Related papers: Membrane-Associated Self-Assembly for Cellular Dec…

Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…

The human brain is able to learn, generalize, and predict crossmodal stimuli. Learning by expectation fine-tunes crossmodal processing at different levels, thus enhancing our power of generalization and adaptation in highly dynamic…

A specific memory is stored in a cell assembly that is activated during fear learning in mice; however, research regarding cell assemblies associated with procedural and habit learning processes is lacking. In modeling studies, simulations…

Convergence extension, the simultaneous elongation of tissue along one axis while narrowing along a perpendicular axis, occurs during embryonic development. A fundamental process that contributes to shaping the organism, it happens in many…

The adhesion of biological membranes is controlled by various types of receptor and ligand molecules. In this letter, we present a statistical-mechanical model for membranes that interact via receptor/ligand bonds of two different lengths.…

Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…

Natural systems integrate the work of many sub-units (cells) toward a large-scale unified goal (morphological and behavioral), which can counteract the effects of unexpected experiences, damage, or simply changes in tasks demands. In this…

Dynamical criticality has been shown to enhance information processing in dynamical systems, and there is evidence for self-organized criticality in neural networks. A plausible mechanism for such self-organization is activity dependent…

We investigate single-cell directional sensing from diffusing chemoattractant signals released by a localized source. We focus on the low-concentration regime in which receptor activity is discrete and cellular decisions are made on…

Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While…

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…

This article reports about a novel extension of dissipative particle dynamics (DPD) that allows the study of the collective dynamics of complex chemical and structural systems in a spatially resolved manner with a combinatorially complex…

Biological systems often involve the self-assembly of basic components into complex and function- ing structures. Artificial systems that mimic such processes can provide a well-controlled setting to explore the principles involved and also…

Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…

Evidence-based decision-making entails collecting (costly) observations about an underlying phenomenon of interest, and subsequently committing to an (informed) decision on the basis of accumulated evidence. In this setting, active sensing…

We model self-assembly of information in networks to investigate necessary conditions for building a global perception of a system by local communication. Our approach is to let agents chat in a model system to self-organize distant…

Motivated by the fine compositional control observed in membraneless droplet organelles in cells, we investigate how a sharp binding-unbinding transition can occur between multivalent client molecules and receptors embedded in a porous…

Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…

In this exploratory paper we introduce the problem of cognitive agents that learn how to modify their environment according to local sensing to reach a global goal. We concentrate on discrete dynamics (cellular automata) on a…

We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…