Article
Chemistry, Physical
Brett Scheiner, Tae Jun Yoon
Summary: This paper applies mean force kinetic theory (MFT) to calculate the self-diffusivity of CO2 in the supercritical fluid regime, with two modifications to allow its application to a system of molecular species. The results obtained are in good agreement with molecular dynamics simulations and have greater potential for application to systems of mixed species and long range interatomic potentials due to electrostatic interactions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Agriculture, Dairy & Animal Science
Nitalo Machado, Michelle Parente, Rui Bessa, Henrique Parente, Ruan Gomes, Ricardo Pinho, Daniele Ferreira, Anderson Zanine, Juliany Costa, Susana Alves
Summary: This research compared the effects of adding babassu oil and buriti oil to the diet of lambs on intake, nutrient digestibility, and fatty acid distribution. The results showed that the babassu supplemented diet caused greater stress to the ruminal bacteria and changed the biohydrogenation of fatty acids in the rumen.
Article
Chemistry, Medicinal
Han Liu, Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai
Summary: In this study, a hybrid quantum mechanical/molecular mechanics approach was used to characterize the interaction of cations and anions, and Lennard-Jones parameters were optimized to improve the description of solvent-exposed salt-bridge interactions. The findings indicate that the new parameters enhance the structural and thermodynamic description of solvent-exposed salt-bridge interactions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Automation & Control Systems
Lihua Zhou, Suping Fang, Kangkang Ding, Yoshiki Kawasaki
Summary: This paper improves the calculation accuracy of the side mill for machining the helicoid by deducing the contact condition formula and proposing an improved method. The calculation accuracy is particularly enhanced in the cases of multi-segment curves and connection points.
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Xiaoshi Wei, Qingyan Yin, Huihui Zhao, Jiajun He, Yangchun Cao, Junhu Yao
Summary: Studies investigated the effects of nicotinamide (NAM) supplementation during postpartum and peripartum periods on rumen fermentation, liver mitochondrial respiratory chain status, lipid metabolism, oxidative status, and liver metabolite profile of does. The results showed that peripartum supplementation improved rumen fermentation pattern and liver energy efficiency, benefiting lipid metabolism.
ANIMAL FEED SCIENCE AND TECHNOLOGY
(2021)
Article
Chemistry, Physical
Timothy J. Giese, Darrin M. York
Summary: We used the modified Bigeleisen-Mayer equation to calculate kinetic isotope effect values for non-enzymatic phosphoryl transfer reactions. The modified equation includes the ratio of vibrational frequencies and the effect of isotopic substitution on the activation free energy. We developed a practical method to estimate the frequency ratio correction directly from umbrella sampling, which avoids the need for normal mode analysis. This method provides a new tool for calculating kinetic isotope effects in complex chemical reactions in the condensed phase.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Fengxuan Jiao, Sheikh I. Hossain, Jianbing Sang, Suvash C. Saha, YuanTong Gu, Zak E. Hughes, Neha S. Gandhi
Summary: This study investigates the interaction between AuNPs and PS using coarse-grained molecular dynamics simulations. It was found that AuNPs with hydrophilic ligands penetrate the monolayer more easily, while those with hydrophobic ligands embed in the monolayer and deform its structure.
Article
Biochemistry & Molecular Biology
Hugo A. L. Filipe, Luis M. S. Loura, Maria Joao Moreno
Summary: Permeation through biomembranes is crucial for drugs to reach their targets, and the asymmetry of cell plasma membrane plays an important role in this process. This study investigates the interaction of a series of NBD-labeled amphiphiles with lipid bilayers of different compositions, including an asymmetric bilayer. The behavior of the amphiphiles during permeation, including their orientation, chain elongation, and H-bonding, is described. The permeability coefficients of the amphiphiles are also calculated, but quantitative agreement with experimental values could not be achieved.
Article
Chemistry, Multidisciplinary
Wannian Zhang, Ming-Yuan Zhang, Kai Wang, Ruixia Sun, Shanlin Zhao, Zhiqiang Zhang, Yu-Peng He, Fang Yu
Summary: The study investigated the effect of surfactant structure on modifying interfacial properties, with the anionic surfactant containing polyethylene oxide groups showing the lowest surface tension at the water/n-decane interface. Molecular dynamics simulations and DFT studies revealed that the structural differences of the surfactants influenced their interactions at the interface, leading to variations in weak interactions and ultimately affecting the properties of the interfaces.
