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1. CSTs for Terabyte-Sized Data

   https://doi.org/10.1109/DCC52660.2022.00017  

   Oliva, Marco; Cenzato, Davide; Rossi, Massimiliano; Liptak, Zsuzsanna; Gagie, Travis; Boucher, Christina (March 2022, Data Compression Conference (DCC))

   Generating pangenomic datasets is becoming increasingly common but there are still few tools able to handle them and even fewer accessible to non-specialists. Building compressed suffix trees (CSTs) for pangenomic datasets is still a major challenge but could be enor- mously beneficial to the community. In this paper, we present a method, which we refer to as RePFP-CST, for building CSTs in a manner that is scalable. To accomplish this, we show how to build a CST directly from VCF files without decompressing them, and to prune from the prefix-free parse (PFP) phrase boundaries whose removal reduces the total size of the dictionary and the parse. We show that these improvements reduce the time and space required for the construction of the CST, and the memory footprint of the finished CST, enabling us to build a CST for a terabyte of DNA for the first time in the literature. 

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2. Single-walled carbon nanotube reptation dynamics in submicron sized pores from randomly packed mono-sized colloids

   https://doi.org/10.1039/D2SM00305H  

   Tang, Zhao; Eichmann, Shannon L.; Lounis, Brahim; Cognet, Laurent; MacKintosh, Frederick C.; Pasquali, Matteo (July 2022, Soft Matter)

   Studying the Brownian motion of fibers and semi-flexible filaments in porous media is the key to understanding the transport and mechanical properties in a variety of systems. The motion of semi-flexible filaments in gel-like porous media including polymer networks and cell cytoskeleton has been studied theoretically and experimentally, whereas the motion of these materials in packed-colloid porous media, advanced foams, and rock-like systems has not been thoroughly studied. Here we use video microscopy to directly visualize the reptation and transport of intrinsically fluorescent, semiflexible, semiconducting single-walled carbon nanotubes (SWCNTs) in the sub-micron pores of packed colloids as fixed obstacles of packed-colloid porous media. By visualizing the filament motion and Brownian diffusion at different locations in the pore structures, we study how the properties of the environment, like the pore shape and pore structure of the porous media, affect SWCNT mobility. These results show that the porous media structure controls SWCNT reorientation during Brownian diffusion. In packed-colloid pores, SWCNTs diffuse along straight pores and bend across pores; conversely, in gel pores, SWCNTs consistently diffuse into curved pores, displaying a faster parallel motion. In both gel and packed-colloid porous media, SWCNT finite stiffness enhances SWCNT rotational diffusion and prevents jamming, allowing for inter-pore diffusion. 

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3. BLUE CARBON AND WETLANDS COMPENSATORY MITIGATION: FITTING A CLIMATE-SIZED PEG INTO A WATERSHED-SIZED HOLE

   Hill, Katie; Spivak, Amanda (January 2024, Sea Grant law and policy journal)

   This Article seeks to provide policymakers and coastal resource managers with detailed insights into the challenges and opportunities for incorporating considerations of “blue carbon” into compensatory mitigation required under Clean Water Act Section 404. As our understanding of blue carbon systems deepens, so too does the urgency of responding to the global climate crisis. Commentators have encouraged the inclusion of blue carbon into existing domestic policies, including Clean Water Act Section 404. It is the authors’ hope that focused articles such as this can shine a light on which approaches might be most tenable under existing law, directing efforts towards workable solutions. 

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4. RADIATION PRESSURE ON FLUFFY SUBMICRON-SIZED GRAINS

   https://doi.org/10.3847/0004-637X/818/2/133  

   Silsbee, Kedron; Draine, Bruce T. (February 2016, The Astrophysical Journal)
5. Linear-Sized Sensor Scheduling Using Regret Minimization

   https://doi.org/10.23919/ACC55779.2023.10155991  

   Vafaee, Reza; Siami, Milad (May 2023, 2023 American Control Conference (ACC))