Related papers: The stochastic behavior of a molecular switching c…
Synaptic connections in neuronal circuits are modulated by pre- and post-synaptic spiking activity. Heuristic models of this process of synaptic plasticity can provide excellent fits to results from in-vitro experiments in which pre- and…
Two synthetic gene circuits -- the genetic toggle switch and the repressilator -- are analyzed quantitatively and discussed in the context of an educational module on gene circuits and feedback that constitutes the final topic of a…
In most studies of the channel capacity of quantum channels, it is assumed that the errors in each use of the channel are independent. However, recent work has begun to investigate the effects of memory or correlations in the error. This…
Neutrino oscillations confirm the presence of mode entanglement, as each flavor eigenstate is composed of a coherent superposition of distinct mass eigenstates. In this work, we investigate the dynamics of quantum resources in neutrino…
Motivated from a wide range of applications, various methods to control synchronization in coupled oscillators have been proposed. Previous studies have demonstrated that global feedback typically induces three macroscopic behaviors:…
We characterize the pre-softmax attention matrix $\mathbf{QK^\top}$ in transformers as an associative memory matrix encoding pairwise associations between input features. By decomposing this matrix into its symmetric and skew-symmetric…
Stochastic resonance is a well established phenomenon, which proves relevant for a wide range of applications, of broad trans-disciplinary breath. Consider a one dimensional bistable stochastic system, characterized by a deterministic…
The topic of this study is the outage behavior of multiple-antenna slow fading channels with quantized feedback and partial power control. A fixed-rate communication system is considered. It is known from the literature that with error-free…
We study decoherence produced by a discrete environment on a charge Josephson qubit by introducing a model of an environment of bistable fluctuators. In particular we address the effect of $1/f$ noise where memory effects play an important…
The development of substrates with a switchable wettability is on a fast pace. The limit of switching frequencies and contact angle differences between substrate states are steadily pushed further. We investigate the behavior of a droplet…
We study associative memory neural networks of the Hodgkin-Huxley type of spiking neurons in which multiple periodic spatio-temporal patterns of spike timing are memorized as limit-cycle-type attractors. In encoding the spatio-temporal…
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of network phenotypes they can exhibit. In this study, we…
Molecular motion through pores plays a crucial role in various natural and industrial processes. One of the most fascinating features of biological channel-facilitated transport is a stochastic gating process, when the channels dynamically…
In many sensory systems, transmembrane receptors are spatially organized in large clusters. Such arrangement may facilitate signal amplification and the integration of multiple stimuli. However, this organization likely also affects the…
An important task in quantitative biology is to understand the role of stochasticity in biochemical regulation. Here, as an extension of our recent work [Phys. Rev. Lett. 107, 148101 (2011)], we study how input fluctuations affect the…
In this paper we describe the solution of a stochastic bistable system from a dynamical perspective. We show how a single framework with variable noise can explain hysteresis at zero temperature and two-state coexistence in the presence of…
Bivalency confers several concentration-dependent phenomena, including avidity, competitive exchange and multi-site competitive exchange. Since these concepts are crucial for a wide variety of topics in cell and molecular biology, their…
Networks of globally coupled, noise activated, bistable elements with connection time delays are considered. The dynamics of these systems is studied numerically using a Langevin description and analytically using (1) a Gaussian…
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We…
Feedback delay has been identified as a key ingredient in the quorum sensing synchronization of synthetic gene oscillators. While this influence has been evidenced at the theoretical level in a simplified system of degrade-and-fire…