Article
Chemistry, Physical
Tian-Tian Xiao, Ru-Yi Li, Gui-Chang Wang
Summary: The role of stabilized Cu+ active sites in propylene epoxidation on Ti2CuO6/Cu(1 1 1) and Cu2O (1 1 1) surfaces was investigated using systematic kinetic Monte Carlo (kMC) studies. The simulation showed that Ti2CuO6/Cu(1 1 1) exhibited better selectivity and activity than Cu2O(1 1 1) due to its active open-shell electronic structure. Understanding the factors influencing the catalytic performance can aid in the design of efficient propylene epoxidation catalysts.
APPLIED SURFACE SCIENCE
(2022)
Article
Chemistry, Physical
Martin Deimel, Hector Prats, Michael Seibt, Karsten Reuter, Mie Andersen
Summary: This study focuses on modeling the CO hydrogenation reaction on Rh catalysts using accelerated first-principles kinetic Monte Carlo simulations, explicitly accounting for adsorbate-adsorbate interactions. The results show that the Rh(111) facet is selective toward methane, while the Rh(211) facet exhibits selectivity toward methane and acetaldehyde, resolving discrepancies with earlier studies.
Article
Chemistry, Multidisciplinary
Alexandre S. Avaro, Juan G. Santiago
Summary: This article presents a quantification of the uncertainty in the experimental determination of kinetic rate parameters for enzymatic reactions. The authors examine several sources of uncertainty and bias and compute typical uncertainties of kcat, KM, and catalytic efficiency. The extraction of these parameters for CRISPR-Cas systems is analyzed as a salient example. Reports of enzymatic kinetic rates for CRISPR diagnostics have been highly unreliable and inconsistent.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Materials Science, Multidisciplinary
Feifei Yu, Jianqiao Yu, Yunping Jia, Huahai Shen, Xia Xiang, Xiaotao Zu, Shuanglin Hu
Summary: The migration paths, barriers, and prefactors of tritium and helium in titanium tritide are calculated by density functional theory calculations, and further applied in kinetic Monte Carlo simulations to determine the overall diffusion rates. The diffusion coefficients of helium with temperature in different titanium tritides are shown as Arrhenius plots. The results indicate that there are two diffusional regimes, migration more via tetrahedral vacancies or octahedral interstitials, depending on temperature and composition. Tritium concentration, temperature, and axial strain can effectively tune the diffusion mechanism and rate of helium atom in titanium tritides.
MATERIALS TODAY COMMUNICATIONS
(2023)
Article
Physics, Multidisciplinary
Timothy Foldes, Antony Lesage, Maria Barbi
Summary: This study reexamines the coil-globule transition of a polymer from a spectral perspective, introducing a new possibility and reintroducing overlooked mature spectral methods. This method not only allows for the determination of the polymer state without information about polymer length or interaction strength, but also proposes an experimental implementation.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Tyler Campbell, Nagendra Dhakal, Marisol Alcantara Ortigoza, Sergey Stolbov
Summary: CO poisoning inhibits the hydrogen oxidation reaction on Pt-based hydrogen fuel cell anodes. Catalysts that are more active in CO removal than Pt must bind OH radicals more strongly and CO more weakly. Pd on Mo(110) and W(110) substrates meet these requirements and are proposed as highly active and CO tolerant HOR catalysts.
Article
Chemistry, Multidisciplinary
Richard S. Graham, Richard J. Wheatley
Summary: Accurate potential energy surfaces (PES) are required for predicting thermophysical properties from molecular principles. This study presents a widely-applicable method that produces first-principles PES using Gaussian Processes (GP) as a machine learning technique. The method accurately interpolates three-body non-additive interaction data and does not require modification for different molecules. It produces highly accurate interpolation from fewer training points and enables more accurate ab initio calculations. The method is exemplified by computing the PES for CO2-Ar mixtures, which allows for accurate first-principles predictions of various thermophysical properties.
