We present a class of efficient parametric closure models for 1D stochastic Burgers equations. Casting it as statistical learning of the flow map, we derive the parametric form by representing the unresolved high wavenumber Fourier modes as functionals of the resolved variable's trajectory. The reduced models are nonlinear autoregression (NAR) time series models, with coefficients estimated from data by least squares. The NAR models can accurately reproduce the energy spectrum, the invariant densities, and the autocorrelations. Taking advantage of the simplicity of the NAR models, we investigate maximal space-time reduction. Reduction in space dimension is unlimited, and NAR models with two Fourier modes can perform well. The NAR model's stability limits time reduction, with a maximal time step smaller than that of the K-mode Galerkin system. We report a potential criterion for optimal space-time reduction: the NAR models achieve minimal relative error in the energy spectrum at the time step, where the K-mode Galerkin system's mean Courant-Friedrichs-Lewy (CFL) number agrees with that of the full model.
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http://dx.doi.org/10.3390/e22121360 | DOI Listing |
Nucleic Acids Res
January 2025
Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States.
The mammalian high mobility group protein AT-hook 2 (HMGA2) is a small DNA-binding protein that specifically targets AT-rich DNA sequences. Structurally, HMGA2 is an intrinsically disordered protein (IDP), comprising three positively charged 'AT-hooks' and a negatively charged C-terminus. HMGA2 can form homodimers through electrostatic interactions between its 'AT-hooks' and C-terminus.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, United Kingdom.
The growing demand for biological products drives many efforts to maximize expression of heterologous proteins. Advances in high-throughput sequencing can produce data suitable for building sequence-to-expression models with machine learning. The most accurate models have been trained on one-hot encodings, a mechanism-agnostic representation of nucleotide sequences.
View Article and Find Full Text PDFNAR Genom Bioinform
March 2025
Department of Computer Science, University of Miami, Coral Gables, FL 33146, United States.
A novel biochemistry experiment named HiRES has been developed to capture both the chromosomal conformations and gene expression levels of individual single cells simultaneously. Nevertheless, when compared to the extensive volume of single-cell Hi-C data generated from individual cells, the number of datasets produced from this experiment remains limited in the scientific community. Hence, there is a requirement for a computational tool that can forecast the levels of gene expression in individual cells using single-cell Hi-C data from the same cells.
View Article and Find Full Text PDFInt J Nanomedicine
January 2025
Department of Drug Sciences, University of Pavia, Pavia, 27100, Italy.
Purpose: The main purpose of the study was the formulation development of nanogels (NHs) composed of chondroitin sulfate (CS) and low molecular weight chitosan (lCH), loaded with a naringenin-β-cyclodextrin complex (NAR/β-CD), as a potential treatment for early-stage diabetic retinopathy.
Methods: Different formulations of NHs were prepared by varying polymer concentration, lCH ratio, and pH and, then, characterized for particle size, zeta potential, particle concentration (particles/mL) and morphology. Cytotoxicity and internalization were assessed in vitro using Human Umbilical Vein Endothelial Cells (HUVEC).
Laryngoscope
January 2025
Department of Otolaryngology, College of Medicine, University of Illinois Chicago, Chicago, Illinois, U.S.A.
Objective: The inflammatory role of female hormones has been garnering increased attention in the literature. Studies suggest a link between estrogen and inflammatory conditions of the airways and nasal mucosa. However, there remains a paucity of literature regarding the associations of hormones with rhinitis.
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