Relationship between extreme pathways and structurally minimal pathways.

The determination of reaction pathways is one of the most important functions that should be performed in exploring the kinetics of catalyzed chemical reactions or biochemical reactions, the latter being generally catalyzed by enzymes. It is proven that the terms, "type-I extreme pathway" and "structurally minimal pathway", both introduced to characterize the kinetics of a catalyzed reaction are equivalent. These two terms are based on two distinct methodologies, one mainly rooted in convex analysis and the other in graph theory. The equivalence promises further even more effective methods for reaction-pathway identification by synergistic integration of existing ones.

Monte Carlo simulation of bacterial disinfection: nonlinear and time-explicit intensity of transition.

Bacteria being disinfected in fluid media are discrete entities and mesoscopic in size; moreover, they are incessantly as well as irregularly in motion and in collision among themselves or with the surrounding solid surfaces. As such, it is highly likely that some of the attributes of the bacterial population, for example, their number concentration, will fluctuate randomly. This is especially the case at the tail-end of disinfection when the population of bacteria is sparse. It might be effectual, therefore, to explore the resultant random fluctuations via a stochastic paradigm. Proposed herein is a Markovian stochastic model for the rate of bacterial disinfection, whose intensity of transition takes into account the contact time of the bacteria with the disinfecting agent to eliminate any given percentage of the bacteria in terms of a nonlinear function of time. The model's master equation has been simulated by resorting to the Monte Carlo method to circumvent the undue complexities in solving it analytically or numerically via conventional numerical techniques. For illustration, the mean, the variance (standard deviation), and the coefficient of variation of the number concentration of bacteria during disinfection have been estimated through Monte Carlo simulation. The results of simulation compare favorably with the available experimental data as well as with those computed from the corresponding deterministic model.

Grain-based activated carbons for natural gas storage.

Natural gas has emerged as a potential alternative to gasoline due to the increase in global energy demand and environmental concerns. An investigation was undertaken to explore the technical feasibility of implementing the adsorbed natural gas (ANG) storage in the fuel tanks of motor vehicles with activated carbons from biomass, e.g., sorghum and wheat. The grain-based activated carbons were prepared by chemical activation; the experimental parameters were varied to identify the optimum conditions. The porosity of the resultant activated carbons was evaluated through nitrogen adsorption; and the storage capacity, through methane adsorption. A comparative study was also carried out with commercial activated carbons from charcoal. The highest storage factor attained was 89 for compacted grain-based activated carbons from grain sorghum with a bulk density of 0.65 g/cm(3), and the highest storage factor attained is 106 for compacted commercial activated carbons (Calgon) with a bulk density of 0.70 g/cm(3). The storage factor was found to increase approximately linearly with increasing bulk density and to be independent of the extent of compaction. This implies that the grain-based activated carbons are the ideal candidates for the ANG storage.

Preparation of carbon molecular sieves by carbon deposition from methane.

To prepare carbon molecular sieves (CMSs), methane was pyrolyzed in an attempt to deposit fine carbon particles on the micropore mouths of the carbon substrates being heated; the carbon substrates included grain-based activated carbons and commercial activated carbons. To explore the effects of heat treatment alone, blank experiments were conducted by heating the samples in N2. The resultant products were characterized by N2-adsorption at 77K. Methane failed to deposit carbon at 800 degrees C. The porosity of activated carbons, however, was substantially influenced by heat treatment alone. The surface areas and micropore volumes of the activated carbons from grain sorghum decreased by 39.32% and 36.84%, respectively, upon heat treatment alone; this is attributable to the destruction of pore structure by sintering. In contrast, the corresponding values of the commercial activated carbons increased by 59.86% and 62.16%, respectively, upon heat treatment alone; this can be attributable to the development of microporosity.

Complementary identification of multiple flux distributions and multiple metabolic pathways.

Cell robustness and complexity have been recognized as unique features of biological systems. Such robustness and complexity of metabolic-reaction systems can be explored by discovering, or identifying, the multiple flux distributions (MFD) and redundant pathways that lead to a given external state; however, this is exceedingly cumbersome to accomplish. It is, therefore, highly desirable to establish an effective computational method for their identification, which, in turn, gives rise to a novel insight into the cellular function. An effective approach is proposed for complementarily identifying MFD in metabolic flux analysis and multiple metabolic pathways (MMP) in structural pathway analysis. This approach judiciously integrates flux balance analysis (FBA) based on linear programming and the graph-theoretic method for determining reaction pathways. A single metabolic pathway, with the concomitant flux distribution and the overall reaction manifesting itself as the desired phenotype under some environmental conditions, is determined by FBA from the initial candidate sequence of metabolic reactions. Subsequently, the graph-theoretic method recovers all feasible MMP and the corresponding MFD. The approach's efficacy is demonstrated by applying it to the in silico Escherichia coli model under various culture conditions. The resultant MMP and MFD attaining a unique external state reveal the surprising adaptability and robustness of the intricate cellular network as a key to cell survival against environmental or genetic changes. These results indicate that the proposed approach would be useful in facilitating drug discovery.

