Article
Physics, Fluids & Plasmas
Othmene Benazieb, Claire Loison, Fabrice Thalmann
Summary: Investigated the friction properties of DSPC lipid bilayer under longitudinal shear, finding significant dependence of membrane mechanical response on physical state, with evidence of linear response in fluid region but not in gel region. Transient viscoelastic response of sheared bilayer accessed, with validity domain of linear response established and timescales discussed.
Review
Physics, Multidisciplinary
Tanja Schilling
Summary: This article discusses the construction of coarse-grained models for systems out of thermal equilibrium, including both equilibrium and non-equilibrium coarse-graining methods and numerical schemes.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
(2022)
Article
Chemistry, Physical
Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth
Summary: The first paper of this series demonstrated the scalability of excess entropy for both fine-grained and coarse-grained systems. However, a more precise determination of the scaling relationship was not possible due to its semi-empirical nature. In this second paper, an analytical scaling relation for excess entropy is derived for bottom-up coarse-grained systems. By constructing effective hard sphere systems at the single-site resolution, the dynamics and excess entropy of the target coarse-grained systems can be accurately approximated.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Michael R. DeLyser, W. G. Noid
Summary: Investigated a new class of one-body potentials called square gradient (SG) potentials that can improve the accuracy and transferability of coarse-grained (CG) models. These SG potentials can tune interfacial properties and enhance the performance of various models.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
Loic Chalamet, David Rodney, Yasushi Shibuta
Summary: In this study, a novel coarse-grained molecular dynamic model is used to extend the time range of atomistic simulations for metallic materials. The model successfully reproduces the mechanical and thermal properties of nickel, and shows good agreement with all-atom molecular dynamics simulations. The method has been applied to simulate crystal growth on a large scale with relative ease, indicating its potential for various applications.
COMPUTATIONAL MATERIALS SCIENCE
(2023)
Article
Physics, Fluids & Plasmas
Takashi Uneyama
Summary: This paper demonstrates the derivation of a coarse-grained dynamics model with a time-dependent and fluctuating potential from microscopic Hamiltonian dynamics. It is shown that the dynamic equations with the transient potential can accurately describe the dynamics of the coupled oscillator model. Additionally, the dynamic equations for the transient potential can be formally derived for the microscopic Hamiltonian dynamics. The use of the transient potential to describe coarse-grained dynamics is justified.
Article
Polymer Science
Chunhua Zhu, Ning Wei, Junhua Zhao
Summary: This study successfully describes the interactions between poly(vinyl alcohol) (PVA) melts and graphene oxide (GO), as well as their interfaces, using coarse-grained potentials. The computational efficiency is significantly improved and the method can be applied to other interfacial systems.
Article
Mechanics
Arghya Das, Mustansir Barma
Summary: Models of particles driven by a one-dimensional fluctuating surface exhibit fluctuation dominated phase ordering (FDPO), with macroscopic order and fluctuations appearing on large scales. Interfacial regions between ordered regions contain many domain walls, violating the Porod law. The total number of domain walls and the length of the largest ordered domain quantify the unique characteristics of FDPO. The study focuses on coarse-grained depth (CD) models and shows that domain wall number fluctuations remain constant during coarsening, while the length of the largest cluster grows with time and system size following a power law with logarithmic terms.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2023)
Article
Polymer Science
Atiyeh Alsadat Mousavi, Behrouz Arash, Raimund Rolfes
Summary: This study developed a coarse-grained model to capture nanoparticle-polymers interactions in nanocomposites and proposed an optimization method for calibrating coarse-grained force fields with epoxy matrix. The elastic properties of polymer reinforced nanocomposites depend on the weight fraction and distribution of nanoparticles, with aggregation reducing their effectiveness.
Article
Green & Sustainable Science & Technology
Erxing Peng, Xiaoying Hu, Yaling Chou, Yu Sheng, Shihao Liu, Fansheng Zhou, Jichun Wu, Wei Cao
Summary: The salinity of soil can cause environmental hazards, but microbially induced carbonate precipitation is an effective and pollution-free treatment modality. Despite the negative effect of salt, this method improves the engineering and mechanical properties of saline soil and reduces the permeability coefficient.
