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Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random…

Biological Physics · Physics 2016-06-29 Édgar Roldán , Ana Lisica , Daniel Sánchez-Taltavull , Stephan W. Grill

We derive an alternative expression for a delayed logistic equation in which the rate of change in the population involves a growth rate that depends on the population density during an earlier time period. In our formulation, the delay in…

Dynamical Systems · Mathematics 2022-06-07 Chiu-Ju Lin , Ting-Hao Hsu , Gail S. K. Wolkowicz

Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria,…

Molecular Networks · Quantitative Biology 2014-12-05 Prasanna M. Bhogale , Robin A. Sorg , Jan-Willem Veening , Johannes Berg

Complex systems, which consist of a large number of interacting constituents, often exhibit universal behavior near a phase transition. A slowdown of certain dynamical observables is one such recurring feature found in a vast array of…

Food-web perturbations stemming from climate change, overexploitation, invasive species, and habitat degradation often cause an initial loss of species that results in a cascade of secondary extinctions, posing considerable challenges to…

Populations and Evolution · Quantitative Biology 2011-03-10 Sagar Sahasrabudhe , Adilson E. Motter

Motivated by modeling the dynamics of a population living in a flowing medium where the environmental factors are random in space, we have studied an asymmetric variant of the one-dimensional contact process, where the quenched random…

Disordered Systems and Neural Networks · Physics 2015-06-16 Róbert Juhász

Mode collapse is a persistent challenge in generative modeling and appears in autoregressive text generation as behaviors ranging from explicit looping to gradual loss of diversity and premature trajectory convergence. We take a…

Computation and Language · Computer Science 2026-05-28 Xin Du , Kumiko Tanaka-Ishii

Subcritical Turing bifurcations of reaction-diffusion systems in large domains lead to spontaneous onset of well-developed localised patterns via the homoclinic snaking mechanism. This phenomenon is shown to occur naturally when balancing…

Pattern Formation and Solitons · Physics 2025-06-10 Víctor Breña-Medina , Alan Champneys

While network abrupt breakdowns due to overloads and cascading failures have been studied extensively, the critical exponents and the universality class of such phase transitions have not been discussed. Here, we study breakdowns triggered…

Physics and Society · Physics 2024-03-07 Ignacio A. Perez , Dana Ben Porath , Cristian E. La Rocca , Lidia A. Braunstein , Shlomo Havlin

We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental…

Statistical Mechanics · Physics 2017-07-04 Hatem Barghathi , Skye Tackkett , Thomas Vojta

We consider subcritical branching processes with immigration which evolve under the influence of a random environment and study the tail distribution of life periods of such processes defined as the length of the time interval between the…

Probability · Mathematics 2020-02-10 Doudou Li , Vladimir Vatutin , Mei Zhang

To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…

Biological Physics · Physics 2017-10-26 Andrés F. López-Lopera , Mauricio A. Álvarez

The emergence and impact of tipping points have garnered significant interest in both the social and natural sciences. Despite widespread recognition of the importance of feedbacks between human and natural systems, it is often assumed that…

We study the effects of noise on the dynamics of a system of coupled self-propelling particles in the case where the coupling is time-delayed, and the delays are discrete and randomly generated. Previous work has demonstrated that the…

Pattern Formation and Solitons · Physics 2012-10-08 Brandon Lindley , Luis Mier-y-Teran-Romero , Ira B. Schwartz

In nonlinear dynamical systems, tipping refers to a critical transition from one steady state to another, typically catastrophic, steady state, often resulting from a saddle-node bifurcation. Recently, the machine-learning framework of…

Chaotic Dynamics · Physics 2026-04-09 Smita Deb , Zheng-Meng Zhai , Mulugeta Haile , Ying-Cheng Lai

Mutation-induced drug resistance in cancer often causes the failure of therapies and cancer recurrence, despite an initial tumor reduction. The timing of such cancer recurrence is governed by a balance between several factors such as…

Probability · Mathematics 2013-07-22 Jasmine Foo , Kevin Leder

We consider a cyclically competing species model on a ring with global mixing at finite rate, which corresponds to the well-known Lotka-Volterra equation in the limit of infinite mixing rate. Within a perturbation analysis of the model from…

Populations and Evolution · Quantitative Biology 2017-03-28 Cilie W. Feldager , Namiko Mitarai , Hiroki Ohta

Root-cause analysis in controlled time dependent systems poses a major challenge in applications. Especially energy systems are difficult to handle as they exhibit instantaneous as well as delayed effects and if equipped with storage, do…

Machine Learning · Statistics 2026-02-05 Philipp Alexander Schwarz , Johannes Oberpriller , Sven Klaassen

We combine infectious disease transmission and the non-pharmaceutical intervention (NPI) response to disease incidence into one closed model consisting of two coupled delay differential equations for the incidence rate and the…

Quantitative Methods · Quantitative Biology 2021-02-24 Kristoffer Rypdal

Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When…

Populations and Evolution · Quantitative Biology 2012-02-02 Jose A. Cuesta