Related papers: Entangled Schr\"odinger Bridge Matching
The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
Interfacial fluctuations in a two-phase binary fluid mixture reveal signatures of underlying physical processes that occur within each phase and on a range of spatial and temporal scales. In this study, we investigate a model binary fluid…
Strongly-coupled gauge theories far from equilibrium may exhibit unique features that could illuminate the physics of the early universe and of hadron and ion colliders. Studying real-time phenomena has proven challenging with…
We present an exact and fully analytical treatment of the entanglement dynamics for an isolated system of $N$ coupled oscillators following a sudden quench of the system parameters. The system is analyzed using the solutions of the time…
We consider the problem of sampling from an unknown distribution for which only a sufficiently large number of training samples are available. In this paper, we build on previous work combining Schr\"odinger bridges and plug & play Langevin…
We propose a new procedure to monitor and forecast the onset of transitions in high dimensional complex systems. We describe our procedure by an application to the Tangled Nature model of evolutionary ecology. The quasi-stable…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
We analyze the bootstrap percolation process on the stochastic block model (SBM), a natural extension of the Erd\"{o}s--R\'{e}nyi random graph that allows representing the "community structure" observed in many real systems. In the SBM,…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…
Projected Entangled Pair States (PEPS) are recognized as a potent tool for exploring two-dimensional quantum many-body systems. However, a significant challenge emerges when applying conventional PEPS methodologies to systems with periodic…
A number of non-Markovian stochastic Schr\"odinger equations, ranging from the numerically exact hierarchical form towards a series of perturbative expressions sequentially presented in an ascending degrees of approximations are revisited…
Conditional generative models represent a significant advancement in the field of machine learning, allowing for the controlled synthesis of data by incorporating additional information into the generation process. In this work we introduce…
The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded…
This work presents a comprehensive framework for enhanced diffusion modeling in fluid-structure interactions by combining the Immersed Boundary Method (IBM) with stochastic trajectories and high-order spectral boundary conditions. Using…
Revealing the structure and dynamics of complex networked systems from observed data is of fundamental importance to science, engineering, and society. Is it possible to develop a universal, completely data driven framework to decipher the…
Three-level quantum systems, which possess some unique characteristics beyond two-level ones, such as electromagnetically induced transparency, coherent trapping, and Raman scatting, play important roles in solid-state quantum information…
We recover the so-called field-road diffusion model as the hydrodynamic limit of an interacting particle system. The former consists of two parabolic PDEs posed on two sets of different dimensions (a "field" and a "road" in a population…
Single-cell data reveal the presence of biological stochasticity between cells of identical genome and environment, in particular highlighting the transcriptional bursting phenomenon. To account for this property, gene expression may be…