Tootfinder

An AI-native experimental laboratory for autonomous biomolecular engineering
Mingyu Wu, Zhaoguo Wang, Jiabin Wang, Zhiyuan Dong, Jingkai Yang, Qingting Li, Tianyu Huang, Lei Zhao, Mingqiang Li, Fei Wang, Chunhai Fan, Haibo Chen
https://arxiv.org/abs/2507.02379

An AI-native experimental laboratory for autonomous biomolecular engineering
Autonomous scientific research, capable of independently conducting complex experiments and serving non-specialists, represents a long-held aspiration. Achieving it requires a fundamental paradigm shift driven by artificial intelligence (AI). While autonomous experimental systems are emerging, they remain confined to areas featuring singular objectives and well-defined, simple experimental workflows, such as chemical synthesis and catalysis. We present an AI-native autonomous laboratory, target…

This https://arxiv.org/abs/2501.05088 has been replaced.
initial toot: https://mastoxiv.page/@arXi…

Effect of particle and substrate wettability on evaporation-driven assembly of colloidal monolayers
Assembled monolayers of colloidal particles are crucial for various applications, including opto-electronics, surface engineering, as well as light harvesting, and catalysis. A common approach for self-assembly is the drying of a colloidal suspension film on a solid substrate using technologies such as printing and coating. However, this approach often presents challenges such as low surface coverage, stacking faults, and the formation of multiple layers. We numerically investigate the influenc…

Deconstructing the Origins of Interfacial Catalysis: Why Electric Fields are Inseparable from Solvation
Solana Di Pino, Debarshi Banerjee, Marta Monti, Gonzalo Diaz Miron, Giuseppe Cassone, Ali Hassanali
https://arxiv.org/abs/2506.23988

Deconstructing the Origins of Interfacial Catalysis: Why Electric Fields are Inseparable from Solvation
In the last decade, there has been a surge of experiments showing that certain chemical reactions undergo an enormous boost when taken from bulk aqueous conditions to microdroplet environments. The microscopic basis of this phenomenon remains elusive and continues to be widely debated. One of the key driving forces invoked are the specific properties of the air-water interface including the presence of large electric fields and distinct solvation at the surface. Here, using a combination of cla…

In-liquid Plasma Catalysis for Nitrogen Reduction
P. Grosse, J. L. Gembus, F. Landwehr, A. R. Silva Olaya, D. Escalera-L\'opez, N. Bibinov, A. R. Gibson, S. Z. Oener, B. Roldan Cuenya
https://arxiv.org/abs/2506.21791

In-liquid Plasma Catalysis for Nitrogen Reduction
Ammonia, a crucial component in fertilizers and fuels, is currently produced by the energy-intensive Haber-Bosch process. However, due to the high upfront investments required for large-scale centralized production, alternative routes for small-scale applications are being sought. We integrate in-liquid plasma with electrocatalysis for ammonia generation via the nitrogen reduction reaction (NRR). Among materials tested, platinum emerged as the most stable and active catalyst - it evolves hydrog…

This https://arxiv.org/abs/2409.16704 has been replaced.
initial toot: https://mastoxiv.page/@a…

Challenges in the Theory and Atomistic Simulation of Metal Electrodeposition
Electrodeposition is a fundamental process in electrochemistry, and has applications in numerous industries, such as corrosion protection, decorative finishing, energy storage, catalysis, and electronics. While there is a long history of using electrodeposition, its application for controlled nanostructure growth is limited. The establishment of an atomic-scale understanding of the electrodeposition process and dynamics is crucial to enable the controlled fabrication of metal nanoparticles and …

Monolayer Two-dimensional Materials Database (ML2DDB) and Applications
Zhongwei Liu, Zhimin Zhang, Xuwei Liu, Mingjia Yao, Xin He, Yuanhui Sun, Xin Chen, Lijun Zhang
https://arxiv.org/abs/2507.00584

Monolayer Two-dimensional Materials Database (ML2DDB) and Applications
The discovery of two-dimensional (2D) materials with tailored properties is critical to meet the increasing demands of high-performance applications across flexible electronics, optoelectronics, catalysis, and energy storage. However, current 2D material databases are constrained by limited scale and compositional diversity. In this study, we introduce a scalable active learning workflow that integrates deep neural networks with density functional theory (DFT) calculations to efficiently explor…

Holographic flavour and neural networks
Veselin G. Filev
https://arxiv.org/abs/2506.20115 https://arxiv.org/pdf/2506.20115

Holographic flavour and neural networks
In holography, flavour probe branes are used to introduce fundamental matter to the AdS/CFT correspondence. At a technical level, the probes are described by extremizing the DBI action and solving the Lagrange-Euler equations of motion. I report on applications of artificial neural networks that allow direct minimization of the regularized DBI action (interpreted as a free energy) without the need to derive and solve the equations of motion. I consider, as examples, magnetic catalysis of chiral…

