Related papers: Gradient sensing limit of a cell when controlling …
Living cells sense noisy biochemical signals crucial for survival, yet models incorporating intracellular signaling are limited. This study examines how cells sense chemotactic concentrations through phosphorylation readouts in Ca2+…
Mathematical modelling of biological population dynamics often involves proposing high fidelity discrete agent-based models that capture stochasticity and individual-level processes. These models are often considered in conjunction with an…
Full-parameter fine-tuning of large language models is constrained by substantial GPU memory requirements. Low-rank adaptation methods mitigate this challenge by updating only a subset of parameters. However, these approaches often limit…
Swimming bacteria detect chemical gradients by performing temporal comparisons of recent measurements of chemical concentration. These comparisons are described quantitatively by the chemotactic response function, which we expect to…
Cells use surface receptors to estimate the concentration of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many…
Image segmentation is a critical step in computational biomedical image analysis, typically evaluated using metrics like the Dice coefficient during training and validation. However, in clinical settings without manual annotations,…
Berg and Purcell [Biophys. J. 20, 193 (1977)] calculated how the accuracy of concentration sensing by single-celled organisms is limited by noise from the small number of counted molecules. Here we generalize their results to the sensing of…
Recent research has shown that motile cells can adapt their mode of propulsion to the mechanical properties of the environment in which they find themselves--crawling in some environments while swimming in others. The latter can involve…
In this paper we extend the adaptive gradient descent (AdaGrad) algorithm to the optimal distributed control of parabolic partial differential equations with uncertain parameters. This stochastic optimization method achieves an improved…
Controlling growth via cell division is crucial in the development of higher organisms, and yet the mechanisms through which this is achieved, e.g., in epithelial tissue, is not yet fully understood. We show that by coupling the cell cycle…
Biomolecular condensates form on timescales of seconds in cells upon environmental or compositional changes. Condensate formation is thus argued to act as a mechanism for sensing such changes and quickly initiating downstream processes,…
We study the fundamental optimization principles of self-attention, the defining mechanism of transformers, by analyzing the implicit bias of gradient-based optimizers in training a self-attention layer with a linear decoder in binary…
How cells reliably infer information about their environment is a fundamentally important question. While sensing and signaling generally start with cell-surface receptors, the degree of accuracy with which a cell can measure external…
Precise alignment of the electron beam is critical for successful application of scanning transmission electron microscopes (STEM) to understanding materials at atomic level. Despite the success of aberration correctors, aberration…
We introduce a notion of inexact model of a convex objective function, which allows for errors both in the function and in its gradient. For this situation, a gradient method with an adaptive adjustment of some parameters of the model is…
Efficient parameter identification of electrochemical models is crucial for accurate monitoring and control of lithium-ion cells. This process becomes challenging when applied to complex models that rely on a considerable number of…
A fast and reliable geometry optimization algorithm is presented that optimizes atomic positions and lattice vectors simultaneously. Using a series of benchmarks, it is shown that the method presented in this paper outperforms in most cases…
In eukaryotic cell chemotaxis, cells extend and retract transient actin-driven protrusions at their membrane that facilitate both the detection of external chemical gradients and directional movement via the formation of focal adhesions…
Contact inhibition refers to a reduction in the rate of cell migration and/or cell proliferation in regions of high cell density. Under normal conditions contact inhibition is associated with the proper functioning tissues, whereas abnormal…
The study of optimal control problems under uncertainty plays an important role in scientific numerical simulations. This class of optimization problems is strongly utilized in engineering, biology and finance. In this paper, a stochastic…