The Multiscale Systems Immunology project: software for cell-based immunological simulation.

BACKGROUND: Computer simulations are of increasing importance in modeling biological phenomena. Their purpose is to predict behavior and guide future experiments. The aim of this project is to model the early immune response to vaccination by an agent based immune response simulation that incorporates realistic biophysics and intracellular dynamics, and which is sufficiently flexible to accurately model the multi-scale nature and complexity of the immune system, while maintaining the high performance critical to scientific computing. RESULTS: The Multiscale Systems Immunology (MSI) simulation framework is an object-oriented, modular simulation framework written in C++ and Python. The software implements a modular design that allows for flexible configuration of components and initialization of parameters, thus allowing simulations to be run that model processes occurring over different temporal and spatial scales. CONCLUSION: MSI addresses the need for a flexible and high-performing agent based model of the immune system.

Strategy in developing cell based therapy for large bone

Regeneration of osseous defects by tissue-engineering approach provides a novel means of treatment utilizing cell biology, materials science, and molecular biology. The concept of in vitro cultured osteoblasts having an ability to induce new bone formation has been demonstrated in the critical size defects using small animal models. The bone derived cells can be incorporated into bioengineered scaffolds and synthesize bone matrix, which on implantation can induce new bone formation. In search of optimal cell delivery materials, the extracellular matrix as cell carriers for the repair and regeneration of tissues is receiving increased attention. We have investigated extracellular matrix formed by osteoblasts in vitro as a scaffold for osteoblasts transplantation and found a mineralized matrix, formed by human osteoblasts in vitro, can initiate bone formation by activating endogenous mesenchymal cells. To repair the large bone defects, osteogenic or stem cells need to be prefabricated in a large three dimensional scaffold usually made of synthetic biomaterials, which have inadequate interaction with cells and lead to in vivo foreign body reactions. The interstitial extracellular matrix has been applied to modify biomaterials surface and identified vitronectin, which binds the heparin domain and RGD (Arg-Gly-Asp) sequence can modulate cell spreading, migration and matrix formation on biomaterials. We also synthesized a tri-block copolymer, methoxy-terminated poly(ethylene glycol)(MPEG)-polyL-lactide(PLLA)-polylysine(PLL) for human osteoblasts delivery. We identified osteogenic activity can be regulated by the molecular weight and composition of the triblock copolymers. Due to the sequential loss of lineage differentiation potential during the culture of bone marrow stromal cells that hinderers their potential clinical application, we have developed a clonal culture system and established several stem cell clones with fast growing and multi-differentiation properties. Using proteomics and subtractive immunization, several differential proteins have been identified and verified their potential application in stem cell characterization and tissue regeneration

Distinguishing between mechanisms of cell aggregation using pair-correlation functions

Many cell types form clumps or aggregates when cultured in vitro through a variety of mechanisms including rapid cell proliferation, chemotaxis, or direct cell-to-cell contact. In this paper we develop an agent-based model to explore the formation of aggregates in cultures where cells are initially distributed uniformly, at random, on a two-dimensional substrate. Our model includes unbiased random cell motion, together with two mechanisms which can produce cell aggregates: (i) rapid cell proliferation, and (ii) a biased cell motility mechanism where cells can sense other cells within a finite range, and will tend to move towards areas with higher numbers of cells. We then introduce a pair-correlation function which allows us to quantify aspects of the spatial patterns produced by our agent-based model. In particular, these pair-correlation functions are able to detect differences between domains populated uniformly at random (i.e. at the exclusion complete spatial randomness (ECSR) state) and those where the proliferation and biased motion rules have been employed - even when such differences are not obvious to the naked eye. The pair-correlation function can also detect the emergence of a characteristic inter-aggregate distance which occurs when the biased motion mechanism is dominant, and is not observed when cell proliferation is the main mechanism of aggregate formation. This suggests that applying the pair-correlation function to experimental images of cell aggregates may provide information about the mechanism associated with observed aggregates. As a proof of concept, we perform such analysis for images of cancer cell aggregates, which are known to be associated with rapid proliferation. The results of our analysis are consistent with the predictions of the proliferation-based simulations, which supports the potential usefulness of pair correlation functions for providing insight into the mechanisms of aggregate formation.

Choosing an appropriate modelling framework for analysing multispecies co-culture cell biology experiments

In vitro cell biology assays play a crucial role in informing our understanding of the migratory, proliferative and invasive properties of many cell types in different biological contexts. While mono-culture assays involve the study of a population of cells composed of a single cell type, co-culture assays study a population of cells composed of multiple cell types (or subpopulations of cells). Such co-culture assays can provide more realistic insights into many biological processes including tissue repair, tissue regeneration and malignant spreading. Typically, system parameters, such as motility and proliferation rates, are estimated by calibrating a mathematical or computational model to the observed experimental data. However, parameter estimates can be highly sensitive to the choice of model and modelling framework. This observation motivates us to consider the fundamental question of how we can best choose a model to facilitate accurate parameter estimation for a particular assay. In this work we describe three mathematical models of mono-culture and co-culture assays that include different levels of spatial detail. We study various spatial summary statistics to explore if they can be used to distinguish between the suitability of each model over a range of parameter space. Our results for mono-culture experiments are promising, in that we suggest two spatial statistics that can be used to direct model choice. However, co-culture experiments are far more challenging: we show that these same spatial statistics which provide useful insight into mono-culture systems are insuffcient for co-culture systems. Therefore, we conclude that great care ought to be exercised when estimating the parameters of co-culture assays.

