Related papers: A core genetic module : the Mixed Feedback Loop
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
In eukaryotic cells, motor proteins (MP) bind to cytoskeletal filaments and move along them in a directed manner generating active stresses. During cell division a spindle structure of overlapping antiparallel microtubules (MT) form whose…
A MEMS Duffing resonator is driven by two adjacent frequency tones into the nonlinear regime. We show that if the two-tone drive is applied at a frequency where a bistable response of the nonlinear oscillator exists, then the system output…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…
We consider the effect of asymmetric temporal delays in a system of two coupled Hopfield neurons. For couplings of opposite signs, a limit cycle emerges via a supercritical Hopf bifurcation when the sum of the delays reaches a critical…
Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation.…
All known life forms are based upon a hierarchy of interwoven feedback loops, operating over a cascade of space, time and energy scales. Among the most basic loops are those connecting DNA and proteins. For example, in genetic networks, DNA…
Instruction tuning in multimodal large language models (MLLMs) generally involves cooperative learning between a backbone LLM and a feature encoder of non-text input modalities. The major challenge is how to efficiently find the synergy…
Feedback is ubiquitous in both biological and engineered control systems. In biology, in addition to typical feedback between plant and controller, we observe feedback pathways within control systems, which we call internal feedback…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
We consider a heteroclinic network in the framework of winnerless competition of species. It consists of two levels of heteroclinic cycles. On the lower level, the heteroclinic cycle connects three saddles, each representing the survival of…
Autonomous sustained oscillations are ubiquitous in living and nonliving systems. As open systems, far from thermodynamic equilibrium, they defy entropic laws which mandate convergence to stationarity. We present structural conditions on…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…
Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies…
GTPases are molecular switches that regulate a wide range of cellular processes, such as organelle biogenesis, position, shape, and signal transduction. These enzymes operate by toggling between an active ("ON") guanosine triphosphate…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
Multi-task learning (MTL) is a paradigm that simultaneously learns multiple tasks by sharing information at different levels, enhancing the performance of each individual task. While previous research has primarily focused on feature-level…
Adaptive dynamical networks appear in various real-word systems. One of the simplest phenomenological models for investigating basic properties of adaptive networks is the system of coupled phase oscillators with adaptive couplings. In this…
Federated learning (FL) is a distributed model for deep learning that integrates client-server architecture, edge computing, and real-time intelligence. FL has the capability of revolutionizing machine learning (ML) but lacks in the…