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| http://dx.doi.org/10.1002/ctm2.294 | DOI Listing |
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Entropy-based methods for formulating bottom-up ultra-coarse-grained models.
J Chem Phys
January 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.
Bottom-up coarse-grained (CG) modeling is an effective means of bypassing the limited spatiotemporal scales of conventional atomistic molecular dynamics while retaining essential information from the atomistic model. A central challenge in CG modeling is the trade-off between accuracy and efficiency, as the inclusion of often pivotal many-body interaction terms in the CG force-field renders simulation markedly slower than simple pairwise models. The Ultra Coarse-Graining (UCG) method incorporates many-body terms through discrete internal state variables that modulate the CG force-field according to, e.
View Article and Find Full Text PDFDesign Principles From Natural Olfaction for Electronic Noses.
Adv Sci (Weinh)
January 2025
Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA.
Natural olfactory systems possess remarkable sensitivity and precision beyond what is currently achievable by engineered gas sensors. Unlike their artificial counterparts, noses are capable of distinguishing scents associated with mixtures of volatile molecules in complex, typically fluctuating environments and can adapt to changes. This perspective examines the multifaceted biological principles that provide olfactory systems their discriminatory prowess, and how these ideas can be ported to the design of electronic noses for substantial improvements in performance across metrics such as sensitivity and ability to speciate chemical mixtures.
View Article and Find Full Text PDFCharacterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize.
BMC Genomics
January 2025
Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
Background: Conserved non-coding sequences (CNS) are islands of non-coding sequences conserved across species and play an important role in regulating the spatiotemporal expression of genes. Identification of CNS provides valuable information about potentially functional genomic elements, regulatory regions, and helps to gain insights into the genetic basis of crop agronomic traits.
Results: Here, we comprehensively analyze CNS in maize, by comparing the genomes of maize inbred line B73 (Zea mays ssp.
Cre-Lox miRNA-delivery technology optimized for inducible microRNA and gene-silencing studies in zebrafish.
Nucleic Acids Res
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Institute for Biomedicine and Glycomics, School of Environment and Science, Griffith University, 46 Don Young Road, Brisbane QLD 4111, Australia., Brisbane, QLD 4111, Australia.
While many genetic tools exist for zebrafish, this animal model still lacks robust gene-silencing and microRNA-delivery technologies enabling spatio-temporal control and traceability. We have recently demonstrated that engineered pri-miR backbones can trigger stable gene knockdown and/or express microRNA(s) of choice in this organism. However, this miRNA-expressing technology presents important limitations.
View Article and Find Full Text PDFOne-core neuron deep learning for time series prediction.
Natl Sci Rev
February 2025
Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China.
The enormous computational requirements and unsustainable resource consumption associated with massive parameters of large language models and large vision models have given rise to challenging issues. Here, we propose an interpretable 'small model' framework characterized by only a single core-neuron, i.e.
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