Phenylalanine modification in plasma-driven biocatalysis revealed by solvent accessibility and reactive dynamics in combination with protein mass spectrometry
Hanna-Friederike Poggemann, Sabrina Klopsch, Simon Homann, Tim Dirks, Sina Sch\"akermann, Julia E. Bandow, Timo Jacob, Christoph Jung
https://arxiv.org/abs/2506.20205…

Phenylalanine modification in plasma-driven biocatalysis revealed by solvent accessibility and reactive dynamics in combination with protein mass spectrometry
Biocatalysis is an emerging field that provides an environmentally friendly alternative to conventional catalysis, but still it faces some challenges. One of the major difficulties for biocatalysts that require reactive species like H2O2 as co-substrates lies in the concentration of these reactive species. On the one hand, they are used as reactants, but on the other hand, they inactivate the enzymes at high concentrations. When utilizing non-thermal plasma to deliver H2O2 for biocatalysis, it …

Structural Stability of Sulfur Depleted MoS2
Ygor M. Jaques, Cristiano F. Woellner, Lucas M. Sassi, Marcelo L. Pereira Jr, Luiz A. Ribeiro Jr, Pulickel M. Ajayan, Douglas S. Galv\~ao
https://arxiv.org/abs/2505.24644

Structural Stability of Sulfur Depleted MoS2
Transition metal dichalcogenides (TMDs), particularly monolayer MoS2, have received increased attention in materials science and have been exploited in diverse applications from photonics to catalysis. Defects in TMDs play a crucial role in modulating their properties, and understanding defect-induced dynamics is of great importance. This study investigates the dynamics of sulfur depletion in defective monolayer MoS2, which yields stable MoS monolayers. Various defect sizes, temperature regimes…

OmniESI: A unified framework for enzyme-substrate interaction prediction with progressive conditional deep learning
Zhiwei Nie, Hongyu Zhang, Hao Jiang, Yutian Liu, Xiansong Huang, Fan Xu, Jie Fu, Zhixiang Ren, Yonghong Tian, Wen-Bin Zhang, Jie Chen
https://arxiv.org/abs/2506.17963

OmniESI: A unified framework for enzyme-substrate interaction prediction with progressive conditional deep learning
Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior knowledge of enzyme catalysis to rationally modulate general protein-molecule features that are misaligned with catalytic patterns. To address this issue, we introduce a two-stage progressive framework, OmniESI, for enzyme-substrate interaction prediction thro…

Multi-Technique Characterization of Rhodium Gem-Dicarbonyls on TiO$_2$(110)
Moritz Eder, Faith J. Lewis, Johanna I. H\"utner, Panukorn Sombut, Maosheng Hao, David Rath, Jan Balajka, Margareta Wagner, Matthias Meier, Cesare Franchini, Ulrike Diebold, Michael Schmid, Florian Libisch, Ji\v{r}\'i Pavelec, Gareth S. Parkinson
https://

Multi-Technique Characterization of Rhodium Gem-Dicarbonyls on TiO$_2$(110)
Gem-dicarbonyls of transition metals supported on metal (oxide) surfaces are common intermediates in heterogeneous catalysis. While infrared (IR) spectroscopy is a standard tool for detecting these species on applied catalysts, the ill-defined crystallographic environment of species observed on powder catalysts renders data interpretation challenging. In this work, we apply a multi-technique surface science approach to investigate rhodium gem-dicarbonyls on a single-crystalline rutile TiO$_2$(1…

This https://arxiv.org/abs/2409.09421 has been replaced.
initial toot: https://mastoxiv.page/@arXi…

One-way catalysis in a solvable lattice model
Catalysts speed up chemical reactions with no energy input and without being transformed in the process, therefore leaving equilibrium constants unchanged. Some catalysts, however, are much more efficient at accelerating one direction of a reaction. Is it possible for catalysis to be strictly unidirectional, accelerating only one direction of a reaction? Can we observe directional catalysis by analyzing the microscopic trajectory of a single reactant undergoing conversions between a substrate a…

Understanding and Controlling V-Doping and S-Vacancy Behavior in Two-Dimensional Semiconductors- Toward Predictive Design
Shreya Mathela (Department of Chemistry, The Pennsylvania State University), Zhuohang Yu (Department of Materials Science and Engineering, The Pennsylvania State University), Zachary D. Ward (Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute), Nikalabh Dihingia (Department of Chemistry, The Pennsylvania State University), Alex Sr…

