21 papers · ranked by Valyu relevance
Akhil Shajan, Madushanka Manathunga, Andreas Goetz, Kenneth Merz
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and…
Akhil Shajan, Madushanka Manathunga, Andreas Goetz, Kenneth Merz
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open- source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and…
AKHIL SHAJAN, Madushanka Manathunga, Andreas Goetz, Kenneth Merz
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open-source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and…
Yuanpeng Liu, Ting-Uei Lee, Anooshe Rezaee Javan, Yi Min Xie
Goldberg polyhedra have been widely studied across multiple fields, as their distinctive pattern can lead to many useful applications. Their topology can be determined using Goldberg’s method through generating topologically equivalent structures, named cages. However, the geometry of Goldberg polyhedra remains…
Zhaocheng Xiang, Yufeng Ge
Maize leaf and canopy are the primary media to interact with environmental factors, including light interception, water evaporation, wind fluctuation, etc. Leaf morphology and canopy architecture affect the interaction process and activity significantly. Maize canopy architecture, a critical determinant of light…
Tommaso Taddei
We develop and assess an optimization-based approach to parametric geometry reduction. Given a family of parametric domains, we aim to determine a parametric diffeomorphism Φ that maps a fixed reference domain Ω into each element of the family, for different values of the parameter; the ultimate goal of our study is to…
Khusrav Yorov, Bolun Wang, Mikhail Skopenkov, Helmut Pottmann + 1 more
Many problems in computational design and fabrication amount to the solution of a system of constraints which is solved by numerical optimization. Despite the presence of constraints, the solution space or design space may still be sufficiently large to be explored by a designer. However, it may be difficult to access…
Stefan Vuckovic
Nearly all electronic structure simulations begin with obtaining approximate geometries, making a systematic quantification of errors in approximate molecular structures of key importance. Recently, the geometric energy offset (GEO) framework based on a single and natural measure for quantifying and analysing these…
Andrew Cheng, Vaibhav Dixit, Melanie Weber
Convex programming plays a fundamental role in machine learning, data science, and engineering. Testing convexity structure in nonlinear programs relies on verifying the convexity of objectives and constraints. Grant et al. (2006) introduced a framework, Disciplined Convex Programming (DCP), for automating this…
Tianbo Kang, Jianpeng Zhang, Xin Zhao, Mingzhu Sun + 2 more
Regular geometric targets under microscopic scenes, such as microspheres, micropores, and microtubes, are characterized by small scales, low contrast, and degraded boundaries. Masks generated by general segmentation methods often fail to directly support high-precision geometric parameter measurement. This paper…
Nikita Belokonev, Artem Melnikov, Maninadh Podapaka, Karan Pinto + 2 more
'Markus Pflitsch' 'Michael Perelshtein'] Chemical component design is a computationally challenging procedure that often entails iterative numerical modeling and authentic experimental testing. We demonstrate a novel optimization method, Tensor train Optimization (TetraOpt), for the shape optimization of components…
Zhihong Tang, Qiang Zou, Hsi-Yung Feng, Shuming Gao + 2 more
'Yusheng Liu'] This paper presents a comprehensive review of geometric constraint solving in parametric computer-aided design (CAD), with the major focus on its advances in the last 15 years. Geometric constraint solving can date back to the very first CAD prototype, Sketchpad, in the 1960s, but serious research…
Yue Li, Logan Numerow, Bernhard Thomaszewski, Stelian Coros
Computing intrinsic distances on discrete surfaces is at the heart of many minimization problems in geometry processing and beyond. Solving these problems is extremely challenging as it demands the computation of onsurface distances along with their derivatives. We present a novel approach for intrinsic minimization of…
Feng Zou, Xia Wang, Weilin Zhang, Qingshui Shi + 3 more
'Heming Jia' 'Gang Hu'] Within computer-aided geometric design (CAGD), Said-Ball curves are primarily adopted in domains such as 3D object skeleton modeling, vascular structure repair, and path planning, owing to their flexible geometric properties. Techniques for curve degree reduction seek to reduce computational and…
Adel Salimi, Saeid Rahmani, Ali Sharifi-Zarchi
Quantification of gene expression is a crucial task in biomedical studies. Although high-throughput methods enable rapid and simultaneous expression quantification of coding or non-coding regions, qPCR is still vastly used due to its high availability, sensitivity, specificity, reproducibility, low cost, and ease of…
Emmanuel Hartman, Yashil Sukurdeep, Eric Klassen, Nicolas Charon + 1 more
'Martin Bauer'] This paper introduces a set of numerical methods for Riemannian shape analysis of 3D surfaces within the setting of invariant (elastic) second-order Sobolev metrics. More specifically, we address the computation of geodesics and geodesic distances between parametrized or unparametrized immersed surfaces…
Maria Evangelia Vlachou, Elizabeth Thomas, Jean Blouin
In this paper, we address the problem of quantifying similarity between planar 2D shapes, which is relevant to studies of internal representations in cognitive, developmental, and neurological research. We designed a set of test shapes arranged along a visually defined perceptual similarity gradient and used them to…
Anoop Praturu, Tatyana Sharpee
Recent studies have increasingly demonstrated that hyperbolic geometry confers many advantages for analyzing hierarchical structure in complex systems. However, available embedding methods do not give a precise metric for determining the dimensionality of the data, and do not vary curvature. These parameters are…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
C. Zhu, C. T. Lee, P. Rangamani
Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to approximation-based methods (e.g., finite element method), the class of discrete mesh models…
Xiaomin Jiang, Yangfei Huang, Feng Zhang, Ding Ma + 1 more
The study of spatial geometric similarity plays a significant role in spatial data retrieval. Many researchers have examined spatial geometric similarity, which is useful for spatial analysis and data retrieval. However, the majority of them focused on objects of the same type. Methods to support the spatial geometric…