Synthetic in vitro transcriptional oscillators

The construction of synthetic biochemical circuits from simple components illuminates how complex behaviors can arise in chemistry and builds a foundation for future biological technologies. A simplified analog of genetic regulatory networks, in vitro transcriptional circuits, provides a modular platform for the systematic construction of arbitrary circuits and requires only two essential enzymes, bacteriophage T7 RNA polymerase and Escherichia coli ribonuclease H, to produce and degrade RNA signals. In this study, we design and experimentally demonstrate three transcriptional oscillators in vitro. First, a negative feedback oscillator comprising two switches, regulated by excitatory and inhibitory RNA signals, showed up to five complete cycles. To demonstrate modularity and to explore the design space further, a positive-feedback loop was added that modulates and extends the oscillatory regime. Finally, a three-switch ring oscillator was constructed and analyzed. Mathematical modeling guided the design process, identified experimental conditions likely to yield oscillations, and explained the system's robust response to interference by short degradation products. Synthetic transcriptional oscillators could prove valuable for systematic exploration of biochemical circuit design principles and for controlling nanoscale devices and orchestrating processes within artificial cells

Sparsing in Real Time Simulation

Modelling of mechatronical systems often leads to large DAEs with stiff components. In real time simulation neither implicit nor explicit methods can cope with such systems in an efficient way: explicit methods have to employ too small steps and implicit methods have to solve too large systems of equations. A solution of this general problem is to use a method that allows manipulations of the Jacobian by computing only those parts that are necessary for the stability of the method. Specifically, manipulation by sparsing aims at zeroing out certain elements of the Jacobian leading t a structure that can be exploited using sparse matrix techniques. The elements to be neglected are chosen by an a priori analysis phase that can be accomplished before the real-time simulaton starts. In this article a sparsing criterion for the linearly implicit Euler method is derived that is based on block diagnonalization and matrix perturbation theory

Kinetic Intersections as a Source of Information on Rate Coefficients

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Sliding mode control of a 2-DOF manipulator with random base vibration based on modified exponential reaching law

To solve the precise position control problem of a two degree of freedom (2-DOF) manipulator with random base vibration, a sliding mode control method based on modified exponential reaching law is studied. The dynamic model of manipulator is established by using the second kind Lagrange equation. The nonlinear term generated by base random vibration is presented as external disturbance term. Based on dynamic models, the sliding mode control using improved exponential reaching law is applied in the manipulator system. It is verified by the simulation result that the control method can effectively suppress the influence of base random vibration, and bring the manipulator from a given initial state to a prescribed terminal state rapidly and precisely