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Structural and electronic properties of liquid, amorphous, and supercooled liquid phases of In <sub/>2</sub> Te <sub/>5</sub> from first-principles
摘要： In2Te5 is a stoichiometric compound in the In–Te system of interest for applications in phase change electronic memories and thermoelectrics. Here, we perform a computational study of the structural, dynamical, and electronic properties of the liquid, supercooled liquid, and amorphous phases of this compound by means of density functional molecular dynamics simulations. Models of the supercooled liquid and amorphous phases have been generated by quenching from the melt. The structure of the liquid phase is characterized by a mixture of defective octahedral and tetrahedral local environments of In atoms, while the amorphous phase displays a mostly tetrahedral local geometry for In atoms with corner and edge sharing tetrahedra similar to those found in the crystalline phases of the In2Te5, InTe, and In2Te3 compounds. Comparison with our previous results on liquid and amorphous In2Te3 and further data on the structural properties of liquid In2Te3 are also discussed. The analysis of the electronic properties highlights the opening of a mobility gap in In2Te5 at about 150 K below the liquidus temperature.
关键词： electronic properties,In2Te5,structural properties,mobility gap,density functional molecular dynamics,phase change materials
更新于2025-09-19 17:13:59
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Enhanced Moisture Stability of Cesium Lead Iodide Perovskite Solar Cells- A First-Principles Molecular Dynamics Study
摘要： An understanding of the interaction of water with perovskite is crucial in improving the structural stability of the perovskite. Hence, in this study, the structural and electronic properties of γ-CsPbI3 (220) perovskite surface upon the adsorption of water molecules have been investigated based on density functional theory calculations. Also, we perform the first-principles ab initio molecular dynamics simulations (AIMD) to explore the structural stability of the γ-CsPbI3 (220) perovskite surface in the presence of water molecules, and the results are compared with the conventional cubic CH3NH3PbI3 (100) perovskite surface. The water molecules show stronger interactions with the (220) surface of γ-CsPbI3 than the (100) of CH3NH3PbI3. However, AIMD results demonstrate that the former is much more stable, and no trace of surface degradation has observed upon the adsorption of water molecules.
关键词： water adsorption,density functional theory,perovskite,ab initio molecular dynamics,structural stability
更新于2025-09-19 17:13:59
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Molecular Recognition and Band Alignment in 3D Covalent Organic Frameworks for Cocrystalline Organic Photovoltaics
摘要： Covalent organic frameworks (COFs) have emerged as versatile, functional materials comprised of low-cost molecular building blocks. The permanent porosity, long-range order, and high surface area of 3D-COFs permit co-crystallization with other materials driven by supramolecular interactions. We designed a new subphthalocyanine-based 3-D covalent organic framework (NEUCOF1) capable of forming co-crystals with fullerene (C60) via periodic ball-and-socket binding motifs. The high co-crystalline surface area and long-range order of NEUCOF1 eliminates the typical surface area vs. structural order trade-off in organic photovoltaics (OPVs). We used plane-wave density functional theory (PBE) to minimize NEUCOF1 and NEUCOF1–C60 co-crystals and determine their electronic band structures. Molecular dynamics (MD) simulations showed that dispersive interactions promoting co-crystallinity NEUCOF1–C60 are stable up to 350 K. The band structures at 0 and 350 K suggest that there is a driving force of 0.27 eV for exciton charge transfer to the pocket-bound fullerenes. Charge separation could then occur at the COF-C60 D-A interface, followed by the transfer of the free electron to the nanowire of C60 acceptors with a driving force of 0.20 eV.
关键词： fullerene,subphthalocyanine,co-crystallization,density functional theory,molecular dynamics,Covalent organic frameworks,organic photovoltaics
更新于2025-09-19 17:13:59
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Glass (Selected Properties and Crystallization) || 9. Crystallization of Undercooled Liquids: Results of Molecular Dynamics Simulations
摘要： The present contribution is devoted to molecular dynamics (MD) simulations modeling of the kinetics of spontaneous crystal nucleation in under-cooled one-component Lennard-Jones liquids and detailed comparison with the basic assumptions and results of classical nucleation theory (CNT). In the MD-computations the following spectrum of properties of the respective nucleating systems under consideration is determined: nucleation rate, J, diffusion coefficient of the crystal clusters in cluster size space, D, non-equilibrium Zeldovich factor, Z, size of the critical crystal nucleus, n?, pressure inside the critical crystal nucleus, p?. Based on these data, the interfacial energy density of the critical crystal nucleus is determined. Simultaneously, the interfacial energy density is computed by molecular dynamics methods for the planar interface liquid-crystal. It is found that for typical sizes of the critical nuclei in the range of 0.7–1.0 nm the value of the effective specific interfacial energy differs from that of the planar interface by less than 15 %. A comparison of the molecular dynamics results with the classical nucleation theory shows that for the considered case of crystallization of one-component liquids MD simulation results are in good agreement with the classical nucleation theory not only with respect to the final result, the nucleation frequency, but also with respect to the parameters D, Z, n?. Consequently, the results of molecular dynamics simulations of crystallization in one-component liquids demonstrate the validity of the basic assumptions and the final results of CNT for this particular case of phase formation.
