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Frank Delvigne

Publications and source records attributed to Frank Delvigne.

2 recordsLinked to original sources

Analog and hybrid computing in the 21st century

Analog computers solve problems through physical representations of mathematical variables and relations, often using the dynamics of electronic circuits and their associated signals. Many analog computers directly represent nonlinear dynamical systems; they encode their solutions in the signals that they generate. Although most modern scientific computing relies on digital architectures with inherently discrete-valued representations and algorithmic approaches, the design constraints of such architectures increasingly limit both performance and energy efficiency. Analog systems can circumvent some of these constraints; they execute specific computations very efficiently by mapping them directly onto physical processes using smaller and simpler computing elements than the ones in digital architectures. In this article, we provide an interdisciplinary perspective on modern analog and hybrid (i.e., analog-digital) computing. We discuss how modern scientific computing workflows can leverage analog approaches in various applications, such as in simulating dynamical systems, performing optimization, and enabling more energy-efficient implementations of artificial intelligence.

math.DS↗

Inherited or produced? Inferring protein production kinetics when protein counts are shaped by a cell's division history

Inferring protein production kinetics for dividing cells is complicated due to protein inheritance from the mother cell. For instance, fluorescence measurements -- commonly used to assess gene activation -- may reflect not only newly produced proteins but also those inherited through successive cell divisions. In such cases, observed protein levels in any given cell are shaped by its division history. As a case study, we examine activation of the glc3 gene in yeast involved in glycogen synthesis and expressed under nutrient-limiting conditions. We monitor this activity using snapshot fluorescence measurements via flow cytometry, where GFP expression reflects glc3 promoter activity. A naïve analysis of flow cytometry data ignoring cell division suggests many cells are active with low expression. Explicitly accounting for the (non-Markovian) effects of cell division and protein inheritance makes it impossible to write down a tractable likelihood -- a key ingredient in physics-inspired inference, defining the probability of observing data given a model. The dependence on a cell's division history breaks the assumptions of standard (Markovian) master equations, rendering traditional likelihood-based approaches inapplicable. Instead, we adapt conditional normalizing flows (a class of neural network models designed to learn probability distributions) to approximate otherwise intractable likelihoods from simulated data. In doing so, we find that glc3 is mostly inactive under stress, showing that while cells occasionally activate the gene, expression is brief and transient.

q-bio.QM↗