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Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) play essential roles in animal reproduction. They exert their function through binding to their cognate receptors, which belong to the large family of G protein-coupled…
Presented with sensory challenges, living cells employ extensive noisy, fluctuating signalling and communication among themselves to compute a physiologically proper response which often results in symmetry breaking. We propose, based on…
In many real-world applications we are interested in approximating costly functions that are analytically unknown, e.g. complex computer codes. An emulator provides a fast approximation of such functions relying on a limited number of…
We describe a process calculus featuring high level constructs for component-oriented programming in a distributed setting. We propose an extension of the higher-order pi-calculus intended to capture several important mechanisms related to…
Pituitary gonadotropins play an essential and pivotal role in the control of human and animal reproduction within the hypothalamic-pituitary-gonadal (HPG) axis. The computational modeling of pituitary gonadotropin signaling encompasses…
Astrocytes express a large variety of G~protein-coupled receptors (GPCRs) which mediate the transduction of extracellular signals into intracellular calcium responses. This transduction is provided by a complex network of biochemical…
An approach to information processing based on the excitation of patterns of activity by non-linear active resonators in response to their input patterns is proposed. Arguments are presented to show that any computation performed by a…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the…
Recent studies have reported that T cells can integrate signals between interrupted encounters with Antigen Presenting Cells (APCs) in such a way that the process of signal integration exhibits a form of memory. Here, we carry out a…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Simulation speed matters for neuroscientific research: this includes not only how quickly the simulated model time of a large-scale spiking neuronal network progresses, but also how long it takes to instantiate the network model in computer…
Mathematical models of transport and reactions in biological systems have been traditionally written in terms of partial differential equations (PDEs) that describe the time evolution of population-level variables. In recent years, the use…
G-protein-coupled receptors (GPCRs), primary targets for over one-third of approved therapeutics, rely on intricate conformational transitions to transduce signals. While Molecular Dynamics (MD) is essential for elucidating this…
Neuro-inspired models and systems have great potential for applications in unconventional computing. Often, the mechanisms of biological neurons are modeled or mimicked in simulated or physical systems in an attempt to harness some of the…
Graph transformation approaches have been successfully used to analyse and design chemical and biological systems. Here we build on top of a DPO framework, in which molecules are modelled as typed attributed graphs and chemical reactions…
The living cell expends energetic and material resources to reliably process information from its environment. To do so, it utilises unreliable molecular circuitry that is subject to thermal and other fluctuations. Here, we argue that…
Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein/protein interactions and post-transcriptional modifications. The response to death receptor stimulation varies significantly from one cell line…
In this article, we review a class of neuro-mimetic computational models that we place under the label of spiking predictive coding. Specifically, we review the general framework of predictive processing in the context of neurons that emit…
P. polycephalum may be considered as a spatially represented parallel unconventional computing substrate, but how can this `computer' be programmed? In this paper we examine and catalogue individual low-level mechanisms which may be used to…