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Handbook of Materials Modeling (Applications: Current and Emerging Materials) || Incorporating Electronic Effects in Molecular Dynamics Simulations of Neutron and Ion-Induced Collision Cascades
摘要： Molecular dynamics offers an ideal method for investigating the evolution of collision cascades and the formation of the resulting primary radiation damage. However, several modifications to classical molecular dynamics are needed in order to facilitate simulating the highly non-equilibrium cascade process. One such modification, which is still a point of active research, concerns methods by which electronic effects, which are expected to be important in collision cascades, can be included in molecular dynamics simulations, where a priori atoms are treated as classical particles and electrons are only present implicitly through the atomic interactions represented by the interatomic potential. This chapter describes current methods by which electronic effects can be accounted for in cascade simulations, with special focus on the developments in the field that have taken place over the last 10 years.
关键词： interatomic potential,collision cascades,electronic effects,radiation damage,Molecular dynamics
更新于2025-09-23 15:21:21
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Prediction of Strong Piezoelectricity in 3R-MoS2 Multilayer Structures
摘要： We present the first calculation of piezoelectric constants of 3R-MoS2 which is one of three known polytypes of MoS2. We demonstrate that the 3R-MoS2 structure with 5 layers has the highest reported piezoelectric constant of all MoS2 multilayer structures. The maximum piezoelectric constant is approximately 13% above the monolayer value. Also 3R-MoS2 structures with 4 and 6 layers have a larger piezoelectric coefficient compared to monolayer MoS2. Results are obtained using the molecular dynamics computational package LAMMPS subject to room temperature simulations. Our results indicate strong potential for multilayer 3R-MoS2 structures in nanosensor and nanogenerator applications.
关键词： Piezoelectric coefficient,3R-MoS2,Multilayers,Molecular dynamics
更新于2025-09-23 15:21:21
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NEXMD Modeling of Photoisomerization Dynamics of 4-Styrylquinoline
摘要： Isomerization of molecular systems is ubiquitous in chemistry and biology, and is also important for many applications. Atomistic simulations can help determine the tunable parameters influencing this process. In this paper, we use the Nonadiabatic EXcited-state Molecular Dynamics (NEXMD) software to study the photoisomerization of a representative molecule, 4-styrylquinoline (SQ). Trans-SQ transforms into dihydrobenzophenanthridine (DHBP) upon irradiation with laser light, with the cis conformer acting as an intermediate. We study how varying three different external stimuli (i.e., apolar versus polar solvent, low versus high photoexcitation energy, and vacuum versus a constant temperature thermostat) affects the trans-to-cis photoisomerization of SQ. Our results show that polarization effects due to implicit solvation and the thermostat play a crucial role in the isomerization process, whereas photoexcitation energy plays a lesser role on the outcome and efficiency. We also show that NEXMD captures the correct energy profile between the ground and first singlet excited state, showing that there are two distinct reaction pathways to the final stable product that vary by the number of photons absorbed, in agreement with experiment. Ultimately, NEXMD proves to be an effective tool for investigating excited state single molecule dynamics subject to various environments and initial conditions.
关键词： Isomerization,Molecular Dynamics,NEXMD,4-styrylquinoline,Photoisomerization
更新于2025-09-23 15:21:21
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Disentangling Coupling Effects in the Infrared Spectra of Liquid Water
摘要： A quantitative characterization of intermolecular and intramolecular couplings that modulate the OH-stretch vibrational band in liquid water has so far remained elusive. Here, we take up this challenge by combining the centroid molecular dynamics (CMD) formalism, which accounts for nuclear quantum effects, with the MB-pol potential energy function, which accurately reproduces the properties of water across all phases, to model the infrared (IR) spectra of various isotopic water solutions with different levels of vibrational couplings, including those that cannot be probed experimentally. Analysis of the different IR OH-stretch lineshapes provides direct evidence for the partially quantum-mechanical nature of hydrogen bonds in liquid water, which is emphasized by synergistic effects associated with intermolecular coupling and many-body electrostatic interactions. Furthermore, we quantitatively demonstrate that intramolecular coupling, which results in Fermi resonances due to the mixing between HOH-bend overtones and OH-stretch fundamentals, are responsible for the shoulder located at ～3250 cm?1 of the IR OH-stretch band of liquid water.
