Design and analysis of nucleic acid reaction pathways

Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.

Design and analysis of a kind of large flattened mode optical fibre

In this paper, a refractive index pro. le design enabling us to obtain a. at modal field around the fibre centre is investigated. The theoretical approach for designing such multilayer large flattened mode (LFM) optical fibres is presented. A comparison is made between the properties of a three-layer LFM structure and a standard step-index pro. le with the same core size. The obtained results indicate that the effective area of the LFM fibre is about twice as large as that of the standard step-index fibre, but the LFM fibre has less effective ability to filter out the higher order modes than the standard step-index fibre with the same bending radius.

Design and analysis of 1.3 mu m GaAs-based quantum dot vertical-cavity surface-emitting lasers

A theoretical study on 1.3 mu m GaAs-based quantum dot vertical-cavity surface-emitting lasers (VCSELs) was made. Investigation of the influence of VCSELs on the optical confinement factors and the optical loss and the calculation of the material gain of the assembled InGaAs/GaAs quantum dots. Analysis of the threshold characteristic was made and the multi-wavelength cavity and multilayer quantum-dot stack structure is found to be more suitable for quantum dot VCSELs.

Design and analysis of kinetic energy recovery system for automobiles: a case study for commuters in Edinburgh.

Transport and its energetic and environmental impacts affect our daily lives. The transport sector is the backbone of the United Kingdom’s economy with 2.3 million people being employed in this sector. With a high dependency on transport for passengers and freight and with the knowledge that oil reserves are rapidly decreasing a solution has to be identified for conserving fuel. Passenger vehicles account for 61% of the transport fuel consumed in the U.K. and should be seen as a key area to tackle. Despite the introduction and development of electric powered cars, the widespread infrastructure that is required is not in place and has attributed to their slow uptake, as well as the fact that the electric car’s performance is not yet comparable with the conventional internal combustion engine. The benefits of the introduction of kinetic energy recovery systems to be used in conjunction with internal combustion engines and designed such that the system could easily be fitted into future passenger vehicles are examined. In this article, a review of automobile kinetic energy recovery system is presented. It has been argued that the ultracapacitor technology offers a sustainable solution. An optimum design for the urban driving cycle experienced in the city of Edinburgh has been introduced. The potential for fuel savings is also presented

Book Review Sharon L. Lohr Sampling: Design and Analysis

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