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1. A gated hydrophobic funnel within BAX binds long-chain alkenals to potentiate pro-apoptotic function

   https://doi.org/10.1101/2024.12.23.630122  

   Gelles, Jesse D; Chen, Yiyang; Luna-Vargas, Mark_P A; Follis, Ariele Viacava; Bayiokos, Stella G; Mohammed, Jarvier N; Sebastian, Tara M; Al_Noman, M Abdullah; Pham, Ngoc Dung; Shi, Yi; et al (December 2024, bioRxiv)

   Mitochondria maintain a biochemical environment that cooperates with BH3–only proteins (e.g., BIM) to potentiate BAX activation, the key event to initiate physiological and pharmacological forms of apoptosis. The sphingosine-1-phosphate metabolite 2-trans-hexadecenal (2t–hexadecenal) is one such component described to support BAX activation, but molecular mechanisms remain largely unknown. Here, we utilize complementary biochemical and biophysical techniques to reveal that 2t-hexadecenal non-covalently interacts with BAX, and cooperates with BIM to stimulate early-activation steps of monomeric BAX. Integrated structural and computational approaches reveal 2t–hexadecenal binds an undefined region – a hydrophobic cavity formed by core-facing residues of α5, α6, and gated by α8 – we now term the “BAX actuating funnel” (BAF). We define alkenal length and α8 mobility as critical determinants for 2t–hexadecenal synergy with BIM and BAX, and demonstrate that proline 168 allosterically regulates BAF function. Collectively, this work imparts detailed molecular insights advancing our fundamental knowledge of BAX regulation and identifies a regulatory region with implications for biological and therapeutic opportunities. 

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2. Modeling thermal and mechanical cancellation of residual stress from hybrid additive manufacturing by laser peening

   https://doi.org/10.1016/j.npe.2019.07.001  

   Madireddy, Guru; Li, Chao; Liu, Jingfu; Sealy, Michael_P (July 2019, Nanotechnology and Precision Engineering)

   Additive manufacturing (AM) of metals often results in parts with unfavorable mechanical properties. Laser peening (LP) is a high strain rate mechanical surface treatment that hammers a workpiece and induces favorable mechanical properties. Peening strain hardens a surface and imparts compressive residual stresses improving the mechanical properties of a material. This work investigates the role of LP on layer-by-layer processing of 3D printed metals using finite element analysis. The objective is to understand temporal and spatial residual stress development after thermal and mechanical cancellation caused by cyclically coupling printing and peening. Results indicate layer peening frequency is a critical process parameter affecting residual stress redistribution and highly interdependent on the heat generated by the printing process. Optimum hybrid process conditions were found to exists that favorably enhance mechanical properties. With this study, hybrid-AM has ushered in the next evolutionary step in AM and has the potential to profoundly change the way high value metal goods are manufactured. 

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3. Suppression of surface charge and its effect on sedimentation and fabric of kaolinite clay

   https://doi.org/10.1680/jgele.24.00104  

   Joo, H-W; Dai, S; Kwon, T-H (June 2025, Géotechnique Letters)

   This study explores the effect of suppressed surface charges on the sedimentation behaviour and fabric of kaolinite clay. In particular, sedimentation behaviours were compared between negatively charged natural kaolin clays and surface-treated and hence electrically suppressed kaolin clays by methylene blue adsorption. The results clearly indicate that the negative surface charge impeded the sedimentation rate of kaolin by resisting particle aggregation. Such an effect appeared the most significant when the surrounding pH was less than the isoelectric point (IEP) of the mineral edges. Under a pH less than IEP, the flocculation time and the final void ratio remarkably dropped after the negative charge neutralisation. This was also corroborated by the scanning electron microscopy images, which further revealed the fabric transition from an edge-to-face flocculated structure to a face-to-face aggregated structure due to the absence of interparticle electrical forces. Conversely, there was no significant fabric change at pH higher than or near the IEP, even though the sedimentation behaviours were accelerated by forming larger flocs. This study imparts important insights into the fundamentals of microstructure and resulting sedimentation behaviour of clayey soils and how they can be changed in electrically neutralised clay. 

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4. Effects of Defects and Presence of Open-Metal Sites on the Structure and Dynamics of Water in Hydrophobic Zeolitic Imidazolate Frameworks

   https://doi.org/10.1021/acs.jcim.3c01077  

   Shi, Yuliang; Limbu, Dil K; Zhang, Zeyu; Momeni, Mohammad R; Shakib, Farnaz A (November 2023, Journal of Chemical Information and Modeling)

   Most of the chemistry in nanoporous materials with small pore sizes and windows takes place on the outer surface, which is in direct contact with the substrate/solvent, rather than within the pores and channels. Here, we report the results of our comprehensive atomistic molecular dynamics (MD) simulations to decipher the interaction of water with a realistic finite ∼5.1 nm nanoparticle (NP) model of ZIF-8, with edges containing undercoordinated Zn metal sites, vs a conventionally employed pristine crystalline bulk (CB) model. The hydrophobic interior surface of the CB model imparts significant dynamical behavior on water molecules with (i) increasing diffusivity from the surface toward the center of the pores and (ii) confined water, at low concentration, showing similar diffusivity to that of the bulk water. On the other hand, water molecules adsorbed on the surface of the NP model exhibit a range of characteristics, including “coordinated”, “confined”, and “bulk-like” behavior. Some of the water molecules form coordinative bonds with the undercoordinated Zn metal centers and act as nucleation sites for the water droplets to form, facilitating diffusion into the pores. However, diffusion of water molecules is limited to the areas near the surface and not all the way to the core of the NP model. Our atomistic MD simulations provide insights into the stability of ZIFs in aqueous solutions despite hydrolysis of their outer surface. Such insights are helpful in designing more robust nanoporous materials for applications in humid environments. 

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5. Solid state photodimerization of 9- tert -butyl anthracene ester produces an exceptionally metastable polymorph according to first-principles calculations

   https://doi.org/10.1039/C8CE01985A  

   Beran, Gregory J. (January 2019, CrystEngComm)

   Molecular crystal engineering seeks to tune the material properties by controlling the crystal packing. However, the range of achievable properties is constrained by the limited energy range of polymorphs which can be crystallized. Here, computational modeling highlights that a solid-state crystal-to-crystal chemical reaction in 9- tert -butyl anthracene ester (9TBAE) nanorods [Al-Kaysi et al. , J. Am. Chem. Soc. , 2006, 128 , 15938] imparts “synthetic memory” into the crystal structure that allows reproducible formation of a highly metastable, yet long-lived polymorph. Specifically, whereas the vast majority of known polymorphs exhibit lattice energy differences below 10 kJ mol −1 , the conformational polymorph formed via solid state reaction chemistry lies 14 kJ mol −1 higher in energy than the form grown from solution, according to calculations that combine a dispersion-corrected second-order Møller–Plesset perturbation theory (MP2D) treatment of the monomer and photodimer with a density functional theory treatment (B86bPBE-XDM) of the intermolecular interactions in the crystal. Moreover, the solid-state reaction environment traps a highly unstable intramolecular photodimer conformation which defies the conventional wisdom surrounding conformational polymorphs. These observations suggest that solid-state reaction chemistry represents an under-appreciated strategy for producing polymorphs that would likely be unobtainable otherwise. 

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