Tootfinder

fullerene_structures: Fullerene molecular structures
Fifteen networks of carbon atoms and the atomic bonds that connect them within molecules of fullerenes, from 60 atoms up to 6000 atoms. A bond is defined to exist whenever the distance of two atoms is less than 1.5 angstrom.
This network has 2940 nodes and 4410 edges.
Tags: Biological, Chemical, Unweighted, Spatial

Molecular Mobility of Extraterrestrial Ices: Surface Diffusion in Astrochemistry and Planetary Science
N. F. W. Ligterink, C. Walsh, H. M. Cuppen, M. N. Drozdovskaya, A. Ahmad, D. M. Benoit, J. T. Carder, A. Das, J. K. D\'iaz-Berr\'ios, F. Dulieu, J. Heyl, A. P. Jardine, T. Lamberts, N. M. Mikkelsen, M. Tsuge
https://arxiv.org/abs/…

Molecular Mobility of Extraterrestrial Ices: Surface Diffusion in Astrochemistry and Planetary Science
Molecules are ubiquitous in space. They are necessary component in the creation of habitable planetary systems and can provide the basic building blocks of life. Solid-state processes are pivotal in the formation of molecules in space and surface diffusion in particular is a key driver of chemistry in extraterrestrial environments, such as the massive clouds in which stars and planets are formed and the icy objects within our Solar System. However, for many atoms and molecules quantitative theo…

🐍 Where did RNA come from? Origin-of-life scientists help to answer the question
#rna

Where did RNA come from? Origin-of-life scientists help to answer the question
In living organisms today, complex molecules like RNA and DNA are constructed with the help of enzymes. So how did these molecules form before life (and enzymes) existed? Why did some molecules end up as the building blocks of life and not others? A new study by Scripps Research scientists helps answer these longstanding questions.

Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integration
Seungyeon Choi, Hwanhee Kim, Chihyun Park, Dahyeon Lee, Seungyong Lee, Yoonju Kim, Hyoungjoon Park, Sein Kwon, Youngwan Jo, Sanghyun Park
https://arxiv.org/abs/2508.21468

Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integration
Recent advances in Structure-based Drug Design (SBDD) have leveraged generative models for 3D molecular generation, predominantly evaluating model performance by binding affinity to target proteins. However, practical drug discovery necessitates high binding affinity along with synthetic feasibility and selectivity, critical properties that were largely neglected in previous evaluations. To address this gap, we identify fundamental limitations of conventional diffusion-based generative models i…

MC-GNNAS-Dock: Multi-criteria GNN-based Algorithm Selection for Molecular Docking
Siyuan Cao, Hongxuan Wu, Jiabao Brad Wang, Yiliang Yuan, Mustafa Misir
https://arxiv.org/abs/2509.26377

MC-GNNAS-Dock: Multi-criteria GNN-based Algorithm Selection for Molecular Docking
Molecular docking is a core tool in drug discovery for predicting ligand-target interactions. Despite the availability of diverse search-based and machine learning approaches, no single docking algorithm consistently dominates, as performance varies by context. To overcome this challenge, algorithm selection frameworks such as GNNAS-Dock, built on graph neural networks, have been proposed. This study introduces an enhanced system, MC-GNNAS-Dock, with three key advances. First, a multi-criteria …

Edge-On Disk Study (EODS) III: Molecular Stratification in the Flying Saucer Disk
A. Dutrey, O. Denis-Alpizar, S. Guilloteau, C. Foucher, S. Gavino, D. Semenov, V. Pietu, E. Chapillon, L. Testi, E. Dartois, E. DiFolco, K. Furuya, U. Gorti, N. Grosso, Th. Henning, J. M. Hur\'e, \'A. K\'osp\'al, F. Le Petit, L. Majumdar, R. Meshaka, H. Nomura, N. T. Phuong, M. Ruaud, Y. W. Tang, S. Wolf

Edge-On Disk Study (EODS) III: Molecular Stratification in the Flying Saucer Disk
Context: Investigating the vertical distribution of molecular content in protoplanetary disks remains difficult in most disks mildly inclined along the line of sight. In contrast, edge-on disks provide a direct (tomographic) view of the 2D molecular brightness. Aims: We study the radial and vertical molecular distribution as well as the gas temperature and density by observing the Keplerian edge-on disk surrounding the Flying Saucer, a Class II object located in Ophiuchus. Methods: We use new a…

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials
Cong Fu, Yuchao Lin, Zachary Krueger, Haiyang Yu, Maho Nakata, Jianwen Xie, Emine Kucukbenli, Xiaofeng Qian, Shuiwang Ji
https://arxiv.org/abs/2507.00407

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials
Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine learning interatomic potential (MLIP) models. To this end, we first curate a large-scale molecular relaxation dataset comprising 3.5 million molecules and 300 million snapshots. Then MLIP foundation models are trained with supervised learning to predict energy and …

Poincar\'e covariant quantum molecular dynamics: a covariant description of a system of interacting wave packets
Yasushi Nara, Asanosuke Jinno, Koichi Murase
https://arxiv.org/abs/2507.23294

Poincaré covariant quantum molecular dynamics: a covariant description of a system of interacting wave packets
We present a new formulation for the mean-field propagation part of the relativistic quantum molecular dynamics, simulating an $N$-body system of interacting Gaussian wave packets via Lorentz scalar and vector potentials. Covariant equations of motion are derived based on the principle of least action. These covariant equations of motion can be solved with a computational cost comparable to that of conventional noncovariant quantum molecular dynamics. Furthermore, the new equations of motion ac…

Electronic-nuclear entanglement in Born-Oppenheimer wave functions and beyond
Juan F. P. Mosquera, Jose Luis Sanz-Vicario
https://arxiv.org/abs/2508.21578 https://

Electronic-nuclear entanglement in Born-Oppenheimer wave functions and beyond
We analyze the entanglement between electronic and nuclear motions in molecular wave functions, by using different widely used ansatzes in molecular Hamiltonian models (H$^+_2$ in 1D and the Shin-Metiu model); namely, i) Born-Oppenheimer separation in both adiabatic and ii) diabatic pictures and beyond it, iii) using a Born-Huang expansion, which involves non-adiabatic couplings in the solution. Any molecule can be considered a bipartite system in terms of electronic and nuclear halfspaces. Acc…

🫀 Revolution in medicine: A molecule produced by gut bacteria causes atherosclerosis, responsible for millions of deaths
https://english.elpais.com/health/2025-07-17/revolut…

Revolution in medicine: A molecule produced by gut bacteria causes atherosclerosis, responsible for millions of deaths
The discovery, made thanks to an experiment involving hundreds of bank employees in Spain, opens the door to new treatments beyond reducing cholesterol