Hydrotalcite intercalated siRNA:computational characterization of the interlayer environment

Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a Mg:Al 2:1 Layered Double Hydroxide (LDH) nanoparticle. An ab initio force field (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies: COMPASS) is used for the MD simulations of the hybrid organic-inorganic systems. The structure, arrangement, mobility, close contacts and hydrogen bonds associated with the intercalated RNA are examined and contrasted with those of the isolated RNA. Computed powder X-ray diffraction patterns are also compared with related LDH-DNA experiments. As a method of probing whether the intercalated environment approximates the crystalline or rather the aqueous state, we explore the stability of the principle parameters (e.g., the major groove width) that differentiate both A- and A'- crystalline forms of siRNA and contrast this with recent findings for the same siRNA simulated in water. We find the crystalline forms remain structurally distinct when intercalated, whereas this is not the case in water. Implications for the stability of hybrid LDH-RNA systems are discussed.

Toward an atomistic understanding of the immune synapse:large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex

T-cell activation requires interaction of T-cell receptors (TCR) with peptide epitopes bound by major histocompatibility complex (MHC) proteins. This interaction occurs at a special cell-cell junction known as the immune or immunological synapse. Fluorescence microscopy has shown that the interplay among one agonist peptide-MHC (pMHC), one TCR and one CD4 provides the minimum complexity needed to trigger transient calcium signalling. We describe a computational approach to the study of the immune synapse. Using molecular dynamics simulation, we report here on a study of the smallest viable model, a TCR-pMHC-CD4 complex in a membrane environment. The computed structural and thermodynamic properties are in fair agreement with experiment. A number of biomolecules participate in the formation of the immunological synapse. Multi-scale molecular dynamics simulations may be the best opportunity we have to reach a full understanding of this remarkable supra-macromolecular event at a cell-cell junction.

Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Resource allocation in decentralised computational systems:an evolutionary market-based approach

We present a novel market-based method, inspired by retail markets, for resource allocation in fully decentralised systems where agents are self-interested. Our market mechanism requires no coordinating node or complex negotiation. The stability of outcome allocations, those at equilibrium, is analysed and compared for three buyer behaviour models. In order to capture the interaction between self-interested agents, we propose the use of competitive coevolution. Our approach is both highly scalable and may be tuned to achieve specified outcome resource allocations. We demonstrate the behaviour of our approach in simulation, where evolutionary market agents act on behalf of service providing nodes to adaptively price their resources over time, in response to market conditions. We show that this leads the system to the predicted outcome resource allocation. Furthermore, the system remains stable in the presence of small changes in price, when buyers' decision functions degrade gracefully. © 2009 The Author(s).

Modelling and simulation of biomass gasification in a circulating fluidized bed reactor