CHEMICAL COMMUNICATIONS
(2022)
Article
Geochemistry & Geophysics
Wenting Wang, Mengchang He, Wei Ouyang, Chunye Lin, Xitao Liu
Summary: Numerous studies have shown that atmospheric surface oxidation significantly affects the surface characteristics and species of pyrite, but the influence on its reaction activity remains controversial. Experimental and simulation studies suggest that atmospheric surface oxidation can impact the production of hydroxyl radicals and hydrogen peroxide by pyrite, altering its reactivity.
Article
Chemistry, Physical
David Mahlberg, Sung Sakong, Axel Gross
Summary: This study investigates the meta-stability of surface alloy systems through kinetic Monte Carlo simulations based on density functional theory calculation. The analysis reveals the factors underlying the stability and structure of bimetallic surface alloys, offering new insights for tuning catalytic activity.
Article
Chemistry, Physical
Ryan B. Jadrich, Christopher Ticknor, Jeffery A. Leiding
Summary: This article utilizes a combination of large scale computing, advanced simulation techniques, and smart data science strategies to analyze the performance of PETN. It reveals important limitations of DFT for EOS prediction and demonstrates a modeling strategy for mapping chemical composition. The study suggests additional molecular species to consider in thermochemical modeling.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Physics, Applied
Hongli Gu, Yu Yao, Qingfang Li, X. G. Wan, Jian Zhou
Summary: The study found that ThMnAsN and ThMnPN are antiferromagnetic semiconductors with C-type antiferromagnetism, with bandgaps of approximately 0.47eV and 0.61eV, and Monte Carlo simulated Néel temperatures of 57K and 55K, respectively.
MODERN PHYSICS LETTERS B
(2021)
Article
Computer Science, Interdisciplinary Applications
Bert Mortier, Pieterjan Robbe, Martine Baelmans, Giovanni Samaey
Summary: We have developed a novel multilevel asymptotic-preserving Monte Carlo method, called Multilevel Kinetic-Diffusion Monte Carlo (ML-KDMC), for simulating the kinetic Boltzmann transport equation. By incorporating this method within a Multilevel Monte Carlo (MLMC) framework and utilizing a hierarchy of larger time step sizes, the simulation cost is further reduced. The ML-KDMC method outperforms the single-level KDMC method by several orders of magnitude, demonstrating its efficiency.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Chemistry, Physical
Ya-Qiong Su, Yan-Yang Qin, Tiantian Wu, De-Yin Wu
Summary: Single-atom catalysis is a hot topic in heterogeneous catalysis, but determining the stability and activity of single atoms on oxide supports compared to clusters and nanoparticles remains challenging. It was found that single Au atoms at step-edges serve as active sites for low-temperature CO oxidation, and the interface between Au nanoparticles and CeO2 can directly catalyze CO oxidation through the Mars-van Krevelen mechanism.
JOURNAL OF CATALYSIS
(2022)
Article
Chemistry, Physical
Yifei Chen, Yanan Zhu, Huaiqiang Dou, Hao Gong
Summary: In this study, the catalytic performance of different Co-N-C models for propylene hydroformylation was investigated. The results showed that the coordination number and mode of N atoms can regulate the electronic density of Co sites, which in turn affects the catalytic activity. Strong interactions between neighboring Co atoms also impact the catalytic activity and lower the reaction energy barrier. Furthermore, the dominant path of propylene hydroformylation varies among different Co-N-C models.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yifei Chen, Yanan Zhu, Huaiqiang Dou, Hao Gong
Summary: In this study, different Co-N-C models were constructed to investigate the catalytic performance of propylene hydroformylation. The results showed that the electronic density of Co sites and the interaction between Co atoms play a crucial role in catalytic activity.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Johannes T. Margraf, Hyunwook Jung, Christoph Scheurer, Karsten Reuter
Summary: Chemical reaction networks are crucial for understanding heterogeneous catalytic processes. However, inferring networks from experiments alone is challenging due to the lack of microscopic information. Computational approaches provide insights but come with uncertainties. This Perspective highlights the applications of machine learning in catalytic reaction networks, aiding in both experimental inference and computational exploration.
