We present a detailed analysis, based on the Forward Flux Sampling (FFS) simulation method, of the switching dynamics and stability of two models of genetic toggle switches, consisting of two mutually-repressing genes encoding transcription factors (TFs); in one model (the exclusive switch), they mu…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic reactions, instead offering only \textit{topological} information …
We have developed a mathematical model of regulation of expression of the Escherichia coli lac operon, and have investigated bistability in its steady-state induction behavior in the absence of external glucose. Numerical analysis of equations describing regulation by artificial inducers revealed tw…
Optimal trade execution is an important problem faced by essentially all traders. Much research into optimal execution uses stringent model assumptions and applies continuous time stochastic control to solve them. Here, we instead take a model free approach and develop a variation of Deep Q-Learning…
The Tsallis $q$-Gaussian distribution is a powerful generalization of the standard Gaussian distribution and is commonly used in various fields, including non-extensive statistical mechanics, financial markets and image processing. It belongs to the $q$-distribution family, which is characterized by…
This paper studies the continuous-time q-learning in mean-field jump-diffusion models when the population distribution is not directly observable. We propose the integrated q-function in decoupled form (decoupled Iq-function) from the representative agent's perspective and establish its martingale c…
We study the dynamics of the out-of-equilibrium nonlinear q-voter model with two types of susceptible voters and zealots, introduced in [EPL 113, 48001 (2016)]. In this model, each individual supports one of two parties and is either a susceptible voter of type $q_1$ or $q_2$, or is an inflexible ze…
Measures of tree balance play an important role in the analysis of phylogenetic trees. One of the oldest and most popular indices in this regard is the Colless index for rooted bifurcating trees, introduced by Colless (1982). While many of its statistical properties under different probabilistic mod…
A self-exciting point process with a continuous-time autoregressive moving average intensity process, named CARMA(p,q)-Hawkes model, has recently been introduced. The model generalizes the Hawkes process by substituting the Ornstein-Uhlenbeck intensity with a CARMA(p,q) model where the associated st…
Modeling financial markets based on empirical data poses challenges in selecting the most appropriate models. Despite the abundance of empirical data available, researchers often face difficulties in identifying the best-fitting model. Long-range memory and self-similarity estimators, commonly used …