Online exercise for the design and simulation of PCR and PCR-RFLP experiments

[EN] Background: Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings: An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes,compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions: The exercise is freely available at http://insilico.ehu.es/edu.

Modelling and Simulation of ERTMS for Current and Future Mobile Technologies

Nowadays, train control in-lab simulation tools play a crucial role in reducing extensive and expensive on-site railway testing activities. In this paper, we present our contribution in this arena by detailing the internals of our European Railway Train Management System in-lab demonstrator. This demonstrator is built over a general-purpose simulation framework, Riverbed Modeler, previously Opnet Modeler. Our framework models both ERTMS subsystems, the Automatic Train Protection application layer based on movement authority message exchange and the telecommunication subsystem based on GSM-R communication technology. We provide detailed information on our modelling strategy. We also validate our simulation framework with real trace data. To conclude, under current industry migration scenario from GSM-R legacy obsolescence to IP-based heterogeneous technologies, our simulation framework represents a singular tool to railway operators. As an example, we present the assessment of related performance indicators for a specific railway network using a candidate replacement technology, LTE, versus current legacy technology. To the best of our knowledge, there is no similar initiative able to measure the impact of the telecommunication subsystem in the railway network availability.

Modelling and simulation of the second-order Doppler error of a laser dual-frequency interferometer

Only the first- order Doppler frequency shift is considered in current laser dual- frequency interferometers; however; the second- order Doppler frequency shift should be considered when the measurement corner cube ( MCC) moves at high velocity or variable velocity because it can cause considerable error. The influence of the second- order Doppler frequency shift on interferometer error is studied in this paper, and a model of the second- order Doppler error is put forward. Moreover, the model has been simulated with both high velocity and variable velocity motion. The simulated results show that the second- order Doppler error is proportional to the velocity of the MCC when it moves with uniform motion and the measured displacement is certain. When the MCC moves with variable motion, the second- order Doppler error concerns not only velocity but also acceleration. When muzzle velocity is zero the second- order Doppler error caused by an acceleration of 0.6g can be up to 2.5 nm in 0.4 s, which is not negligible in nanometric measurement. Moreover, when the muzzle velocity is nonzero, the accelerated motion may result in a greater error and decelerated motion may result in a smaller error.

Theory and simulation of the optical response of novel nanomaterials from visible to terahertz

133 p.