1. #### Reactive controllers for differentially flat systems with temporal logic constraints

Liu, Jun; Topcu, Ufuk; Ozay, Necmiye; Murray, Richard M.
We propose a procedure for the synthesis of control protocols for systems governed by nonlinear differential equations and constrained by temporal logic specifications. This procedure relies on a particular finite-state abstraction of the underlying continuous dynamics and a discrete representation of the external environmental signals. A two-player game formulation provides computationally efficient means to construct a discrete strategy based on the finite-state model. We focus on systems with differentially flat outputs, which, in a straightforward manner, allows the construction of continuous control signals from the discrete transitions dictated by the discrete strategy. The resulting continuous-time output trajectories are provably guaranteed...

2. #### Towards definition of an ECM parts list: An advance on GO categories

Naba, Alexandra; Hoersch, Sebastian; Hynes, Richard O.; Hynes, Richard O
Those of us interested in the extracellular matrix (ECM) are faced with significant challenges of definition. ECM proteins are large, complex and assembled into crosslinked insoluble matrices. This has meant that defining the biochemical composition of ECMs has been difficult. Nonetheless, protein chemistry and molecular biology have defined many familiar ECM proteins — collagens, proteoglycans, laminins, thrombospondins, tenascins, fibronectins, etc. With the completion of many genomes it should now be possible to develop complete “parts lists” for the ECM. Such lists are needed for analyzing data from “omic” approaches such as expression arrays, latest-generation sequencing and proteomics. These approaches generate...

3. #### Studies of amino acid sensing by the mTORC 1 pathway

Wang, Shuyu, Ph. D. Massachusetts Institute of Technology
The mTOR complex 1 (mTORC 1) protein kinase is a master growth regulator that responds to multiple cues from the local and systemic environment surrounding the cell. Nutrients and growth factors are both required to activate mTORC 1 and to promote growth. While the mechanisms of growth factor signaling have been reasonably well established, we have only begun to unravel in recent years how amino acids signal to mTORC 1, thanks in large part to the identification of the Rag GTPases, which recruit mTORC 1 to the lysosomal surface for catalytic activation, and of the regulators of Rag function. An...

4. #### The Function and Organization of the Motor System Controlling Flight Maneuvers in Flies

Lindsay, Theodore; Sustar, Anne; Dickinson, Michael
Animals face the daunting task of controlling their limbs using a small set of highly constrained actuators. This problem is particularly demanding for insects such as Drosophila, which must adjust wing motion for both quick voluntary maneuvers and slow compensatory reflexes using only a dozen pairs of muscles. To identify strategies by which animals execute precise actions using sparse motor networks, we imaged the activity of a complete ensemble of wing control muscles in intact, flying flies. Our experiments uncovered a remarkably efficient logic in which each of the four skeletal elements at the base of the wing are equipped...

5. #### Model predictive control with signal temporal logic specifications

Raman, Vasumathi; Donzé, Alexandre; Maasoumy, Mehdi; Murray, Richard M.; Sangiovanni-Vincentelli, Alberto; Seshia, Sanjit A.
We present a mathematical programming-based method for model predictive control of discrete-time cyber-physical systems subject to signal temporal logic (STL) specifications. We describe the use of STL to specify a wide range of properties of these systems, including safety, response and bounded liveness. For synthesis, we encode STL specifications as mixed integer-linear constraints on the system variables in the optimization problem at each step of a model predictive control framework. We present experimental results for controller synthesis for building energy and climate control.

6. #### Automata theory meets approximate dynamic programming: Optimal control with temporal logic constraints

Papusha, Ivan; Fu, Jie; Topcu, Ufuk; Murray, Richard M.
We investigate the synthesis of optimal controllers for continuous-time and continuous-state systems under temporal logic specifications. The specification is expressed as a deterministic, finite automaton (the specification automaton) with transition costs, and the optimal system behavior is captured by a cost function that is integrated over time. We construct a dynamic programming problem over the product of the underlying continuous-time, continuous-state system and the discrete specification automaton. To solve this dynamic program, we propose controller synthesis algorithms based on approximate dynamic programming (ADP) for both linear and nonlinear systems under temporal logic constraints. We argue that ADP allows treating the...

