Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Mao, Qian; Feng, Muye; Ren, Yihua; Luo, Kai H.; Duin, Adri C. T. van

doi:10.1016/j.pecs.2023.101084

Cited by 60 publications

(22 citation statements)

References 455 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The approach is capable of investigating the phenomena containing a chemical reaction, charge transfer, and electron excitation and hence is beyond the complexity required for understanding PFAS dynamics. 44,47,50 In contrast to AIMD, for classic MD simulations, electronic structures are not directly considered, while atomic-level resolution is retained. Solving Newton's equation of motion for a system of atoms and/or molecules forms the central task of classical MD, just as solving the Schrodinger equation is the central tenant of quantum mechanics.…”

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

“…The disadvantage, however, is that in a classical MD simulation the subatomic electronic structure and dynamics are not computed, so inherently quantum-mechanical events, such as chemical reactions (i.e., chemical bond breaking and formation), photoinduced processes, and charge transfer are excluded. 50 To ensure numerical stability, the time steps in an MD simulation must be short, typically only a few femtoseconds (10 −15 s) each. Most of the events of biochemical interest take place on time scales of nanoseconds, microseconds, or longer.…”

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

“…This method is very accurate but computationally intensive and, hence, is appropriate for systems containing 100–1000 atoms within a time duration of 1–100 ps. The approach is capable of investigating the phenomena containing a chemical reaction, charge transfer, and electron excitation and hence is beyond the complexity required for understanding PFAS dynamics. ,, …”

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

“…Once the trajectories and velocities of individual atoms and/or molecules, subjected to interatomic and/or intermolecular forces, are obtained by MD, the system’s macroscopic behaviors and properties might also be determined (upscaling). The disadvantage, however, is that in a classical MD simulation the subatomic electronic structure and dynamics are not computed, so inherently quantum-mechanical events, such as chemical reactions (i.e., chemical bond breaking and formation), photoinduced processes, and charge transfer are excluded …”

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

See 3 more Smart Citations

The Dynamics of Per- and Polyfluoroalkyl Substances (PFAS) at Interfaces in Porous Media: A Computational Roadmap from Nanoscale Molecular Dynamics Simulation to Macroscale Modeling

Sookhak Lari,

Davis,

Kumar

et al. 2024

ACS Omega

View full text Add to dashboard Cite

Managing and remediating perfluoroalkyl and polyfluoroalkyl substance (PFAS) contaminated sites remains challenging. The major reasons are the complexity of geological media, partly unknown dynamics of the PFAS in different phases and at fluid− fluid and fluid−solid interfaces, and the presence of cocontaminants such as nonaqueous phase liquids (NAPLs). Critical knowledge gaps exist in understanding the behavior and fate of PFAS in vadose and saturated zones and in other porous media such as concrete and asphalt. The complexity of PFAS−surface interactions warrants the use of advanced characterization and computational tools to understand and quantify nanoscale behavior of the molecules. This can then be upscaled to the microscale to develop a constitutive relationship, in particular to distinguish between surface and bulk diffusion. The dominance of surface diffusion compared to bulk diffusion results in the solutocapillary Marangoni effect, which has not been considered while investigating the fate of PFAS. Without a deep understanding of these phenomena, derivation of constitutive relationships is challenging. The current Darcy scale mass-transfer models use constitutive relationships derived from either experiments or field measurements, which makes their applicability potentially limited. Here we review current efforts and propose a roadmap for developing Darcy scale transport equations for PFAS. We find that this needs to be based on systematic upscaling of both experimental and computational studies from nano-to microscales. We highlight recent efforts to undertake molecular dynamics simulations on problems with similar levels of complexity and explore the feasibility of conducting nanoscale simulations on PFAS dynamics at the interface of fluid pairs.

show abstract

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

Section: Nanoscale Molecular Dynamicsmentioning

confidence: 99%

See 2 more Smart Citations

The Dynamics of Per- and Polyfluoroalkyl Substances (PFAS) at Interfaces in Porous Media: A Computational Roadmap from Nanoscale Molecular Dynamics Simulation to Macroscale Modeling

