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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,…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…
The linear programming (LP) approach is, together with value iteration and policy iteration, one of the three fundamental methods to solve optimal control problems in a dynamic programming setting. Despite its simple formulation,…
Smart systems are characterised by their ability to analyse measured data in live and to react to changes according to expert rules. Therefore, such systems exploit appropriate data models together with actions, triggered by domain-related…
The branching algorithm is a fundamental technique for designing fast exponential-time algorithms to solve combinatorial optimization problems exactly. It divides the entire solution space into independent search branches using…
We introduce a high-performance simulation framework that permits the semi-independent, task-based solution of sets of partial differential equations, typically manifesting as updates to a collection of `patches' in space-time. A hybrid…
This paper presents a spectral element finite element scheme that efficiently solves elliptic problems on unstructured hexahedral meshes. The discrete equations are solved using a matrix-free preconditioned conjugate gradient algorithm. An…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Robust Model Predictive Control (MPC) for nonlinear systems is a problem that poses significant challenges as highlighted by the diversity of approaches proposed in the last decades. Often compromises with respect to computational load,…
We develop a novel formulation of the Performance Estimation Problem (PEP) for decentralized optimization whose size is independent of the number of agents in the network. The PEP approach allows computing automatically the worst-case…
Despite being recognized as neurobiologically plausible, active inference faces difficulties when employed to simulate intelligent behaviour in complex environments due to its computational cost and the difficulty of specifying an…
All simulation approaches eventually face limits in computational scalability when applied to large spatiotemporal domains. This challenge becomes especially apparent in molecular-level particle simulations, where high spatial and temporal…
Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a…
It is well known that physical phenomena may be of great help in computing some difficult problems efficiently. A typical example is prime factorization that may be solved in polynomial time by exploiting quantum entanglement on a quantum…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
We introduce a parallel machine scheduling problem in which the processing times of jobs are not given in advance but are determined by a system of linear constraints. The objective is to minimize the makespan, i.e., the maximum job…
This paper presents a new approach to solve linear and nonlinear model predictive control (MPC) problems that requires small memory footprint and throughput and is particularly suitable when the model and/or controller parameters change at…
Modern `smart' materials have complex microscale structure, often with unknown macroscale closure. The Equation-Free Patch Scheme empowers us to non-intrusively, efficiently, and accurately simulate over large scales through computations on…
Timing aspects in formalisms with explicit resources and parallelism are investigated, and it is presented a formal link between timed membrane systems and timed Petri nets with localities. For both formalisms, timing does not increase the…
In our daily lives and industrial settings, we often encounter dynamic problems that require reasoning over time and metric constraints. These include tasks such as scheduling, routing, and production sequencing. Dynamic logics have…