A computer simulation of surface microcolony formation during microbial colonization

Several models of microbial surface colonization have been devised to quantitate growth and attachment rates on surfaces. One of these, the surface growth rate equation, is based on the assumption that the number of microcolonies of a given size (C_i) reaches a constant value (C_max) that is equal to the attachment rate (A) divided by the specific growth rate (Μ). In this study, a computer simulation was used to determine the time required to reach C_max. It was shown that C_i approaches C_max asymptotically. The time required is dependent solely upon the growth rate and size of microcolonies. The number of one-celled microcolonies reaches 95% of C_max after 4.3 generations. At low growth rates, a relatively long incubation period is required. Alternate methods that shorten the incubation time are considered.     

A new modeling technique and computer simulation of bacterial growth

A mathematical model that describes substrate utilization and cell growth in terms of two potentially rate-limiting enzyme systems has been developed. Consideration of substrate inhibition and enzyme repression have been incorporated. The model provides a rational approach for characterizing non-steady-state phenomena. The model has been used to analyze batch test data to illustrate the effects of inhibition, repression, and concurrent substrate utilization. Its utility lies in the fact that it provides a quantitative framework for describing changes in the activity levels of cells that result from changes in substrate concentration and/or substrate type. The lag phase resulting from exposure to a new substrate can be modeled.     

Strategies for computer modeling

Modeling is a ubiquitous and often misunderstood enterprise in which data from diverse disciplines are analyzed by techniques from other diverse disciplines in an attempt to confirm or falsify a set of hypotheses about the real world. Guidelines are offered for designing models to match the goals of modeling biological systems. Techniques for the construction and interpretation of models are discussed. The requirements for credibility of models are detailed, and tests are suggested for their validation.     

Neurite branching pattern formation: modeling and computer simulation.

A model for nerve cell pattern formation is proposed in this paper. The model is based on some experimental results and an assumption that there is a kind of inhibitive interaction between growing neurites on the same nerve cell. In this paper, this interaction is termed lateral inhibition. A group of ordinary differential equations are used to describe the elongation of the terminal neurite segments of individual nerve cells. Computer simulation and comparison of it with in vitro studies are also made in this paper.     

Conduction-based modeling of the biofilm anode of a microbial fuel cell

The biofilm of a microbial fuel cell (MFC) experiences biofilm-related (growth and mass transport) and electrochemical (electron conduction and charger-transfer) processes. We developed a dynamic, one-dimensional, multi-species model for the biofilm in three steps. First, we formulated the biofilm on the anode as a "biofilm anode" with the following two properties: (1) The biofilm has a conductive solid matrix characterized by the biofilm conductivity (kappa(bio)). (2) The biofilm matrix accepts electrons from biofilm bacteria and conducts the electrons to the anode. Second, we derived the Nernst-Monod expression to describe the rate of electron-donor (ED) oxidation. Third, we linked these components using the principles of mass balance and Ohm's law. We then solved the model to study dual limitation in biofilm by the ED concentration and local potential. Our model illustrates that kappa(bio) strongly influences the ED and current fluxes, the type of limitation in biofilm, and the biomass distribution. A larger kappa(bio) increases the ED and current fluxes, and, consequently, the ED mass-transfer resistance becomes significant. A significant gradient in ED concentration, local potential, or both can develop in the biofilm anode, and the biomass actively respires only where ED concentration and local potential are high. When kappa(bio) is relatively large (i.e., > or =10(-3) mS cm(-1)), active biomass can persist up to tens of micrometers away from the anode. Increases in biofilm thickness and accumulation of inert biomass accentuate dual limitation and reduce the current density. These limitations can be alleviated with increases in the specific detachment rate and biofilm density.     

Control of microbial contamination for large-scale photoautotrophic micropropagation

Summary Photoautotrophic (sugar-free) micropropagation has been examined for many different plant species. One of the advantages of photoautotrophic micropropagation is the low risk of contamination, which facilitates the use of large culture vessels, and thus contributes to the reduction in production cost. In this article, pathogenic and nonpathogenic contaminations are discussed, and guidelines for development of large-scale, pathogen-free, photautotrophic micropropagation systems are introduced. A preliminary experiment was conducted for producing pathogen-free plantlets by large-scale photoautotrophic micropropagation. Addition of AgNO₃ in the medium was shown to suppress growth of nonpathogenic contaminants without reducing fresh and dry weight, and number of leaves of the tomato plantlets.     