关键词： molecular dynamics simulations,nucleation rate,critical crystal nucleus,Lennard-Jones liquids,classical nucleation theory,interfacial energy density,crystallization,undercooled liquids
更新于2025-09-16 10:30:52
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Electrons and Phonons Cooperate in the Laser-Induced Desorption of CO from Pd(111)
摘要： Femtosecond laser induced desorption of CO from a CO-covered Pd(111) surface is investigated with ab initio molecular dynamics with electronic friction that incorporates effects due to the excited electronic and phononic systems, as well as out-of-phase coadsorbate interactions. Our simulations show evidence of an important electron-phonon synergy in promoting CO desorption that has largely been neglected in other similar systems. At the saturated coverage of 0.75 ML, effects due to CO-CO interadsorbate energy exchange are also important. Our dynamics simulations, in concert with site-specific desorption energy calculations, allow us to understand the large coverage dependence of the desorption yields observed in experiments.
关键词： electron-phonon synergy,Pd(111),desorption,femtosecond laser,CO,electronic friction,ab initio molecular dynamics
更新于2025-09-16 10:30:52
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Atomic-level description of the CH3NH3PbI3perovskite solar cell absorber surface
摘要： Methylammonium lead halide CH3NH3PbI3 (MAPI)-based hybrid organic-inorganic perovskite has recently emerged as a promising solar photovoltaic absorber exhibiting an energy conversion efficiency higher than 20 %. An atomic-level description of a clean MAPI surface is a first step to understand its behavior when interfaced with oxides o molecules. Here, we perform classical molecular dynamics simulations of MAPI by using a MYP force field which was derived from ab initio calculations by Mattoni et al. The slab method is applied to model a thin film with two (001) PbI2-terminated surfaces. Temperature evolution of the structural properties are reported, analyzing in particular the changes of the orientations of the MA+cations at the surface and along the growth direction.
关键词： Molecular Dynamics,Solar cell,hybrid perovskite
更新于2025-09-16 10:30:52
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Simulated revelation of the adsorption behaviours of acetylcholinesterase on charged self-assembled monolayers
摘要： An acetylcholinesterase (AChE)-based electrochemical biosensor, as a promising alternative to detect organophosphates (OPs) and carbamate pesticides, has gained considerable attention in recent years, due to the advantages of simplicity, rapidity, reliability and low cost. The bio-activity of AChE immobilized on the surface and the direct electron transfer (DET) rate between an enzyme and an electrode directly determined the analytical performances of the AChE-based biosensor, and experimental studies have shown that the charged surfaces have a strong impact on the detectability of the AChE-based biosensor. Therefore, it is very important to reveal the behaviour of AChE in bulk solution and on charged surfaces at the molecular level. In this work, the adsorption orientation and conformation of AChE from Torpedo californica (TcAChE) on oppositely charged self-assembled monolayers (SAMs), COOH-SAM and NH2-SAM with different surface charge densities, were investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics simulations (AAMD). Simulation results show that TcAChE could spontaneously and stably adsorb on two oppositely charged surfaces by the synergy of an electric dipole and charged residue patch, and opposite orientations were observed. The active-site gorge of TcAChE is oriented toward the surface with the “end-on” orientation and the active sites are close to the surface when it is adsorbed on the positively charged surface and the tunnel cost for the substrate is lower than that on the negatively charged surface and in bulk solution, while for TcAChE adsorbed on the negatively charged surface, the active site of TcAChE is far away from the surface and the active-site gorge is oriented toward the solution with a “back-on” orientation. It suggests that the positively charged surface could provide a better microenvironment for the efficient bio-catalytic reaction and quick DET between TcAChE and the electrode surface. Moreover, the RMSD, RMSF, dipole moment, gyration radius, eccentricity and superimposed structures show that only a slight conformational change occurred on the relatively flexible structure of TcAChE during simulations, and the native conformation is well preserved after adsorption. This work helps us better comprehend the adsorption mechanism of TcAChE on charged surfaces and might provide some guidelines for the development of new TcAChE-based amperometric biosensors for the detection of organophosphorus pesticides.
