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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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Argon clustering in silicon under low-energy irradiation: Molecular dynamics simulation with different Ar–Si potentials
摘要： In this paper, the authors carried out a molecular dynamics simulation of crystal and amorphous silicon sputtering by low-energy (200 eV) Ar ions at normal incidence. The gradual damage of silicon caused by the ion bombardment was taken into account in order to study the dynamics of argon accumulation and clustering. For describing interatomic Ar–Si interaction, they used three different potentials: two binary screened Coulomb potentials (Molière and Ziegler–Biersack–Littmark) and the potential developed on the basis of density functional theory. The obtained results demonstrated the substantial influence of the chosen Ar–Si potential on calculated sputtering yields and on the processes of argon accumulation and clustering.
关键词： silicon sputtering,molecular dynamics simulation,Ar–Si potentials,argon clustering,low-energy irradiation
更新于2025-09-23 15:21:01
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A study of deformation behavior and phase transformation in 4H-SiC during nanoindentation process via molecular dynamics simulation
摘要： The deformation behavior and phase transformation of 4H silicon carbide (4H-SiC) during nanoindentation process is investigated with a cube corner diamond indenter through molecular dynamics simulation. It is found through the research that the basal dislocations are most likely to be generated in (0001) face and the indentation process contributes to the distortion of 4H-SiC lattice. In addition, phase transformation from 4H-SiC to 3C-SiC is firstly observed via MD simulations during indentation process. Cross-sectional observation in (12 10) plain shows that 3C-SiC layers appear firstly during nanoindentation process, and the layers are observed at small indentation depth. 3C-SiC grain is generated based on 3C-SiC layers, and the transformation is more likely to appear at larger indentation depth. The phase transformation from 4H-SiC to 3C-SiC results from the shear stress induced by indenter during loading process. 3C-SiC grain and layers are both generated from the slip of 3C seeds under the influence of shear stress, and the condition of 3C-SiC grain formation is stricter. Moreover, the P-h curve is studied and the vertical deformation mode during indentation process on 4H-SiC can be reflected on P-h curve as small pop-in events. The findings are meaningful for the study of deformation mechanism of SiC and the application of SiC in precision machining.
关键词： molecular dynamics simulation,cube corner diamond indenter,3C-SiC grain,4H-SiC,phase transformation,3C-SiC layer
更新于2025-09-23 15:21:01
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Grain size dependence of tensile properties in nanocrystalline diamond
摘要： Nanocrystalline diamond (NCD) is a promising material due to its extraordinary mechanical properties, however, the research on the dependence of mechanical properties on the grain size (d) of NCD is still limited. In this paper, the mechanical behavior of 3D NCD with various d is investigated using molecular dynamics (MD) simulations. It was found that the mechanical properties of NCD are sensitive to d. The Young's modulus (E) increases with the increase of d due to the increasing fraction of grain interiors (GIs), while the failure strain (εf) decreases with the increase of d due to the decreasing fraction of grain boundaries (GBs). It was also found that the failure strength (σf) decreases with the increase of d, which could be attributed to that for larger d the stress concentration in the GBs is severer, which may make cracks initiate more easily. Similar to εf and σf, the deformation work density was found to increase with the decrease of d, indicating the enhancement of toughness of NCD when d is small. For the samples of different d, the nucleation and propagation of both transgranular and intergranular cracks are the main failure mechanisms, which is consistent with experimental observations.
关键词： Molecular dynamics simulation,Mechanical property,Nanocrystalline diamond,Tension,Grain size
更新于2025-09-23 15:21:01
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Structural Evolutions of Vertically-Aligned Two-Dimensional MoS <sub/>2</sub> Layers Revealed by <i>In Situ</i> Heating Transmission Electron Microscopy
摘要： Benefited from a large density of layer edges exposed on the surface, vertically-aligned two-dimensional (2D) molybdenum disulfide (MoS2) layers have recently harvested excellent performances in the field of electrochemical catalysis and chemical sensing. With their increasing versatility for high-temperature demanding applications, it is vital to identify their thermally-driven structural and chemical stability as well as clarify its underlying principle. Despite various ex situ and in situ characterizations on horizontally-aligned 2D MoS2 layers, the direct in situ heating of vertically-aligned 2D MoS2 layers and the real-time observation of their near-atomic scale dynamics have never been approached, leaving their thermal stability poorly understood. Moreover, the geometrical advantage of the surface-exposed vertically-aligned 2D MoS2 layers is anticipated to unveil the structural dynamics of interlayer van der Waals (vdW) gaps and its correlation with thermal energy, unattainable with 2D MoS2 layers in any other geometry. Herein, we report a comprehensive in situ heating TEM study on cleanly transferred vertically-aligned 2D MoS2 layers up to 1000 °C. Several striking phenomena were newly observed in the course of heating: (1) formation and propagation of voids between the domains of vertical 2D MoS2 layers with distinct grain orientations starting at ~875 °C, (2) subsequent decompositions of the 2D MoS2 layers accompanying a formation of Mo nanoparticles at ~950 °C, much lower than the melting temperature of their bulk counterpart, and (3) initiation of decomposition from the surface-exposed 2D layer vertical edge sites, congruently supported by molecular dynamics (MD) simulation. These new findings will offer critical insights into better understanding the thermodynamic principle that governs the structural stability of general vdW 2D crystals as well as providing useful technological guidance for materials design and optimization in their potential high-temperature applications.