Downstream process synthesis for biochemical production of butanol, ethanol, and acetone from grains: generation of optimal and near-optimal flowsheets with conventional operating units.

Manufacturing butanol, ethanol, and acetone through grain fermentation has been attracting increasing research interest. In the production of these chemicals from fermentation, the cost of product recovery constitutes the major portion of the total production cost. Developing cost-effective flowsheets for the downstream processing is, therefore, crucial to enhancing the economic viability of this manufacturing method. The present work is concerned with the synthesis of such a process that minimizes the cost of the downstream processing. At the outset, a wide variety of processing equipment and unit operations, i.e., operating units, is selected for possible inclusion in the process. Subsequently, the exactly defined superstructure with minimal complexity, termed maximal structure, is constructed from these operating units with the rigorous and highly efficient graph-theoretic method for process synthesis based on process graphs (P-graphs). Finally, the optimal and near-optimal flowsheets in terms of cost are identified.

Modeling growth of a heterogeneous tumor.

It has long been recognized that the growth of tumor population depends on the initial age distribution of the cells in the tumor and the age-dependent cellular birth rate. Deterministic dual-cell models have been available for sometime; these models take into account the effects of the resultant cell heterogeneity. Nevertheless, these models ignore various variables significantly affecting the growth, such as those characterizing the cells' inherent properties and environmental factors. Uncertainties, or fluctuations, arise when the growth is simulated with the models. Stochastic analysis of these fluctuations is the focus of the current work. Two types of cells are visualized to proliferate separately and to transform mutually during the process. The master equations of the system have been formulated through probabilistic population balance around a particular state by considering all mutually exclusive events. The governing equations for the means, variances, and covariance of the random variables have been derived through the system-size expansion of these nonlinear master equations. The stochastic pathways of the two different types of cells have been numerically simulated by the algorithm derived from the master equation for two different physical situations, one without and, the other, with the chemotherapeutic treatment. The results of the current study illuminate the significance of stochastically modeling the responses of the tumor to a variety of medicinal treatments: The coefficient of variation of the malignant cells' population magnifies with time under chemotherapeutic regimens. Consequently, the impact of the uncertainties in the exact number of malignant cells as expressed by this coefficient of variation is highly unpredictable. For example, it becomes increasingly uncertain if or how fast these cells will reactivate to become a full-blown carcinogenic tumor after treatment.

A graph-theoretic method to identify candidate mechanisms for deriving the rate law of a catalytic reaction.

Stoichiometrically, exact candidate pathways or mechanisms for deriving the rate law of a catalytic or complex reaction can be determined through the synthesis of networks of plausible elementary reactions constituting such pathways. A rigorous algorithmic method is proposed for executing this synthesis, which is exceedingly convoluted due to its combinatorial complexity. Such a method for synthesizing networks of reaction pathways follows the general framework of a highly exacting combinatorial method established by us for process-network synthesis. It is based on the unique graph-representation in terms of P-graphs, a set of axioms, and a group of combinatorial algorithms. In the method, the inclusion or exclusion of a step of each elementary reaction in the mechanism of concern hinges on the general combinatorial properties of feasible reaction networks. The decisions are facilitated by solving linear programming problems comprising a set of mass-balance constraints to determine the existence or absence of any feasible solution. The search is accelerated further by exploiting the inferences of preceding decisions, thereby eliminating redundancy. As a result, all feasible independent reaction networks, i.e. pathways, are generated only once; the pathways violating any first principle of either stoichiometry or thermodynamics are eliminated. The method is also capable of generating those combinations of independent pathways directly, which are not microscopically reversible. The efficiency and efficacy of the method are demonstrated with the identification of the feasible mechanisms of ammonia synthesis involving as many as 14 known elementary reactions.

Activated carbons prepared from phosphoric acid activation of grain sorghum.