Computational Fluid Dynamics (CFD) has found great acceptance among the engineering community as a tool for research and design of processes that are practically difficult or expensive to study experimentally. One of these processes is the biomass gasification in a Circulating Fluidized Bed (CFB). Biomass gasification is the thermo-chemical conversion of biomass at a high temperature and a controlled oxygen amount into fuel gas, also sometime referred to as syngas. Circulating fluidized bed is a type of reactor in which it is possible to maintain a stable and continuous circulation of solids in a gas-solid system. The main objectives of this thesis are four folds: (i) Develop a three-dimensional predictive model of biomass gasification in a CFB riser using advanced Computational Fluid Dynamic (CFD) (ii) Experimentally validate the developed hydrodynamic model using conventional and advanced measuring techniques (iii) Study the complex hydrodynamics, heat transfer and reaction kinetics through modelling and simulation (iv) Study the CFB gasifier performance through parametric analysis and identify the optimum operating condition to maximize the product gas quality. Two different and complimentary experimental techniques were used to validate the hydrodynamic model, namely pressure measurement and particle tracking. The pressure measurement is a very common and widely used technique in fluidized bed studies, while, particle tracking using PEPT, which was originally developed for medical imaging, is a relatively new technique in the engineering field. It is relatively expensive and only available at few research centres around the world. This study started with a simple poly-dispersed single solid phase then moved to binary solid phases. The single solid phase was used for primary validations and eliminating unnecessary options and steps in building the hydrodynamic model. Then the outcomes from the primary validations were applied to the secondary validations of the binary mixture to avoid time consuming computations. Studies on binary solid mixture hydrodynamics is rarely reported in the literature. In this study the binary solid mixture was modelled and validated using experimental data from the both techniques mentioned above. Good agreement was achieved with the both techniques. According to the general gasification steps the developed model has been separated into three main gasification stages; drying, devolatilization and tar cracking, and partial combustion and gasification. The drying was modelled as a mass transfer from the solid phase to the gas phase. The devolatilization and tar cracking model consist of two steps; the devolatilization of the biomass which is used as a single reaction to generate the biomass gases from the volatile materials and tar cracking. The latter is also modelled as one reaction to generate gases with fixed mass fractions. The first reaction was classified as a heterogeneous reaction while the second reaction was classified as homogenous reaction. The partial combustion and gasification model consisted of carbon combustion reactions and carbon and gas phase reactions. The partial combustion considered was for C, CO, H2 and CH4. The carbon gasification reactions used in this study is the Boudouard reaction with CO2, the reaction with H2O and Methanation (Methane forming reaction) reaction to generate methane. The other gas phase reactions considered in this study are the water gas shift reaction, which is modelled as a reversible reaction and the methane steam reforming reaction. The developed gasification model was validated using different experimental data from the literature and for a wide range of operating conditions. Good agreement was observed, thus confirming the capability of the model in predicting biomass gasification in a CFB to a great accuracy. The developed model has been successfully used to carry out sensitivity and parametric analysis. The sensitivity analysis included: study of the effect of inclusion of various combustion reaction; and the effect of radiation in the gasification reaction. The developed model was also used to carry out parametric analysis by changing the following gasifier operating conditions: fuel/air ratio; biomass flow rates; sand (heat carrier) temperatures; sand flow rates; sand and biomass particle sizes; gasifying agent (pure air or pure steam); pyrolysis models used; steam/biomass ratio. Finally, based on these parametric and sensitivity analysis a final model was recommended for the simulation of biomass gasification in a CFB riser.

Solving Travelling Salesman Problem in a Simulation of Genetic Algorithms with DNA

In this paper it is explained how to solve a fully connected N-City travelling salesman problem (TSP) using a genetic algorithm. A crossover operator to use in the simulation of a genetic algorithm (GA) with DNA is presented. The aim of the paper is to follow the path of creating a new computational model based on DNA molecules and genetic operations. This paper solves the problem of exponentially size algorithms in DNA computing by using biological methods and techniques. After individual encoding and fitness evaluation, a protocol of the next step in a GA, crossover, is needed. This paper also shows how to make the GA faster via different populations of possible solutions.

Numerical simulation of mass transfer during the osmotic dehydration of biological tissues

In this paper a mathematical model based on mass transfer in plant tissues is developed. The model takes into account the diffusion and convection of each constituent within the tissue. The driving force for the convection is assumed to be the gradient of hydrostatic pressure. The mass balance equation for the transport of each constituent is established separately for intracellular and extracellular volumes but taking into account the mass exchange across the cell membrane between the intracellular and extracellular volumes. The mass transfer results in not only the change of intracellular and extracellular volumes but also the shrinkage of whole tissue. The model allows us to quantitatively simulate the time evolution of intracellular and extracellular volumes, which was observed in histological sections under the microscope. © 2005 Elsevier B.V. All rights reserved.

DNA Simulation of Genetic Algorithms: Fitness Computation

* This work has been partially supported by Spanish Project TIC2003-9319-c03-03 “Neural Networks and Networks of Evolutionary Processors”.

A DNA Codification for Genetic Algorithms Simulation

In this paper we propose a model of encoding data into DNA strands so that this data can be used in the simulation of a genetic algorithm based on molecular operations. DNA computing is an impressive computational model that needs algorithms to work properly and efficiently. The first problem when trying to apply an algorithm in DNA computing must be how to codify the data that the algorithm will use. In a genetic algorithm the first objective must be to codify the genes, which are the main data. A concrete encoding of the genes in a single DNA strand is presented and we discuss what this codification is suitable for. Previous work on DNA coding defined bond-free languages which several properties assuring the stability of any DNA word of such a language. We prove that a bond-free language is necessary but not sufficient to codify a gene giving the correct codification.

Grid and Simulation of Digital Communication Systems

The purpose of this paper is to turn researchers' attention to the use of grid computing for simulating digital communications and its large potential for decreasing significantly the duration of the experiments and for improving the statistical representativeness and reliability of the obtained results.

