Article
Chemistry, Physical
Vladimir G. Baidakov, Sergey P. Protsenko, Vasiliy M. Bryukhanov
Summary: The nucleation of bubbles in a stretched Lennard-Jones liquid between two flat smooth solid walls was investigated using molecular dynamics. The centers of bubbles are mainly located at a distance of (1.5-3) molecular diameters from the walls, with the nucleation rate near the walls being two orders of magnitude higher than in a homogeneous liquid. The liquid boiling-up in the presence of smooth wettable walls proceeds by the mechanism of homogeneous nucleation, regardless of the bubble formation location.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Yu-Jie Chen, Xue-Jiao Chen, Bo Yu, Wen-Jing Zhou, Qun Cao, Wen-Quan Tao
Summary: In this study, molecular dynamics simulation method was used to investigate bubble nucleation of water on a grooved copper substrate with hydrophilicity, and a concept based on the competition between molecular kinetic energy and potential restriction was proposed to explain the mechanism of bubble nucleus formation. Simulation results showed that this concept effectively clarifies the intrinsic regimes of bubble nucleation and the nucleation differences between different cases.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Elise Rosky, Will Cantrell, Tianshu Li, Raymond A. Shaw
Summary: Recent experiments suggest that pressure fluctuations play a role in ice nucleation. By evaluating homogeneous ice nucleation rates under different pressures, researchers found that the density difference between water and ice is crucial in controlling the effect of pressure on nucleation rate. A linear approximation of lines of constant nucleation rate was found to be useful in experimental predictions for studying ice nucleation mechanisms.
CHEMICAL PHYSICS LETTERS
(2022)
Review
Chemistry, Physical
Yu-Jie Chen, Wei Lu, Bo Yu, Wen-Quan Tao, Wenjing Zhou, Qun Cao
Summary: Bubble nucleation in boiling heat transfer is a microscale phenomenon. The commonly used molecular dynamics simulation method often requires an unreasonable heating temperature to achieve bubble nucleation in liquid argon. This study proposes a revised potential model for bubble nucleation study of argon, which can lower the onset nucleation temperature and avoid the unreasonable change of liquid argon properties.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Joel Puibasset
Summary: The spontaneous formation of tiny bubbles in a liquid is crucial for understanding liquid-to-vapor transitions. These spatially correlated bubbles should be considered as one single density depression of the liquid, known as LDR, instead of multiple independent bubbles. This has significant implications for the characterization of bubble density, understanding the transition process, and molecular simulations.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Joel Puibasset
Summary: This study presents an improved relation that corrects the approximation between the probability size distribution of the largest nucleus and the size distribution of any nucleus, allowing for an accurate calculation of free energy barriers from biased simulations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Thermodynamics
Lin Shi, Chengzhi Hu, Changli Yi, Jizu Lyu, Minli Bai, Dawei Tang
Summary: A model of nucleate boiling of liquid on the structured surface was constructed, and the processes of nucleate generation and bubble growth were directly observed using molecular dynamics simulation. The research found that the position and number of interfaces are mainly determined by the potential energy restriction generated by structures, which significantly affects the critical heat flux. In addition, liquid retention also affects interfaces and critical heat flux.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2022)
Article
Biochemistry & Molecular Biology
Bhawna Pandey, Krishnendu Sinha, Aditya Dev, Himal K. Ganguly, Smarajit Polley, Suman Chakrabarty, Gautam Basu
Summary: Phosphorylation is a key post-translational modification that alters the functional state of many proteins. In the case of the Escherichia coli toxin HipA, autophosphorylation of Ser150 inactivates its ability to phosphorylate glutamyl-tRNA synthetase and trigger bacterial persistence. However, Ser150 is buried in the crystal structure of HipA and is not phosphorylation-competent. A molten-globule-like intermediate of HipA with a solvent-exposed Ser150 has been identified, suggesting a phosphorylation-competent metastable state. This study provides insights into the mechanism of HipA autophosphorylation and sheds light on the transient exposure of buried residues for phosphorylation.
Article
Chemistry, Physical
Vladimir G. Baidakov, Sergey P. Protsenko, Vasiliy M. Bryukhanov
Summary: The kinetics of homogeneous nucleation of the vapour-gas phase was studied using the molecular dynamics method in systems with partial and complete solubility. The density and concentration of the solution were found to affect the formation and growth of the vapour-gas nucleus.
MOLECULAR SIMULATION
(2022)
Article
Chemistry, Physical
Katsuhiro Endo, Daisuke Yuhara, Kenji Yasuoka
Summary: In this study, a new sampling method called continuous normalizing molecular flow (CNMF) is proposed for Monte Carlo molecular simulation. The CNMF method generates samples by solving a first-order differential equation with two-body intermolecular interaction terms. It is demonstrated that Monte Carlo molecular simulation using CNMF is more efficient than the standard simulation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Review
Biochemistry & Molecular Biology
Hangjin Jiang, Xiaodan Fan
Summary: Understanding the energy landscape and conformational dynamics is crucial for studying biological or chemical processes, with Molecular Dynamics (MD) simulations being a major source of dynamic structure information. While many methods have been proposed for learning metastable states from MD data, there are still key issues that require further investigation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Thermodynamics
Zirui Li, Zhenyu Wang, Wei Shao, Qun Cao, Zheng Cui
Summary: The nucleate boiling process on rectangular grooved surfaces with varying aspect ratio is studied through molecular dynamics simulation. The rectangular grooves can significantly accelerate the initial bubble nucleation time and delay the transition from bubble nucleation to film boiling. However, when the groove width is extremely narrow, bubbles cannot be generated first due to the limitation of geometric structure and low potential energy region inside the groove.
THERMAL SCIENCE AND ENGINEERING PROGRESS
(2023)
Article
Nuclear Science & Technology
Huaqiang Liu, Wei Deng, Peng Ding, Jiyun Zhao
Summary: The study investigates the nanoscale liquid-vapor phase change process of argon above solid copper substrates with different surface wettability and roughness, and finds that variations in wettability and surface roughness significantly impact the heat transfer and evaporation rate. Increased wettability enhances heat transfer and evaporation flux, while surface roughness advances the boiling inception and increases the evaporation rate.
NUCLEAR ENGINEERING AND DESIGN
(2021)
Article
Thermodynamics
Longyan Zhang, Yin Yang, Jianing Han
Summary: In this study, the impact of nanostructure morphology on liquid argon bubble nucleation on a platinum solid surface was investigated using molecular dynamics methods. Nucleation behavior on smooth and nanostructured surfaces, including trapezoidal, rectangular, and reentrant cavities, was compared. The simulation results revealed that nanostructured surfaces outperformed smooth surfaces in terms of bubble nucleation, with the reentrant cavity showing the shortest nucleation time.
NUMERICAL HEAT TRANSFER PART A-APPLICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Pietro Sacchi, Petros Neoptolemou, Roger J. Davey, Susan M. Reutzel-Edens, Aurora J. Cruz-Cabeza
Summary: The phenomenon of molecular crystal polymorphism is important for industries relying on crystallisation. Computational methods for evaluating thermodynamic properties of polymorphs are accurate, but the prediction of crystallisation kinetics impacting polymorphism has received less attention. This study measures the crystal growth kinetics of three polymorphs of tolfenamic acid in isopropanol solutions and compares their growth rates. The metastable forms TFA-II and TFA-IX grow faster than the stable TFA-I.
