- 标题
- 摘要
- 关键词
- 实验方案
- 产品
-
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
-
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
-
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
-
Van der Waals Integration of Bismuth Quantum Dots–Decorated Tellurium Nanotubes (Te@Bi) Heterojunctions and Plasma‐Enhanced Optoelectronic Applications
摘要： Crystallization is relevant to many disciplines, and the control of crystallization of molecules is of importance to a great range of technological applications. It has been well established that a variety of surfaces can serve as possible nucleation sites for heterogeneous crystallization. However, it is still unknown what features of such system may be crucial and whether just a single molecule might serve as a nucleation site for crystallization. Therefore, to probe this question, we have investigated the nucleation of a prototypical multicomponent crystal, clathrate hydrates. As multicomponent crystalline compounds, clathrate hydrates have drawn considerable attention because of their scientific and industrial importance. Clathrate hydrates can occur in several possible structures, where the size of guest molecules and their ability to fit into water cages is a crucial factor. Despite the fact that in most applications, for example in oil?gas pipelines, clathrate hydrates form from gas mixtures that feature a variety of sizes of guest molecules, the possible roles of these species in hydrate formation has remained essentially unexplored. Herein, we investigate the impact of the presence of 2,2-dimethylbutane (DMB) on the nucleation of methane hydrate. Our simulation results provide clear evidence that DMB can serve as a nucleation site and can promote the formation of methane hydrates. The low mobility of the DMB molecule, and the longer residence time and hydrate-like structure of water molecules in its hydration shell appear as important contributors to its behavior. These results demonstrate that the presence of a somewhat larger hydrocarbon in low concentration can significantly impact hydrate nucleation and hence have immediate impact in, for example, flow assurance in oil?gas pipelines. More generally, the results presented herein indicate that single molecules in an otherwise homogeneous solution can promote crystal nucleation by stabilizing early stage structural fluctuations in the liquid.
关键词： crystallization,clathrate hydrates,molecular dynamics simulations,methane hydrate,2,2-dimethylbutane,nucleation
更新于2025-09-11 14:15:04
-
Influence of π spacer of donor-acceptor-π-acceptor sensitizers on photovoltaic properties in dye-sensitized solar cells
摘要： On the basis of organic dyes (E)-3-(6-(7-(bis(4-methoxyphenyl)amino)benzo[c] [1,2,5]thiadiazol-4-yl)-4,4-dimethyl-4H-cyclopenta[2,1-b:3,4-b']dithiophen-2-yl)-2-cyanoacrylic acid (1) and (E)-3-(6-(7-(bis(4-methoxyphenyl)amino)benzo[c] [1,2,5]thiadiazol-4-yl)-4-methyl-4H-dithieno[3,2-b:2′,3′-d]pyrrol-2-yl)-2-cyanoacrylic acid (2), two new D-A-π-A dyes, (E)-3-(7-(7-(bis(4-methoxyphenyl)amino)benzo[c] [1,2,5]thiadiazol-4-yl)benzo [2,1-b:3,4-b']dithiophen-2-yl)-2-cyanoacrylic acid (3) and (E)-3-(9-(7-(bis(4-methoxyphenyl)amino)benzo[c] [1,2,5]thiadiazol-4-yl)-2,3-dihydrodithieno[3′,2':3,4; 2″,3'':5,6]benzo[1,2-b] [1,4]dioxin-6-yl)-2-cyanoacrylic acid (4) are designed with diphenylamine as donor, 2-cyanoacrylic acid as acceptor along with different π group. Besides the frontier orbital energy levels and absorption spectra, the interfacial properties of dye-TiO2 adsorbed system is considered. After adsorption, the energy level of both dye and TiO2 surface shifts, which would affect the overall performance. More important, the short-circuit current density (JSC), open-circuit voltage (VOC), and photon-to-electron conversion efficiency (PCE) are calculated, which is helpful to determine the effect of π group on the donor-acceptor-π-acceptor dyes. The negative influence of aggregation for the dye-TiO2 adsorbed system is also considered to evaluate the overall photovoltaic performance. The molecular simulations are carried out to explore the dynamic properties of aggregation.
关键词： Dye sensitized solar cells,Molecular dynamics simulations,Photon-to-electron conversion efficiency,Electronic coupling,Aggregation
更新于2025-09-11 14:15:04
-
Dewetting of monolayer water and isopropanol between MoS2 nanosheets
摘要： Understanding dewetting of solvent molecules confined to layered material (LM) interfaces is crucial to the synthesis of two-dimensional materials by liquid-phase exfoliation. Here, we examine dewetting behavior of water and isopropanol/water (IPA/H2O) mixtures between molybdenum disulfide (MoS2) membranes using molecular dynamics (MD) simulations. We find that a monolayer of water spontaneously ruptures into nanodroplets surrounded by dry regions. The average speed of receding dry patches is close to the speed of sound in air. In contrast, monolayer mixtures of IPA/H2O between MoS2 membranes slowly transform into percolating networks of nanoislands and nanochannels in which water molecules diffuse inside and IPA molecules stay at the periphery of islands and channels. These contrasting behaviors may explain why IPA/H2O mixtures are much more effective than H2O alone in weakening interlayer coupling and exfoliating MoS2 into atomically thin sheets.
