Article
Engineering, Chemical
Suwei Liu, Sinan Keten, Richard M. Lueptow
Summary: This study investigates the performance of three commonly used water models in simulating NF membrane systems at different temperatures and thermostat settings. The results show that the TIP4P water model accurately reproduces water dynamics, especially water self-diffusivity. Additionally, TIP4P outperforms the other two water models in describing ion diffusivities and water solvation shells. Therefore, TIP4P is an appropriate water model for MD simulations of polyamide membranes.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Tomas Nemec
Summary: Nucleation rates for droplet formation in water vapor were measured using molecular dynamics simulations. The results showed that the measured rates were roughly in agreement with the predictions of classical nucleation theory.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Materials Science, Multidisciplinary
Akshay Krishna Ammothum Kandy, Kevin Rossi, Alexis Raulin-Foissac, Gaetan Laurens, Julien Lam
Summary: Atomic simulations using machine learning interatomic potential (MLIP) have gained popularity due to their accuracy. However, the transferability of MLIP to systems outside the training set is challenging. This study compares the transferability of three MLIP approaches and shows the superiority of neural network potentials (NNP) and physical LassoLars interactions potential (PLIP) models. Linear models perform poorly for nanoscale systems and liquid phases, while NNP performs poorly for structural optimization of nanoparticles and molecular dynamics simulation of liquid phases.
Article
Chemistry, Physical
Raymond Weldon, Feng Wang
Summary: This study investigates two methods to convert flexible models into rigid models. The rigid model can be created based on the Model's Geometry (MG) without molecular interaction or the ensemble averaged geometry (EG) under specific thermodynamic conditions. While the MG model is more straightforward, it has relatively poor performance compared to the EG model, which behaves similarly to the corresponding flexible model (FL model) and agrees better with experiments. The difference between the EG and FL models is mainly due to flexibility, and the MG and EG models have different dipole moments in the condensed phase.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Mahabir Prasafd, Niall J. English, Somendra Nath Chakraborty
Summary: The asymmetry of donor-acceptor hydrogen bonds in liquid water is observed through molecular dynamics simulation, with one bond strengthening within donors/acceptors as temperature increases. This asymmetry is present among donors/acceptors but absent in the strongest donor-acceptor pair, highlighting the limitations of using a non-polarisable water model to capture hydrogen bond asymmetry in liquid water.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Kara K. Grotz, Nadine Schwierz
Summary: Research has made progress in accurately simulating magnesium ions in physiological processes through optimized force fields, providing a new approach to address the shortcomings of existing 12-6 Lennard-Jones potential force fields. These parameters can accurately reproduce experimental results in various water models.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Mahabir Prasad, Somendra Nath Chakraborty
Summary: The structure and dynamics of liquid water at 1 GPa and temperatures ranging from 300-230 K were investigated using molecular dynamics simulations of the TIP4P/2005 water model. The study revealed proportions of hydrogen bonded water molecules and average local coordination numbers were temperature-dependent. Additionally, similarities between high pressure liquid water and ice V were noted, along with an increase in intensities of bending and stretching modes as temperature decreased.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Yu Hu, Shuai Wang, Yurong He, Liang An
Summary: This study investigates the chemical degradation of Nafion membranes on proton transport and solvation effect using the MS-EVB method. The results show that membrane degradation alters the connectivity and coordination number of the hydrophilic domain, hindering proton transport along the membrane side chain.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Itai Leven, Hongxia Hao, Songchen Tan, Xingyi Guan, Katheryn A. Penrod, Dooman Akbarian, Benjamin Evangelisti, Md Jamil Hossain, Md Mahbubul Islam, Jason P. Koski, Stan Moore, Hasan Metin Aktulga, Adri C. T. van Duin, Teresa Head-Gordon
Summary: This perspective summarizes recent efforts to improve the performance of reactive force fields, focusing on the ReaxFF model. Recent advances in improving accuracy include reformulating charge equilibration schemes, accounting for explicit electrons, and addressing energy conservation issues. Enhancements in transferability involve explicit treatment of electrons and hybrid simulations, while efforts to address computational cost are seen in extended Lagrangian schemes and software performance improvements in LAMMPS.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
S. Blazquez, M. M. Conde, J. L. F. Abascal, C. Vega
Summary: This work presents an extension of the Madrid-2019 force field, which adds several ions and accurately describes the properties of aqueous solutions. The developed force field shows good agreement with experimental results and provides insights on the ion pair effects in electrolyte solutions.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Federica Lodesani, Maria Cristina Menziani, Shingo Urata, Alfonso Pedone
Summary: This study systematically investigates the effects of simulation conditions on crystallization in highly viscous systems and finds that bias factor and temperature are the most effective parameters. Moreover, temperature rescaling proves to be a reliable approach for recovering free energy surfaces at lower temperatures.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Kohler
Summary: The introduction of flexibility in water force fields during molecular dynamics simulations of nanoconfined water has a significant impact on viscosity, diffusion, and dipole orientation. The level of confinement and the choice of force-field family greatly influence the behavior of water molecules in nanoconfined systems.