JOURNAL OF CLEANER PRODUCTION
(2022)
Review
Biochemistry & Molecular Biology
Jun Li, Shi-Jie Chen
Summary: Understanding the 3D structures of RNA molecules is crucial for their biological functions, leading to the development of computational methods due to the laborious and difficult experimental determination. All-atom simulations are suitable for small RNA systems, while coarse-grained models are more widely applied.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Metallurgy & Metallurgical Engineering
Yong-long Qu, Geng-she Yang, Jia-mi Xi, Wan-kui Ni, Xiao Ding, Bing-quan Wu
Summary: The strength and deformation properties of sandstones under different low temperatures were investigated, and the energy characteristics and microstructure features were analyzed. Results show that sandstones have a noticeable pore compression stage, with medium-grained sandstone being more pronounced. The rock strength decreases with increasing temperature and increases with increasing confining stress, with the elastic modulus and Poisson ratio exhibiting opposite changes. The study also reveals the evolution laws of total strain energy, elastic energy, and dissipated energy of sandstones, providing insights into the deformation and damage mechanism of rocks.
JOURNAL OF CENTRAL SOUTH UNIVERSITY
(2023)
Article
Polymer Science
Chengyuan Wen, Roy Odle, Shengfeng Cheng
Summary: A coarse-grained model is developed for large-scale MD simulations of a branched polyetherimide, using systematic protocols based on chemistry-informed grouping of atoms and parameterization methods. The model has been successfully applied to explore the mechanical, structural, and rheological properties of the polymer.
Article
Chemistry, Physical
Liuyang Zhang, Ning Liu, Xianqiao Wang
Summary: The present study evaluates the effect of physical factors on the nuclear uptake of nanoparticles (NPs) using a computational model. Size, surface modification, and rigidity were found to be crucial factors. Larger NPs require more energy to enter the nucleus, highlighting the importance of size in NP design. Surface modification and rigidity also impact the nuclear uptake pathway and efficiency, providing insights for precise and controllable NP-nucleus interaction design.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Evan Pretti, M. Scott Shell
Summary: Bottom-up coarse-graining methods provide systematic tools for creating simplified models of molecular systems, but the resulting coarse-grained models often fail to accurately reproduce all thermodynamic properties of the reference atomistic systems. This work introduces a new strategy for creating temperature-transferable CG models based on effective entropy functions and relative entropy minimization, allowing for improved temperature dependence predictions and parameterization. The approach is demonstrated to be successful for creating temperature-transferable CG models for complex molecular liquids.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yong Han, Puranjan Chatterjee, Sardar B. Alam, Tanya Prozorov, Igor I. Slowing, James W. Evans
Summary: The pillaring of synthetic layered crystalline silicates and aluminosilicates enhances their adsorption and separation performance, providing insights into the behavior of complex natural clays. First-principles density functional theory calculations were performed to investigate the pillaring of a pure silica polymorph of an MCM-22 type molecular sieve. The results show that pillaring agents can bridge adjacent internal surfaces, leading to changes in interlayer spacing.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Katherine E. McCullough, Ian L. Peczak, Robert M. Kennedy, Yi-Yu Wang, James Lin, Xun Wu, Alexander L. Paterson, Frederic A. Perras, Jacklyn Hall, A. Jeremy Kropf, Ryan A. Hackler, Youngho Shin, Jens Niklas, Oleg G. Poluektov, Jianguo Wen, Wenyu Huang, Aaron D. Sadow, Kenneth R. Poeppelmeier, Massimiliano Delferro, Magali S. Ferrandon
