Related papers: Memory Consistency Conditions for Self-Assembly Pr…
The recently introduced Thermodynamic Binding Networks (TBN) model was developed with the purpose of studying self-assembling systems by focusing on their thermodynamically favorable final states, and ignoring the kinetic pathways through…
Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external…
Tile displacement is a newly-recognized mechanism in DNA nanotechnology that exploits principles analogous to toehold-mediated strand displacement but within the context of self-assembled DNA origami tile arrays. Here, we formulate an…
Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for all $N \in \mathbb{N}$, there is a tile set that uniquely self-assembles into an $N \times N$ square shape at temperature 1 with optimal…
In this paper we propose a research programme for getting structural characterisations for 2-dimensional languages generated by self-assembling tiles. This is part of a larger programme on getting a formal foundation of parallel,…
In this paper, we introduce an SMT-based method that automatically synthesizes a distributed self-stabilizing protocol from a given high-level specification and network topology. Unlike existing approaches, where synthesis algorithms…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…
A memory consistency model specifies the allowed behaviors of shared memory concurrent programs. At the language level, these models are known to have a non-trivial impact on the safety of program optimizations, limiting the ability to…
This paper presents unifying results for subspace identification (SID) and dynamic mode decomposition (DMD) for autonomous dynamical systems. We observe that SID seeks to solve an optimization problem to estimate an extended observability…
We present a framework that provides deterministic consistency algorithms for given memory models. Such an algorithm checks whether the executions of a shared-memory concurrent program are consistent under the axioms defined by a model. For…
Non-volatile memory (NVM), also known as persistent memory, is an emerging paradigm for memory that preserves its contents even after power loss. NVM is widely expected to become ubiquitous, and hardware architectures are already providing…
For the last thirty years, a large variety of memory allocators have been proposed. Since performance, memory usage and energy consumption of each memory allocator differs, software engineers often face difficult choices in selecting the…
Stochastic neural networks are a prototypical computational device able to build a probabilistic representation of an ensemble of external stimuli. Building on the relationship between inference and learning, we derive a synaptic plasticity…
We propose a new method for computing Dynamic Mode Decomposition (DMD) evolution matrices, which we use to analyze dynamical systems. Unlike the majority of existing methods, our approach is based on a variational formulation consisting of…
We study the problem of determining whether a given temporal specification can be implemented by a symmetric system, i.e., a system composed from identical components. Symmetry is an important goal in the design of distributed systems,…
Patterned self-assembly tile set synthesis (PATS) aims at finding a minimum tile set to uniquely self-assemble a given rectangular color pattern. For $k \ge 1$, $k$-PATS is a variant of PATS that restricts input patterns to those with at…
Finite-state models, such as finite-state machines (FSMs), aid software engineering in many ways. They are often used in formal verification and also can serve as visual software models. The latter application is associated with the…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…
We ask the question of how small a self-assembling set of tiles can be yet have interesting computational behaviour. We study this question in a model where supporting walls are provided as an input structure for tiles to grow along: we…
The complexity class $NP$ can be logically characterized both through existential second order logic $SO\exists$, as proven by Fagin, and through simulating a Turing machine via the satisfiability problem of propositional logic SAT, as…