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Koehler
Summary: This study investigates the effects of introducing flexibility in water force fields on molecular dynamics simulations of nanoconfined water. The results show that viscosity, diffusion, and dipole orientation are greatly influenced by the flexibility and the family of force fields used.
Article
Chemistry, Physical
Johan Aqvist, Florian van der Ent
Summary: This study investigates the impact of heat capacity changes on temperature optima in enzyme catalysis, proposing methods to calculate the activation free energy's temperature dependence and absolute heat capacities of reactants and transition states through molecular dynamics simulations. It also provides a new scheme for calculating absolute heat capacity changes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
David Montes de Oca Zapiain, Mitchell A. Wood, Nicholas Lubbers, Carlos Z. Pereyra, Aidan P. Thompson, Danny Perez
Summary: Advances in machine learning have made it possible to develop interatomic potentials with both the accuracy of first principles methods and the efficiency of empirical potentials. However, achieving transferability remains a challenge for machine learning-based potentials. This study focuses on developing systematic and scalable approaches to generate diverse training sets, and evaluates the performance of different potentials trained on these datasets.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Chemistry, Physical
Noura Dawass, Jilles Langeveld, Mahinder Ramdin, Elena Perez-Gallent, Angel A. Villanueva, Erwin J. M. Giling, Jort Langerak, Leo J. P. van den Broeke, Thijs J. H. Vlugt, Othonas A. Moultos
Summary: In this study, molecular simulations were used to compute the properties of mixed solvents composed of deep eutectic solvents (DES) and organic solvents. The results show that adding DES to the organic solvents can increase the solubilities of oxalic and formic acids, but also increases the density and viscosity of the mixed solvents. Additionally, the self-diffusivities and ionic conductivities decrease as more DES is added to the mixtures.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Thermodynamics
W. A. van Rooijen, P. Habibi, K. Xu, P. Dey, T. J. H. Vlugt, H. Hajibeygi, O. A. Moultos
Summary: In this study, molecular dynamics and continuous fractional component Monte Carlo simulations were conducted to fill in the gaps in thermodynamic and transport property data for hydrogen technologies. New data sets were obtained for interfacial tensions, self-diffusivities, and solubilities of hydrogen in aqueous sodium chloride solutions. The simulation results showed excellent agreement with available experimental data, with average deviations lower than 10%.
JOURNAL OF CHEMICAL AND ENGINEERING DATA
(2023)
Review
Chemistry, Multidisciplinary
Vikram Korede, Nagaraj Nagalingam, Frederico Marques Penha, Noah van der Linden, Johan T. Padding, Remco Hartkamp, Huseyin Burak Eral
Summary: Crystallization is widely present in nature and industrial practices, but our control over the process is incomplete. This limits our ability to engineer crystalline products and hinders progress towards a sustainable circular economy. Laser-induced crystallization approaches show promise in manipulating crystallization using light-material interactions. In this review, we discuss various mechanisms and experimental setups for laser-induced nucleation and crystallization, emphasizing interdisciplinary exchange of ideas.