Summary: This study presents a scalable synthesis method for Pt/STO by surface organometallic chemistry (SOMC) techniques using Pt(ii) acetylacetonate or trimethyl(methylcyclopentadienyl)platinum. The Pt/STO catalysts effectively hydrogenolyzed polyolefins into hydrocarbon oils, offering a promising approach for upcycling plastic waste. This new synthesis method overcomes the cost and resource-intensive issues associated with the previous atomic layer deposition (ALD) technique.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Nanoscience & Nanotechnology
Xingyi Lyu, Max Meirow, Xun Wu, Xinwei Zhou, Yuzi Liu, Wenyu Huang, Tao Li, Byeongdu Lee
Summary: The mesoporous silica shell coating the hydrogenolysis nano-catalyst alters the molecular weight distributions of cleaved polymer chains compared to catalysts without a shell. The shell reduces low-valued gaseous products and increases the median molecular weight of the product, enhancing the value of the products for polymer upcycling. The spatial distribution of polystyrene chains in the nanochannels reveals a non-uniform distribution for longer chains.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Physical
Yong Han, Marek Kolmer, Michael C. Tringides, James W. Evans
Summary: SiC-supported graphene intercalated by a two-dimensional Pb monolayer is a promising platform for spintronic applications. The thermodynamic stability of this structure has been confirmed in recent experiments. However, the details of intercalated phases, location of atoms, thermodynamic preference, and intercalation pathways are still not fully understood. In this study, extensive density functional theory calculations were conducted to investigate the thermodynamics and kinetics of Pb intercalation on graphene/SiC(0001). The results suggest that intercalation of complete Pb layers in the gallery is strongly favored over other configurations, and more complex intercalation pathways are involved.
Article
Chemistry, Physical
King C. C. Lai, Da-Jiang Liu, James W. W. Evans
Summary: The shape stability of metallic nanocrystals is critical for optimizing properties in catalysis and plasmonics. Reshaping of facetted nanocrystals is controlled by surface diffusion-mediated nucleation and growth. However, classical nucleation theory fails to accurately predict the reshaping barrier and rate due to the low nucleation barriers and lack of local equilibrium before crossing the barrier.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Alexander Volkov, Jiashan Mi, Kanika Lalit, Puranjan Chatterjee, Dapeng Jing, Scott L. Carnahan, Yunhua Chen, Simin Sun, Aaron J. Rossini, Wenyu Huang, Levi M. Stanley
Summary: The library of imine-linked covalent organic frameworks (COFs) has significantly expanded in the past two decades, offering a wide range of morphologies, pore sizes, and applications. While various synthetic methods have been developed to enhance COF functionalities, most of them are specific to certain applications. This study presents a general strategy to introduce functional group handles in COFs through the Ugi multicomponent reaction, enabling the functionalization of any COFs containing imine linkages.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Shaojiang Chen, Akalanka Tennakoon, Kyung-Eun You, Alexander L. L. Paterson, Ryan Yappert, Selim Alayoglu, Lingzhe Fang, Xun Wu, Tommy Yunpu Zhao, Michelle P. P. Lapak, Mukunth Saravanan, Ryan A. A. Hackler, Yi-Yu Wang, Long Qi, Massimiliano Delferro, Tao Li, Byeongdu Lee, Baron Peters, Kenneth R. R. Poeppelmeier, Salai C. C. Ammal, Clifford R. R. Bowers, Frederic A. Perras, Andreas Heyden, Aaron D. D. Sadow, Wenyu Huang
Summary: Non-reducible zirconia catalysts can efficiently hydrogenolytically cleave polyolefins, achieving similar activity as precious metal nanoparticles.
