Related papers: Dynamical hysteresis in multisite protein modifica…
Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade, where in each layer of the cascade a protein is phosphorylated at two sites. It has…
In this manuscript we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics of protein density is governed by a random differential…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
Multivariate functional data from a complex system are naturally high-dimensional and have complex cross-correlation structure. The complexity of data structure can be observed as that (1) some functions are strongly correlated with similar…
In the perspective of developing smart hybrid materials with customized features, ferrogels and magnetorheological elastomers allow a synergy of elasticity and magnetism. The interplay between elastic and magnetic properties gives rise to a…
Recent evidence suggests that physiological signals under healthy conditions may have a fractal temporal structure. We investigate the possibility that time series generated by certain physiological control systems may be members of a…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation…
Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing computational methods that predict…
We consider a cell population structured by a positive real number, describing the number of P-glycoproteins carried by the cell. We are interested in the effect of those proteins on the growth of the population: those proteins are indeed…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical…
Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling.…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
This paper studies the emergence of multi-stability and hysteresis in those systems that arise, under positive feedback, starting from monotone systems with well-defined steady-state responses. Such feedback configurations appear routinely…
Cell fate determination, the process through which cells commit to differentiated states is commonly mediated by gene regulatory motifs with mutually exclusive expression states. The classical deterministic picture for cell fate…
Frequency evolutions of hysteresis loop area and hysteresis tools such as remanence and coercivity of a kinetic Ising model in the presence of quenched bond dilution are investigated in detail. The kinetic equation describing the time…
We study the classical dynamics of resonantly modulated large-spin systems in a strong magnetic field. We show that these systems have special symmetry. It leads to characteristic nonlinear effects. They include abrupt switching between…