Article
Biochemistry & Molecular Biology
Aleksandra Drajkowska, Andrzej Molski
Summary: The amyloidogenicity and toxicity of amyloid peptides are influenced by their aggregation and interactions with lipid bilayers. The study using MARTINI model found that A/3(1-28) fragments form irreversible aggregates with strong peptide-peptide and peptide-lipid interactions. On the other hand, A/3(25-35) fragments form reversible aggregates with weaker interactions and accumulate at the membrane-solution interface irrespective of their initial spatial arrangement.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Leila Bechtella, Edward Chalouhi, Paula Milan Rodriguez, Marine Cosset, Delphine Ravault, Francoise Illien, Sandrine Sagan, Ludovic Carlier, Olivier Lequin, Patrick F. J. Fuchs, Emmanuelle Sachon, Astrid Walrant
Summary: In this study, the role of the negatively charged lipid phosphatidylinositol-4,5-bisphosphate (PI(4,5)P-2) in the internalization of Penetratin was analyzed. The results showed that Penetratin has a strong affinity for PI(4,S)P-2 and PI(4,5)P-2 plays an important role in Penetratin internalization.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Daniel L. Vigil, Mark J. Stevens, Amalie L. Frischknecht
Summary: We conducted all-atom molecular dynamics simulations of lithium triflate in 1,2-dimethoxyethane using six different literature force fields. The results showed that several commonly used force fields for lithium ions produced qualitatively incorrect outcomes compared to experimental and quantum chemistry findings. This highlights the importance of accurately selecting force field parameters and provides recommendations for choosing force fields in lithium electrolyte applications.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Alyson Shoji, Christopher Kang, Kazuumi Fujioka, John P. Rose, Rui Sun
Summary: This manuscript presents a novel computational method to accurately assess the intestinal permeability of small molecule compounds. The method shows remarkable agreement with experimental results and provides insights into the interplay between drug structure and permeability, which is crucial for drug optimization.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Review
Physiology
Milan Holecek
Summary: The aim of the article is to investigate the side effects of increased dietary intake of amino acids. The study highlights the potential risks and harmful effects of most amino acid supplements and calls for further research on their impact on the immune system, brain function, muscle protein balance, synthesis of toxic metabolites, and tumor growth.
PHYSIOLOGICAL RESEARCH
(2022)
Article
Chemistry, Medicinal
Christophe Chipot
Summary: Predicting the rate of passive permeation of small molecules across the biological membrane is a promising strategy for drug discovery. The estimation of permeation rates through computer simulations and the solubility-diffusion model requires determining the free-energy change and diffusivity of the substrate along the translocation pathway. This Perspective clarifies the physical meaning of membrane permeability from computer simulations and discusses the challenges and potential research directions to improve the predictive power and practical usefulness of physics-based rates of passive permeation.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Daohui Zhao, Chu Huang, Xuebo Quan, Libo Li, Yuqing Wang, Jian Zhou
Summary: The study demonstrated that lysozyme can effectively adsorb on Ti3C2Tx surfaces, controlled by electrostatics and van der Waals interactions. The orientation distribution of lysozyme on Ti3C2O2 and Ti3C2F2 surfaces is more concentrated, with stable conformation during adsorption. The distribution of interfacial water layer on Ti3C2Tx surface also impacts protein adsorption.
Article
Engineering, Chemical
Luxi Lyu, Houxiao Wu, Libo Li, Yanying Wei, Haihui Wang
Summary: Research shows that the flexibility of metal-organic frameworks has little impact on adsorption separation behavior, but the stiffened ZIF-8 formed under an external electric field significantly reduces the diffusion rate of C3H8, resulting in a higher separation factor for C3H6/C3H8.
CHEMIE INGENIEUR TECHNIK
(2022)
Article
Multidisciplinary Sciences
Anu Tyagi, Tofayel Ahmed, Shi Jian, Saumya Bajaj, Seow Theng Ong, Stephanie Shee Min Goay, Yue Zhao, Igor Vorobyov, Changlin Tian, K. George Chandy, Shashi Bhushan
Summary: This study reports two structures of the human voltage-gated potassium channel Kv1.3 – apo-Kv1.3 and dalazatide-Kv1.3. Both structures are in an activated state and show remarkable rearrangements in the selectivity filter. In apo-Kv1.3, the aromatic residue Y447 adopts a unique position diverging from other K+ channels, while in dalazatide-Kv1.3, binding of dalazatide narrows the selectivity filter and stabilizes Y447 in a position similar to other K+ channels. These structural changes play a crucial role in Kv1.3's transition into the drug-blocked state.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Materials Science, Multidisciplinary
Chongxiong Duan, Kuan Liang, Jiahui Lin, Jingjing Li, Libo Li, Le Kang, Yi Yu, Hongxia Xi
Summary: H-MOFs, as a popular class of crystalline porous materials with hierarchical porous structures, have been widely studied in heterogeneous catalysis. They exhibit excellent catalytic activity, selectivity, stability, and recyclability, showing great potential for future research and applications.
SCIENCE CHINA-MATERIALS
(2022)
Article
Chemistry, Physical
Donglei Bu, Duocheng Bu, Wei Chen, Changgeng Huang, Libo Li, Hao Lei, Shaoming Huang
Summary: Three new Cu-X-bpy (X = Cl/Br, Cl/I or Br/I) photocatalytic materials were synthesized and their hydrogen production performance was systematically investigated. It was found that the hydrogen productivity can be significantly enhanced by varying the anions in the materials.