关键词： van der Waals gaps,in situ heating,structural evolution,MoS2,two-dimensional,vertically-aligned,transmission electron microscopy,thermal stability,molecular dynamics simulation
更新于2025-09-23 15:19:57
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Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies
摘要： The precise positioning of catalytic amino acids against the substrate in an enzyme active site is a crucial factor in biocatalysis. Biosynthesis of the chromophores of fluorescent proteins (FPs) is an autocatalytic process that must conform to these requirements. Here, we show that, in addition to the internal amino acid residues in the proximity of the chromophore, chromophore biosynthesis is influenced by the remote amino acids exposed on the outer surface of the β-barrel structure of the FP. It has been shown earlier that chromophore biosynthesis of the red FP from Zoanthus sp. (zoan2RFP) proceeds via an immature green state. At the same time, the green state is the final stage of chromophore biosynthesis of green FP (zoanGFP), which is highly homologous to zoan2RFP. It was also shown that a single N66D substitution in the chromophore-forming sequence of zoanGFP might trigger the synthesis of the red chromophore. However, in this case, the synthesis of the red chromophore is incomplete and occurs only at elevated temperatures. Here, we tried to uncover additional structural determinants that govern the biosynthesis of the red chromophore. A comparison of zoanGFP and zoan2RFP revealed intrabarrel amino acid differences at five positions. Exhaustive substitutions of these five positions in zoanGFP-N66D gave rise to zoanGFPmut with the same intrabarrel amino acid composition as zoan2RFP. zoanGFPmut showed only partial green-to-red chromophore transformation at elevated temperatures. To elucidate the extra factors that can affect red chromophore biosynthesis, we performed comparative molecular dynamics simulations of zoan2RFP and zoanGFPmut. The simulations revealed several external amino acids that might influence the arrangement and flexibility of the chromophore-surrounding amino acid residues in these proteins. Mutagenesis experiments confirmed the crucial role of these residues in red chromophore biosynthesis. The obtained zoanGFPmut2 exhibited complete green-to-red transformation, suggesting that the mutated amino acids exposed on the surface of the β-barrel contribute to red chromophore biosynthesis.
关键词： autocatalysis,chromophore,protein engineering,fluorescent protein,molecular dynamics simulation,long-range interaction
更新于2025-09-23 15:19:57
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Self-assembled nanorods in YBCO matrix a?? a computational study of their effects on critical current anisotropy
摘要： In order to understand how the doping with self-assembled nanorods of different sizes and concentrations as well as applied magnetic fields affect the critical current anisotropy in YBa2Cu3O7?x (YBCO) thin films close to YBCO c-axis, we present an extensive and systematic computational study done by molecular dynamics simulation. the simulations are also used to understand experimentally measured Jc(θ) curves for BaHfO3, BaZrO3 and BaSnO3 doped YBCO thin films with the help of nanorod parameters obtained from transmission electron microscopy measurements. our simulations reveal that the relation between applied and matching field plays a crucial role in the formation of Jc(θ)-peak around YBCO c-axis (c-peak) due to vortex-vortex interactions. We also find how different concentrations of different size nanorods effect the shape of the c-peak and explain how different features, such as double c-peak structures, arise. In addition to this, we have quantitatively explained that, even in an ideal superconductor, the overdoping of nanorods results in decrease of the critical current. our results can be widely used to understand and predict the critical current anisotropy of YBco thin films to improve and develop new pinscapes for various transport applications.
