodegradation kinetic data for a set of 208 chemicals. The new model allows the prediction of biodegradation multi-pathways, primary and ultimate half-lives and simulation of related kinetic biodegradation parameters such as biological oxygen demand (BOD), carbon dioxide production, and the nature and amount of metabolites as a function of time. The model may also be used for evaluating the OECD ready biodegradability potential of a chemical within the ‘10-day window’ criterion.     

Heuristic-based tabu search algorithm for folding two-dimensional AB off-lattice model proteins

The protein structure prediction problem is a classical NP hard problem in bioinformatics. The lack of an effective global optimization method is the key obstacle in solving this problem. As one of the global optimization algorithms, tabu search (TS) algorithm has been successfully applied in many optimization problems. We define the new neighborhood conformation, tabu object and acceptance criteria of current conformation based on the original TS algorithm and put forward an improved TS algorithm. By integrating the heuristic initialization mechanism, the heuristic conformation updating mechanism, and the gradient method into the improved TS algorithm, a heuristic-based tabu search (HTS) algorithm is presented for predicting the two-dimensional (2D) protein folding structure in AB off-lattice model which consists of hydrophobic (A) and hydrophilic (B) monomers. The tabu search minimization leads to the basins of local minima, near which a local search mechanism is then proposed to further search for lower-energy conformations. To test the performance of the proposed algorithm, experiments are performed on four Fibonacci sequences and two real protein sequences. The experimental results show that the proposed algorithm has found the lowest-energy conformations so far for three shorter Fibonacci sequences and renewed the results for the longest one, as well as two real protein sequences, demonstrating that the HTS algorithm is quite promising in finding the ground states for AB off-lattice model proteins.     

A new model for the kinetic analysis of thermal degradation of polymers driven by random scission

In this paper, a series of f(α) kinetic equations able to describe the random scission degradation of polymers is formulated in such a way that the reaction rate of the thermal degradation of polymers that go through a random scission mechanism can be directly related to the reacted fraction. The proposed equations are validated by a study of the thermal degradation of poly(butylene terephthalate) (PBT). The combined kinetic analysis of thermal degradation curves of this polymer obtained under different thermal pathways have shown that the proposed equation fits all these curves while other conventional models used in literature do not.     

A kinetic model for the thermal evolution of sedimentary and meteoritic organic carbon using Raman spectroscopy

Small samples of Murchison meteorite were flash pyrolysed at a range of temperatures (250–1000 degrees centigrade) for short durations (10–80 s). Raman spectroscopic analysis of the feedstock-pyrolysate revealed that with increased level of thermal alteration the R1 parameter (also known as the ID/IG and D/O ratio) increased in value. This appears to be a phenomena unique to low levels of thermal alteration and is most easily observed in homogeneous materials. An empirically derived kinetic model of the rise of the R1 parameter was obtained from the experimental data and used to successfully reproduce field measurements and experimental work from a number of short duration high temperature heating events. Results indicate that the use of this parameter and its predictor equation are limited to levels of thermal alteration less than that associated with the end of the oil window and the onset of condensate formation. It is also limited to situations where durations of heating are short. Even within these boundaries a high level of variation is observed in data from all settings which can make the parameter imprecise.     

A kinetic model for nonisothermic homogeneous nucleation

A model for isothermal homogeneous nucleation is proposed that improves the classical model. A quasiequilibrium distribution of clusters was calculated on a basis of the Frenkel’-Lothe-Pound theory. The dependence of the free energy of clusters on their size was represented by an interpolation formula relating the free energy of dimers and large clusters to which a notion of macroscopic surface tension is applicable. The nucleation rate and the dependence of the cluster temperature on their size were calculated by balance equations describing the heating of from a cluster due to the condensation of monomers and its cooling due to collisions with an ambient gas. It is shown that the nucleation rate in excess buffer gas is higher than for the pure condensing gas by approximately two orders of magnitude. The model adequately describes the experimental data for the nucleation of methanol supersaturated vapor.     

Statistical mechanics of a two-dimensional lattice model of benzene adsorption in zeolites

In this Letter, we present a mean field calculation of the statistical mechanics of a lattice model of benzene adsorption in the quasi two-dimensional network of pores in zeolites. A lattice fluid model is introduced with monomer states to represent molecules standing perpendicular to the principle axis of the pore, dimer states to represent molecules lying flat against the pore wall, and vacant sites or holes. For a wide range of interaction parameters the model gives steps in adsorption isotherms similar to those observed experimentally for benzene adsorption in silicalite. Our treatment attributes the experimentally observed steps in the level of adsorption with rising pressure, to orientational transitions amongst molecules in the adsorbed phase with two possible ground states arrangements of the benzene molecules in the zeolite pores energetically competing with each other.     