The production of activated carbons from grain sorghum with phosphoric acid activation has been studied by means of two processes, i.e., one-stage and two-stage. The former comprises simultaneous carbonization and activation after impregnation; the latter, the carbonization of the precursor at 300 degrees C for 15 min, followed by the activation of the resultant char after impregnation with phosphoric acid. The preparation conditions, e.g., activation duration, phosphoric acid concentration, and activation temperature, have been varied to determine the optimal processing conditions. The optimal activation conditions for the highest surface areas have been determined to be 600 and 500 degrees C with a phosphoric acid concentration of 35% for the one-stage and two-stage processes, respectively. The two-stage process has been found to greatly enhance the porosity development, especially the microporosity.

The ligament of Marshall: a structural analysis in human hearts with implications for atrial arrhythmias.

OBJECTIVES: We sought to study the anatomy of human ligament of Marshall (LOM). BACKGROUND: Although the LOM has been implicated in the genesis of focal atrial tachyarrhythmias, its gross anatomic and microscopic features in humans hearts have not been completely defined. METHODS: We studied seven postmortem human hearts from five men and two women with a mean age of 52 +/- 26 years. Four did not have any heart disease. One woman had dilated cardiomyopathy, and two men had chronic atrial fibrillation. A block of tissue encompassing the LOM from the coronary sinus (CS) cephalad, between the atrial appendage and left pulmonary veins, was dissected. Serial sections from this tissue were then stained with hematoxylin and eosin, trichrome, and/or tyrosine hydroxylase. RESULTS: The LOM consists of multiple sympathetic nerve fibers, ganglia, blood vessels and multiple myocardial tracts (Marshall Bundles) insulated by fibrofatty tissue. One or more myocardial tracts was inserted directly into the left atrial free wall and CS. The distance between insertion sites was 7.8 +/- 2.5 mm. Nerve fibers, some tyrosine hydroxylase positive, were present within the fibrofatty matrix and within the myocardial tracts. CONCLUSIONS: Human LOM 1) is innervated by sympathetic nerve fibers; 2) is more complex than the LOM in canine hearts; and 3) has multiple myocardial tract insertions into the left atrial free wall and CS, forming a substrate of reentry. Radiofrequency catheter ablation from the CS may fail to reach the free wall insertion.

Promotion of oxygen transfer in three-phase fluidized-bed bioreactors by floating bubble breakers.

The objective of the present study was to investigate a method to enhance the volumetric rate of oxygen transfer in three-phase fluidized-bed bioreactors. The rates of oxygen transfer from air bubbles to viscous liquid media were promoted by floating bubble breakers in three-phase fluidized beds operated in the bubble coalescing regime. The liquid-phase volumetric oxygen transfer coefficient has been recovered by fitting the axial dispersion model to the resultant data, and its dependence on the experimental variables, such as the gas and liquid flow rates, particle size, concentration of bubble breakers, and liquid viscosity, has been examined. The results indicate that the liquid-phase volumetric oxygen transfer coefficient can be enhanced up to 20-25%. The coefficient exhibits a maximum with respect to the volume ratio of the floating bubble breakers to the fluidized solid particles; it increases with increases in the gas and liquid flow rates and size of fluidized particles, while it decreases with an increase in the liquid viscosity. An expression has been developed to correlate the liquid-phase volumetric oxygen transfer coefficient with the experimental variables.

A generalized model for swelling-controlled release systems.

A generalized model has been developed for simultaneous transport of an active agent and an organic penetrant in a planar glassy polymer matrix. The active agent diffuses out of the matrix undergoing macromolecular chain relaxation and volume expansion due to absorption of the organic penetrant from the environment into the matrix. The swelling behavior of the polymer is characterized by a stress-induced drift velocity term "v" corresponding to the so-called case-II velocity. The change of volume due to the relaxation phenomenon is assumed instantaneous. The model incorporates convective transport of the two species induced by volume expansion and by stress gradient. The proposed phenomenological model reduces to a number of special cases depending on polymer-penetrant system behavior.

Kinetic studies of enzymatic hydrolysis of insoluble cellulose: Derivation of a mechanistic kinetic model.

A comprehensive mechanistic kinetic model for enzymatic hydrolysis of insoluble cellulose has been synthesized by combining models for several key aspects which have been derived independent of each other. The model takes into account the major contributing factors: the nature of the enzyme system, the structure of cellulose, and the mode of interaction between the enzyme and cellulose molecules. It consists of a set of simultaneously occurring ordinary differential equations with ten kinetic constants. All of the kinetic constants have been determined independently by carrying out critically designed experiments, and they appear in the comprehensive model without any arbitrary manipulations. The governing equations of the model have been numerically simulated by means of the computer subroutine CSMP III. The model predicts the progress of hydrolysis of cellulose over a wide range of experimental conditions and hydrolysis times reasonably well. The model can even be applied to predict the progress of hydrolysis for intensively pretreated cellulose with a minor adjustment. The applicability of the model for the actual process development is also discussed.

