Related papers: ShEPhERD: Diffusing shape, electrostatics, and pha…
Obtaining high-quality particle distributions for stable and accurate particle-based simulations poses significant challenges, especially for complex geometries. We introduce a preprocessing technique for 2D and 3D geometries, optimized for…
Materials performance is deeply linked to their microstructures, which govern key properties such as strength, durability, and fatigue resistance. EBSD is a major technique for characterizing these microstructures, but acquiring large and…
We present a diffusion-based, generative model for conformer generation. Our model is focused on the reproduction of bonded structure and is constructed from the associated terms traditionally found in classical force fields to ensure a…
The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…
Diffusion models show promise for 3D molecular generation, but face a fundamental trade-off between sampling efficiency and conformational accuracy. While flow-based models are fast, they often produce geometrically inaccurate structures,…
Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models…
Existing works based on molecular knowledge neglect the 3D geometric structure of molecules and fail to learn the high-dimensional information of medications, leading to structural confusion. Additionally, it does not extract key…
The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to…
We present a highly accurate numerical method based on a boundary integral formulation and the leaky dielectric model to study the dynamics of surfactant-covered drops in the presence of an applied electric field. The method can simulate…
Recent advances in microphysiological systems have underscored the need for novel sensing and monitoring systems specifically designed for three-dimensional (3D) cell culture. In this article, an original architecture of a cell-culture…
Advanced simulations of the mechanical behavior of soft tissues frequently rely on structure-based constitutive models, including smeared descriptions of collagen fibers. Among them, the so-called Discrete Fiber Dispersion (DFD) model is…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
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…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
Recent methods for molecular generation face a trade-off: they either enforce strict equivariance with costly architectures or relax it to gain scalability and flexibility. We propose a frame-based diffusion paradigm that achieves…
In this article we propose and numerically implement a mathematical model for the simulation of three-dimensional semiconductor devices characterized by an heterogeneous material structure. The model consists of a system of nonlinearly…
Protein binder design is central to therapeutics, diagnostics, and synthetic biology, yet practical deployment remains challenging due to fragmented workflows, high computational costs, and complex tool integration. We present…
In the past decade, Artificial Intelligence driven drug design and discovery has been a hot research topic, where an important branch is molecule generation by generative models, from GAN-based models and VAE-based models to the latest…