Article
Computer Science, Interdisciplinary Applications
Robin Fingerhut, Gabriela Guevara-Carrion, Isabel Nitzke, Denis Saric, Joshua Marx, Kai Langenbach, Sergei Prokopev, David Celny, Martin Bernreuther, Simon Stephan, Maximilian Kohns, Hans Hasse, Jadran Vrabec
Summary: The new version 4.0 of the molecular simulation tool ms2 introduces two additional potential functions and enhances computational efficiency. It also provides new properties, functionalities, and features, such as thermodynamic factor, thermal diffusion coefficients, and non-Gaussian parameters, to improve the application-oriented thermodynamic properties and microscopic structure analysis.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Sheida Jamalzadeh, Sogand Aghamohammadi, Aligholi Niaei, Hamid Erfan-Niya
Summary: In this study, Molecular Dynamics and Monte Carlo methods were used to investigate the adsorption and diffusion behavior of molecules in the catalytic process of NOx reduction. The results showed that Cu-ZSM5 catalyst achieved high selectivity of desired products.
MOLECULAR CATALYSIS
(2022)
Article
Chemistry, Applied
Zahra Keyvanloo, Ali Nakhaei Pour, Fatemeh Moosavi
Summary: The adsorption and diffusion behaviors of H-2, CO2, CO, MeOH, and EtOH in ZIF-8 were studied in pure and mixed states. The results showed different trends for the diffusion coefficients and adsorption isotherms of the guest molecules. The separation of MeOH from other molecules in the mixture was also investigated.
MICROPOROUS AND MESOPOROUS MATERIALS
(2022)
Review
Green & Sustainable Science & Technology
Tianyu Wang, Shouceng Tian, Gensheng Li, Liyuan Zhang, Mao Sheng, Wenxi Ren
Summary: This article provides an overview of the adsorption mechanism of shale gas and the importance of molecular simulation, emphasizing the crucial role of accurate description of shale compositions and structures for simulation.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2021)
Article
Thermodynamics
Junqing Chen, Fujie Jiang, Qi Cong, Xiongqi Pang, Kuiyou Ma, Kanyuan Shi, Bo Pang, Dongxia Chen, Hong Pang, Xiaobin Yang, Yuying Wang, Bingyao Li
Summary: With the development of shale gas exploration technology, shale gas has become the primary energy source, and understanding the adsorption of gas in organic-inorganic slit pores is crucial for evaluating shale reservoirs and improving shale gas recovery. This study used molecular simulations to investigate the adsorption behavior of methane in organic-inorganic slit pores in Songliao Basin shale. The results showed that methane is more strongly adsorbed on graphene surfaces than on kaolinite surfaces, and the adsorption capacity is affected by temperature, pressure, and pore size. The findings contribute to accurate evaluation of shale reservoir gas content and enhancement of shale gas recovery.
Article
Environmental Sciences
Shuai Wang, Huiyan Zhu, Cheng Zhang, Yupei Ye, Rui Zhang, Xiaoxiang Wang, Chongxuan Liu
Summary: Understanding the adsorption behavior of antibiotics on minerals is crucial for determining their fate in soils and waters. This study used molecular dynamics simulations to investigate the adsorption of two common antibiotics, tetracycline and sulfathiazole, on montmorillonite. The results revealed the molecular orientation and conformation of the antibiotics during the adsorption process, providing insights into the complexity of antibiotics adsorption to soil and their environmental transport and fate.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Physics, Multidisciplinary
K. L. Zhang, Z. Song
Summary: The study reveals that applying a nonlocal non-Hermitian perturbation to an Ising chain merges the topological Kramer-like degeneracy in the ferromagnetic phase, with distinct dynamic responses for different quantum phases. The phase diagram at zero temperature is completely preserved at finite temperatures.
PHYSICAL REVIEW LETTERS
(2021)
Article
Materials Science, Multidisciplinary
Rong-Guang Xu, Qi Rao, Yuan Xiang, Motong Bian, Yongsheng Leng
Summary: Hybrid GCMC/MD simulations were used to study the adsorption-desorption isotherms of argon molecules confined in nanoscale thickness between commensurate and incommensurate contacts. The mid-density scheme was applied to hysteresis loops to generate equilibrium phases of nanoconfined fluids. Equilibrium structures obtained from GCMC/MD simulations with appropriate chemical potentials can be used as initial configurations for future metadynamics free energy calculations.