Review
Biotechnology & Applied Microbiology
Yadong Chen, Tianxing Gong, Nan Jiang, Aoxiang Zhao, Tongyu Wang, Xiangdong Wang, Wenfeng Han
Summary: In clinical practice, ACL rupture is commonly repaired by the single-beam reconstruction method. Surgeons make diagnosis based on medical images before surgery. However, the biomechanical effects on the biological nature of femoral tunnel position are not well understood. This study used motion capture and medical image reconstruction to analyze the effects of different femoral tunnel positions on ACL biomechanics. The results showed significant differences in the direct mechanical effects of the ACL at different femoral tunnel locations.
BIOTECHNOLOGY AND GENETIC ENGINEERING REVIEWS
(2023)
Review
Environmental Sciences
Tongyu Wang, Naoko Kaida, Kosuke Kaida
Summary: The review critically summarizes the findings and potential areas for future research on the effects of outdoor artificial light at night (ALAN) on human health and behaviors. The lack of studies on the effects of outdoor ALAN on human behaviors and health, including social interaction, is identified as a crucial gap in scientific research. The review highlights the importance of investigating the complex relationships between outdoor ALAN, health, and behaviors with sleep as a key factor.
ENVIRONMENTAL POLLUTION
(2023)
Article
Chemistry, Physical
Simiam Ghan, Elias Diesen, Christian Kunkel, Karsten Reuter, Harald Oberhofer
Summary: We investigate the electronic coupling between an adsorbate and a metal surface by directly calculating tunneling matrix elements H-ad based on first principles. Using a projection-operator diabatization approach, we project the Kohn-Sham Hamiltonian onto a diabatic basis. By integrating the couplings over the Brillouin zone, we are able to calculate a size-convergent Newns-Anderson chemisorption function, which measures the broadening of an adsorbate frontier state upon adsorption. This function reveals not only the lifetime of the electron state, but also provides rich information on orbital phase interactions on the surface.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
R. Dupuy, J. Filser, C. Richter, T. Buttersack, F. Trinter, S. Gholami, R. Seidel, C. Nicolas, J. Bozek, D. Egger, H. Oberhofer, S. Thuermer, U. Hergenhahn, K. Reuter, B. Winter, H. Bluhm
Summary: The determination of depth profiles across interfaces is crucial in various scientific and technological fields. While photoemission spectroscopy is a suitable method for this purpose, investigating liquid-vapor interfaces has been hindered by a lack of understanding of electron-scattering processes in liquids. However, recent studies have shown that core-level photoelectron angular distributions can provide information on the depth distribution of species across the interface. This study further explores this concept and demonstrates that the experimental anisotropy parameter scales linearly with the average distance of atoms along the surface normal, achieving excellent depth resolution.
PHYSICAL REVIEW LETTERS
(2023)
Article
Psychology, Experimental
Yuqing Zhao, Ting Zeng, Tongyu Wang, Fang Fang, Yi Pan, Jianrong Jia
Summary: This study found that statistical encoding compresses redundant information from multiple items into a single summary metric. The researchers examined the involvement of the subcortex in processing summary statistics and found that invisible circles were automatically included in the statistical representation, but only when presented to the same eye as visible circles.