Article
Nanoscience & Nanotechnology
Hengzhou Liu, Jiaqi Yu, Yifu Chen, Jungkuk Lee, Wenyu Huang, Wenzhen Li
Summary: Electrocatalytic oxidative dehydrogenation (EOD) of aldehydes allows for the production of bipolar H-2 at ultra-low voltage with carboxylic acid co-generation. This study presents a simple galvanic replacement method to prepare CuM (M = Pt, Pd, Au, and Ag) bimetallic catalysts, enabling industrially relevant current densities in the EOD of furfural. The incorporation of noble metals onto the Cu surface and the subsequent enlargement of its surface area significantly improve the EOD performance, with CuPt achieving a record-high current density of 498 mA cm(-2) and a Faradaic efficiency of >80% to H-2 at a low cell voltage of 0.6 V. Further research is required to understand the synergistic effects of Cu-M on furfural EOD and enhance the catalyst stability, thus facilitating the future production of green hydrogen and carbon chemicals with practical rates and low-carbon footprints.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Physical
Da-Jiang Liu, James W. Evans
Summary: Supported metallic nanoparticles are important in catalysis, but predicting their behavior is challenging due to their complex structure and interface with the support materials. Recent advances in machine learning allow for molecular dynamics simulations with near-DFT accuracy, which can provide insights into the growth, relaxation, and reactions of these nanoparticles. We studied the adsorption of fluorine atoms on ceria and silica supported palladium nanoparticles using machine learning potential trained by DFT data. The results show that defects on the ceria and Pd/ceria interfaces are crucial for the initial adsorption of fluorine, while the interplay between Pd and ceria and the reverse oxygen migration control the spillover of fluorine from Pd to ceria at later stages. In contrast, silica supports do not induce fluorine spillover from Pd particles.
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
Yong Han, Shen Chen, Joseph Hall, Samuel Roberts, Marek Kolmer, James W. W. Evans, Michael C. C. Tringides
Summary: First-principles density functional theory (DFT) is used to analyze the stability of Pb intercalated phases under buffer layer graphene on SiC(0001). It is found that there exists a family of structurally distinct thermodynamically preferred Pb subsurface configurations with minute stability differences. High-resolution surface-diffraction experiments confirm the high degree of degeneracy of the Pb intercalated phases.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Akalanka Tennakoon, Xun Wu, Max Meirow, Daniel Howell, Jarod Willmon, Jiaqi Yu, Jessica V. Lamb, Massimiliano Delferro, Erik Luijten, Wenyu Huang, Aaron D. Sadow
Summary: By embedding active platinum nanoparticles between linear, hexagonal mesoporous silica and gyroidal cubic MCM-48 silica, the new catalyst design emphasizes the pore effect and selectively deconstructs polyolefins into valuable hydrocarbon chains while generating minimal volatile byproducts, including methane.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Nanoscience & Nanotechnology
Siying Yu, Ranjan Kumar Behera, Jung Hyun Park, Shihyun Park, Wenyu Huang, Hong Yang
Summary: In this study, the control over particle size and uniformity of ultrafine PtZn intermetallic nanoparticles was achieved using a dual-ligand metal-organic framework as atomically dispersed precursors in a one-pot synthesis. The resulting PtZn intermetallic nanoparticles exhibited highly selective hydrogenation catalytic properties for the conversion of 1-iodo-4-nitrobenzene and 1-bromo-4-nitrobenzene to the corresponding semihydrogenated products exclusively.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Physical
King C. Lai, Charles T. Campbell, James W. Evans
Summary: Nanostructured systems are prone to coarsening, which can lead to deactivation when used as catalysts. The dependence of diffusivity on nanocluster size controls coarsening kinetics. Traditional mean-field theory is refined to account for different densities and hop rates on different facets, capturing the occurrence of local minima in diffusivity versus size. However, this approach has fundamental shortcomings and a beyond-mean-field treatment is needed to capture the cooperative multi-step diffusion process in faceted nanoclusters.
NANOSCALE HORIZONS
(2023)
Article
Chemistry, Multidisciplinary
William S. Salvia, Tommy Yunpu Zhao, Puranjan Chatterjee, Wenyu Huang, Frederic A. Perras
Summary: The study confirmed that the active sites in amorphous silica-alumina are zeolitic bridging Bronsted sites, using selective isotope labeling and quantitative NMR distance measurements.
CHEMICAL COMMUNICATIONS
(2023)