Simulation of nonisothermal reactive liquid chromatography using two-dimensional lumped kinetic model

A nonisothermal two-dimensional lumped kinetic model of reactive liquid chromatography is formulated and applied to simulate the separation of multicomponent mixtures in a fixed-bed cylindrical column operating under nonisothermal condition. The axial and radial variations of concentration and temperature as well as reversibility of the chemical reactions are incorporated in the model equations. The model comprises a system of convection-diffusion-reaction partial differential equations coupled with algebraic and differential equations. Due to the nonlinearity of adsorption and reaction kinetics, it is required to apply an accurate numerical scheme for solving the model equations. In this study, an efficient and accurate high-resolution flux-limiting finite-volume scheme is proposed to solve the model equations. A number of stoichiometrical reactions are numerically simulated to determine the level of coupling between the temperature and concentration profiles. Moreover, the effects of various critical parameters on the process performance are examined. The results obtained are beneficial for understanding reaction and separation processes inside a liquid chromatographic reactor and to improve its performance.     

Applications of type I antifreeze proteins: studies with model membranes & cryoprotectant properties

Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs), found in the body fluids of many species of polar fish allow them to survive in waters colder than the equilibrium freezing point of their blood and other internal fluids. Despite their structural diversity, all AF(G)Ps kinetically depress the temperature at which ice grows in a non-colligative manner and hence exhibit thermal hysteresis. AF(G)Ps also share the ability to interact with and protect mammalian cells and tissues from hypothermic damage (e.g., improved storage of human blood platelets at low temperatures), and are able to stabilize or disrupt membrane composition during low temperature and freezing stress (e.g., cryoprotectant properties in stabilization of sperm and oocytes). This review will summarize studies of AFPs with phospholipids and plant lipids, proposed mechanisms for inhibition of leakage from membranes, and cryoprotectant studies with biological samples. The major focus will be on the alpha-helical type I antifreeze proteins, and synthetic mutants, that have been most widely studied. For completeness, data on glycoproteins will also be presented. While a number of models to explain stabilization and destabilization of different lipid systems have been proposed, it is currently not possible to predict whether a particular AFP will stabilize or destabilize a given lipid system. Furthermore the relationship between the antifreeze property of thermal hysteresis and membrane stabilization is unknown. This lack of detailed knowledge about how AFPs function in the presence of different types of materials has hampered progress toward the development of antifreezes for cold storage of cells, tissues, and organs.     

A simple adsorption model for ionic surfactants

In the past, few theoretical attempts have been made to describe quantitatively the adsorption of ionic surfactants at liquid interfaces. Well-known adsorption isotherms due to Frumkin or Hill–de Boer cannot respond to the specific electrostatic and geometric properties of the surfactant molecules. Our approach is based on a combination of the Gouy–Chapman theory with a modified Frumkin isotherm. The modification implies that the system is free to choose an optimal head group area and an optimal arrangement of the surfactant molecules in the interface as a function of bulk concentration. Interaction energies between neighbouring adsorbed surfactant molecules and between surfactant and water molecules are taken into consideration. The minimum of the Gibbs free energy of the system is equivalent to a minimal interfacial tension. Thus, the thermodynamically stable isotherm can be obtained as the lower envelope of the family of σ versus ln c isotherms resulting from different choices of the model parameters, including the area per molecule. According to the Gibbs equation, the Γ versus ln c adsorption isotherm is obtained as the derivative of this envelope. By variation of the model parameters, the envelope of the calculated adsorption isotherms can be fitted to experimental data of the interfacial tension versus bulk concentration. A computer program is used to calculate the σ versus c and the Γ versus ln c curves as well as to fit the parameters. Received: 28 October 1999/Accepted: 8 February 2000     

An improved model for the kinetic description of the thermal degradation of cellulose

In spite of the large amount of work performed by many investigators during last decade, the actual understanding of the kinetics of thermal degradation of cellulose is still largely unexplained. In this paper, recent findings suggesting a nucleation and growth of nuclei mechanism as the main step of cellulose degradation have been reassessed and a more appropriate model involving chain scission and volatilization of fragments has been proposed instead. The kinetics of cellulose pyrolysis have been revisited by making use of a novel kinetic method that, without any previous assumptions regarding the kinetic model, allows performing the kinetic analysis of a set of experimental curves recorded under different heating schedules. The kinetic parameters and kinetic model obtained allows for the reconstruction of the whole set of experimental TG curves.