A computer simulation of cell stacking for even thickness in mammalian epidermis

The method of even stacking of epidermal cells in mammalian skin was studied by computer simulation. The epidermis consists of neat vertical columns of stacked, flattened, tetrakaidecahedral cells. Cells which have been proliferated in a basal layer migrate upwards, occupy the bottom regions of vertical columns, and become members constituting columns. Computer simulations demonstrated that the column height becomes considerably varied if the cells are randomly supplied from the basal layer. In contrast, if the cells are assumed to have an ability to find the uppermost region among the column's bases consisting of one base where the cell has reached and its neighbouring bases, the cells stack into columns whose heights are remarkably uniform even if the cells are randomly supplied. The results indicated that an epidermal structure consisting of the flattened polyhedral cells could itself function as a control mechanism of the epidermal thickness.     

A computer simulation of geometrical configurations during cell division

A process of cell division in the blastular wall of the starfish, Asterina pectinifera, was observed, and an attempt was made to model with a computer simulation the way in which cell number increases in such a tissue. Dividing cells at stages between the 2(11)-cell and the beginning of rotation were observed to shift these positions to the outer surface of the cell sheet by rounding up, after which they divide and slip back into the sheet as two columnar daughter cells. The change of a polygonal pattern of the blastular wall by cell division was simulated by making use of geometrical models of polygonal cells and the rule of the direction of cell division which was confirmed by observation. The simulation proves valid for describing changes of polygonal patterns of cell sheets including dividing cells.     

Mathematical modeling and computer simulation of isoelectric focusing with electrochemically defined ampholytes

A mathematical model of isoelectric focusing at the steady state has been developed for an M-component system of electrochemically defined ampholytes. The model is formulated from fundamental principles describing the components' chemical equilibria, mass transfer resulting from diffusion and electromigration, and electroneutrality. The model consists of ordinary differential equations coupled with a system of algebraic equations. The model is implemented on a digital computer using FORTRAN-based simulation software. Computer simulation data are presented for several two-component systems showing the effects of varying the isoelectric points and dissociation constants of the constituents.     

Continuum modeling and numerical simulation of cell motility

This work proposes a continuum-mechanical model of cell motility which accounts for the dynamics of motility-relevant protein species. For the special case of fish epidermal keratocytes, the stress and cell-substrate traction responses are postulated to depend on selected protein densities in accordance with the structural features of the cells. A one-dimensional version of the model is implemented using Arbitrary Lagrangian–Eulerian finite elements in conjunction with Lagrange multipliers for the treatment of kinematic constraints related to surface growth. Representative numerical tests demonstrate the capacity of the proposed model to simulate stationary and steady crawling states.     

Biodynamic modeling and simulation of multistage cell mutations

The aim of this study is to present a mathematical computer simulation model for multistage carcinogenesis. The population genetic model is developed based on the reaction diffusion, logistic behavior, and Hollings Type II interactions between normal, benign, and premalignant cells. The simple form of the Fisher-Haldane-Wright equation of the genetic model of tumor suppressor gene and oncogenes is used to describe this type of interaction. Through computer simulation, we observe the behavior, stability, and traveling wave solution of the premalignant stage mutation as well as its survival under natural selection pressure. As a simple case of this model, the interaction between normal and tumor cells with one or two stages of mutations is analyzed.     

Molecular basis for microbial adhesion to geochemical surfaces: computer simulation of Pseudomonas aeruginosa adhesion to goethite

The adhesion of Pseudomonas aeruginosa to the goethite mineral is investigated using classical molecular simulation. A fragment model for goethite has been integrated into a fully atomistic membrane model. Properties for the resulting system are evaluated for a 1.5-ns simulation in the isothermal-isobaric ensemble. The response of the membrane to the presence of the mineral is investigated. Radial distribution functions are used to present an average picture of the hydrogen bonding. Orientational vectors, assigned to the saccharide groups, reveal the extent of the mineral's perturbations on the membrane. Significant structural changes were observed for the outermost saccharide groups, several of which rotate to form hydrogen bonds with the mineral surface. The structure of the inner core, and the corresponding integrity of the membrane, is maintained. The mineral surface dehydrates slightly in the presence of the membrane as saccharide hydroxyl groups compete with water molecules for hydrogen-bonding sites on its surface.     

