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Delays and stochasticity have both served as crucially valuable ingredients in mathematical descriptions of control, physical, and biological systems. In this work, we investigate how explicitly dynamical stochasticity in delays modulates…
A discrete delay is included to model the time between the capture of the prey and its conversion to viable biomass in the simplest classical Gause type predator-prey model that has equilibrium dynamics without delay. As the delay increases…
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
It has recently been observed that the occurrence of sudden cardiac death has a close statistical relationship with the time of day, viz., ventricular fibrillation is most likely to occur between 12 am-6 am, with 6 pm-12 am being the next…
We consider application of the multiple time delayed feedback for control of anharmonic (nonlinear) oscillators subject to noise. In contrast to the case of a single delay feedback, the multiple one exhibits resonances between feedback and…
Time delay in general leads to instability in some systems, while a specific feedback with delay can control fluctuated motion in nonlinear deterministic systems to a stable state. In this paper, we consider a non-stationary stochastic…
DNA methylation is an important biological mechanism to regulate gene expression and control cell development. Mechanistic modeling has become a popular approach to enhance our understanding of the dynamics of methylation pattern formation…
We show how the recurrence phenomenon characteristic of the nonlinear stage of induced modulational instability in a passive fiber is affected by forcing. An additional linear amplification, even if extremely weak, induces separatrix…
We study control of synchronization in weakly coupled oscillator networks by using a phase reduction approach. Starting from a general class of limit cycle oscillators we derive a phase model, which shows that delayed feedback control…
The cosinor model is frequently used to represent the oscillatory behavior of different genes over time. When data are collected from multiple individuals, the cosinor model is estimated with recorded gene expression levels and the 24 hour…
Various field and laboratory experiments show that prey refuge plays a significant role in the stability of prey-predator dynamics. On the other hand, theoretical studies show that delayed system exhibits a much more realistic dynamics than…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
Amplification of quantum transfer and ratchet--type processes are important for quantum technologies. We also expect that quantum ratchet works in quantum photosynthesis, where possible role of quantum effects is now widely discussed but…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
The theoretical analysis and numerical simulations of the magnetron operation with a feedback loop were performed assuming that the delay of the electromagnetic wave propagating in the loop is constant whereas the phase of the complex…
Proposing an optomechanical cavity modulated periodically, we study the modulation synchronization of mechanical modes of the mirrors. A periodic modulation is applied to one of the mirrors, where the second mirror has the capability of…
The suprachiasmatic nucleus (SCN), also known as the circadian master clock, consists of a large population of oscillator neurons. Together, these neurons produce a coherent signal that drives the body's circadian rhythms. What properties…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…