关键词： molecular dynamics simulations,liquid-phase exfoliation,isopropanol/water mixtures,two-dimensional materials,layered material interfaces,dewetting,solvent molecules,MoS2 membranes
更新于2025-09-10 09:29:36
-
Strength and toughness anisotropy in hexagonal boron nitride: An atomistic picture
摘要： Strength and toughness are two crucial mechanical properties of a solid that determine its ability to function reliably without undergoing failure in extreme conditions. While hexagonal boron nitride (hBN) is known to be elastically isotropic in the linear regime of mechanical deformation, its directional response to extreme mechanical loading remains less understood. Here, using a combination of density functional theory calculations and molecular dynamics simulations, we show that strength and crack nucleation toughness of pristine hBN are strongly anisotropic and chirality dependent. They vary nonlinearly with the chirality of the lattice under symmetry breaking deformation, and the anisotropic behavior is retained over a large temperature range with a decreasing trend at higher temperatures. An atomistic analysis reveals that bond deformation and associated distortion of electron density are nonuniform in the nonlinear regime of mechanical deformation, irrespective of the loading direction. This nonuniformity forms the physical basis for the observed anisotropy under static conditions, whereas reduction in nonuniformity and thermal softening reduce anisotropy at higher temperatures. The chirality-dependent anisotropic effects are well predicted by inverse cubic polynomials.
关键词： chirality,anisotropy,hexagonal boron nitride,molecular dynamics simulations,density functional theory,strength,toughness
更新于2025-09-10 09:29:36
-
Coupling to Charge Transfer States Is the Key to Modulate the Optical Bands for Efficient Light-Harvesting in Purple Bacteria.
摘要： The photosynthetic apparatus of purple bacteria uses exciton delocalization and static disorder to modulate the position and broadening of its absorption bands, leading to efficient light harvesting. Its main antenna complex, LH2, contains two rings of identical bacteriochlorophyll pigments, B800 and B850, absorbing at 800 nm and at 850 nm, respectively. It has been an unsolved problem why static disorder of the strongly coupled B850 ring is several times larger than that of the B800 ring. Here we show that mixing between excitons and charge transfer states in the B850 ring is responsible for the effect. The linear absorption spectrum of the LH2 system is simulated by using a multi-scale approach with an exciton Hamiltonian generalized to include the charge transfer states that involve adjacent pigment pairs, with static disorder modelled microscopically by molecular dynamics simulations. Our results show that a sufficient inhomogeneous broadening of the B850 band, needed for efficient light-harvesting, is only obtained by utilizing static disorder in the coupling between local excited and inter-pigment charge transfer states.
关键词： exciton delocalization,B850,B800,charge transfer states,purple bacteria,LH2,molecular dynamics simulations,static disorder,bacteriochlorophyll pigments,photosynthetic apparatus,light harvesting
更新于2025-09-10 09:29:36
-
In situ monitoring of molecular aggregation using circular dichroism
摘要： The aggregation of molecules plays an important role in determining their function. Electron microscopy and other methods can only characterize the variation of microstructure, but are not capable of monitoring conformational changes. These techniques are also complicated, expensive and time-consuming. Here, we demonstrate a simple method to monitor in-situ and in real-time the conformational change of (R)-1,1′-binaphthyl-based polymers during the aggregation process using circular dichroism. Based on results from molecular dynamics simulations and experimental circular dichroism measurements, polymers with “open” binaphthyl rings are found to show stronger aggregation-annihilated circular dichroism effects, with more negative torsion angles between the two naphthalene rings. In contrast, the polymers with “locked” rings show a more restrained aggregation-annihilated circular dichroism effect, with only a slight change of torsion angle. This work provides an approach to monitor molecular aggregation in a simple, accurate, and efficient way.
关键词： molecular aggregation,binaphthyl-based polymers,conformational change,circular dichroism,molecular dynamics simulations
更新于2025-09-09 09:28:46
-
Complexities of atomic structure at CdO/MgO and CdO/Al 2O 3 interfaces
摘要： We report the interface structures of CdO thin films on (001)-MgO and (0001)-Al2O3 substrates. Using aberration corrected scanning transmission electron microscopy, we show that epitaxial growth of (001)-CdO||(001)-MgO occurs with a lattice misfit greater than 10%. A high density of interface misfit dislocations is found to form. In combination with molecular dynamics simulations, we show that dislocation strain fields form and overlap in very thin heterostructures of CdO and MgO (< 3 nm). On the c-Al2O3 substrate, we find that CdO grows with a surface normal of [025]. We show that three rotation variants form due to the symmetry of the sapphire surface. These results contribute insights into the epitaxial growth of these rock-salt oxides.
关键词： CdO,epitaxial growth,Al2O3,scanning transmission electron microscopy,molecular dynamics simulations,MgO,interface structures
更新于2025-09-09 09:28:46