Related papers: Patterning the insect eye: from stochastic to dete…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
Despite the enormous theoretical and application interests, a fundamental understanding of the glassy dynamics remains elusive. The static properties of glassy and ordinary liquids are similar, but their dynamics are dramatically different.…
Disordered systems like liquids, gels, glasses, or granular materials are not only ubiquitous in daily life and in industrial applications but they are also crucial for the mechanical stability of cells or the transport of chemical and…
To make decisions organisms often accumulate information across multiple timescales. However, most experimental and modeling studies of decision-making focus on sequences of independent trials. On the other hand, natural environments are…
Aging affects almost all aspects of an organism -- its morphology, its physiology, its behavior. Isolating which biological mechanisms are regulating these changes, however, has proven difficult, potentially due to our inability to…
Mixed positive and negative feedback loops are often found in biological systems which support oscillations. In this work we consider a prototype of such systems, which has been recently found at the core of many genetic circuits showing…
Stochastic models, based on random processes, may lead to power law distributions, which provide long range correlations. The observation of power law behavior and the presence of long range correlations in biological systems has been…
The seemingly stochastic transient dynamics of neocortical circuits observed in vivo have been hypothesized to represent a signature of ongoing stochastic inference. In vitro neurons, on the other hand, exhibit a highly deterministic…
Separating synapses into different classes based on their appearance in EM images has many applications in biology. Examples may include assigning a neurotransmitter to a particular class, or separating synapses whose strength can be…
A parametric point process model is developed, with modeling based on the assumption that sequential observations often share latent phenomena, while also possessing idiosyncratic effects. An alternating optimization method is proposed to…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Evolutionary success depends on the capacity to adapt: organisms must respond to environmental challenges through both genetic innovation and lifetime learning. The gene-centric paradigm attributes evolutionary causality exclusively to…
A general theory of stochastic decision forests is developed to bridge two concepts of information flow: decision trees and refined partitions on the one side, filtrations from probability theory on the other. Instead of the traditional…
We model hypothetical bio-dispersal within a single Galactic region using the stochastic infection dynamics process, which is inspired by these local properties of life dispersal on Earth. We split the population of stellar systems into…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
Statistical mechanics determines the abundance of different arrangements of matter depending on cost-benefit balances. Its formalism and phenomenology percolate throughout biological processes and set limits to effective computation. Under…
The classification of the long-term behavior of dynamical systems is a fundamental problem in mathematics. For both deterministic and stochastic dynamics specific classes of models verify Palis' conjecture: the long-term behavior is…
Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology,…