Related papers: Noise in Biomolecular Systems: Modeling, Analysis,…
This paper investigates the impact of control field noise on the optimal manipulation of quantum dynamics. Simulations are performed on several multilevel quantum systems with the goal of population transfer in the presence of significant…
Synthetic biology is an interdisciplinary field aiming to design biochemical systems with desired behaviors. To this end, molecular controllers have been developed which, when embedded into a pre-existing ambient biochemical network,…
Brain functions require both segregated processing of information in specialized circuits, as well as integration across circuits to perform high-level information processing. One possible way to implement these seemingly opposing demands…
We have analyzed the effects of the addition of external noise to non-dynamical systems displaying intrinsic noise, and established general conditions under which stochastic resonance appears. The criterion we have found may be applied to a…
Both for the theoretical and practical treatment of Inverse Problems, the modeling of the noise is a crucial part. One either models the measurement via a deterministic worst-case error assumption or assumes a certain stochastic behavior of…
In animal groups, individual decisions are best characterised by probabilistic rules. Furthermore, animals of many species live in small groups. Probabilistic interactions among small numbers of individuals lead to a so called intrinsic…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Experimental evidences of phenotypic differentiation are given by the presence of bimodal distributions…
A stochastic model is here introduced to investigate the molecular mechanisms which trigger the perception of pain. The action of analgesic drug compounds is discussed in a dynamical context, where the competition with inactive species is…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
A modelling framework, based on the theory of signal processing, for characterising the dynamics of systems driven by the unravelling of information is outlined, and is applied to describe the process of decision making. The model input of…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
Fluctuations in intracellular reactions (intrinsic noise) reduce the information transmitted from an extracellular input to a cellular response. However, recent studies have demonstrated that the decrease in the transmitted information with…
We discuss two aspects, the in vivo and in vitro difference and the modeling of noise, of integrative modeling of network dynamics in biology, using phage lambda as an example. We believe those two aspects have not been seriously…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
We examine the effect of noise on societies of agents using an agent-based model of evolutionary norm emergence. Generally, we see that noisy societies are more selfish, smaller and discontent, and are caught in rounds of perpetual…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…
The ergodicity and the output-controllability of stochastic reaction networks have been shown to be essential properties to fulfill to enable their control using, for instance, antithetic integral control. We propose here to extend those…
In this paper, we focus on the influence of heterogeneity and stochasticity of the population on the dynamical structure of a basic susceptible-infected-susceptible (SIS) model. First we prove that, upon a suitable mathematical…