CRYSTAL GROWTH & DESIGN
(2023)
Review
Engineering, Chemical
Mahinder Ramdin, Othonas A. Moultos, Leo J. P. van den Broeke, Prasad Gonugunta, Peyman Taheri, Thijs J. H. Vlugt
Summary: Electrochemical reduction of carbon dioxide (CO2) to useful products with renewable electricity is a promising concept. However, carbonation, the formation of (bi)carbonate, is a major challenge in scaling up the process. It leads to various issues including low carbon utilization efficiencies and additional costs. In this review, the causes, consequences, and potential solutions for carbonation effect in CO2 electrolyzers are discussed, aiming to provide guidance for research in low-temperature CO2 electrolysis in alkaline media.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Chemistry, Physical
Silvestros Oikonomidis, Mahinder Ramdin, Othonas A. Moultos, Albert Bos, Thijs J. H. Vlugt, Ahmadreza Rahbari
Summary: This research develops a transient model of a multi-cell stack for alkaline water electrolyzers, which accurately describes the operation of the electrolyzer under dynamically changing conditions. The study finds that the geometrical volume of the gas separators and the number of cells in the stack significantly affect the dynamic response and transition to steady state. This model serves as a tool for sizing and process management of the electrolyzer system, particularly in relation to explosion safety.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2023)
Article
Chemistry, Physical
H. Mert Polat, Frederick de Meyer, Celine Houriez, Othonas A. Moultos, Thijs J. H. Vlugt
Summary: We developed an open-source chemical reaction equilibrium solver in Python (CASpy) to compute the concentration of species in any reactive liquid-phase absorption system. The computed CO2 absorption isotherms and speciations showed excellent agreement with experimental data, demonstrating the accuracy and precision of our solver. However, the computed CO2 pressures were significantly underestimated due to the sensitivity of the simulations to the point charges used.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Othonas A. A. Moultos, Ioannis N. N. Tsimpanogiannis
Summary: This study compares experimental and molecular simulation data for the intra-diffusivities of H-2 and O-2 in H2O, as well as the self-diffusivity of pure H2O, with calculations based on theoretical methods. A novel methodology is proposed to extrapolate the intra-/self-diffusivities data computed from molecular dynamics simulations at low pressures. The extrapolated values are used to refine a recent molecular simulation-based correlation of intra-/self-diffusivities as a function of pressure and temperature with the solvent in the vapor phase.
Article
Engineering, Electrical & Electronic
Nagaraj Nagalingam, Aswin Raghunathan, Vikram Korede, Edwin F. J. Overmars, Shih-Te Hung, Remco Hartkamp, Johan T. Padding, Carlas S. Smith, Huseyin Burak Eral
Summary: Optofluidic devices have greatly advanced the manipulation and transport of fluid at small scales. In this study, we present a specialized optical setup for investigating laser-induced cavitation within microchannels. By evaporating a dye-laced solution with a tightly focused laser beam, we can create a microbubble and track its interface using high-speed microscopy and digital image analysis. Additionally, we demonstrate how this system can be adapted for fluid flow analysis through fluorescence-Particle Image Velocimetry (PIV) technique. We also provide guidelines for constructing a fluorescence microscope from scratch using standard optical components, offering flexibility in design and cost-effectiveness compared to commercial alternatives.
Article
Engineering, Chemical
Parsa Habibi, Julien R. T. Postma, Johan T. Padding, Poulumi Dey, Thijs J. H. Vlugt, Othonas A. Moultos
Summary: In this study, molecular dynamics simulations were used to calculate the viscosities, electrical conductivities, and self-diffusivities of the NaBH4 hydrolysis reaction solution, as well as the solubilities and activities of H2 and water in the solution. By developing a new force field model, the densities and viscosities of the solution can be accurately simulated, and engineering equations were proposed for the design and modeling of NaBH4 hydrolysis reactors.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Thermodynamics
Bin Fang, Parsa Habibi, Othonas A. Moultos, Tao Lu, Fulong Ning, Thijs J. H. Vlugt
Summary: Continuous Fractional Component Monte Carlo (CFCMC) and molecular dynamics (MD) simulations were used to calculate the solubilities and self-diffusion coefficients of four light n-alkanes in aqueous NaCl solutions, as well as the thermodynamic properties of their corresponding hydrate crystals. Correction factors for alkane groups (CH3) and water were optimized by fitting excess chemical potentials to experimental data. Using these values, the solubilities of the four alkanes in NaCl solutions with different molalities and temperatures, and the diffusion coefficients in NaCl solutions were calculated. The lattice parameters and thermodynamic properties of the hydrates with different guest molecules were also computed. This research provides valuable thermodynamic data for understanding natural gas hydrate science.
