Article
Chemistry, Physical
Theodore L. Fobe, Christopher C. Walker, Garrett A. Meek, Michael R. Shirts
Summary: In this study, researchers use computational modeling techniques to address the challenges in designing non-biological foldamers. They developed CG PyRosetta, an extension to PyRosetta, which allows the folding of toy CG foldamer models. By systematically varying CG parameters in these models, they investigate different folding hypotheses and provide insights for the design process of new foldamer chemistries.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Polymer Science
Aditi Khot, Brett M. Savoie
Summary: This study presents a coarse-grained modeling framework flexible enough to explore the structure-function relationships of organic mixed conductors exhibiting both ionic and electronic conductivity. The model successfully replicates experimental trends and reveals the complex interplay between polymer morphology, ionic-electronic coupling, and electrolyte distribution. This framework provides validation for future applications in establishing structure-function relationships in this important material class and suggests near-term opportunities for tailoring mixed conduction via side-chain design.
Article
Computer Science, Artificial Intelligence
Yanhai Gan, Feng Gao, Junyu Dong, Sheng Chen
Summary: This paper proposes a method to generate textures directly from coarse-grained control or high-level guidance, dividing the texture generation process into a three-level Bayesian hierarchical model and using a fully convolutional network to produce diverse textures in real-time.
IEEE TRANSACTIONS ON IMAGE PROCESSING
(2022)
Article
Chemistry, Physical
Carles Navarro, Maciej Majewski, Gianni De Fabritiis
Summary: Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended time scales. This study presents a methodology that utilizes molecular dynamics simulations and neural networks to train a model that can accurately simulate protein folding events. The method eliminates the need for extensive simulations or labeled data and showcases extrapolation capabilities.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Mingwei Wan, Junjie Song, Ying Yang, Lianghui Gao, Weihai Fang
Summary: This study proposes a combined strategy to parameterize the self- and cross-termed interactions of zwitterionic phospholipids in water solution through a piecewise Morse potential. The self-interacting force parameters were optimized by matching experimental data, while the cross-termed interactions were optimized by fitting pseudo properties obtained from atomistic simulations. The proposed coarse-grained force field shows good accuracy and transferability in predicting the structural and thermodynamic properties of lipid membranes, as well as the vesicle self-assembly and fusion processes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Paul Appshaw, Annela M. Seddon, Simon Hanna
Summary: In order to accurately represent the morphological and elastic properties of a human red blood cell, Fu et al. developed a coarse-grained molecular dynamics model. By simulating cells of different diameters, they assessed the validity of the model and found that cells with a diameter of at least 0.5μm were able to form the characteristic shape of human red blood cells.
Article
Biochemistry & Molecular Biology
Yusuke Miyazaki, Wataru Shinoda
Summary: This study investigates the actions of melittin on a lipid membrane through coarse-grained molecular dynamics simulations. Different pore formation modes were observed depending on the peptide concentration and local arrangement, revealing the complexity of melittin's interaction with the membrane.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Engineering, Mechanical
Kek Tang, Jie Tian, Yujie Xiang, Zheng Zhong, Xianqiao Wang
Summary: Motivated by computational flexibility and efficiency, this paper presents a novel approach for coarse-grained modeling of notched 2D metamaterials. The approach utilizes an adaptive triangular mesh and Morse bond potential, optimized using the CMA-ES algorithm. The results demonstrate that the proposed approach provides smooth boundaries and good adaptability, and is effective in studying the mechanical properties of notched 2D metamaterials.
THEORETICAL AND APPLIED FRACTURE MECHANICS
(2023)
Article
Chemistry, Physical
Abhilash Sahoo, Pei-Yin Lee, Silvina Matysiak
Summary: The application of classical MD simulations at atomic resolution to biomolecular processes is limited by computational complexity. This study presents a transferable CG force field with an explicit representation of the environment for accurate protein simulations. The force field consists of pseudoatoms that can be joined together to create different biomolecular systems. Validations with well-studied aqueous protein systems show the effectiveness of the CG model.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Pharmacology & Pharmacy
Xiaoyu Liu, Mostafa Sulaiman, Jari Kolehmainen, Ali Ozel, Sankaran Sundaresan
Summary: This study evaluated the effectiveness of two coarse-grained CFD-DEM approaches in drug delivery via dry powder inhalers, finding that the representative particle approach can approximate CFD-DEM results with reasonable accuracies.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Biochemistry & Molecular Biology
Iga Biskupek, Cezary Czaplewski, Justyna Sawicka, Emilia Ilowska, Maria Dzierzynska, Sylwia Rodziewicz-Motowidlo, Adam Liwo
Summary: The UNited RESidue (UNRES) model was used to study the aggregation behavior of 20 peptides with different lengths. The majority of peptides showed inter-strand beta-sheet formation, except for glutamine- and asparagine-rich peptides, which require modification of the UNRES model.
Article
Engineering, Chemical
Jia Yu, Liqiang Lu, Yupeng Xu, Xi Gao, Mehrdad Shahnam, William Rogers
Summary: Industrial-scale gasifier design was assisted by CFD-CGDEM model, providing important parameters such as syngas compositions and temperature distributions. The study also explored steady-state and transient operations, showing variations in syngas components under different conditions and the time required for shutdown and bed material recovery from sudden loss.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2022)
Article
Construction & Building Technology
Qinlong Liu, Wei Lu, Jing Zhu, Qinde Qi, Guangzhou Li, Dongbo Li
Summary: In this study, the mechanical properties of polydisperse C-S-H were investigated through coarse-grained mesoscale simulations and statistical theory. The simulations showed good agreement with nanoindentation data and revealed that the bulk modulus and indentation modulus of C-S-H colloidal structure are closely related to the packing fraction, with significant linear positive correlations. The results also demonstrated the significant impact of grain size on the packing fraction, and suggested that increasing the range of grain diameter can enhance the packing fraction and strengthen the mechanical properties of C-S-H structure.
CONSTRUCTION AND BUILDING MATERIALS
(2023)
Article
Chemistry, Physical
Iryna Zaporozhets, Cecilia Clementi
Summary: Coarse-grained models are useful for studying biomolecular processes on long time and length scales. In this study, experimental data on mutant stability is used to develop coarse-grained models for two proteins, with and without many-body terms. It is shown that many-body terms are necessary to accurately simulate the effect of point mutations on protein stability, particularly considering the solvent effect.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Saientan Bag, Melissa K. Meinel, Florian Mueller-Plathe
Summary: In this paper, a data-driven approach to generate coarse-grained models that preserve the all-atom molecular mobility is presented. The researchers designed an artificial neural network model that can predict the simulation-ready coarse-grained potential based on the input of all-atom force field parameters. Experimental results showed that the predicted coarse-grained potential can significantly reduce the artificial acceleration in molecular mobility, making the coarse-grained models more accurate.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)