Related papers: Optimal Path to Epigenetic Switching
Optimal designs minimize the number of experimental runs (samples) needed to accurately estimate model parameters, resulting in algorithms that, for instance, efficiently minimize parameter estimate variance. Governed by knowledge of past…
We study the stationary states of variants of the noisy voter model, subject to fluctuating parameters or external environments. Specifically, we consider scenarios in which the herding-to-noise ratio switches randomly and on different time…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
Consider a supercritical birth and death process where the children acquire mutations. We study the mutation rates along the ancestral lineages in a sample of size $n$ from the population at time $T$. The mutation rate is time-inhomogenous…
In this paper we provide a novel approach to the analysis of kinetic models for label switching, which are used for particle systems that can randomly switch between gradient flows in different energy landscapes. Besides problems in biology…
The dynamical organization in the presence of noise of a Boolean neural network with random connections is analyzed. For low levels of noise, the system reaches a stationary state in which the majority of its elements acquire the same…
We consider potential type dynamical systems in finite dimensions with two meta-stable states. They are subject to two sources of perturbation: a slow external periodic perturbation of period $T$ and a small Gaussian random perturbation of…
The study of biochemical pathways usually focuses on a small section of a protein interactions network. Two distinct sources contribute to the noise in such a system: intrinsic noise, inherent in the studied reactions, and extrinsic noise…
The problem of optimal switching between nonlinear autonomous subsystems is investigated in this study where the objective is not only bringing the states to close to the desired point, but also adjusting the switching pattern, in the sense…
Systems of differential equations have been used to model biological systems such as gene and neural networks. A problem of particular interest is to understand the number of stable steady states. Here we propose conjunctive networks…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
We study barrier crossing in a two-state system, namely the kinetic Ising model, in the presence of a weak bias field and spatially homogeneous, but time-dependent, Gaussian random fields. We find that the bias field determines the location…
This paper develops a predictive switching control algorithm for stochastic gene regulatory networks described by a Partial Integro-Differential Equation (PIDE) model, which enables direct shape control of the probability density function.…
Realistic large-scale networks display an heterogeneous distribution of connectivity weights, that might also randomly vary in time. We show that depending on the level of heterogeneity in the connectivity coefficients, different…
The synthetic toggle switch, first proposed by Gardner & Collins [1] is a MIMO control system that can be controlled by varying the concentrations of two inducer molecules, aTc and IPTG, to achieve a desired level of expression of the two…
Since the advent of new nanotechnologies, the variability of gate delay due to process variations has become a major concern. This paper proposes a new gate delay model that includes impact from both process variations and multiple input…
We present an experimental study of stochastic resonance in an electronic Chua circuit operating in the chaotic regime. We study in detail the switch-phase distribution and the phase-shift between sinusoidal forcing for two responses of the…