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A stochastic model of excitatory and inhibitory interactions which bears universality traits is introduced and studied. The endogenous component of noise, stemming from finite size corrections, drives robust inter-nodes correlations, that…
Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication networks, as well as systems constrained in…
Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…
Non-equilibrium dynamics are present in many aspects of our lives, ranging from microscopic physical systems to the functioning of the brain. What characterizes stochastic models of non-equilibrium processes is the breaking of the…
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…
How to induce differentiated cells into pluripotent cells has elicited researchers' interests for a long time since pluripotent stem cells are able to offer remarkable potential in numerous subfields of biological research. However, the…
Animal locomotion employs different periodic patterns known as animal gaits. In 1993 Collins and Stewart achieved the characterization in quadrupeds and bipeds by using permutation symmetries groups which impose constrains in the locomotion…
Some mechanisms of cardiac arrhythmias can be presented as a composition of elementary acts of block and reflection on the contacts of homogeneous areas of the conducting tissue. For study this phenomena we use an axiomatic one-dimensional…
Circadian rhythms are archetypical examples of nonlinear oscillations. While these oscillations are usually attributed to circuits of biochemical interactions among clock genes and proteins, recent experimental studies reveal that they are…
Motif discovery is a powerful and insightful method to quantify network structures and explore their function. As a case study, we present a comprehensive analysis of regulatory motifs in the connectome of the model organism Caenorhabditis…
Biophysical signals such as Electrocardiogram (ECG) and Photoplethysmogram (PPG) are key to the sensing of vital parameters for wellbeing. Coincidentally, ECG and PPG are signals, which provide a "different window" into the same phenomena,…
Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and…
From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory…
Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by…
We study the pattern formation in a lattice of coupled phase oscillators with quenched disorder. In the synchronized regime concentric waves can arise, which are induced and increase in regularity by the disorder of the system. Maximal…
Coupling among neural rhythms is one of the most important mechanisms at the basis of cognitive processes in the brain. In this study we consider a neural mass model, rigorously obtained from the microscopic dynamics of an inhibitory…
Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site…
Living creatures exhibit a remarkable diversity of locomotion mechanisms, evolving structures specialised for interacting with their environment. In the vast majority of cases, locomotor behaviours such as flying, crawling, and running, are…
Many questions in science center around the fundamental problem of understanding causal relationships. However, most constraint-based causal discovery algorithms, including the well-celebrated PC algorithm, often incur an exponential number…