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1. A local mode study of ring puckering effects in the infrared spectra of cyclopentane

   https://doi.org/10.1063/5.0095010  

   Sibert, Edwin L.; Bernath, Peter F. (June 2022, The Journal of Chemical Physics)

   We report and interpret recently recorded high-resolution infrared spectra for the fundamentals of the CH 2 scissors and CH stretches of gas phase cyclopentane at −26.1 and −50 °C, respectively. We extend previous theoretical studies of this molecule, which is known to undergo barrierless pseudorotation due to ring puckering, by constructing local mode Hamiltonians of the stretching and scissor vibrations for which the frequencies, couplings, and linear dipoles are calculated as functions of the pseudorotation angle using B3LYP/6-311++(d,p) and MP2/cc-pVTZ levels of theory. Symmetrization ( D 5 h ) of the vibrational basis sets leads to simple vibration/pseudorotation Hamiltonians whose solutions lead to good agreement with the experiment at medium resolution, but which miss interesting line fractionation when compared to the high-resolution spectra. In contrast to the scissor motion, pseudorotation leads to significant state mixing of the CH stretches, which themselves are Fermi coupled to the scissor overtones. 

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2. Quadrilateral layout generation and optimization using equivalence classes of integral curves: theory and application to surfaces with boundaries

   https://doi.org/10.1093/jom/ufac002  

   Shepherd, Kendrick M.; Gu, Xianfeng David; Hiemstra, René R.; Hughes, Thomas J. R. (April 2022, Journal of Mechanics)

   Abstract Extracting quadrilateral layouts from surface triangulations is an important step in texture mapping, semi-structured quadrilateral meshing for traditional analysis and spline reconstruction for isogeometric analysis. Current methods struggle to yield high-quality layouts with appropriate connectivity between singular nodes (known as “extraordinary points” for spline representations) without resorting to either mixed-integer optimization or manual constraint prescription. The first of these is computationally expensive and comes with no guarantees, while the second is laborious and error-prone. In this work, we rigorously characterize curves in a quadrilateral layout up to homotopy type and use this information to quickly define high-quality connectivity constraints between singular nodes. The mathematical theory is accompanied by appropriate computational algorithms. The efficacy of the proposed method is demonstrated in generating quadrilateral layouts on the United States Army’s DEVCOM Generic Hull vehicle and parts of a bilinear quadrilateral finite element mesh (with some linear triangles) of a 1996 Dodge Neon. 

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3. QuadriFlow: A Scalable and Robust Method for Quadrangulation

   Huang, J.; Zhou, Y.; Niessner, M.; Shewchuk, J. R.; Guibas, L. J. (July 2018, Symposium on Geometry Processing)

   QuadriFlow is a scalable algorithm for generating quadrilateral surface meshes based on the Instant Field-Aligned Meshes of Jakob et al. (ACM Trans. Graph. 34(6):189, 2015). We modify the original algorithm such that it efficiently produces meshes with many fewer singularities. Singularities in quadrilateral meshes cause problems for many applications, including parametrization and rendering with Catmull-Clark subdivision surfaces. Singularities can rarely be entirely eliminated, but it is possible to keep their number small. Local optimization algorithms usually produce meshes with many singularities, whereas the best algorithms tend to require non-local optimization, and therefore are slow. We propose an efficient method to minimize singularities by combining the Instant Meshes objective with a system of linear and quadratic constraints. These constraints are enforced by solving a global minimum-cost network flow problem and local boolean satisfiability problems. We have verified the robustness and efficiency of our method on a subset of ShapeNet comprising 17,791 3D objects in the wild. Our evaluation shows that the quality of the quadrangulations generated by our method is as good as, if not better than, those from other methods, achieving about four times fewer singularities than Instant Meshes. Other algorithms that produce similarly few singularities are much slower; we take less than ten seconds to process each model. Our source code is publicly available. 

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4. Does Inter-Residue Hydrogen Bonding in β-(1→4)-Linked Disaccharides Influence Linkage Conformation in Aqueous Solution?

   https://doi.org/10.1021/acs.jpcb.3c07448  

   Zhang, Wenhui; Meredith, Reagan J.; Wang, Xiaocong; Woods, Robert J.; Carmichael, Ian; Serianni, Anthony S. (March 2024, The Journal of Physical Chemistry B)

   Two disaccharides, methyl β-d-galactopyranosyl-(1→4)-α-d-glucopyranoside (1) and methyl β-d-galactopyranosyl-(1→4)-3-deoxy-α-d-ribo-hexopyranoside (3), were prepared with selective 13C-enrichment to allow measurement of six trans-O-glycosidic J-couplings (2JCOC, 3JCOCH, and 3JCOCC) in each compound. Density functional theory (DFT) was used to parameterize Karplus-like equations that relate these J-couplings to either ϕ or ψ. MA’AT analysis was applied to both linkages to determine mean values of ϕ and ψ in each disaccharide and their associated circular standard deviations (CSDs). Results show that deoxygenation at C3 of 1 has little effect on both the mean values and librational motions of the linkage torsion angles. This finding implies that, if inter-residue hydrogen bonding between O3H and O5′ of 1 is present in aqueous solution and persistent, it plays little if any role in dictating preferred linkage conformation. Hydrogen bonding may lower the energy of the preferred linkage geometry but does not determine it to any appreciable extent. Aqueous 1-μs MD simulation supports this conclusion and also indicates greater conformational flexibility in deoxydisaccharide 3 in terms of sampling several, conformationally distinct, higher-energy conformers in solution. The populations of these latter conformers are low (3–14%) and could not be validated by MA’AT analysis. If the MD model is correct, however, C3 deoxygenation does enable conformational sampling over a wider range of ϕ/ψ values, but linkage conformation in the predominant conformer is essentially identical in both 1 and 3. 

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5. Linkage Attack on Skeleton-based Motion Visualization

   Thomas Carr, Aidong Lu (January 2023, ACM International Conference on Information and Knowledge Management)

   Skeleton-based motion capture and visualization is an important computer vision task, especially in the virtual reality (VR) envi- ronment. It has grown increasingly popular due to the ease of gathering skeleton data and the high demand of virtual socializa- tion. The captured skeleton data seems anonymous but can still be used to extract personal identifiable information (PII). This can lead to an unintended privacy leakage inside a VR meta-verse. We propose a novel linkage attack on skeleton-based motion visual- ization. It detects if a target and a reference skeleton are the same individual. The proposed model, called Linkage Attack Neural Net- work (LAN), is based on the principles of a Siamese Network. It incorporates deep neural networks to embed the relevant PII then uses a classifier to match the reference and target skeletons. We also employ classical and deep motion retargeting (MR) to cast the target skeleton onto a dummy skeleton such that the motion sequence is anonymized for privacy protection. Our evaluation shows that the effectiveness of LAN in the linkage attack and the effectiveness of MR in anonymization. The source code is available at https://github.com/Thomasc33/Linkage-Attack 

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