JOURNAL OF CATALYSIS
(2022)
Article
Chemistry, Physical
Shiyuan Liu, Yuehua Deng, Weiqi Liu, Zhiqiang Li, Libo Li, Rui Zhang, Yanbin Jiang
Summary: This study demonstrates the use of modified chitosan hydrogel as a template to control the polymorphism of a drug through competitive crystallization and gelation mechanisms. The results offer a promising approach for the design of drug delivery systems.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2022)
Article
Chemistry, Physical
Shouwei Liao, Qia Ke, Yanying Wei, Libo Li
Summary: This study focuses on the molecular dynamics simulations of water-graphene systems. By developing accurate non-bonded Lennard-Jones parameters based on experimental results, valuable insights have been obtained through thorough comparison and analysis of various simulation data.
APPLIED SURFACE SCIENCE
(2022)
Article
Chemistry, Physical
Qia Ke, Xiaoting Gong, Shouwei Liao, Chongxiong Duan, Libo Li
Summary: The choice of thermostats/barostats has a significant impact on the accuracy of simulated properties in molecular dynamics simulations. Nose-Hoover/V-rescale thermostat and Parrinello-Rahman barostat with moderate coupling strength are recommended for common NVT/NPT production simulations.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Engineering, Chemical
Wenjin Li, Shouwei Liao, Zhipeng Xiang, Mingbao Huang, Zhiyong Fu, Libo Li, Zhenxing Liang
Summary: The concentration and redox state of a bipyridinium derivative (12+) have been found to impact the microstructure of the electrolyte solution in a flow battery. Molecular dynamics simulation shows that the 12+ remains discrete, while the singly-reduced monoradical (1 center dot+) tends to aggregate and form a nano-heterogeneous structure (NHS). The addition of tetrabutylammonium chloride (TBAC) can regulate the NHS and improve the battery cyclability, reducing the capacity decay rate.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Chemistry, Inorganic & Nuclear
Xiaoya Bi, Libo Li, Qijian Niu, Xiaohong Liu, Lijun Luo, Huihui Jiang, Tianyan You
Summary: The development of multi-functional materials for the synchronous detection and removal of mercury ions (Hg2+) is highly demanded. In this study, magnetic Fe3O4 nanoparticles (MNPs) and 6-aza-2-thiothymine-protected gold nanoclusters (ATT-AuNCs) were assembled into a zeolitic imidazolate framework 8 (ZIF-8) structure. The resulting nanocomposite showed enhanced fluorescence emission and improved sensitivity for Hg2+ detection and removal, without the need for another detection method. The nanocomposite also exhibited satisfactory Hg2+ removal capability with short capture time, high removal efficiency, and excellent reusability.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Shouwei Liao, Qia Ke, Yanying Wei, Libo Li
Summary: This study investigates the behavior of water confined in graphene or MoS2 nanochannels using molecular dynamics simulations. The results show that the diffusivity of water is linearly correlated with its mean square displacement along the z-direction, regardless of changes in system variables. This work is significant for designing high-performance 2D nanochannels and discovering novel principles in nano-fluidics and membrane separation fields.
Article
Engineering, Chemical
Lan Chen, Shouwei Liao, Dongkun Yu, Libo Li, Tiancheng Mu, Zhimin Xue
Summary: Efficient absorption is crucial for removing environmental pollutants, and innovative and sustainable absorbents are needed. In this study, an innovative aryl-based deep eutectic solvent (DES) was designed and shown to efficiently adsorb RhB and PS nanoparticles. The absorption efficiency of DPA:BZP-1:1 was higher than that of commercial activated carbon. The study provides new insights into the efficient absorption of dyes and nanoplastics by aryl-based DESs.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Neurosciences
Pei-Chi Yang, Adam Rose, Kevin R. DeMarco, John R. D. Dawson, Yanxiao Han, Mao-Tsuen Jeng, Robert D. Harvey, L. Fernando Santana, Crystal M. Ripplinger, Igor Vorobyov, Timothy J. Lewis, Colleen E. Clancy
Summary: Cardiac function is regulated by the autonomic nervous system (ANS), with sympathetic activation increasing cardiac output and parasympathetic stimulation slowing heart rate. Imbalance in autonomic control can lead to arrhythmias and heart failure. A multiscale neurocardiac model and simulator tool predicts the effect of ANS stimulation on the heart and can be used to study neuromodulatory therapy.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
Article
Nanoscience & Nanotechnology
Chongxiong Duan, Kuan Liang, Zena Zhang, Jingjing Li, Ting Chen, Daofei Lv, Libo Li, Le Kang, Kai Wang, Han Hu, Hongxia Xi
Summary: This review focuses on recent advances in the synthesis strategies of nanoscale hierarchically porous metal-organic frameworks (NHP-MOFs) based on different metal ions, and discusses their advantages, disadvantages, and prospects for commercialization.
NANO MATERIALS SCIENCE
(2022)
Article
Chemistry, Physical
Yi Kong, Libo Li, Shiyu Fu
Summary: Molecular dynamics simulations were used to investigate the adsorption and conformational adaptation of xylan on cellulose microfibers. The results showed that xylan preferred to adsorb parallel to the cellulose microfibrils in the presence of water molecules. The adsorption on hydrophilic planes was found to be superior to that on hydrophobic planes. Additionally, the study revealed that xylan could adopt a two-fold helical conformation on the (200) plane of cellulose microfibrils.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)