Kinetic studies of enzymatic hydrolysis of insoluble cellulose: (II). Analysis of extended hydrolysis times.

The kinetics of enzymatic hydrolysis of pure insoluble cellulose by means of unpurified culture filtrate of Trichoderma reesei was studied, emphasizing the kinetic characteristics associated with the extended hydrolysis times. The changes in the hydrolysis rate and extent of soluble protein adsorption during the progress of reaction, either apparent or intrinsic, were investigated. The hydrolysis rate declined drastically during the initial hours of hydrolysis. The factors causing the reduction in the hydrolysis rate were examined; these include the transformation of cellulose into a less digestible form and product inhibition. The structural transformation can be partially explained by changes in the crystallinity index and surface area. The product inhibition was caused by the deactivation of the adsorbed soluble protein by the products, which essentially represents the so-called "un-competitive" inhibition. The kinetics of beta-glucosidase were also studied. The result has shown that the action of beta-glucosidase is competitively inhibited by glucose. It has been found that the integrated form of the initial rate expression cannot be used in predicting the progress of reaction because the digestibility of cellulose changes drastically as the hydrolysis proceeds, and that the rate expression for enzymatic hydrolysis of cellulose cannot be simplified or approximated by resorting to the pseudo-steady-state assumption. A mechanistic kinetic model of cellulose hydrolysis should include the following major influencing factors: (1)mode of action of enzyme, (2) structure of cellulose, and (3) mode of interaction between the enzyme and cellulose molecules.

Structural modification of lignocellulosics by pretreatments to enhance enzymatic hydrolysis.

In this work an evaluation was made of a wide variety of single and multiple pretreatment methods for enhancing the rate of enzymatic hydrolysis of wheat straw. A multiple pretreatment consisted of a physical pretreatment followed by a chemical pretreatment. The structural features of wheat straw, including the specific surface area, crystallinity index, and lignin content, were measured to understand the mechanism of the enhancement in the hydrolysis rate upon pretrement. It has been found that, in general, multiple pretreatments were not promising, since the hydrolysis rates rarely exceeded those achieved by single pretreatments. Ballmilling pretreatment was found to be effective in increasing the specific surface area and decreasing the crystallinity index. Treatment with ethylene glycol was highly effective in increasing the specific surface area, in addition to a high degree of delignification. Peracetic acid pretreatment was highly effective in delignifying substrate. Among multiple pretreatments, those involving peracetic acid treatment generally had lower crystallinity indices and lignin content values. The relationship between the hydrolysis rate and the set of structural features indicated that an increase in surface area and a decrease in the crystallinity and lignin content enhance the hydrolysis; the specific surface area is the most influential of the structural features, followed by the lignin content.

Kinetic studies of enzymatic hydrolysis of insoluble cellulose: analysis of the initial rates.

A study was conducted on the kinetics of enzymatic hydrolysis of pure insoluble cellulose using unpurified culture filtrate Trichoderma reesei, with the emphasis on the initial reaction period. The initial hydrolysis rate and extent of enzyme (soluble protein)adsorption, either apparent or initial, were evaluated under various experimental conditions. It has been found that the various mass-transfer steps do not control the overall hydrolysis rate and that the hydrolysis rate is mainly controlled by the surface reaction step promoted by the adsorbed enzyme. It has also been found that the initial hydrolysis rate strongly depends on the initial extent of soluble protein adsorption and the effectiveness of the adsorbed soluble protein to promote the hydrolysis. The initial extent of soluble protein adsorption, in turn, is related to the initial cellulose concentration, enzyme concentration, and specific surface area of cellulose, whereas the effectiveness of the initially adsorbed soluble protein to promote the derived to interrelate these parameters without resorting to the Michaelis-Menten kinetics. The present result appear to imply that the role of enzyme-substrate complex formation should not be ignored in deriving a mechanistic kinetic model for enzymatic hydrolysis of cellulose.

Oxygen transfer and axial dispersion in an aeration tower containing static mixers.

Oxygen transfer from gas to liquid under steady-state cocurrent flow conditions was modeled using the dispersion model, and the oxygen transfer coefficients were estimated from available data for a column with Koch motionless mixers. The dispersion in the column was estimated for several different gas and liquid flow rates using steady-state tracer experiments. The estimated oxygen transfer coefficients were compared with those estimated using complete mixing and plug flow models. The results indicate that the dispersion model is the most appropriate model for estimating the mass transfer coefficient from the available data.