7. #### Simultaneous model identification and task satisfaction in the presence of temporal logic constraints

Chinchali, Sandeep P.; Livingston, Scott C.; Pavone, Marco; Burdick, Joel W.
Recent proliferation of cyber-physical systems, ranging from autonomous cars to nuclear hazard inspection robots, has exposed several challenging research problems on automated fault detection and recovery. This paper considers how recently developed formal synthesis and model verification techniques may be used to automatically generate information-seeking trajectories for anomaly detection. In particular, we consider the problem of how a robot could select its actions so as to maximally disambiguate between different model hypotheses that govern the environment it operates in or its interaction with other agents whose prime motivation is a priori unknown. The identification problem is posed as selection of...

8. #### Planning Education for Economic Development

Fields, Gary S
[Excerpt] This paper presents the most important approaches to the economics of education. Three topics are developed: The logic of economic analysis of educational planning Three approaches to educational planning Evaluating the social rate-of-return approach in a developing country context.

9. #### Compositional reactive synthesis for multi-agent systems

Moarref, Salar
With growing complexity of systems and guarantees they are required to provide, the need for automated and formal design approaches that can guarantee safety and correctness of the designed system is becoming more evident. To this end, an ambitious goal in system design and control is to automatically synthesize the system from a high-level specification given in a formal language such as linear temporal logic. The goal of this dissertation is to investigate and develop the necessary tools and methods for automated synthesis of controllers from high-level specifications for multi-agent systems. We consider systems where a set of controlled agents...

10. #### Program auto-tuning through population-based stochastic optimization

Zhan, Minshu
Program optimization often can and need to be decoupled from the programs innate logic. In various domains, program autotuners have been developed which can automatically search for optimal program configurations using established optimization methods. OpenTuner is a general-purpose autotuner which provides a flexible search domain representation and robust optimization techniques. This thesis extends Open-Tuner with the family of population-based stochastic optimization (PBSO) algorithms to boost OpenTuner's search capability on discrete-valued tuning problems.

11. #### A tool for automated inference in rule-based biological models

Voss, Chelsea (Chelsea S.)
Rule-based biological models help researchers investigate systems such as cellular signalling pathways. Although these models are generally programmed by hand, some research efforts aim to program them automatically using biological facts extracted from papers via natural language processing. However, NLP facts cannot always be directly converted into mechanistic reaction rules for a rule-based model. Thus, there is a need for tools that can convert biological facts into mechanistic rules in a logically sound way. We construct such a tool specifically for Kappa, a model programming language, by implementing Iota, a logic language for Kappa models. Our tool can translate biological...

12. #### Design for a mind with many bodies : cybernetic micro-interventions in the cryosphere

Gonzalez Ramirez, Ricardo Jnani
Historically, designs that function within the realm of ecological interventions have heavily gravitated towards attempting to gain full authority and control over the particular ecosystem in order to reform it. This approach is seen far more often than that of working in tandem with the ecosystem through an adaptive and autopoietic manner. [1] According to Pickering, this predominant, hegemonic, and static mode of operations "ignores emergence [and] assumes that we know all the chains of cause and effect." The thesis proposed here instead suggests that through a soft, cybernetic approach of aggregated micro-interventions a higher degree of adaptability and autopoiesis...

13. #### Probabilistic seismic hazard maps for the sultanate of Oman

El-Hussain, I.; Deif, A.; Al-Jabri, K.; El-Hady, S.; Al-Hashmi, S.; Al-Toubi, K.; Al-Shijbi, Y.; Al-Saifi, M.; Kuleli, Huseyin Sadi; Toksoz, M. Nafi
This study presents the results of the first probabilistic seismic hazard assessment (PSHA) in the framework of logic tree for Oman. The earthquake catalogue was homogenized, declustered, and used to define seismotectonic source model that characterizes the seismicity of Oman. Two seismic source models were used in the current study; the first consists of 26 seismic source zones, while the second is expressing the alternative view that seismicity is uniform along the entire Makran and Zagros zones. The recurrence parameters for all the seismogenic zones were determined using the doubly bounded exponential distribution except the zones of Makran, which were...

