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Deep generative models provide a promising approach to de novo 3D peptide design. Most of them jointly model the distributions of peptide's position, orientation, and conformation, attempting to simultaneously converge to the target pocket.…

Quantitative Methods · Quantitative Biology 2025-11-04 Dengdeng Huang , Shikui Tu

A sensitive porosity adjoint method (SPAM) for optimizing the topology of fluid machines has been proposed. A sensitivity function with respect to the porosity has been developed. In the first step of the optimization process, porous media…

Fluid Dynamics · Physics 2015-12-29 B. Philippi , Y. Jin

This paper addresses the problem of designing a sparse {\em fault-tolerant} BFS tree, or {\em FT-BFS tree} for short, namely, a sparse subgraph $T$ of the given network $G$ such that subsequent to the failure of a single edge or vertex, the…

Data Structures and Algorithms · Computer Science 2013-02-22 Merav Parter , David Peleg

Multiscale topology optimization is crucial for designing porous infill structures with high stiffness-to-weight ratios and excellent energy absorption. Although gradient-based methods provide a rigorous framework, they are computationally…

Optimization and Control · Mathematics 2025-10-13 Shuzhi Xu , Yifan Guo , Hiroki Kawabe , Kentaro Yaji

This paper presents a homogenized topology optimization (TO) method for spatially optimizing cell-size distribution of triply-periodic minimal surface (TPMS) structures, with high accuracy in the optimized structural response after…

Optimization and Control · Mathematics 2026-05-08 Hiroki Kawabe , Kaito Ohtani , Yusibo Yang , Musaddiq Al Ali , Kentaro Yaji

In the current industry, the development of optimized mechanical components able to satisfy the customer requirements evolves quickly. Therefore, companies are asked for efficient solutions to improve their products in terms of stiffness…

Computational Engineering, Finance, and Science · Computer Science 2023-07-31 Rafael Merli , Antolín Martínez-Martínez , Juan José Ródenas , Marc Bosch-Galera , Enrique Nadal

Tensor B-spline methods are a high-performance alternative to solve partial differential equations (PDEs). This paper gives an overview on the principles of Tensor B-spline methodology, shows their use and analyzes their performance in…

Numerical Analysis · Computer Science 2019-04-08 Dmytro Shulga , Oleksii Morozov , Volker Roth , Felix Friedrich , Patrick Hunziker

This work presents a novel algorithm for generating porous structures as an alternative to the PoreSpy program suite. Unlike PoreSpy, which often produces structures whose porosity deviates from the target value, our proposed algorithm…

Soft Condensed Matter · Physics 2026-01-06 Shota Arai , Takashi Yoshidome

3D porous scaffolds based on agarose and nanocrystalline apatite, two structural components that act as a temporary mineralized extracellular matrix, were prepared by the GELPOR3D method. This shaping technology allows the introduction of…

Tissues and Organs · Quantitative Biology 2021-03-18 Juan L. Paris , Nuria Lafuente-Gomez , M. Victoria Cabanas , Jesus Roman , Juan Pena , Maria Vallet-Regi

It has recently been shown that triply periodic two-phase bicontinuous composites with interfaces that are the Schwartz primitive (P) and diamond (D) minimal surfaces are not only geometrically extremal but extremal for simultaneous…

Soft Condensed Matter · Physics 2007-05-23 Y. Jung , S. Torquato

Stochastic porous structures are ubiquitous in natural phenomena and have gained considerable traction across diverse domains owing to their exceptional physical properties. The recent surge in interest in microstructures can be attributed…

Graphics · Computer Science 2023-05-17 Zhongren Wang , Lihao Tian , Xiaokang Liu , Andrei Sharf , Lin Lu

Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current…

Biomolecules · Quantitative Biology 2023-03-21 Brian L. Trippe , Jason Yim , Doug Tischer , David Baker , Tamara Broderick , Regina Barzilay , Tommi Jaakkola

Navigating the vast chemical space of druggable compounds is a formidable challenge in drug discovery, where generative models are increasingly employed to identify viable candidates. Conditional 3D structure-based drug design (3D-SBDD)…

Machine Learning · Computer Science 2025-02-04 Kiwoong Yoo , Owen Oertell , Junhyun Lee , Sanghoon Lee , Jaewoo Kang

Additively manufactured hollow strut bioceramic scaffolds present a promising strategy towards enhanced performance in patient-tailored bone tissue engineering. The channels in such scaffolds offer pathways for nutrient and cell transport…

Materials Science · Physics 2023-03-21 Shumin Pang , Dongwei Wu , Aleksander Gurlo , Jens Kurreck , Dorian A H Hanaor

The development of porous polymeric membranes remains a labor-intensive process, often requiring extensive trial and error to identify optimal fabrication parameters. In this study, we present a fully automated platform for membrane…

Porous media are ubiquitous in energy storage and conversion, catalysis, biomechanics, hydrogeology, as well as many other fields. These materials possess high surface-to-volume ratios and their complex channels can restrict and guide the…

High-quality quadrilateral mesh generation is a fundamental challenge in computer graphics. Traditional optimization-based methods are often constrained by the topological quality of input meshes and suffer from severe efficiency…

Graphics · Computer Science 2026-03-12 Yuguang Chen , Xinhai Liu , Xiangyu Zhu , Yiling Zhu , Zhuo Chen , Dongyu Zhang , Chunchao Guo

Tomography is a widely used tool for analyzing microstructures in three dimensions (3D). The analysis, however, faces difficulty because the constituent materials produce similar grey-scale values. Sometimes, this prompts the image…

Materials Science · Physics 2021-09-28 Anand V. Patel , Tao Hou , Juan D. Beltran Rodriguez , Tamal K. Dey , Dunbar P. Birnie

Fault tolerant distance preservers (spanners) are sparse subgraphs that preserve (approximate) distances between given pairs of vertices under edge or vertex failures. So-far, these structures have been studied mainly from a centralized…

Distributed, Parallel, and Cluster Computing · Computer Science 2020-10-06 Merav Parter

Boundary representation (B-rep) of geometric models is a fundamental format in Computer-Aided Design (CAD). However, automatically generating valid and high-quality B-rep models remains challenging due to the complex interdependence between…

Computer Vision and Pattern Recognition · Computer Science 2025-03-18 Jing Li , Yihang Fu , Falai Chen