关键词： liquid water,nuclear quantum effects,infrared spectra,Fermi resonances,centroid molecular dynamics,hydrogen bonds,intramolecular coupling,intermolecular coupling,MB-pol potential energy function
更新于2025-09-23 15:21:21
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Characterizing Molecular Adsorption on Biodegradable MnO <sub/>2</sub> Nanoscaffolds
摘要： Biodegradable MnO2 nanoscaffolds have recently been designed for advanced stem cell therapy. These nanomaterials strongly bind extracellular matrix proteins and effectively deliver therapeutic molecules, which significantly enhance stem cell survival and neuronal differentiation both in vitro and in vivo. In this work, we combine molecular dynamics simulations, density functional theory calculations and UV-Vis spectroscopy experiments to examine the selectivity and efficiency of a MnO2 nanosheet in adsorbing neurogenic drugs. To uncover the fundamental principles governing the drug loading process, we have systematically examined a series of model aromatic and alkyl compounds with characteristic functional groups and demonstrated that molecular adsorption on the MnO2 nanosheet results from an interplay of dispersion, electrostatic and charge transfer interactions. We have then proposed a metric that efficiently predicts the qualitative adsorption affinity of a guest molecule on the MnO2 nanosheet based on its structural and chemical features, which will facilitate the experimental screening of proper adsorbates for efficient molecular delivery and aid the development of MnO2-based nanoscaffolds for biomedical applications.
关键词： adsorption affinity,molecular dynamics simulations,density functional theory,MnO2 nanoscaffolds,neurogenic drugs,UV-Vis spectroscopy
更新于2025-09-23 15:21:21
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Structural determination of phosphosilicate glass based on first-principles molecular dynamics calculation
摘要： We report static and dynamic first-principles calculations determining the structure and electronic properties of phosphosilicate glass (PSG). A stable structure of PSG with composition of (SiO2)x(P2O5)y was calculated by simulated annealing based on Car–Parrinello molecular dynamics (CPMD) with a real-space density functional theory (RSDFT) code. As a result, phosphorus (P) atoms in PSG were four-fold coordinated with oxygen (O) atoms and one of the four PO bonds was dangling toward the interstitial region (an –O3PO configuration). We also compared the structures having a different number of O atoms to discuss the stable configuration of PSG in the realistic situation of phosphoryl chloride (POCl3) annealing. We found that –O3PO is most stable for O2-rich conditions, whereas three-coordinate P (an –O3P configuration) becomes stable in O2-poor conditions. The candidates of the states which create levels inside the bandgap of PSG were also calculated.
关键词： phosphosilicate glass,molecular dynamics,first-principles calculation,electronic properties,POCl3 annealing
更新于2025-09-23 15:21:21
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Effects of vacancy defects location on thermal conductivity of silicon nanowire: a molecular dynamics study
摘要： The improvement of thermoelectric ?gure of merit of silicon nanowire (SiNW) can be achieved by lowering its thermal conductivity. In this work, non-equilibrium molecular dynamics method was used to demonstrate that the thermal conductivity of bulk silicon crystal is drastically reduced when it is crafted as SiNW and that it can be reduced remarkably by including vacancy defects. It has been found that ‘centre vacancy defect’ contributes much more in reducing the thermal conductance than ‘surface vacancy defect’. The lowest thermal conductivity that occurs is about 52.1% of that of pristine SiNW, when 2% vacancy defect is introduced in the nanowire. The vibrational density of states analysis was performed to understand the nature of this reduction and it has been found that the various boundary scatterings of phonon signi?cantly reduce the thermal conductivity. Also, larger mass difference due to voids induces smaller thermal conductivity values. These results indicate that the inclusion of vacancy defects can enhance the thermoelectric performance of SiNWs.
