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Spatio-temporal modulation has shown great promise as a strong time-reversal symmetry breaking mechanism that enables integrated nonreciprocal devices and topological materials at optical frequencies. However, optical modulation has its own…
We introduce and analyze an extension of the mixed feedback loop model of Fran\c{c}ois and Hakim. Our extension includes an additional promoter state and allows for reversible protein sequestration, which was absent from the original…
We present a theory of vibrational modulation of two-dimensional coherent Fourier transformed electronic spectra. Based on an expansion of the system's energy gap correlation function in terms of Huang-Rhys factors, we explain the…
We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. We find that multisite calcium-binding…
Control-based continuation (CBC) is an experimental method that can reveal stable and unstable dynamics of physical systems. It extends the path-following principles of numerical continuation to experiments, and provides systematic…
Discrete time crystals (DTCs) refer to a novel many-body steady state that spontaneously breaks the discrete time-translational symmetry in a periodically-driven quantum system. Here, we study DTCs in a Bose-Einstein condensate (BEC)…
We investigate the anomalous energy change of the measurement apparatus when a qubit is measured in bases that do not commute with energy. We model two possible measurement implementations: one is a quantum clock model with a completely…
Adiabatic approximations are a powerful tool for simplifying nonlinear quantum dynamics, and are applicable whenever a system exhibits a hierarchy of time scales. Current interest in small nonlinear quantum systems, such as few-mode…
We develop a detailed theoretical framework for various types of transcription factor gene oscillators. We further demonstrate that one can build genetic-oscillators which are tunable and robust against perturbations in the critical control…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…
Echo protocols provide a means to investigate the arrow of time in macroscopic processes. Starting from a nonequilibrium state, the many-body quantum system under study is evolved for a certain period of time $\tau$. Thereafter, an…
Vector clock algorithms are basic wait-free building blocks that facilitate causal ordering of events. As wait-free algorithms, they are guaranteed to complete their operations within a finite number of steps. Stabilizing algorithms allow…
Understanding the oscillating behaviors that govern organisms' internal biological processes requires interdisciplinary efforts combining both biological and computer experiments, as the latter can complement the former by simulating…
In this note, we show how certain properties of Goldbeter's 1995 model for circadian oscillations can be proved mathematically, using techniques from the recently developed theory of monotone systems with inputs and outputs. The theory…
Ordinary differential equations (ODEs) can model the transition of cell states over time. Bifurcation theory is a branch of dynamical systems which studies changes in the behavior of an ODE system while one or more parameters are varied. We…
We simulate the dynamics of paramagnetic colloidal particles that are placed above a magnetic hexagonal pattern and exposed to an external field periodically changing its direction along a control loop. The conformation of three colloidal…
Time crystals, a unique non-equilibrium quantum phenomenon with promising applications in current quantum technologies, mark a significant advance in quantum mechanics. Although traditionally studied in atom-cavity and optical lattice…
We present a scheme for creating tight and adiabatic time-averaged atom-traps through the piezoelectric actuation of nanomagnetic structures. We show that potentials formed by the circular translation of magnetic structures have several…
Circadian rhythms regulate the physiology and behavior of humans and animals. Despite advancements in understanding these rhythms and predicting circadian phases at the transcriptional level, predicting circadian phases from proteomic data…
The study of synchronization in biological systems is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. In this paper, by using simple dynamical systems theory, we present a…