CRN++ : molecular programming language

Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness of chemical reactions, defining representations that are faithful, efficient, and practical remains challenging. This work introduces CRN++, a new language for programming deterministic (mass-action) chemical kinetics to perform computation. We present its syntax and semantics, and build a compiler translating CRN++ programs into chemical reactions, thereby laying the foundation of a comprehensive framework for molecular programming. Our language addresses the key challenge of embedding familiar imperative constructs into a set of chemical reactions happening simultaneously and manipulating real-valued concentrations. Although some deviation from ideal output value cannot be avoided, we develop methods to minimize the error, and implement error analysis tools. We demonstrate the feasibility of using CRN++ on a suite of well-known algorithms for discrete and real-valued computation. CRN++ can be easily extended to support new commands or chemical reaction implementations, and thus provides a foundation for developing more robust and practical molecular programs.Electrical and Computer Engineerin

10271 Abstracts Collection -- Verification over discrete-continuous boundaries

From 4 July 2010 to 9 July 2010, the Dagstuhl Seminar 10271 ``Verification over discrete-continuous boundaries\u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Variations on the Theme of Conning in Mathematical Economics

The mathematization of economics is almost exclusively in terms of the mathematics of real analysis which, in turn, is founded on set theory (and the axiom of choice) and orthodox mathematical logic. In this paper I try to point out that this kind of mathematization is replete with economic infelicities. The attempt to extract these infelicities is in terms of three main examples: dynamics, policy and rational expectations and learning. The focus is on the role and reliance on standard xed point theorems in orthodox mathematical economics

Novel linear and nonlinear optical signal processing for ultra-high bandwidth communications

The thesis is articulated around the theme of ultra-wide bandwidth single channel signals. It focuses on the two main topics of transmission and processing of information by techniques compatible with high baudrates. The processing schemes introduced combine new linear and nonlinear optical platforms such as Fourier-domain programmable optical processors and chalcogenide chip waveguides, as well as the concept of neural network. Transmission of data is considered in the context of medium distance links of Optical Time Division Multiplexed (OTDM) data subject to environmental fluctuations. We experimentally demonstrate simultaneous compensation of differential group delay and multiple orders of dispersion at symbol rates of 640 Gbaud and 1.28 Tbaud. Signal processing at high bandwidth is envisaged both in the case of elementary post-transmission analog error mitigation and in the broader field of optical computing for high level operations (“optical processor”). A key innovation is the introduction of a novel four-wave mixing scheme implementing a dot-product operation between wavelength multiplexed channels. In particular, it is demonstrated for low-latency hash-key based all-optical error detection in links encoded with advanced modulation formats. Finally, the work presents groundbreaking concepts for compact implementation of an optical neural network as a programmable multi-purpose processor. The experimental architecture can implement neural networks with several nodes on a single optical nonlinear transfer function implementing functions such as analog-to-digital conversion. The particularity of the thesis is the new approaches to optical signal processing that potentially enable high level operations using simple optical hardware and limited cascading of components

Quantum Simulation for High Energy Physics

It is for the first time that Quantum Simulation for High Energy Physics (HEP) is studied in the U.S. decadal particle-physics community planning, and in fact until recently, this was not considered a mainstream topic in the community. This fact speaks of a remarkable rate of growth of this subfield over the past few years, stimulated by the impressive advancements in Quantum Information Sciences (QIS) and associated technologies over the past decade, and the significant investment in this area by the government and private sectors in the U.S. and other countries. High-energy physicists have quickly identified problems of importance to our understanding of nature at the most fundamental level, from tiniest distances to cosmological extents, that are intractable with classical computers but may benefit from quantum advantage. They have initiated, and continue to carry out, a vigorous program in theory, algorithm, and hardware co-design for simulations of relevance to the HEP mission. This community whitepaper is an attempt to bring this exciting and yet challenging area of research to the spotlight, and to elaborate on what the promises, requirements, challenges, and potential solutions are over the next decade and beyond.Comment: This is a whitepaper prepared for the topical groups CompF6 (Quantum computing), TF05 (Lattice Gauge Theory), and TF10 (Quantum Information Science) within the Computational Frontier and Theory Frontier of the U.S. Community Study on the Future of Particle Physics (Snowmass 2021). 103 pages and 1 figur