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Caitlin Hult

Publications and source records attributed to Caitlin Hult.

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Stochastic Gradient-Descent Calibration of Pyragas Delayed-Feedback Control for Chaos Suppression in the Sprott Circuit

This paper explores chaos control in the Sprott circuit by leveraging Stochastic Gradient Descent (SGD) to calibrate Pyragas delayed feedback control. Using a third-order nonlinear differential equation, we model the circuit and aim to suppress chaos by optimizing control parameters (gain $K$, delay $T_{\text{con}}$) and the variable resistor $R_v$. Experimental voltage data, extracted from published figures via WebPlotDigitizer, serve as the calibration target. We compare two calibration techniques: sum of squared errors (SSE) minimization via grid search and stochastic gradient descent (SGD) with finite differences. Joint optimization of $K$, $T_{\text{con}}$, and $R_v$ using SGD achieves superior alignment with experimental data, capturing both phase and amplitude with high fidelity. Compared to grid search, SGD excels in phase synchronization, though minor amplitude discrepancies persist due to model simplifications. Phase space analysis confirms the model ability to replicate the chaotic attractor geometry, despite slight deviations. We analyze the trade-off between calibration accuracy and computational cost, highlighting scalability challenges. Overall, SGD-based calibration demonstrates significant potential for precise control of chaotic systems, advancing mathematical modeling and applications in electrical engineering.

nlin.CD

Transient crosslinking kinetics optimize gene cluster interactions

Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and cohesin that stochastically generate loops within and between chains, and entrap proximal strands of sister chromatids. In this paper, we explore the ability of transient, protein-mediated, gene-gene crosslinks to induce clusters of genes, thereby dynamic architecture, within the highly repeated ribosomal DNA that comprises the nucleolus of budding yeast. We implement three approaches: live cell microscopy; computational modeling of the full genome during G1 in budding yeast, exploring four decades of timescales for transient crosslinks between 5k bp domains in the nucleolus on Chromosome XII; and, temporal network models with automated community detection algorithms applied to the full range of 4D modeling datasets. The data analysis tools detect and track gene clusters, their size, number, persistence time, and their plasticity. Of biological significance, our analysis reveals an optimal mean crosslink lifetime that promotes pairwise and cluster gene interactions through "flexible" clustering. In this state, large gene clusters self-assemble yet frequently interact, marked by gene exchanges between clusters, which in turn maximizes global gene interactions in the nucleolus. This regime stands between two limiting cases each with far less global gene interactions: with shorter crosslink lifetimes, "rigid" clustering emerges with clusters that interact infrequently; with longer crosslink lifetimes, there is a dissolution of clusters. These observations are compared with imaging experiments on a normal yeast strain and two condensin-modified mutant cell strains, applying the same image analysis pipeline to the experimental and simulated datasets.

q-bio.GN