Implementing nonlinear feedback controllers using DNA strand displacement reactions

We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs

Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud

Methods developed at the Texas Advanced Computing Center (TACC) are described and demonstrated for automating the construction of an elastic, virtual cluster emulating the Stampede2 high performance computing (HPC) system. The cluster can be built and/or scaled in a matter of minutes on the Jetstream self-service cloud system and shares many properties of the original Stampede2, including: i) common identity management, ii) access to the same file systems, iii) equivalent software application stack and module system, iv) similar job scheduling interface via Slurm. We measure time-to-solution for a number of common scientific applications on our virtual cluster against equivalent runs on Stampede2 and develop an application profile where performance is similar or otherwise acceptable. For such applications, the virtual cluster provides an effective form of "cloud bursting" with the potential to significantly improve overall turnaround time, particularly when Stampede2 is experiencing long queue wait times. In addition, the virtual cluster can be used for test and debug without directly impacting Stampede2. We conclude with a discussion of how science gateways can leverage the TACC Jobs API web service to incorporate this cloud bursting technique transparently to the end user.Comment: 6 pages, 0 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Design Environments for Complex Systems

The paper describes an approach for modeling complex systems by hiding as much formal details as possible from the user, still allowing verification and simulation of the model. The interface is based on UML to make the environment available to the largest audience. To carry out analysis, verification and simulation we automatically extract process algebras specifications from UML models. The results of the analysis is then reflected back in the UML model by annotating diagrams. The formal model includes stochastic information to handle quantitative parameters. We present here the stochastic -calculus and we discuss the implementation of its probabilistic support that allows simulation of processes. We exploit the benefits of our approach in two applicative domains: global computing and systems biology

Design and analysis of genetic feedback architectures for synthetic biology

Synthetic Biology seeks to design and assemble novel biological systems with favourable properties. It allows us to comprehend and modify the fundamental mechanisms of life and holds significant promise in revolutionizing current technologies ranging from medicine and biomanufacturing to energy and environmental protection. Biological processes constitute remarkably complex dynamical systems operating impeccably well in messy and constantly changing environments. Their ability to do so is rooted in sophisticated molecular control architectures crafted by natural evolutionary innovation over billions of years. Such control architectures, often blended with human-engineering approaches, are the key to realizing efficient and reliable synthetic biological systems. Aiming to accelerate the development of the latter, the present thesis addresses some fundamental challenges in biomolecular systems and control design. We begin by elucidating biological mechanisms of temporal gradient computation, enabling cells to adjust their behaviour in response to anticipated environmental changes. Specifically, we introduce biomolecular motifs capable of functioning as highly tunable and accurate signal differentiators to input molecular signals around their nominal operation. We investigate strategies to deal with high-frequency input signal components which can be detrimental to the performance of most differentiators. We ascertain the occurrence of such motifs in natural regulatory networks and demonstrate the potential of synthetic experimental realizations. Our motifs can serve as reliable speed biosensors and can form the basis for derivative feedback control. Motivated by the pervasiveness of Proportional-Integral-Derivative (PID) controllers in modern technological applications, we present the realization of a PID controller via biomolecular reactions employing, among others, our differentiator motifs. This biomolecular architecture represents a PID control law with set point weighting and filtered derivative action, offering robust regulation of a single-output biological process with enhanced dynamic performance and low levels of stochastic noise. It is characterized by significant ease of tuning and can be of particular experimental interest in molecular programming applications. Finally, we investigate efficient regulation strategies for multi-output biological processes with internal coupling interactions, expanding previously established single-output control approaches. More specifically, we propose control schemes allowing for robust manipulation of the outputs in various ways, namely manipulation of their product/ratio, linear combinations of them as well as manipulation of each of the outputs independently. Our analysis is centered around two-output biological processes, yet the scalability of the proposed regulation strategies to processes with a higher number of outputs is highlighted. In parallel, their experimental implementability is explored in both in vivo and in vitro settings

Energy efficient torus networks with on/off links

[EN] Future exascale computing systems will require energy and performance efficient interconnection networks to respond to the high data movement demands of new applications, such as those coming from big-data and artificial intelligence areas. The network structure plays a major role in the overall interconnect performance, for this reason torus is a common topology used in the current largest supercomputers. There are several proposals to improve energy efficiency of interconnection networks. However, few works combine both energy and performance, and sometimes they are treated as opposed issues. In this paper, we try to determine which torus network configuration offers the best performance/energy ratio when high-radix switches are used to build the interconnect system. The performance/energy evaluation has been performed by trace-driven simulation under realistic scenarios, where several mixes of scientific applications share a supercomputer system and are scheduled to be executed with the available resources at each moment.This work has been supported by the Spanish MINECO and European Commission (FEDER funds) under project TIN2015-66972-05-1-R and project TIN2015-66972-05-2-R. Francisco J. Andujar is also funded by the Spanish MINECO under a Juan de la Cierva grant FJCI-2015-26080.Andújar, FJ.; Coll, S.; Alonso Díaz, M.; Martínez-Rubio, J.; López Rodríguez, PJ.; Sánchez, JL.; Alfaro, FJ.... (2019). Energy efficient torus networks with on/off links. Journal of Parallel and Distributed Computing. 130:37-49. https://doi.org/10.1016/j.jpdc.2019.03.015S374913

POWAR: Power-Aware Routing in HPC Networks with On/Off Links

[EN] In order to save energy in HPC interconnection networks, one usual proposal is to switch idle links into a low-power mode after a certain time without any transmission, as IEEE Energy Efficient Ethernet standard proposes. Extending the low-power mode mechanism, we propose POWer-Aware Routing (POWAR), a simple power-aware routing and selection function for fat-tree and torus networks. POWAR adapts the amount of network links that can be used, taking into account the network load, and obtaining great energy savings in the network (55%-65%) and the entire system (9%-10%) with negligible performance overhead.This work has been supported by the Spanish MINECO and European Commission (FEDER funds) under project TIN2015-66972-C5-1-R. Francisco J. 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