25 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…
Max Kochurov, Rasul Karimov, Sergei Kozlukov
Geoopt is a research-oriented modular opensource package for Riemannian Optimization in PyTorch. The core of Geoopt is a standard Manifold interface that allows for the generic implementation of optimization algorithms (Bcigneul & Ganea, 2018). Geoopt supports basic Riemannian SGD as well as adaptive optimization…
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…
Dario Wirtz, Claus Horn
The vastness of the space of possible protein variations is often regarded an insurmountable challenge for effective optimization. Traditional approaches focus primarily on substitutions near the binding pocket but are frequently hindered by epistatic effects and non-convex optimization landscapes. Current AI-aided…
Praveen S. Vulimiri, Hao Deng, Florian Dugast, Xiaoli Zhang + 2 more
'Albert C. To' 'Tuhin Mukherjee'] This research proposes a novel topology optimization method using neural style transfer to simultaneously optimize both structural performance for a given loading condition and geometric similarity for a reference design. For the neural style transfer, the convolutional layers of a…
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…
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…
Kosala Bandara, Thomas Rüberg, Fehmi Cirak
We develop a new optimisation technique that combines multiresolution subdivision surfaces for boundary description with immersed finite elements for the discretisation of the primal and adjoint problems of optimisation. Similar to wavelets multiresolution surfaces represent the domain boundary using a coarse control…
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…
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…
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…
Khusrav Yorov, Bolun Wang, Mikhail Skopenkov, Helmut Pottmann + 1 more
We introduce the following auxiliary variables and constraints. Discrete A-nets. Consider an A-net , so that , −1,, ,−1, +1,, and ,+ 1 are coplanar for each 0 < , < . This condition is encoded by the quadratic constraints (3-16)$\langle \mathbf{n}_{ij}, f_{ij} - f_{i\pm 1,j} \rangle = 0, \quad \langle \mathbf{n}_{ij}…
Ahmed A. G. AbdAllah, Zhengtao Wang
Geodetic networks are important for most engineering projects. Generally, a geodetic network is designed according to precision, reliability, and cost criteria. This paper provides a new criterion considering the distances between the Net Points (NPs) and the Project Border (PB) in terms of Neighboring (N).…
Daniel Dörfler, Andreas Löhne
In 2011, Luc [8] introduced parametric duality for multiple objective linear programs. He showed that geometric duality, introduced in 2008 by Heyde and L¨ohne [3], is a consequence of parametric duality. We show the converse statement: parametric duality can be derived from geometric duality. We point out that an easy…
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…
Xiaoqiu Ma
The traditional methods deal with large sample data sets of architectural engineering drawings and they have high time complexity and space complexity as well. Their searching time is long and sometimes the results are unsatisfactory. Therefore, this paper proposes an optimization method designed for architectural…
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…
Jose Sergio Hleap, Christian Blouin
A phenotype is defined as an organism’s physical traits. In the macroscopic world, an animal’s shape is a phenotype. Geometric morphometrics (GM) can be used to analyze its shape. Let’s pose protein structures as microscopic three dimensional shapes, and apply principles of GM to the analysis of macromolecules. In this…
Benqi Zhang, Guofan Jin, Jun Zhu
Design of an optical system, whether classic or novel, in the past or the present, requires significant effort from the designer. In addition to design methods and theories, the designer’s skills and experience in optical system design are particularly important, which may require years of practice to learn. The…
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…
Ali Fozooni, Osman Kamari, Mostafa Pourtalebiyan, Masoud Gorgich + 2 more
'Mohammad Khalilzadeh' 'Amin Valizadeh'] In this study, we evaluate several nongradient (evolutionary) search strategies for minimizing mathematical function expressions. We developed and tested the genetic algorithms, particle swarm optimization, and differential evolution in order to assess their general efficacy in…
Fabian Fröhlich, Peter K. Sorger
Ordinary differential equation (ODE) models are widely used to describe biochemical processes, since they effectively represent mass action kinetics. Optimization-based calibration of ODE models on experimental data can be challenging, even for low-dimensional problems. However, reliable model calibration is a…