Related papers: Spatial Dynamic Structures and Mobility in Computa…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Membrane computing and P systems are a paradigm of massively parallel natural computing introduced by Gheorghe P\u{a}un in 1999, inspired by the structure of the living cell and by its biochemical reactions. In spite of this explicit…
P systems with active membranes were used to generate languages, in the sense of languages associated with the structure of membrane systems. Here, we analyze the power of P systems with membrane creation and dissolution restricted to…
The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the…
Many real-world dynamic systems, both natural and artificial, are understood to be performing computations. For artificial dynamic systems, explicitly designed to perform computation - such as digital computers - by construction, we can…
We investigate computing models that are presented as families of finite computing devices with a uniformity condition on the entire family. Examples of such models include Boolean circuits, membrane systems, DNA computers, chemical…
In present day technology, storing and processing of information occur on physically distinct regions of space. Not only does this result in space limitations; it also translates into unwanted delays in retrieving and processing of relevant…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location…
The dynamics of a membrane is a coupled system comprising a moving elastic surface and an incompressible membrane fluid. We will consider a reduced elastic surface model, which involves the evolution equations of the moving surface, the…
Over the last decade, the term spatial computing has grown to have two different, though not entirely unrelated, definitions. The first definition of spatial computing stems from industry, where it refers primarily to new kinds of…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Trying to be effective (no matter who exactly and in what field) a person face the problem which inevitably destroys all our attempts to easily get to a desired goal. The problem is the existence of some insuperable barriers for our mind,…
Understanding how biological constraints shape neural computation is a central goal of computational neuroscience. Spatially embedded recurrent neural networks provide a promising avenue to study how modelled constraints shape the combined…
Physical reservoir computing is a computational framework that implements spatiotemporal information processing directly within physical systems. By exciting nonlinear dynamical systems and creating linear models from their state, we can…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
In this work, we present a computational formulation based on continuum mechanics to study the interaction of fluid membranes embedded with semiflexible filaments. This is motivated by systems in membrane biology, such as cytoskeletal…