JOURNAL OF CHEMICAL AND ENGINEERING DATA
(2023)
Article
Chemistry, Physical
Samuel Blazquez, Jose L. F. Abascal, Jelle Lagerweij, Parsa Habibi, Poulumi Dey, Thijs J. H. Vlugt, Othonas A. Moultos, Carlos Vega
Summary: In this study, the electrical conductivities of aqueous NaCl and KCl solutions under ambient conditions were computed using the Einstein-Helfand equation. Conventional force fields could not accurately predict the experimental values of electrical conductivities, viscosities, and diffusion coefficients. However, by introducing the concept of using different charges to describe the potential energy surface and the dipole moment surface, excellent agreement with experimental results was achieved for the first time for the entire concentration range.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Polymer Science
Christos Gioldasis, Apostolos Gkamas, Othonas A. Moultos, Costas Hristos Vlahos
Summary: In this study, the chemical feedback between building blocks in the templated polymerization of diblock copolymers and their consecutive micellization was investigated using coarse-grained molecular dynamics simulations. The simulation results were in agreement with experimental findings, showing that templated micellization forms more spherical micelles with a smaller radius of gyration compared to traditional two-step micellization. Molecular simulation offers advantages over traditional kinetic models by allowing for a detailed study of heterogeneous polymerization in the presence of oppositely charged templates and accounting for the incompatibility between reacted species, which has a significant influence on the reaction process.
Article
Thermodynamics
H. Mert Polat, Casper van der Geest, Frederick de Meyer, Celine Houriez, Thijs J. H. Vlugt, Othonas A. Moultos
Summary: Through molecular dynamics simulations, the effects of temperature and N-methyldiethanolamine (MDEA) concentration on the self-diffusivities of CO2 and H2S in aqueous MDEA solutions were studied. The densities and viscosities of the solutions were computed, showing good agreement with experimental data. The self-diffusivities of CO2 and H2S were found to depend significantly on temperature and MDEA concentration, and were slower compared to aqueous MEA solutions. The strong interactions between H2S and surrounding molecules were observed, leading to slower diffusion in aqueous MDEA solutions. The results will contribute to the design and optimization of acid gas removal units.
FLUID PHASE EQUILIBRIA
(2023)
Article
Chemistry, Physical
Eleni Ntone, Benjamin Rosenbaum, Simha Sridharan, Stan B. J. Willems, Othonas A. A. Moultos, Thijs J. H. Vlugt, Marcel B. J. Meinders, Leonard M. C. Sagis, Johannes H. H. Bitter, Constantinos V. V. Nikiforidis
Summary: It has been reported that lipid droplets, known as oleosomes, have the ability to inflate or shrink when absorbing or fueling lipids in cells due to the dilatable property of their phospholipid/protein membrane. By extracting oleosomes from rapeseeds, researchers were able to observe the rearrangement of phospholipids on the droplet surface and confirmed weak lateral interactions on the oleosome membrane. They also discovered that the weak lateral interactions can be triggered by external forces, resulting in the destabilization of oleosomes and targeted release of oil. This unique property could have applications in the food, pharmaceutical, and cosmetic industries.
Article
Construction & Building Technology
Lili Ma, Hirad S. Salehi, Ruxin Jing, Sandra Erkens, Thijs J. H. Vlugt, Othonas A. Moultos, Michael L. Greenfield, Aikaterini Varveri
Summary: This study investigates the water transport in bitumen and the clustering behavior of water molecules using molecular dynamics simulations. The results reveal that the water concentration in bitumen is low, and additional water molecules tend to form large clusters via hydrogen bonding, indicating micro-phase separation of water and bitumen. Hydrogen bonding and water clustering have a significant impact on the self-diffusion coefficient of water and the physical properties of bitumen.
CONSTRUCTION AND BUILDING MATERIALS
(2023)
