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This thesis describes work on two applications of probabilistic programming: the learning of probabilistic program code given specifications, in particular program code of one-dimensional samplers; and the facilitation of sequential Monte…
Studies of issues related to computability and computational complexity involve the use of a model of computation. Pivotal to such a model are the computational processes considered. Processes of this kind can be described using an…
Modelling, simulation and optimization form an integrated part of modern design practice in engineering and industry. Tremendous progress has been observed for all three components over the last few decades. However, many challenging issues…
Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each…
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo…
We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
PLACES 2015 (full title: Programming Language Approaches to Concurrency- and Communication-Centric Software) is the eighth edition of the PLACES workshop series. After the first PLACES, which was affiliated to DisCoTec in 2008, the workshop…
The Computing Community Consortium (CCC) sponsored a workshop on "Robotic Materials" in Washington, DC, that was held from April 23-24, 2018. This workshop was the second in a series of interdisciplinary workshops aimed at transforming our…
We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To…
This is the first volume of Electronic Proceedings in Theoretical Computer Science (EPTCS), a free international refereed open access venue for the rapid electronic publication of the proceedings of workshops and conferences, and of…
We report recent research on computing with biology-based neural network models by means of physics-based opto-electronic hardware. New technology provides opportunities for very-high-speed computation and uncovers problems obstructing the…
Hybrid systems are complex dynamical systems that combine discrete and continuous components. Reachability questions, regarding whether a system can run into a certain subset of its state space, stand at the core of verification and…
Understanding the functional architecture of complex systems is crucial to illuminate their inner workings and enable effective methods for their prediction and control. Recent advances have introduced tools to characterise emergent…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
We summarise some of the key statements made at the workshop Form Follows Function at ISC High Performance 2016. The summary highlights what type of co-design the presented projects experience; often in the absence of an explicit co-design…
Much of the controversy about methods for automated decision making has focused on specific calculi for combining beliefs or propagating uncertainty. We broaden the debate by (1) exploring the constellation of secondary tasks surrounding…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…