Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

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.

Quantum Simulation of Dissipative Processes without Reservoir Engineering

We present a quantum algorithm to simulate general finite dimensional Lindblad master equations without the requirement of engineering the system-environment interactions. The proposed method is able to simulate both Markovian and non-Markovian quantum dynamics. It consists in the quantum computation of the dissipative corrections to the unitary evolution of the system of interest, via the reconstruction of the response functions associated with the Lindblad operators. Our approach is equally applicable to dynamics generated by effectively non-Hermitian Hamiltonians. We confirm the quality of our method providing specific error bounds that quantify its accuracy.