Modeling, simulation, and optimization of bacterial leaching reactors

Bacterial leaching represents an unusual problem in biochemical engineering, because the substrate for bacterial growth is not supplied directly, but is a product of another reaction, the leaching of mineral particles. In addition, leaching is a heterogeneous reaction dependent on the particle-size distribution in the feed and on the kinetics of particle shrinkage. In this study, these effects are incorporated in the material balance for each mineral by the number balance. Examination of the number balance gives rise to a novel analysis of the competing technologies for leaching. The model is completed by the addition of material balances for the ferrous and ferric ions, the dissolved oxygen, and for each bacterial species to the number balance for each mineral present in the feed. The model is compared with pilot plant data for three different ores. It is shown that the model is in excellent agreement with the data. The performance of a bacterial leaching reactor is explored using the model, and the washout and sensitivity criteria are determined. It is shown that there are three washout conditions, in which the leaching conversion drops to zero. The washout conditions are dependent on the growth rate of the bacteria, on the rate of dissolution of the mineral, and on the rate of mass transfer of oxygen to the reactor. The critical washout condition is that arising from the rate of mineral dissolution. The optimization of a plant in which continuous tank reactors are configured in series is addressed. This analysis shows that the primary reactor should be between 1.5 and 2 times the size of each of the secondary reactors in a series combination.     

Modeling, docking, and simulation of the major facilitator superfamily

X-ray structures are known for three members of the Major Facilitator Superfamily (MFS) of membrane transporter proteins, thus enabling the use of homology modeling to extrapolate to other MFS members. However, before employing such models for, e.g., mutational or docking studies, it is essential to develop a measure of their quality. To aid development of such metrics, two disparate MFS members (NupG and GLUT1) have been modeled. In addition, control models were created with shuffled sequences, to mimic poor quality homology models. These models and the template crystal structures have been examined in terms of both static and dynamic indicators of structural quality. Comparison of the behavior of modeled structures with the crystal structures in molecular dynamics simulations provided a metric for model quality. Docking of the inhibitor forskolin to GLUT1 and to a control model revealed significant differences, indicating that we may identify accurate models despite low sequence identity between target sequences and templates.     

Charles Darwin,embryology, evolution and skeletal plasticity

Darwin provided us with the theory of evolutionary change through natural selection. Just as important to the science of biology was Darwin’s recognition that all organisms could be classified and were related to one another because they arose from a single common universal ancestor – what we know as the universal tree of life (UtoL). All the features of the skeletal biology of fish therefore can be explained, both in an evolutionary framework (ultimate causation) and in the framework of development, growth and physiology (proximate causation). Neither approach is complete without the other. I will outline the elements of Darwin’s theories on evolution and classification and, as importantly, discuss what was missing from Darwin’s theories. An important class of evidence for evolution used by Darwin came from embryology, both comparative embryology and the existence of vestiges and atavisms. After discussing this evidence I examine some fundamental features of skeletal development and evolution These include: the presence of four skeletal systems in all vertebrates; the existence of two skeletons, one based on cartilage, the other on bone and dentine; the modular nature of skeletal development and evolution; and the plasticity of the skeleton in response to either genetic or environmental changes.     

Modeling,analysis and simulation of ant-based network routing protocols

Using the metaphor of swarm intelligence, ant-based routing protocols deploy control packets that behave like ants to discover and optimize routes between pairs of nodes. These ant-based routing protocols provide an elegant, scalable solution to the routing problem for both wired and mobile ad hoc networks. The routing problem is highly nonlinear because the control packets alter the local routing tables as they are routed through the network. We mathematically map the local rules by which the routing tables are altered to the dynamics of the entire networks. Using dynamical systems theory, we map local protocol rules to full network performance, which helps us understand the impact of protocol parameters on network performance. In this paper, we systematically derive and analyze global models for simple ant-based routing protocols using both pheromone deposition and evaporation. In particular, we develop a stochastic model by modeling the probability density of ants over the network. The model is validated by comparing equilibrium pheromone levels produced by the global analysis to results obtained from simulation studies. We use both a Matlab simulation with ideal communications and a QualNet simulation with realistic communication models. Using these analytic and computational methods, we map out a complete phase diagram of network behavior over a small multipath network. We show the existence of both stable and unstable (inaccessible) routing solutions having varying properties of efficiency and redundancy depending upon the routing parameters. Finally, we apply these techniques to a larger 50-node network and show that the design principles acquired from studying the small model network extend to larger networks.     