Article
Chemistry, Physical
M. Laabd, Y. Brahmi, B. El Ibrahimi, A. Hsini, E. Toufik, Y. Abdellaoui, H. Abou Oualid, M. El Ouardi, A. Albourine
Summary: This study reported the effective removal of Ciprofloxacin (Cipro) antibiotic from aqueous solutions using a novel Hydroxyapatite@Montmorillonite (HAP@Mt) hybrid composite synthesized via a facile co-precipitation route. The composite showed a high adsorption capacity for Cipro, controlled mainly by electrostatic interactions, hydrophobic interactions, hydrogen bonding, and n-It electron donor/acceptor interactions. Monte Carlo/SA simulations provided atomic-level insights on the interactions between Cipro molecule and HAP@Mt surface.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Engineering, Chemical
Hongling Zhang, Haihua Xu, Mingzhu Xia, Fengyun Wang, Xia Wan
Summary: The novel ampholytic surfactant modified montmorillonite showed better adsorption performance for BTH and 2-OH-BTH compared to acidified Na-Mt, mainly through electrostatic interaction and hydrophobic partitioning.
ADVANCED POWDER TECHNOLOGY
(2021)
Article
Materials Science, Multidisciplinary
Carl Degitz, Manuel Konrad, Simon Kaiser, Wolfgang Wenzel
Summary: This paper compares two different modeling approaches to investigate the structure and properties of films during physical vapor deposition (PVD) process. The results show that films generated by the molecular dynamics approach have a density approximately 10% higher than those generated by the Metropolis Monte Carlo approach. Additionally, the anisotropic nature of the films is studied by calculating the refractive index, and electron and hole mobilities are calculated using a Kinetic Monte Carlo protocol.
ORGANIC ELECTRONICS
(2022)
Article
Engineering, Environmental
Danqi Wang, Ruicong Wang, Wencai Peng, Jinli Zhang, Yi Wang, Minghui Huang, Na Zhang, Yanan Duan, Ying Fang
Summary: This study reported the experimental and theoretical studies on the adsorption of Cu(II) on Na-montmorillonite surface. The adsorption reached equilibrium within 80 min with an adsorption capacity of 35.230 mg middot g(-1) at 25 degrees C. The adsorption data of Cu(II) followed pseudo-second-order kinetic and Langmuir isotherm models. The simulation results showed no significant differences in the adsorption energy of Cu(II) at different sites on the montmorillonite surface, and Cu(II) had more electron transfer than Na(I).
WATER SCIENCE AND TECHNOLOGY
(2023)
Article
Chemistry, Physical
Haiyan Wang, Qinghua Yang, Zhaosong Li, Yuan Xie, Fanping Kong, Derui Liang, Caifeng Xia, Hanhan Huang, Jialiang Li, Zilin Meng
Summary: The removal effect of montmorillonite (Mt) on antibiotics, specifically ciprofloxacin (CIP) and erythromycin (ERY), was investigated in this study. Adsorption kinetics and isotherm experiments confirmed the effectiveness of the generalized Langmuir model in describing the adsorption process, with higher adsorption capacity observed for CIP. The intercalation and adsorption behaviors of CIP and ERY on Mt surface were analyzed using various techniques, revealing the competitive adsorption mechanism of these antibiotics. Moreover, the adsorption of antibiotics on Mt under different pH conditions was studied, and the competitive adsorption results were supported by the potential energy distribution.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Polymer Science
Xiaozheng Duan, An-Chang Shi, Lijia An
Summary: This study demonstrates a simple and novel approach for fabricating large ionomer microparticles in dilute aqueous solutions using coarse-grained molecular dynamics simulations. By adding cationic polyelectrolytes, the size of the microparticles can be precisely controlled and bare microparticles can be obtained in saline solution.
