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Compositionality is a key property for dealing with complexity, which has been studied from many points of view in diverse fields. Particularly, the composition of individual computations (or programs) has been widely studied almost since…
Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have…
A bio tissue model consisting of multilayer spherical cells including four nested radial domains (nucleus, nuclear membrane, cytoplasm and plasma membrane) is worked out to derive the cell heating dynamics in presence of membrane…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed…
We need much better understanding of information processing and computation as its primary form. Future progress of new computational devices capable of dealing with problems of big data, internet of things, semantic web, cognitive robotics…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
Dynamics play a critical role in computation. The principled evolution of states over time enables both biological and artificial networks to represent and integrate information to make decisions. In the past few decades, significant…
The term ``neuromorphic'' refers to systems that are closely resembling the architecture and/or the dynamics of biological neural networks. Typical examples are novel computer chips designed to mimic the architecture of a biological brain,…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
We analyze classical theory of a membrane propagating in a singular background spacetime. The algebra of the first-class constraints of the system defines the membrane dynamics. A membrane winding uniformly around compact dimension of…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Neural computation is associated with the emergence, reconfiguration and dissolution of cell assemblies in the context of varying oscillatory states. Here, we describe the complex spatio-temporal dynamics of cell assemblies through temporal…
Computational modeling and simulation have become essential tools in the quest to better understand the brain's makeup and to decipher the causal interrelations of its components. The breadth of biochemical and biophysical processes and…
Memcomputing is a novel non-Turing paradigm of computation that uses interacting memory cells (memprocessors for short) to store and process information on the same physical platform. It was recently proved mathematically that memcomputing…
Capturing the structure of a data-generating process by means of appropriate inductive biases can help in learning models that generalize well and are robust to changes in the input distribution. While methods that harness spatial and…
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…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
A novel language system has given rise to promising alternatives to standard formal and processor network models of computation. An interstring linked with a abstract machine environment, shares sub-expressions, transfers data, and…