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While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
We discovered a class of self-similar solutions in nonlinear models describing the formation of morphogen gradients, the concentration fields of molecules acting as spatial regulators of cell differention in developing tissues. These models…
Non-genetic heterogeneity is key to cellular decisions, as even genetically identical cells respond in very different ways to the same external stimulus, e.g., during cell differentiation or therapeutic treatment of disease. Strong…
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…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Signals recorded from neurons with extracellular planar sensors have a wide range of waveforms and amplitudes. This variety is a result of different physical conditions affecting the ion currents through a cellular membrane. The…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
Instance segmentation enables the analysis of spatial and temporal properties of cells in microscopy images by identifying the pixels belonging to each cell. However, progress is constrained by the scarcity of high-quality labeled…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
We present a pipeline to study the device performance of organic solar cells in silico. We introduce a mathematical model that includes the dynamics of excitons as well as their dissociation at bulk heterojunctions within the nanomorphology…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
We review theoretical results for the adhesion-induced phase behavior of biomembranes. The focus is on models in which the membranes are represented as discretized elastic sheets with embedded adhesion molecules. We present several…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…