arXiv subjects

Adrian Jacobo

Publications and source records attributed to Adrian Jacobo.

5 recordsLinked to original sources

arXiv2024

WaveOrder: A differentiable wave-optical framework for scalable biological microscopy with diverse modalities

Correlative computational microscopy can accelerate imaging and modeling of cellular dynamics by relaxing trade-offs inherent to dynamic imaging. Existing computational microscopy frameworks are either specialized or overly generic, limiting use to fixed configurations or domain experts. We introduce WaveOrder, a generalist wave-optical framework for imaging the architectural order of biomolecules. WaveOrder reconstructs diverse specimen properties from multi-channel acquisitions, with or without fluorescence. It provides a unified representation of linear optical properties and differentiable physics-based image formation models spanning widefield, confocal, light-sheet, and oblique label-free geometries. WaveOrder uses physics-informed ML to auto-tune model parameters and solve blind shift-variant restoration problems. This open-source, PyTorch-based framework enables scalable quantitative imaging across scales from organelles to adult zebrafish, and improves restoration of cellular structures in high-throughput experiments. We validate WaveOrder on diverse imaging applications, demonstrating its ability to recover biomolecular structure beyond the limits of existing approaches.

physics.optics↗

arXiv2018

Fluctuation theory in space and time: white noise in reaction-diffusion models of morphogenesis

The precision of reaction-diffusion models for mesoscopic physical systems is limited by fluctuations. To account for this uncertainty, Van Kampen derived a stochastic Langevin-like reaction-diffusion equation that incorporates spatio-temporal white noise. The resulting solutions, however, have infinite standard deviation. Ad hoc modifications that address this issue by introducing microscopic correlations are inconvenient in many physical contexts of wide interest. We instead estimate the magnitude of fluctuations by coarse-graining solutions of the Van Kampen equation at a relevant mesoscopic scale. The ensuing theory yields fluctuations of finite magnitude. Our approach is demonstrated for a specific biophysical model--the encoding of positional information. We discuss the properties of the fluctuations and the role played by the macroscopic parameters of the underlying reaction-diffusion model. The analysis and numerical methods developed here can be applied in physical problems to predict the magnitude of fluctuations. This general approach can also be extended to other classes of dynamical systems that are described by partial differential equations.

cond-mat.stat-mech↗

arXiv2012

Logical operations with Localized Structures

We show how to exploit excitable regimes mediated by localized structures (LS) to perform AND, OR, and NOT logical operations providing full logical functionality. Our scheme is general and can be implemented in any physical system displaying LS. In particular, LS in nonlinear photonic devices can be used for all-optical computing applications where several reconfigurable logic gates can be implemented in the transverse plane of a single device, allowing for parallel computing.

nlin.PS↗

arXiv2008

Effects of a localized beam on the dynamics of excitable cavity solitons

We study the dynamical behavior of dissipative solitons in an optical cavity filled with a Kerr medium when a localized beam is applied on top of the homogeneous pumping. In particular, we report on the excitability regime that cavity solitons exhibits which is emergent property since the system is not locally excitable. The resulting scenario differs in an important way from the case of a purely homogeneous pump and now two different excitable regimes, both Class I, are shown. The whole scenario is presented and discussed, showing that it is organized by three codimension-2 points. Moreover, the localized beam can be used to control important features, such as the excitable threshold, improving the possibilities for the experimental observation of this phenomenon.

physics.optics↗

arXiv2007

Phase-space structure of two-dimensional excitable localized structures

In this work we characterize in detail the bifurcation leading to an excitable regime mediated by localized structures in a dissipative nonlinear Kerr cavity with a homogeneous pump. Here we show how the route can be understood through a planar dynamical system in which a limit cycle becomes the homoclinic orbit of a saddle point (saddle-loop bifurcation). The whole picture is unveiled, and the mechanism by which this reduction occurs from the full infinite-dimensional dynamical system is studied. Finally, it is shown that the bifurcation leads to an excitability regime, under the application of suitable perturbations. Excitability is an emergent property for this system, as it emerges from the spatial dependence since the system does not exhibit any excitable behavior locally.

nlin.PS↗