关键词： critical current anisotropy,molecular dynamics simulation,YBCO,flux pinning,self-assembled nanorods
更新于2025-09-23 15:19:57
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Enhanced heat capacity of binary nitrate eutectic salt-silica nanofluid for solar energy storage
摘要： In concentrating solar power plants, the heat capacity of thermal storage media is a key factor that affects the cost of electricity generation. This work investigated the effective specific heat capacity of binary nitrate eutectic salts seeded with silica nanoparticles, using both experimental measurements and molecular dynamics simulations. The effects of the mass concentration (0–2.0 wt%) and average size (10, 20, and 30 nm) of the nanoparticles on the specific heat capacity value of nanofluids were analyzed. The results show that specific heat capacity increases when adding 10 nm silica nanoparticles up to 1.0 wt%, and then it decreases at higher concentrations. At this optimal mass concentration, the 20 nm nanoparticles displayed a maximum enhancement in the average specific heat capacity (by ~26.7%). The simulation results provided information about the different energy components in the system. The rate of potential energy change versus nanoparticle mass concentration was found to be maximized at 1.0 wt% concentration, which agrees with the experimental measurements. The potential energy components in the simulation system indicate that the change of Coulombic energy contributes the most to the variation of specific heat capacity.
关键词： Molten salt based nanofluids,Molecular dynamics simulation,Solar energy storage,Specific heat capacity
更新于2025-09-23 15:19:57
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Self-assembled monolayer for polymer-semiconductor interface with improved interfacial thermal management
摘要： Reliability and lifespan of highly miniaturized and integrated devices will be effectively improved if excessive accumulated heat can be quickly transported to heat sinks. In this study, both molecular dynamics (MD) simulations and experiments were performed to demonstrate that self-assembled monolayers (SAMs) have high potential in interfacial thermal management and can enhance thermal transport across polystyrene (PS) / silicon (Si) interface, modelling the common polymer/semiconductor interfaces in actual devices. The influence of packing density and alkyl-chain length of SAMs are investigated. Firstly, MD simulations show that the interfacial thermal transport efficiency of SAM is higher with high packing density. The interfacial thermal conductance (ITC) between PS and Si can be improved up to 127 ± 9 MW m-2 K-1, close to the ITC across metal and semiconductor interface. At moderate packing density, the SAMs with less than 8 carbon atoms in alkyl-chain show superior improvements over those with more carbons due to the assembled structure variation. Secondly, time-domain thermoreflectance technique was employed to characterize the ITCs of a bunch of Al/PS/SAM/Si samples. C6-SAM enhances the ITC by 5 folds, from 11 ± 1 MW m-2 K-1 to 56 ± 17 MW m-2 K-1. The interfacial thermal management efficiency will weaken when alkyl-chain exceeds 8 carbon atoms, which agrees with the ITC trend from MD simulations at moderate packing density. The relationship between SAM morphology and interfacial thermal management efficiency is also discussed in detail. This study demonstrates the feasibility of molecular level design for interfacial thermal management from both theoretical calculation and experiment, and may provide a new idea for improving the heat dissipation efficiency of micro devices.
关键词： polymer/semiconductor interface,time-domain thermoreflectance,molecular dynamics simulation,self-assembled monolayer,interfacial thermal management
更新于2025-09-11 14:15:04
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[Advances in Experimental Medicine and Biology] Glycobiophysics Volume 1104 || Synchrotron-Radiation Vacuum-Ultraviolet Circular-Dichroism Spectroscopy for Characterizing the Structure of Saccharides
摘要： Circular-dichroism (CD) spectroscopy is a powerful tool for analyzing the structures of chiral molecules and biomolecules. The development of CD instruments using synchrotron radiation has greatly expanded the utility of this method by extending the spectra to the vacuum-ultraviolet (VUV) region below 190 nm and thereby yielding information that is unobtainable by conventional CD instruments. This technique is especially advantageous for monitoring the structure of saccharides that contain hydroxy and acetal groups with high-energy transitions in the VUV region. Combining VUVCD spectra with theoretical calculations provides new insight into the contributions of anomeric hydroxy groups and rotational isomers of hydroxymethyl groups to the dynamics, intramolecular hydrogen bonds, and hydration of saccharides in aqueous solution.
关键词： Glycoprotein,Hydration,Circular dichroism,Synchrotron radiation,Time-dependent density functional theory,Molecular dynamics simulation,Saccharide,Intramolecular hydrogen bond,Solution structure,Structural dynamics,Vacuum ultraviolet,Glycosaminoglycan
更新于2025-09-10 09:29:36