skip to main content


Title: A Unified Analysis of Penalty-Based Collision Energies
We analyze a wide class of penalty energies used for contact response through the lens of a reduced frame. Applying our analysis to both spring-based and barrier-based energies, we show that we can obtain closed-form, analytic eigensystems that can be used to guarantee positive semidefiniteness in implicit solvers. Our approach is both faster than direct numerical methods, and more robust than approximate methods such as Gauss-Newton. Over the course of our analysis, we investigate physical interpretations for two separate notions of length. Finally, we showcase the stability of our analysis on challenging strand, cloth, and volume scenarios with large timesteps on the order of 1/40 s.  more » « less
Award ID(s):
2132280
NSF-PAR ID:
10431370
Author(s) / Creator(s):
;
Editor(s):
Ye, Yuting; Wang Huamin
Date Published:
Journal Name:
Proceedings of the ACM on computer graphics and interactive techniques
ISSN:
2577-6193
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Objective

    Solar ultraviolet (UV) radiation is ubiquitous in human life and well known to cause skin damage that can lead to harmful conditions such as erythema. Although sunscreen is a popular form of protection for some of these conditions, it is unclear whether sunscreen can maintain the mechanical barrier properties of skin. The objective of this study was to determine whetherin vitrothin‐film mechanical analysis techniques adapted for biological tissue are able to characterize the efficacy of commonly used UV inhibitors and commercial sunscreens to protect the biomechanical barrier properties of stratum corneum (SC) from UV exposure.

    Methods

    The biomechanical properties of SC samples were assayed through measurements of the SC's drying stress profile and delamination energy. The drying stresses within SC were characterized from the curvature of a borosilicate glass substrate onto which SC had been adhered. Delamination energies were characterized using a double‐cantilever beam (DCB) cohesion testing method. Successive DCB specimens were prepared from previously separated specimens by adhering new substrates onto each side of the already tested specimen to probe delamination energies deeper into the SC. These properties of the SC were measured before and after UV exposure, both with and without sunscreens applied, to determine the role of sunscreen in preserving the barrier function of SC.

    Results

    The drying stress in SC starts increasing sooner and rises to a higher plateau stress value after UVA exposure as compared to non‐UV‐exposed control specimens. For specimens that had sunscreen applied, the UVA‐exposed and non‐UV‐exposed SC had similar drying stress profiles. Additionally, specimens exposed to UVB without protection from sunscreen exhibited significantly lower delamination energies than non‐UV‐exposed controls. With commercial sunscreen applied, the delamination energy for UV‐exposed and non‐UV‐exposed tissue was consistent, even up to large doses of UVB.

    Conclusion

    In vitrothin‐film mechanical analysis techniques can readily characterize the effects of SC's exposure to UV radiation. The methods used in this study demonstrated commercial sunscreens were able to preserve the biomechanical properties of SC during UV exposure, thus indicating the barrier function of SC was also maintained.