Modeling and simulation of luminescence detection platforms

Motivated by the design of an integrated CMOS-based detection platform, a simulation model for CCD and CMOS imager-based luminescence detection systems is developed. The model comprises four parts. The first portion models the process of photon flux generation from luminescence probes using ATP-based and luciferase label-based assay kinetics. An optics simulator is then used to compute the incident photon flux on the imaging plane for a given photon flux and system geometry. Subsequently, the output image is computed using a detailed imaging sensor model that accounts for photodetector spectral response, dark current, conversion gain, and various noise sources. Finally, signal processing algorithms are applied to the image to enhance detection reliability and hence increase the overall system throughput. To validate the model, simulation results are compared to experimental results obtained from a CCD-based system that was built to emulate the integrated CMOS-based platform.     

系统生物学中建模方法的研究现状及展望

系统生物学倡导利用系统论的思想和方法,从整体的高度分析、研究生命的复杂特性。这一点与实验生物学仅关注某一个或者某一些生物大分子是迥然不同的。系统生物学既要同时考虑多个层次、多种类型的生物信息,还要考虑时间因素。由于系统特性是由于不同组成部分、不同层次间相互作用而“涌现”出的新性质,因此,如果只是针对组成部分或单一层次的分析并不能真正准确地预测整体或高层次的行为。如何通过研究和整合去发现和理解“涌现”出的新的系统性质,是系统生物学面临的一个根本性的挑战。为了应对这一挑战,系统生物学,特别是计算系统生物学必须建立有效的方法,通过整合系统各个层次的信息,建立可反映该系统目前已知或已可测量的性质的物理、数学模型,并通过这样的模型来研究或预测目前还未知晓的系统性状。可以说：建模是系统生物学的最重要的研究手段之一。目前,生命科学的研究正逐步由对单一现象、单一过程的机械论式的描述型研究转向运用高通量实验技术获取海量生物信息,并在这些生物信息基础上建立物理、数学模型,最终通过建模与实验相接合的研究手段来定量阐述生命现象的本质规律。由于建模方法在系统生物学研究中的重要性,本文将对一些主要的建模类型,如定性建模方法;基于约束的建模方法;基于常微分/偏微分方程的定量建模和基于随机微分方程的定量建模方法等等分别予以简要介绍。     

Modeling and simulation of cancer immunoprevention vaccine

We present an in silico model that simulates the immune system responses to tumor cells in naive and vaccinated mice. We have demonstrated the ability of this model to accurately reproduce the experimental results. MOTIVATION: In vivo experiments on HER-2/neu mice have shown the effectiveness of Triplex vaccine in the protection of mice from mammary carcinoma. Full protection was conferred using chronic (prophylactic) vaccination protocol while therapeutic vaccination was less efficient. Our in silico model was able to closely reproduce the effects of various vaccination protocols. This model is the first step towards the development of in silico experiments searching for optimal vaccination protocols. RESULTS: In silico experiments carried out on two large statistical samples of virtual mice showed very good agreements with in vivo experiments for all experimental vaccination protocols. They also show, as supported by in vivo experiments, that the humoral response is fundamental in controlling the tumor growth and therefore suggest the selection and timing of experiments for measuring the activity of T cells. CONTACT: francesco@dmi.unict.it SUPPLEMENTARY INFORMATION: http://www.dmi.unict.it/CIG/suppdata_bioinf.html.     

Zebrafish embryology and neural development

The zebrafish is rapidly increasing in popularity with developmental biologists. Driving this interest are the elegant methods for in vivo observations and recovery of early developmental mutations. The past year has seen the introduction of additional methods for in vivo manipulation of identified cells and the application of these methods to mutant analysis.     

The embryology and relationships ofOliniaceae

Two of the five species ofOliniaceae (Olinia emarginata andO. ventosa), a monotypic and problematic family of theMyrtales, were investigated embryologically.Oliniaceae clearly agree with otherMyrtales in their basic embryological characteristics, and are characterized further by having an ephemeral endothecium, a campylotropous ovule, and a thick, three-five-layered, outer integument. A combination of these three characteristic features is unknown elsewhere inMyrtales, so that embryological features do not support a close relationship with any other member of the order. Shared distinctive anther characteristics (i.e. ephemeral endothecium) suggest thatOliniaceae are derived from the common ancestor ofCrypteroniaceae s. str.,Rhynchocalycaceae, Alzateaceae, andPenaeaceae.     

Genomics and embryology in amphibians

A report on the Eighth Biannual Xenopus Conference, Estes Park, Colorado, August 16-20, 2000.