Related papers: Lumpability Abstractions of Rule-based Systems

Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…

Stochastic kinetic models describe systems across biology, chemistry, and physics where discrete events and small populations render deterministic approximations inadequate. Parameter inference and inverse design in these systems require…

We consider stability analysis of constrained switching linear systems in which the dynamics is unknown and whose switching signal is constrained by an automaton. We propose a data-driven Lyapunov framework for providing probabilistic…

We consider multiple-period states in systems of periodically modulated qubits. In such states the discrete time-translation symmetry imposed by the modulation is broken. We explicitly show how multiple-period states emerge in the simplest…

We define the syntax and reduction relation of a recursively typed lambda calculus with a parallel case-function (a parallel conditional). The reduction is shown to be confluent. We interpret the recursive types as information systems in a…

We study the stochastic dynamics of a system of interacting species in a stochastic environment by means of a continuous-time Markov chain with transition rates depending on the state of the environment. Models of gene regulation in systems…

Coupling an isolated emitter to a single mode of the electromagnetic field is now routinely achieved and well understood. Current efforts aim to explore the coherent dynamics of emitters coupled to several electromagnetic modes (EM).…

We address the challenge of crosstalk in quantum multiplexing -an obstacle to scaling throughput in quantum communication networks. Crosstalk arises when physically coupled quantum modes interfere, degrading signal fidelity. We propose a…

Answering complex questions that require making latent decisions is a challenging task, especially when limited supervision is available. Recent works leverage the capabilities of large language models (LMs) to perform complex question…

Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…

Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…

Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…

Existing approaches to analogue quantum simulations of time-dependent quantum systems rely on perturbative corrections to quantum simulations of time-independent quantum systems. We overcome this restriction to perturbative treatments with…

Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…

In many real-world problems, recovering sparse signals from underdetermined linear systems remains a fundamental challenge. Although $\ell_1$ norm minimization is widely used, it suffers from estimation bias that prevents it from reaching…

Evolutionary symbolic regression approaches are powerful tools that can approximate an explicit mapping between input features and observation for various problems. However, ensuring that explored expressions maintain consistency with…

We consider a combinatorial problem occurring naturally in a group theoretical setting and provide a constructive solution in a special case. More precisely, in 1999 the author established a logarithmic bound for the derived length of the…

This work develops a rigorous framework for analysing ergodicity and mixing in time-inhomogeneous quantum dynamics. It considers quantum evolutions generated by sequences of quantum channels and examines in detail the relationship between…

We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example, and show that its transition paths are…

For a model nonlinear dynamical system, we show how one may obtain its bifurcation behavior by introducing noise into the dynamics and then studying the resulting Langevin dynamics in the weak-noise limit. A suitable quantity to capture the…