     
    more » « less
  2. The molecules 1,4-cyclohexadiene (unconjugated 1,4-CHD) and 1,3-cyclohexadiene (conjugated 1,3-CHD) both have two double bonds, but these bonds interact in different ways. These molecules have long served as examples of through-bond and through-space interactions, respectively, and their electronic structures have been studied in detail both experimentally and theoretically, with the experimental assignments being especially complete. The existence of Rydberg states interspersed with the valence states makes the quantum mechanical calculation of their spectra a challenging task. In this work, we explore the electronic excitation energies of 1,4-CHD and 1,3-CHD for both valence and Rydberg states by means of complete active space second-order perturbation theory (CASPT2), extended multi-state CASPT2 (XMS-CASPT2), and multiconfiguration pair-density functional theory (MC-PDFT); it is shown by comparison to experiment that MC-PDFT yields the most accurate results. We found that the inclusion of Rydberg orbitals in the active space not only enables the calculation of Rydberg excitation energies but also improves the accuracy of the valence ones. A special characteristic of the present analysis is the calculation of the second moments of the excited-state orbitals. Because we find that the CASPT2 densities agree well with the CASSCF ones and since the MC-PDFT methods gets accurate excitation energies based on the CASSCF densities, we believe that we can trust these moments as far as giving a more accurate picture of the diffuseness of the excited-state orbitals in these prototype molecules than has previously been available. 
    more » « less
  3. Ultra-high-energy (UHE) photons are an important tool for studying the high-energy Universe. A plausible source of photons with exa-eV (EeV) energy is provided by UHE cosmic rays (UHECRs) undergoing the Greisen–Zatsepin–Kuzmin process (Greisen 1966; Zatsepin & Kuzmin 1966) or pair production process (Blumenthal 1970) on a cosmic background radiation. In this context, the EeV photons can be a probe of both UHECR mass composition and the distribution of their sources (Gelmini, Kalashev & Semikoz 2008; Hooper, Taylor & Sarkar 2011). At the same time, the possible flux of photons produced by UHE protons in the vicinity of their sources by pion photoproduction or inelastic nuclear collisions would be noticeable only for relatively near sources, as the attenuation length of UHE photons is smaller than that of UHE protons; see, for example, Bhattacharjee & Sigl (2000) for a review. There also exists a class of so-called top-down models of UHECR generation that efficiently produce the UHE photons, for instance by the decay of heavy dark-matter particles (Berezinsky, Kachelriess & Vilenkin 1997; Kuzmin & Rubakov 1998) or by the radiation from cosmic strings (Berezinsky, Blasi & Vilenkin 1998). The search for the UHE photons was shown to be the most sensitive method of indirect detection of heavy dark matter (Kalashev & Kuznetsov 2016, 2017; Kuznetsov 2017; Kachelriess, Kalashev & Kuznetsov 2018; Alcantara, Anchordoqui & Soriano 2019). Another fundamental physics scenario that could be tested with UHE photons (Fairbairn, Rashba & Troitsky 2011) is the photon mixing with axion-like particles (Raffelt & Stodolsky 1988), which could be responsible for the correlation of UHECR events with BL Lac type objects observed by the High Resolution Fly’s Eye (HiRes) experiment (Gorbunov et al. 2004; Abbasi et al. 2006). In most of these scenarios, a clustering of photon arrival directions, rather than diffuse distribution, is expected, so point-source searches can be a suitable test for photon - axion-like particle mixing models. Finally, UHE photons could also be used as a probe for the models of Lorentz-invariance violation (Coleman & Glashow 1999; Galaverni & Sigl 2008; Maccione, Liberati & Sigl 2010; Rubtsov, Satunin & Sibiryakov 2012, 2014). The Telescope Array (TA; Tokuno et al. 2012; Abu-Zayyad et al. 2013c) is the largest cosmic ray experiment in the Northern Hemisphere. It is located at 39.3° N, 112.9° W in Utah, USA. The observatory includes a surface detector array (SD) and 38 fluorescence telescopes grouped into three stations. The SD consists of 507 stations that contain plastic scintillators, each with an area of 3 m2 (SD stations). The stations are placed in the square grid with 1.2 km spacing and cover an area of ∼700 km2. The TA SD is capable of detecting extensive air showers (EASs) in the atmosphere caused by cosmic particles of EeV and higher energies. The TA SD has been operating since 2008 May. A hadron-induced EAS significantly differs from an EAS induced by a photon because the depth of the shower maximum Xmax for a photon shower is larger, and a photon shower contains fewer muons and has a more curved front (see Risse & Homola 2007 for a review). The TA SD stations are sensitive to both muon and electromagnetic components of the shower and therefore can be triggered by both hadron-induced and photon-induced EAS events. In the present study, we use 9 yr of TA SD data for a blind search for point sources of UHE photons. We utilize the statistics of the SD data, which benefit from a high duty cycle. The full Monte Carlo (MC) simulation of proton-induced and photon-induced EAS events allows us to perform the photon search up to the highest accessible energies, E ≳ 1020 eV. As the main tool for the present photon search, we use a multivariate analysis based on a number of SD parameters that make it possible to distinguish between photon and hadron primaries. While searches for diffuse UHE photons were performed by several EAS experiments, including Haverah Park (Ave et al. 2000), AGASA (Shinozaki et al. 2002; Risse et al. 2005), Yakutsk (Rubtsov et al. 2006; Glushkov et al. 2007, 2010), Pierre Auger (Abraham et al. 2007, 2008a; Bleve 2016; Aab et al. 2017c) and TA (Abu-Zayyad et al. 2013b; Abbasi et al. 2019a), the search for point sources of UHE photons has been done only by the Pierre Auger Observatory (Aab et al. 2014, 2017a). The latter searches were based on hybrid data and were limited to the 1017.3 < E < 1018.5 eV energy range. In the present paper, we use the TA SD data alone. We perform the searches in five energy ranges: E > 1018, E > 1018.5, E > 1019, E > 1019.5 and E > 1020 eV. We find no significant evidence of photon point sources in all energy ranges and we set the point-source flux upper limits from each direction in the TA field of view (FOV). The search for unspecified neutral particles was also previously performed by the TA (Abbasi et al. 2015). The limit on the point-source flux of neutral particles obtained in that work is close to the present photon point-source flux limits. 
    more » « less
  4. Abstract Motivation