Sookhak Lari,

Davis,

Kumar

et al. 2024

ACS Omega

View full text Add to dashboard Cite

show abstract

“…However, the SEI layer may trap Li + ions, resulting in irreversible capacity loss simultaneously . Recently, several computational modeling approaches, ranging from the electronic level to the atomic/molecular scale, have been widely applied in various fields including catalysis and energy materials. , Table summarizes various computational methods with respect to the simulation time/length scale, key features, and limitations. − Each computational method with a different simulation time and length scale focuses on its distinctive features, and consequently, limitations are also evident. In this Perspective, we present the history of strategies used to model the anode/electrolyte interface structure in the field of atomic and molecular simulations and propose a perspective for interface modeling in the anode materials in lithium-ion batteries.…”

Section: Introductionmentioning

confidence: 99%

Atomistic Scale Modeling of Anode/Electrolyte Interfaces in Li-Ion Batteries

You,

Yoon,

et al. 2024

Langmuir

View full text Add to dashboard Cite

A key issue in lithium-ion batteries is understanding the solid electrolyte interphase (SEI) resulting from a reductive reaction on the anode/ electrolyte interface. The presence of the SEI layer affects the transport behavior of the ions and electrons between the anode and electrolyte. Despite the influence on interfacial properties, the formation and evolution mechanism of the SEI layer are unclear owing to their complexity and dynamic nature. Atomistic-scale simulations have promoted the understanding of the reaction mechanism on the anode/ electrolyte interface, the formation and evolution of the SEI layer, and their fundamental properties. This Perspective discusses the modeling and interpretations of anode/SEI/electrolyte interfaces through computational methods at the atomicscale and highlights interfacial modeling techniques for a realistic interface design, which can overcome the limited time and length scale with high accuracy.

show abstract

Kinetics and energetics of biodiesel oxidation stability: The impact of Uapaca kirkiana‐derived natural antioxidants

Kahimbi,

Kichonge,

Kivevele

2024

Biofuels Bioprod Bioref

View full text Add to dashboard Cite

Despite considerable progress in understanding biodiesel autoxidation inhibition, the kinetics and energetics of the inhibition reactions involving natural antioxidants remain underexplored. Most existing research on natural antioxidants has focused on enhancing oxidation stability and other fuel properties. This study aimed to investigate the oxidative stability of croton biodiesel (CBD) and assess the kinetics and energetics of natural antioxidants derived from the roots, pulp, and fruit peels of the Uapaca kirkiana plant. The oxidation stability of biodiesel samples was assessed using the OXITEST method at temperatures of 90, 100, 110, and 120 °C. These tests enabled the calculation of kinetic parameters such as reaction rates and activation energies, crucial for understanding the inhibition role of antioxidants during oxidative degradation. Activation energy for antioxidant consumption, determined using the Arrhenius equation, was found to be 81.39 kJ mol−1 for fruit peel extracts, 77.73 kJ mol−1 for pulp extracts, and 63.85 kJ mol−1 for root bark extracts. The higher activation energy for fruit peel extracts suggests that they are more effective at preventing oxidation, especially under high‐temperature conditions. Enthalpy, entropy, and Gibbs free energy parameters were calculated using the Eyring equation, indicating a nonspontaneous endothermic process for the antioxidant samples. The study found an inverse relationship between antioxidant concentration and rate constants, demonstrating the antioxidants' effectiveness in slowing down the oxidation process. These kinetics and energetics analyses provide detailed insights into how antioxidants function, facilitating the optimization, selection, and validation of their efficiency in stabilizing biodiesel.

show abstract

Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Cited by 60 publications

References 455 publications

The Dynamics of Per- and Polyfluoroalkyl Substances (PFAS) at Interfaces in Porous Media: A Computational Roadmap from Nanoscale Molecular Dynamics Simulation to Macroscale Modeling

The Dynamics of Per- and Polyfluoroalkyl Substances (PFAS) at Interfaces in Porous Media: A Computational Roadmap from Nanoscale Molecular Dynamics Simulation to Macroscale Modeling

Atomistic Scale Modeling of Anode/Electrolyte Interfaces in Li-Ion Batteries

Kinetics and energetics of biodiesel oxidation stability: The impact of Uapaca kirkiana‐derived natural antioxidants

Contact Info

Product

Resources

About