14. #### Ramsey Algebras and Formal Orderly Terms

Teh, Wen Chean
Hindman’s theorem says that every finite coloring of the natural numbers has a monochromatic set of finite sums. A Ramsey algebra is a structure that satisfies an analogue of Hindman’s theorem. In this paper, we present the basic notions of Ramsey algebras by using terminology from mathematical logic. We also present some results regarding classification of Ramsey algebras.

15. #### Models as Universes

Halimi, Brice
Kreisel’s set-theoretic problem is the problem as to whether any logical consequence of ZFC is ensured to be true. Kreisel and Boolos both proposed an answer, taking truth to mean truth in the background set-theoretic universe. This article advocates another answer, which lies at the level of models of set theory, so that truth remains the usual semantic notion. The article is divided into three parts. It first analyzes Kreisel’s set-theoretic problem and proposes one way in which any model of set theory can be compared to a background universe and shown to contain internal models. It then defines logical...

16. #### Locally Finite Reducts of Heyting Algebras and Canonical Formulas

Bezhanishvili, Guram; Bezhanishvili, Nick
The variety of Heyting algebras has two well-behaved locally finite reducts, the variety of bounded distributive lattices and the variety of implicative semilattices. The variety of bounded distributive lattices is generated by the $\to$ -free reducts of Heyting algebras, while the variety of implicative semilattices is generated by the $\vee$ -free reducts. Each of these reducts gives rise to canonical formulas that generalize Jankov formulas and provide an axiomatization of all superintuitionistic logics (si-logics for short). ¶ The $\vee$ -free reducts of Heyting algebras give rise to the $(\wedge,\to)$ -canonical formulas that we studied in an earlier work. Here we introduce the...

17. #### Disarming a Paradox of Validity

Field, Hartry
Any theory of truth must find a way around Curry’s paradox, and there are well-known ways to do so. This paper concerns an apparently analogous paradox, about validity rather than truth, which JC Beall and Julien Murzi (“Two flavors of Curry’s paradox”) call the v-Curry. They argue that there are reasons to want a common solution to it and the standard Curry paradox, and that this rules out the solutions to the latter offered by most “naive truth theorists.” To this end they recommend a radical solution to both paradoxes, involving a substructural logic, in particular, one without structural contraction. ¶ In...

18. #### Layered graph logic as an assertion language for access control policy models

Pym, D; Collinson, M; McDonald, K
We describe a uniform logical framework, based on a bunched logic that combines classical additives and very weak multiplicatives, for reasoning compositionally about access control policy models. We show how our approach takes account of the underlying system architecture, and so provides a way to identify and reason about how vulnerabilities may arise (and be removed) as a result of the architecture of the system. We consider, using frame rules, how local properties of access control policies are maintained as the system architecture evolves.

19. #### SAT-based optimal hypergraph partitioning with replication

Wrighton, Michael G.; DeHon, André M.
We propose a methodology for optimal k-way partitioning with replication of directed hypergraphs via Boolean satisfiability. We begin by leveraging the power of existing and emerging SAT solvers to attack traditional logic bipartitioning and show good scaling behavior. We continue to present the first optimal partitioning results that admit generation and assignment of replicated nodes concurrently. Our framework is general enough that we also give the first published optimal results for partitioning with respect to the maximum subdomain degree metric and the sum of external degrees metric. We show that for the bipartitioning case we can feasibly solve problems of...

20. #### Toward molecular programming with DNA

Winfree, Erik
Biological organisms are beautiful examples of programming. The program and data are stored in biological molecules such as DNA, RNA, and proteins; the algorithms are carried out by molecular and biochemical processes; and the end result is the creation and function of an organism. If we understood how to program molecular systems, what could we create? Lifelike technologies whose basic operations are chemical reactions? The fields of chemistry, physics, biology, and computer science are converging as we begin to synthesize molecules, molecular machines, and molecular systems of ever increasing complexity, leading to subdisciplines such as DNA nanotechnology, DNA computing, and...

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