On the Mathematical Modelling of Microbial Growth: Some Computational Aspects

We propose a new approach to the mathematical modelling of microbial growth. Our approach differs from familiar Monod type models by considering two phases in the physiological states of the microorganisms and makes use of basic relations from enzyme kinetics. Such an approach may be useful in the modelling and control of biotechnological processes, where microorganisms are used for various biodegradation purposes and are often put under extreme inhibitory conditions. Some computational experiments are performed in support of our modelling approach.

A Computational Approach for the Statistical Estimation of Discrete Time Branching Processes with Immigration

2010 Mathematics Subject Classification: 60J80.

Effect of blood flow patterns on localized platelet adhesion under physiologic flow conditions using two-dimensional and three-dimensional stent models: An experimental and computational approach

This dissertation presents dynamic flow experiments with fluorescently labeled platelets to allow for spatial observation of wall attachment in inter-strut spacings, to investigate their relationship to flow patterns. Human blood with fluorescently labeled platelets was circulated through an in vitro system that produced physiologic pulsatile flow in (1) a parallel plate blow chamber that contained two-dimensional (2D) stents that feature completely recirculating flow, partially recirculating flow, and completely reattached flow, and (2) a three-dimensional (3D) cylindrical tube that contained stents of various geometric designs. ^ Flow detachment and reattachment points exhibited very low platelet deposition. Platelet deposition was very low in the recirculation regions in the 3D stents unlike the 2D stents. Deposition distal to a strut was always high in 2D and 3D stents. Spirally recirculating regions were found in 3D unlike in 2D stents, where the deposition was higher than at well-separated regions of recirculation. ^

Secure information flow via stripping and fast simulation

Type systems for secure information flow aim to prevent a program from leaking information from H (high) to L (low) variables. Traditionally, bisimulation has been the prevalent technique for proving the soundness of such systems. This work introduces a new proof technique based on stripping and fast simulation, and shows that it can be applied in a number of cases where bisimulation fails. We present a progressive development of this technique over a representative sample of languages including a simple imperative language (core theory), a multiprocessing nondeterministic language, a probabilistic language, and a language with cryptographic primitives. In the core theory we illustrate the key concepts of this technique in a basic setting. A fast low simulation in the context of transition systems is a binary relation where simulating states can match the moves of simulated states while maintaining the equivalence of low variables; stripping is a function that removes high commands from programs. We show that we can prove secure information flow by arguing that the stripping relation is a fast low simulation. We then extend the core theory to an abstract distributed language under a nondeterministic scheduler. Next, we extend to a probabilistic language with a random assignment command; we generalize fast simulation to the setting of discrete time Markov Chains, and prove approximate probabilistic noninterference. Finally, we introduce cryptographic primitives into the probabilistic language and prove computational noninterference, provided that the underling encryption scheme is secure.

Computational evaluation of wind loads on low- and highrise buildings

Buildings and other infrastructures located in the coastal regions of the US have a higher level of wind vulnerability. Reducing the increasing property losses and causalities associated with severe windstorms has been the central research focus of the wind engineering community. The present wind engineering toolbox consists of building codes and standards, laboratory experiments, and field measurements. The American Society of Civil Engineers (ASCE) 7 standard provides wind loads only for buildings with common shapes. For complex cases it refers to physical modeling. Although this option can be economically viable for large projects, it is not cost-effective for low-rise residential houses. To circumvent these limitations, a numerical approach based on the techniques of Computational Fluid Dynamics (CFD) has been developed. The recent advance in computing technology and significant developments in turbulence modeling is making numerical evaluation of wind effects a more affordable approach. The present study targeted those cases that are not addressed by the standards. These include wind loads on complex roofs for low-rise buildings, aerodynamics of tall buildings, and effects of complex surrounding buildings. Among all the turbulence models investigated, the large eddy simulation (LES) model performed the best in predicting wind loads. The application of a spatially evolving time-dependent wind velocity field with the relevant turbulence structures at the inlet boundaries was found to be essential. All the results were compared and validated with experimental data. The study also revealed CFD's unique flow visualization and aerodynamic data generation capabilities along with a better understanding of the complex three-dimensional aerodynamics of wind-structure interactions. With the proper modeling that realistically represents the actual turbulent atmospheric boundary layer flow, CFD can offer an economical alternative to the existing wind engineering tools. CFD's easy accessibility is expected to transform the practice of structural design for wind, resulting in more wind-resilient and sustainable systems by encouraging optimal aerodynamic and sustainable structural/building design. Thus, this method will help ensure public safety and reduce economic losses due to wind perils.