关键词： electrochemical biosensor,carbamate pesticides,molecular dynamics simulations,conformation,organophosphates,acetylcholinesterase,self-assembled monolayers,adsorption orientation
更新于2025-09-16 10:30:52
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Revealing Conformational Transitions in G-Protein Coupled Receptor Rhodopsin upon Phosphorylation
摘要： GPCRs have evolved as highly specialized cellular machinery that can dictate biological outcomes in response to diverse stimuli. Specifically, they induce multiple pathway responses upon structural perturbations induced at local protein sites. GPCRs utilize concurrent strategy involving a central transmembrane topology and biochemical modifications for precise functional implementation. However, the specific role of latter is not decomposed due to the lack of precise probing techniques that can characterize receptor dynamics upon biochemical modifications. Phosphorylation is known to be one of the critical biochemical modifications in GPCRs that aids in receptor desensitization via arrestin binding. Here, we carried out all-atom molecular dynamics (MD) simulations of rhodopsin in membrane environment to study its conformational dynamics induced upon phosphorylation. Interestingly, our comparative analysis of non-phosphorylated and phosphorylated rhodopsin structure demonstrated enhanced receptor stability upon phosphorylation at the C-terminal region that leads to the opening of the extracellular part of the transmembrane helices. In addition, monitoring of the distinct number of phosphorylation states showed that less number of phosphorylated residues does not bring about appropriate conformational changes in the extracellular region. Since phosphorylation results in receptor desensitization and recycling of ligand, our findings provide significant insights into the conformational dynamics of the mechanism of ligand exit from the receptor.
关键词： conformational dynamics,molecular dynamics simulations,GPCRs,phosphorylation,rhodopsin
更新于2025-09-12 10:27:22
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Emergent biaxiality in nematic microflows illuminated by a laser beam
摘要： Anisotropic fluids (e.g. liquid crystals) offer a remarkable promise as optofluidic materials owing to the directional, tunable, and coupled interactions between the material, flow, and the optical fields. Here we present a comprehensive in silico treatment of this anisotropic interaction by performing nonequilibrium molecular dynamics simulations. We quantify the response of a nematic liquid crystal (NLC) undergoing a Poiseuille flow in the Stokes regime, while being illuminated by a laser beam incident perpendicular to the flow direction. We adopt a minimalistic model to capture the interactions, accounting for two features: first, the laser heats up the NLC locally; and second, the laser polarises the NLC and exerts an optical torque that tends to reorient molecules of the nematic phase. Because of this reorientation the liquid crystal exhibits small regions of biaxiality, where the nematic director is one symmetry axis and the axis of rotation for the reorientation of the molecules is the other one. We find that the relative strength of the viscous and the optical torques mediates the flow-induced response of the biaxial regions, thereby tuning the emergence, shape and location of the regions of enhanced biaxiality. The mechanistic framework presented here promises experimentally tractable routes toward novel optofluidic applications based on material-flow-light interactions.
关键词： optofluidics,Liquid crystal,biaxiality,nematic phase,nonequilibrium molecular dynamics
更新于2025-09-12 10:27:22
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Growth mechanism of gold nanorods: the effect of tip-surface curvature as revealed by molecular dynamics simulations
摘要： To understand the anisotropic growth mechanism of gold nanorods (AuNRs) during colloidal synthesis is critical for controlling the nanocrystal size and shape and thus has implications in tuning the properties for applications in a wide range of research and technology fields. In order to investigate the role of the cetyltrimethylammonium bromide (CTAB) coating in the anisotropic growth mechanism of AuNRs, we used molecular dynamics (MD) simulations and built a computational model that considered explicitly the effect of the curvature of the gold surface on CTAB adsorption and therefore differentiated the CTAB arrangements on flat and curved surfaces, representing the lateral and tip facets of growing AuNRs, respectively. We verified that on a curved surface, a lower CTAB coverage density and larger intermicellar channels are generated compared to those on a flat surface. Using umbrella sampling simulations, we measured the free energy profile and verified that the environment around a curved surface corresponds to an easier migration from the solution to the gold surface for the [AuBr2]? species than does a flat surface. Long unbiased molecular dynamics simulations also corroborated the umbrella sampling results. Therefore, the [AuBr2]? diffusion through the environment of the tips is much more favorable than in the case of lateral facets. This shows that the surface curvature is an essential component of the anisotropic growth mechanism.
关键词： molecular dynamics,growth mechanism,CTAB,umbrella sampling,surface curvature,gold nanorod synthesis
更新于2025-09-12 10:27:22