Article
Chemistry, Physical
Martin Vondrak, Karsten Reuter, Johannes T. T. Margraf
Summary: This paper presents the q-pac Python package, which implements several algorithmic and methodological advances to the kQEq method and provides an extendable framework for the development of ML charge equilibration models.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
King Chun Lai, Sebastian Matera, Christoph Scheurer, Karsten Reuter
Summary: The nature of an atom in a bonded structure depends on its local atomic environment. Identifying groups of atoms with equivalent environments is a frequent task in atomic-scale modeling and simulation, and we present a machine-learning framework to automate this task.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Sina Stocker, Hyunwook Jung, Gabor Csanyi, C. Franklin Goldsmith, Karsten Reuter, Johannes T. Margraf
Summary: This study demonstrates that machine-learning methods can be used to predict the rate constants of elementary reaction steps in catalytic processes. The results show that thermal effects have a significant impact on the free energy barriers, which can be different from the predictions based on the harmonic transition state theory approximation. This finding calls into question the previously reported mechanisms established by microkinetic models.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Ke Chen, Christian Kunkel, Bingqing Cheng, Karsten Reuter, Johannes T. Margraf
Summary: Machine learning is widely used in predicting chemical properties, especially energies and forces in molecules and materials. However, some electronic properties do not scale linearly with system size, leading to large errors when using size-extensive models. This study explores different strategies to learn intensive and localized properties, focusing on HOMO energies in organic molecules.
Article
Mathematical & Computational Biology
Tongyu Wang, Yadong Chen
Summary: This paper studies the vibration suppression control of a flexible manipulator system modeled by partial differential equation (PDE) with state constraints. The problem of joint angle constraint and boundary vibration deflection is solved using the Barrier Lyapunov function (BLF) based on the backstepping recursive design framework. Furthermore, an event-triggered mechanism is proposed based on the relative threshold strategy to save communication workload and improve system efficiency. Simulation results prove the effectiveness of the proposed control strategy in achieving good damping effect on vibration and elevated system performance.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2023)
Article
Chemistry, Physical
Nicolas Bergmann, Nicolas G. Hoermann, Karsten Reuter
Summary: This study investigates the approximations used in computationally efficient calculations for the electrosorption of Br ions on an Ag(100) model electrode. The combination of an implicit solvation model, a perturbative second order account of capacitive double layer effects, and a constant-potential grand-canonical Monte Carlo sampling of the adsorbate layer accurately describes the experimental results. However, error cancellation at lower levels of theory may also lead to good descriptions, despite inadequate treatment of key underlying physics, such as the disorder-order transition of the Br adlayer.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Tobias Weiss, Aleksandr Baklanov, Georg S. Michelitsch, Karsten Reuter, Martin Schwarz, Manuela Garnica, Willi Auwarter
Summary: This study presents the first real space characterization of borazine molecules and their self-assemblies on solid supports. The adsorption of borazine on Ag(111) surface is weak and non-dissociative, with the ring aligned parallel to the surface plane. Borazine molecules prefer hollow adsorption sites, leading to the assembly of both porous and dense-packed structures. STM-based manipulation is demonstrated to modify the borazine adsorption configuration.
ADVANCED MATERIALS INTERFACES
(2023)
Article
Chemistry, Physical
Simeon D. Beinlich, Georg Kastlunger, Karsten Reuter, Nicolas G. Hoermann
Summary: Understanding the electrochemical activation energies under applied potential conditions is crucial for comprehending catalytic activity at electrochemical interfaces. This study introduces a novel approach to compute electrochemical barriers, which achieves accuracy comparable to constant potential grand canonical methods without the need for a potentiostat. By Legendre transforming a set of constant charge canonical reaction paths, this method offers the possibility to calculate electrochemical barriers with lower computational cost and complexity. Additionally, the analytical inclusion of geometric response emphasizes the significance of incorporating both electronic and geometric degrees of freedom when evaluating electrochemical barriers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Doudou Zhang, Haobo Li, Haijiao Lu, Zongyou Yin, Zelio Fusco, Asim Riaz, Karsten Reuter, Kylie Catchpole, Siva Karuturi
Summary: This study fabricates a highly active ternary metal (hydro)oxide OER catalyst and uses machine learning methods to analyze its activity mechanism, demonstrating that adding Fe and Co can reduce overpotential and enhance activity. This study provides new insights into the activity mechanism of ternary metal (hydro)oxide amorphous catalysts.
ENERGY & ENVIRONMENTAL SCIENCE
(2023)