Article
Multidisciplinary Sciences
Zhen Zhang, Jun Ding, Evan Ma
Summary: Plastic flow in metallic glasses is not caused by identifiable local defect regions. Through a realistic model, we found that shear transformations involve only a small percentage of atoms and their locations and distribution vary under different mechanical loading conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Energy & Fuels
Tao Zhang, Jie Liu, Shuyu Sun
Summary: Energy transition has become a significant topic in recent years due to the urgent need to tackle carbon emissions, address climate change, and find a balance between environmental protection and economic growth. As the world moves away from fossil fuels towards renewable energy sources like hydrogen, there is still a need for conventional energy development to ensure stable supply and leverage mature technologies. The utilization of advanced simulation techniques developed for oil and gas reservoir studies can contribute to the development of hydrogen energy and its applications in transportation, power generation, chemicals, and housing.
ADVANCES IN GEO-ENERGY RESEARCH
(2023)
Article
Mathematics, Applied
Jisheng Kou, Huangxin Chen, Xiuhua Wang, Shuyu Sun
Summary: In this paper, an efficient numerical method is proposed for solving a comprehensive infection model. The method preserves the positivity of variables and is easy to implement. The unique existence and positivity-preserving property of the method are rigorously proved using discrete variational principles.
COMMUNICATIONS ON PURE AND APPLIED ANALYSIS
(2023)
Article
Biochemistry & Molecular Biology
Jie Liu, Tao Zhang, Shuyu Sun
Summary: The ion transport in protein nanochannels during peritoneal dialysis was investigated using molecular dynamics (MD) simulations and the MD Monte Carlo (MDMC) algorithm. The spatial distribution of ions and their temporal properties were accurately predicted, validating the suitability of the MDMC method for handling ion transport problems in protein nanochannels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Computer Science, Interdisciplinary Applications
Yuze Zhang, Xuguang Yang, Lei Zhang, Yiteng Li, Tao Zhang, Shuyu Sun
Summary: With the increasingly accurate modeling and simulation demands, a new method for phase equilibrium prediction is proposed to resolve the shortages in computational efficiency and stability in the conventional iterative flash calculation. This method uses the HiSD algorithm and the Rosenbrock-Euler ETD format to calculate the saddle points and simplify the phase equilibrium calculations.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Xiaoyu Feng, Zhonghua Qiao, Shuyu Sun, Xiuping Wang
Summary: This paper presents a pioneering study on the energy-stable smoothed particle hydrodynamics (SPH) discretization of the Navier-Stokes-Cahn-Hilliard (NSCH) model for incompressible two-phase flows. The proposed numerical scheme inherits mass and momentum conservation and the energy dissipation properties at the fully discrete level, and it satisfies the divergence-free condition through the projection procedure. Numerical experiments are conducted to verify the performance of the energy-stable SPH method for solving the two-phase NSCH model.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Mathematics, Applied
L. I. N. A. Zhao, S. H. U. Y. U. Sun
Summary: In this paper, a strongly mass conservative and stabilizer-free scheme is proposed for the coupled Brinkman-Darcy flow and transport, which incorporates the interface conditions naturally without introducing additional variables. The proposed scheme exhibits uniform robustness for different values of viscosity. A novel upwinding staggered discontinuous Galerkin scheme in mixed form is used to solve the transport equation, and rigorous convergence analysis and stability estimates are provided. Numerical experiments are conducted to validate the theoretical findings and demonstrate the performance of the method.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2023)
Article
Energy & Fuels
Piyang Liu, Xue Kong, Gaocheng Feng, Kai Zhang, Shuyu Sun, Jun Yao
Summary: Acidization is commonly used for stimulating carbonate reservoirs by removing formation damage and creating wormholes. This paper enhances the two-scale continuum model to include fractured-vuggy porous media and proposes a method for generating random pore-fracture-vuggy models. The simulation results show that both fractures and vugs have a significant impact on wormhole development, with fractures in different directions playing a crucial role in determining the growth direction of wormholes.