Blast cell and granulocyte production in human leukemia: pathophysiological concepts based on computer simulation using discrete modeling techniques

The granulocyte production of two patients suffering from leukemia was studied extensively by means of the tritiated thymidine method of cellular kinetics. The data obtained (1-h labeling index, pattern of cell labeling, labeling intensity, as well as other conventional parameters of bone marrow and blood) were used to develop a computer model (GPSS-language) to fit the observations. From these models, it was concluded that patients with leukemia may have an abnormal granulopoiesis, characterized by a high degree of inefficiency (premature cell death, skipping of divisions with undisturbed maturation). However, the underlying mechanisms may be quite different. While it cannot be excluded that in acute myelocytic leukemia there is a stem and/or progenitor cell pool that is highly ineffective but still capable of feeding some cells into the granulocytic pathway, it is nevertheless possible, as shown in plasma cell leukemia, that the ineffective granulopoiesis may be the result of direct or indirect interaction between the "leukemic" and the "normal" cell clone.     

Design of experiments for predictive microbial modeling

Summary Good predictive microbial models can be built with appropriate data from well-designed experiments. Anyone setting up an experiment should consider the sources of variability, possible screening experiments, optimum spacing between points on a continuous scale, and the most appropriate type of design, e.g. factorial, screening, or central composite.     

Comparison of three classes of snake neurotoxins by homology modeling and computer simulation graphics

We present a systematic structure comparison of three major classes of postsynaptic snake toxins, which include short and long chain alpha-type neurotoxins plus one angusticeps-type toxin of black mamba snake family. Two novel alpha-type neurotoxins isolated from Taiwan cobra (Naja naja atra) possessing distinct primary sequences and different postsynaptic neurotoxicities were taken as exemplars for short and long chain neurotoxins and compared with the major lethal short-chain neurotoxin in the same venom, i.e., cobrotoxin, based on the derived three-dimensional structure of this toxin in solution by NMR spectroscopy. A structure comparison among these two alpha-neurotoxins and angusticeps-type toxin (denoted as FS2) was carried out by the secondary-structure prediction together with computer homology-modeling based on multiple sequence alignment of their primary sequences and established NMR structures of cobrotoxin and FS2. It is of interest to find that upon pairwise superpositions of these modeled three-dimensional polypeptide chains, distinct differences in the overall peptide flexibility and interior microenvironment between these toxins can be detected along the three constituting polypeptide loops, which may reflect some intrinsic differences in the surface hydrophobicity of several hydrophobic peptide segments present on the surface loops of these toxin molecules as revealed by hydropathy profiles. Construction of a phylogenetic tree for these structurally related and functionally distinct toxins corroborates that all long and short toxins present in diverse snake families are evolutionarily related to each other, supposedly derived from an ancestral polypeptide by gene duplication and subsequent mutational substitutions leading to divergence of multiple three-loop toxin peptides.     

两种自然保护区设计方法——数学建模和计算机模拟

传统的自然保护区设计方法是打分法和Gap分析法,这两种方法简单易行但可靠性不高;地理信息系统(GIS)在保护区设计领域的应用也为人熟悉.关注近年来快速发展而国内使用不多的两种方法——数学建模和计算机模拟.数学建模主要用来从一组备选地块中选择一部分组成自然保护区,包括线性和非线性模型,用启发式算法或最优化算法求解.启发式算法具有速度快、灵活等优点,但解通常不是最优的,不能保证稀缺资源的最优化利用.最优化算法运算效率低,变量较多比如数百时就可能遇到计算困难,但解是最优的.预计两种算法都将继续发展.计算机模拟主要用于保护区评价、功能区划分、预测特定环境比如空间特征和气候变化对物种的影响等,多用启发式算法,与其它软件结合把结果以图画显示出来.两种方法特别是计算机模拟均要求保护区设计者有较强的专业知识.讨论了两种方法面临的问题和新的研究方向,至少包括:1)基础数据依然需要完善;2)一些新的因素比如动态性和不确定性如何在模型中考虑并与其它因素结合;3)气候变化预景下模拟参数如何评估和调整;4)如何协调保护与发展的关系;5)方法的实际应用需要研究者与决策者之间建立交流机制;6)多领域专家和相关利益方应有机会参与保护区设计.     

Model for computer simulation of bone tissue

The paper deals with the dependence of the torsional moment on the angle of the compact bone torsion in laboratory animals and humans. Based on the data for laboratory animals obtained by measurements, the data on dependence of the torsional moment and the angle of torsion were predicted for humans. The measurements were carried out in four groups of laboratory animals. One was the control group, and the other three groups were treated by various vitamin D3 metabolites. The same measurements were performed also in only one group of humans, due to the impossibility to treat humans with vitamin D3 metabolites. The functional relationship between the angle of torsion and the torsional moment for all the groups of animal bone tissue were determined by measurements, and results were used to predict the reaction of the human compact bone tissue if treated by vitamin D3 metabolites.