Understanding and Controlling V-Doping and S-Vacancy Behavior in Two-Dimensional Semiconductors- Toward Predictive Design
Doping in transition metal dichalcogenide (TMD) monolayers provides a powerful method to precisely tailor their electronic, optical, and catalytic properties for advanced technological applications, including optoelectronics, catalysis, and quantum technologies. However, doping efficiency and outcomes in these materials are strongly influenced by the complex interactions between introduced dopants and intrinsic defects, particularly sulfur vacancies. This coupling between dopants and defects ca…

Tracking and controlling monolayer water in gold nanogaps using extreme plasmonic spectroscopy
Elle W. Wyatt, Sarah May Sibug-Torres, Rakesh Arul, Marika Niihori, Tabitha Jones, James W. Beattie, Bart de Nijs, Jeremy J. Baumberg
https://arxiv.org/abs/2506.10199

Tracking and controlling monolayer water in gold nanogaps using extreme plasmonic spectroscopy
Nanogaps are ubiquitous across science, confining molecules and thus changing chemistries which influence many areas such as catalysis, corrosion, photochemistry, and sensing. However in ambient conditions, it is unclear how water solvates nanogaps and even if nominally dry, what water structure persists. Despite its low Raman cross-section, surface-enhanced Raman spectroscopy (SERS) enables study of water at coinage metal surfaces. Using multi-layer aggregates of close-packed gold nanoparticle…

Ultrafast interband transitions in nanoporous gold metamaterial
Tlek Tapani, Jonas M. Pettersson, Nils Henriksson, Erik Z\"all, Nils V. Hauff, Lakshmi Das, Gianluca Balestra, Massimo Cuscun\`a, Aitor De Andr\'es, Tommaso Giovannini, Denis Garoli, Nicol\`o Maccaferri
https://arxiv.org/abs/2506.08536

Ultrafast interband transitions in nanoporous gold metamaterial
Nanoporous metals have emerged as promising functional architectures due to their tunable optical and electronic properties, high surface areas, and versatile use in real-life applications such as sensing, catalysis, and biomedicine. While the optical and morphological properties of nanoporous metals have been extensively studied, their electronic properties at ultrafast timescales remain largely unexplored. Here, we study the transient response of a nanoporous gold metamaterial and compare it …

Electron conductive self-assembled hybrid low-molecular weight glycolipid-nanosilver gels
Korin Gasia Ozkaya (LCMCP-SMiLES), Othmane Darouich (LCMCP), Hynd Remita (ICP), Isabelle Lampre (ICP), Lionel Porcar (ILL), Alain Carvalho (ICS), M. Schmutz (ICS), Sandra Casale (LRS), Christel Laberty-Robert (LCMCP), Niki Baccile (LCMCP-SMiLES)
https://

Electron conductive self-assembled hybrid low-molecular weight glycolipid-nanosilver gels
Low-molecular weight (LMW) hydrogels are gaining interest over macromolecular gels due to their reversible, dynamic and stimuli-responsive nature. They are potentially interesting functional materials for advanced applications such as catalysis, nanoelectronics or regenerative medicine. One common strategy to enhance the functional properties is to incorporate inorganic nanostructures. However, simultaneous control of the gel mechanics, shape and size of the nanostructures and functional proper…

Automatic generation of density fitting auxiliary basis sets for all electron Dirac-Kohn-Sham calculations
Nicolo' Antonini, Enrico Ronca, Loriano Storchi, Leonardo Belpassi
https://arxiv.org/abs/2506.15631

Automatic generation of density fitting auxiliary basis sets for all electron Dirac-Kohn-Sham calculations
In this study, we present a general workflow that enables the automatic generation of auxiliary density basis sets for all elements of the periodic table (from H to Og) to facilitate the general applicability of relativistic Dirac-Kohn-Sham calculations. It is an important tool for the accurate description of relativistic effects, including spin-orbit coupling, in molecules containing heavy elements. The latter are very important in various fields ranging from catalysis to quantum technologies.…

Single Cu Atom Sites on Co3O4 Activate Interfacial Oxygen for Enhanced Reactivity and Selective Gas Sensing at Low Temperature
Hamin Shin, Matteo D'Andria, Jaehyun Ko, Dong-Ha Kim, Frank Krumeich, Andreas T. Guentner
https://arxiv.org/abs/2506.09761

Single Cu Atom Sites on Co3O4 Activate Interfacial Oxygen for Enhanced Reactivity and Selective Gas Sensing at Low Temperature
Controlling the redox landscape of transition metal oxides is central to advancing their reactivity for heterogeneous catalysis or high-performance gas sensing. Here we report single Cu atom sites (1.42 wt%) anchored on Co3O4 nanoparticles (Cu1-Co3O4) that dramatically enhance reactivity and molecular sensing properties of the support at low temperature. The Cu1 are identified by X-ray adsorption near edge structure and feature strong metal-support interaction between Cu2+ and Co3O4, as reveale…