关键词： molecular dynamics,silicon nanowire,thermoelectric performance,thermal conductivity,vacancy defects
更新于2025-09-23 15:21:21
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Laser control of molecular rotation: Expanding the utility of an optical centrifuge
摘要： Since its invention in 1999, the optical centrifuge has become a powerful tool for controlling molecular rotation and studying molecular dynamics and molecular properties at extreme levels of rotational excitation. This technique has been applied to a variety of molecular species, from simple linear molecules to symmetric and asymmetric tops, to molecular ions and chiral enantiomers. Properties of isolated ultrafast rotating molecules, the so-called molecular superrotors, have been investigated, as well as their collisions with one another and the interaction with external fields. The ability of an optical centrifuge to spin a particular molecule of interest depends on both the molecular structure and the parameters of the centrifuge laser pulse. An interplay between these two factors dictates the utility of an optical centrifuge in any specific application. Here, we discuss the strategy of assessing and adjusting the properties of the centrifuge to those of the molecular rotors and describe two practical examples of optical centrifuges with very different characteristics, implemented experimentally in our laboratory.
关键词： laser control,molecular rotation,molecular dynamics,molecular superrotors,optical centrifuge
更新于2025-09-23 15:21:01
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Fluorinated graphene nanoparticles with 1-3 nm electrically active graphene quantum dots
摘要： A new perspective approach to how to create a new and locally nanostructured graphene-based material is reported on. We studied the electric and structural properties for the partially fluorinated graphene (FG) films obtained from a FG-suspension and nanostructured by high-energy Xe ions. Local shock heating in ion tracks is suggested to be the main driving force of the changes. It was found that ion irradiation leads to the formation of locally thermal expanded FG and its cracking into nanosized nanoparticles with embedded small (~1.5-3 nm) graphene quantum dots, which band gap was estimated as 1-1.5 eV, into them. A further developed approach was applied to correction of the functional properties of the printed FG-based crossbar memristors. Dielectric FG films with small quantum dots may offer prospects in graphene-based electronics due to their stability and promising properties.
关键词： memristor,molecular dynamics simulation,nanostructuring,swift ion irradiation,fluorinated graphene,graphene quantum dots
更新于2025-09-23 15:21:01
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Graphene Foam: Hole-Flake Network for Uniaxial Supercompression and Recovery Behavior
摘要： We employed the coarse-grained molecular dynamics simulation method to systematically study the uniaxial supercompression and recovery behavior of multi-porous graphene foam, in which a mesoscopic three-dimensional network with hole-graphene flakes was proposed. The network model not only considers the physical cross-links and interlayer van der Waals interactions, but also introduces a hole in the flake to approach the imperfection of pristine graphene and the hierarchical porous configuration of real foam material. We first recreated a typical two-stage supercompression stress?strain relationship and the corresponding time-dependent recovery as well as a U-type nominal Poisson ratio. Then the recovery unloading at different strains and multicycle compression?uncompression were both conducted; the initial elastic moduli in the multicycles were found to be the same, and a multilevel residual strain was disclosed. Importantly, the residual strain is not exactly the plastic one, part of which can resurrect in the subsequent loading?unloading?holding. The mesoscopic mechanism of viscoelastic and residual deformation for the recovery can be attributed to the van der Waals repulsion and mechanical interlocking among the hole-flakes; interestingly, the local tensile stress was observed in the virial stress distribution. Particularly, an abnormal turning point in the length-time curve for the mean bead-bond length was captured during the supercompression. After the point, the length abnormally increases for different size ratios of the hole to the flake, which is in line with the mesostructure evolution. The finding may provide a mesoscopic criterion for the supercompression of graphene foam related materials.
关键词： supercompression,strain history,recovery behavior,mesoscale,van der Waals interaction,viscoelastoplasticity,graphene foam,coarse-grained molecular dynamics
更新于2025-09-23 15:21:01