ADVANCES IN GEO-ENERGY RESEARCH
(2023)
Article
Chemistry, Physical
Yafan Yang, Jingyu Wan, Xiangyu Shang, Shuyu Sun
Summary: The fluid-solid interfacial tension is of great importance and has been studied through extensive molecular dynamics simulations in a H2O + gas + solid three-phase system. The results show the influence of temperature, pressure, and wettabilities on the interfacial tension and highlight the caution needed when applying assumptions of pressure independence in systems with non-hydrophilic surfaces.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Seokgyun Ham, Xin Wang, Arun Kumar Narayanan Nair, Shuyu Sun, Brian Lattimer, Rui Qiao
Summary: This study investigates the transport of heptane across water-vapor interfaces covered by sodium dodecyl sulfate (SDS) surfactants using molecular dynamics simulations. The potential of mean force (PMF) and local diffusivity profiles are calculated to determine the transport resistance of heptane molecules across SDS monolayers with varying densities. The results demonstrate that heptane experiences a finite resistance due to high PMF and slow diffusion in the SDS headgroup region. This resistance increases linearly with SDS density and jumps at saturation, equivalent to a 5 nm thick layer of bulk water. The implications for designing surfactants to suppress heptane transport through water-vapor interfaces are discussed.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Energy & Fuels
Manojkumar Gudala, Suresh Kumar Govindarajan, Zeeshan Tariq, Bicheng Yan, Shuyu Sun
Summary: The Puga geothermal reservoir in India has shown potential for geothermal energy extraction, however, there have been limited studies on its thermo-hydrogeomechanical behavior. This study enhances the THM model and proposes an integrated assessment approach to improve heat extraction possibilities. The evaluation results demonstrate the effectiveness of the proposed techniques. Overall, the article highlights the importance of understanding the behavior of geothermal reservoirs and provides valuable insights for future geothermal energy exploitation.
GEOENERGY SCIENCE AND ENGINEERING
(2023)
Article
Energy & Fuels
Zeeshan Tariq, Manojkumar Gudala, Bicheng Yan, Shuyu Sun, Mohamed Mahmoud
Summary: This study used six machine learning techniques to predict the NMR-based effective porosity in carbonate rocks, achieving accurate results. The study also provided an empirical model for quickly estimating NMR-based effective porosity, based on well logs.
GEOENERGY SCIENCE AND ENGINEERING
(2023)
Article
Mechanics
Yuanqing Wu, Shuyu Sun
Summary: Pressure-temperature (PT) flash calculations are a performance bottleneck of compositional-flow simulations. The computing burden of PT flash calculations is shifted from the online stage to the offline stage with the sparse grid surrogate, achieving great acceleration. Physics-informed neural networks remove the computing burden of PT flash calculations in the offline stage by not carrying out the heavy-burden routines. Numerical experiments validate the correctness and applicability of this approach. To the best of our knowledge, this is the first work to remove the performance bottleneck of PT flash calculations during both the online and offline stages of compositional-flow simulations.
Article
Energy & Fuels
Gang Qiu, Haijian Yang, Jisheng Kou, Shuyu Sun
Summary: The paper presents a scalable framework for modeling and simulating flow in unconventional shale gas reservoirs, using a chemical potential-based modeling approach and the fully implicit method. A thermodynamically consistent mathematical model is developed to satisfy the second law of thermodynamics and accurately capture the flow physics in shale media. The proposed approach achieves parallel scalability through the use of Newton-Krylov methods and the domain decomposition technique. Numerical experiments demonstrate the robustness and efficiency of the solution strategies for shale gas flow problems in two or three dimensions.
GEOENERGY SCIENCE AND ENGINEERING
(2023)
Article
Thermodynamics
Yuanqing Wu, Shuyu Sun
Summary: The sparse-grid guided PINN training method improves the accuracy of the PINN surrogate model by rearranging collocation points and reduces the training time complexity. Experimental results demonstrate its clear advantages in terms of convergence, stability, and accuracy.
FLUID PHASE EQUILIBRIA
(2024)
Review
Thermodynamics
Mohammad Ferdows, Sultana Jahan, Efstratios Tzirtzilakis, Shuyu Sun
Summary: This research aims to investigate how temperature-dependent fluid properties can improve the heat transfer efficiency and performance evolution of hybrid nanofluid in the presence of a transverse magnetic field. The study explores the effects of varying the magnetic field strength and the volume fraction of Fe3O4 nanoparticles on fluid motion and energy transport. The results show that increasing the volume fraction of Fe3O4 enhances heat generation and thermal conductivity, leading to a rise in thermal boundary layer, while increasing the variable Prandtl number significantly improves the heat transfer rate.
ADVANCES IN MECHANICAL ENGINEERING
(2023)