    Cell shape provides both geometry for, and a reflection of, cell function. Numerous methods for describing and modeling cell shape have been described, but previous evaluation of these methods in terms of the accuracy of generative models has been limited.

    Results

    Here we compare traditional methods and deep autoencoders to build generative models for cell shapes in terms of the accuracy with which shapes can be reconstructed from models. We evaluated the methods on different collections of 2D and 3D cell images, and found that none of the methods gave accurate reconstructions using low dimensional encodings. As expected, much higher accuracies were observed using high dimensional encodings, with outline-based methods significantly outperforming image-based autoencoders. The latter tended to encode all cells as having smooth shapes, even for high dimensions. For complex 3D cell shapes, we developed a significant improvement of a method based on the spherical harmonic transform that performs significantly better than other methods. We obtained similar results for the joint modeling of cell and nuclear shape. Finally, we evaluated the modeling of shape dynamics by interpolation in the shape space. We found that our modified method provided lower deformation energies along linear interpolation paths than other methods. This allows practical shape evolution in high dimensional shape spaces. We conclude that our improved spherical harmonic based methods are preferable for cell and nuclear shape modeling, providing better representations, higher computational efficiency and requiring fewer training images than deep learning methods.

    Availability and implementation

    All software and data is available at http://murphylab.cbd.cmu.edu/software.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
    more » « less
  5. Abstract

    We report the application of our fragment‐based quantum chemistry model MIM (Molecules‐In‐Molecules) with electrostatic embedding. The method is termed “EE‐MIM (ElectrostaticallyEmbeddedMolecules‐In‐Molecules)” and accounts for the missing electrostatic interactions in the subsystems resulting from fragmentation. Point charges placed at the atomic positions are used to represent the interaction of each subsystem with the rest of the molecule with minimal increase in the computational cost. We have carefully calibrated this model on a range of different sizes of clusters containing up to 57 water molecules. The fragmentation methods have been applied with the goal of reproducing the unfragmented total energy at the MP2/6‐311G(d,p) level. Comparative analysis has been carried out between MIM and EE‐MIM to gauge the impact of electrostatic embedding. Performance of several different parameters such as the type of charge and levels of fragmentation are analyzed for the prediction of absolute energies. The use of background charges in subsystem calculations improves the performance of both one‐ and two‐layer MIM while it is noticeably important in the case of one‐layer MIM. Embedded charges for two‐layer MIM are obtained from a full system calculation at the low‐level. For one‐layer MIM, in the absence of a full system calculation, two different types of embedded charges, namely, Geometry dependent (GD) and geometry independent (GI) charges, are used. A self‐consistent procedure is employed to obtain GD charges. We have further tested our method on challenging charged systems with stronger intermolecular interactions, namely, protonated ammonia clusters (containing up to 30 ammonia molecules). The observations are similar to water clusters with improved performance using embedded charges. Overall, the performance of NPA charges as embedded charges is found to be the best.

     
    more » « less