Effect of TiO2 electrode thickness on photovoltaic properties of dye sensitized solar cell based on randomly oriented Titania nanotubes

Anatase titania nanotubes (TNTs) have been synthesized from P25 TiO2 powder by alkali hydrothermal method followed by post annealing. The microstructure analysis by X-ray diffraction (XRD), transmission electron microscopy (TEM) and scanning electron microscopy (SEM) revealed the formation of anatase nanotubes with a diameter of 9-10 nm. These NTs are used to make photo anode in dye-sensitized solar cells (DSSCs). Layer by layer deposition with curing of each layer at 350 C is employed to realize films of desired thickness. The performance of these cells is studied using photovoltaic measurements. Electrochemical impedance spectroscopy (EIS) is used to quantitatively analyze the effect of thickness on the performance of these cells. These studies revealed that the thickness of TiO2 has a pronounced impact on the cell performance and the optimum thickness lies in the range of 10-14 mu m. In comparison to dye solar cells made of P25, TNTs based cells exhibit an improved open circuit voltage and fill factor (FF) due to an increased electron lifetime, as revealed by EIS analysis. (C) 2011 Elsevier B.V. All rights reserved.

The promise of fuel cell-based automobiles

Fuel cell-based automobiles have gained attention in the last few years due to growing public concern about urban air pollution and consequent environmental problems. From an analysis of the power and energy requirements of a modern car, it is estimated that a base sustainable power of ca. 50 kW supplemented with short bursts up to 80 kW will suffice in most driving requirements. The energy demand depends greatly on driving characteristics but under normal usage is expected to be 200 Wh/km. The advantages and disadvantages of candidate fuel-cell systems and various fuels are considered together with the issue of whether the fuel should be converted directly in the fuel cell or should be reformed to hydrogen onboard the vehicle. For fuel cell vehicles to compete successfully with conventional internal-combustion engine vehicles, it appears that direct conversion fuel cells using probably hydrogen, but possibly methanol, are the only realistic contenders for road transportation applications. Among the available fuel cell technologies, polymer-electrolyte fuel cells directly fueled with hydrogen appear to be the best option for powering fuel cell vehicles as there is every prospect that these will exceed the performance of the internal-combustion engine vehicles but for their first cost. A target cost of $ 50/kW would be mandatory to make polymer-electrolyte fuel cells competitive with the internal combustion engines and can only be achieved with design changes that would substantially reduce the quantity of materials used. At present, prominent car manufacturers are deploying important research and development efforts to develop fuel cell vehicles and are projecting to start production by 2005.

Dye sensitized solar cell based on platinum decorated multiwall carbon nanotubes as catalytic layer on the counter electrode

In this study we have employed multiwall carbon nanotubes (MWCNT), decorated with platinum as catalytic layer for the reduction of tri-iodide ions in dye sensitized solar cell (DSSC). MWCNTs have been prepared by a simple one step pyrolysis method using ferrocene as the catalyst and xylene as the carbon source. Platinum decorated MWCNTs have been prepared by chemical reduction method. The as prepared MWCNTs and Pt/MWCNTs have been characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). In combination with a dye adsorbed TiO(2) photoanode and an organic liquid electrolyte, Pt/MWCNT composite showed an enhanced short circuit current density of 16.12 mA/cm(2) leading to a cell efficiency of 6.50% which is comparable to that of Platinum. (C) 2011 Elsevier Ltd. All rights reserved.

A quantum dot sensitized solar cell based on vertically aligned carbon nanotube templated ZnO arrays

We report on a quantum dot sensitized solar cell (QDSSC) based on ZnO nanorod coated vertically aligned carbon nanotubes (VACNTs). Electrochemical impedance spectroscopy shows that the electron lifetime for the device based on VACNT/ZnO/CdSe is longer than that for a device based on ZnO/CdSe, indicating that the charge recombination at the interface is reduced by the presence of the VACNTs. Due to the increased surface area and longer electron lifetime, a power conversion efficiency of 1.46% is achieved for the VACNT/ZnO/CdSe devices under an illumination of one Sun (AM 1.5G, 100 mW/cm2). © 2010 Elsevier B.V.

Biofunctionalization of alginate microcapsules: advances in cell-based drug delivery systems

172 p.

A solid-state dye-sensitized solar cell based on a novel ionic liquid gel and ZnO nanoparticles on a flexible polymer substrate.

This paper describes a new strategy to make a full solid-state, flexible, dye-sensitized solar cell (DSSC) based on novel ionic liquid gel, organic dye, ZnO nanoparticles and carbon nanotube (CNT) thin film stamped onto a polyethylene terephthalate (PET) substrate. The CNTs serve both as the charge collector and as scaffolds for the growth of ZnO nanoparticles, where the black dye molecules are anchored. It opens up the possibility of developing a continuous roll to roll processing for THE mass production of DSSCs.

A nanowire magnetic memory cell based on a periodic magnetic superlattice

We analyse the operation of a semiconductor nanowire-based memory cell. Large changes in the nanowire conductance result when the magnetization of a periodic array of nanoscale magnetic gates, which comprise the other key component of the memory cell, is switched between distinct configurations by an external magnetic field. The resulting conductance change provides the basis for a robust memory effect, which can be implemented in a semiconductor structure compatible with conventional semiconductor integrated circuits.