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Pressure-induced phase transformation in iron and its alloys is a classic research topic in solid-state physics, material science, and geophysics. The crystal structure of iron undergoes a phase transformation at a hydrostatic pressure of 13 GPa, changing from a body-centered cubic system to a hexagonal close-packed system. Although extensive research has been carried out on the transformation in iron by using molecular dynamics simulations, there is very limited literature that focuses on the contribution of parent phase orientations, system size, and impurities to the phase evolution. In this work, classic molecular dynamics simulations have been employed to investigate the effects of system size, lattice orientation, and impurity concentration on the pressure-induced phase transformation of iron and iron alloys for the first time. Our results show that the lattice orientation has a strong influence on the phase transition behavior, while the influence of carbon is small. The phase transition is slightly delayed with increasing carbon content, whereas the transition pressure increases from [001] to [011] to [111] orientation. The amount of twinning and stacking faults highly depends on the orientation. It is easiest for solitary waves to travel through [111] lattice orientation. The addition of carbon has a slow-down effect on shock velocities, and this effect increases with carbon content and lattice orientation of the samples from [001] to [011] to [111]. [ABSTRACT FROM AUTHOR]

Using non-equilibrium molecular dynamics simulations, we investigate thermal transport in organic/inorganic Au/molecular nanolayer (MNL) nanolaminate. We examine the tunability of thermal conductivity via interfacial bonding by (i) homogeneous change of bonding strength and heterogeneous change of (ii) bond density and (iii) molecular coverage at the interface. By comparing the thermal conductivity of the nanolaminates with the interfacial thermal conductance of corresponding individual interfaces, we conclude that phenomenologically the thermal conductivity can be predicted from independent interfacial resistors connected in a series model, particularly at higher temperatures. However, interfacial thermal conductance shows a moderate increase with temperature, whereas the thermal conductivity of Au/MNL nanolaminates shows the opposite effect. We elucidate this apparent contradiction via phonon wave packet simulations at individual and multiple interface structures. [ABSTRACT FROM AUTHOR]

In our recent publication, we have proposed a revised base excision repair pathway in which DNA polymerase β (Polβ) catalyzes Schiff base formation prior to the gap-filling DNA synthesis followed by β-elimination. In addition, the polymerase activity of Polβ employs the "three-metal ion mechanism" instead of the long-standing "two-metal ion mechanism" to catalyze phosphodiester bond formation based on the fact derived from time-resolved x-ray crystallography that a third Mg2+ was captured in the polymerase active site after the chemical reaction was initiated. In this study, we develop the models of the uncross-linked and cross-linked Polβ complexes and investigate the "three-metal ion mechanism" vs the "two-metal ion mechanism" by using the quantum mechanics/molecular mechanics molecular dynamics simulations. Our results suggest that the presence of the third Mg2+ ion stabilizes the reaction-state structures, strengthens correct nucleotide binding, and accelerates phosphodiester bond formation. The improved understanding of Polβ's catalytic mechanism provides valuable insights into DNA replication and damage repair. [ABSTRACT FROM AUTHOR]

Focused ultrasound has experimentally been found to enhance the diffusion of nanoparticles; our aim with this work is to study this effect closer using both experiments and non-equilibrium molecular dynamics. Measurements from single particle tracking of 40 nm polystyrene nanoparticles in an agarose hydrogel with and without focused ultrasound are presented and compared with a previous experimental study using 100 nm polystyrene nanoparticles. In both cases, we observed an increase in the mean square displacement during focused ultrasound treatment. We developed a coarse-grained non-equilibrium molecular dynamics model with an implicit solvent to investigate the increase in the mean square displacement and its frequency and amplitude dependencies. This model consists of polymer fibers and two sizes of nanoparticles, and the effect of the focused ultrasound was modeled as an external oscillating force field. A comparison between the simulation and experimental results shows similar mean square displacement trends, suggesting that the particle velocity is a significant contributor to the observed ultrasound-enhanced mean square displacement. The resulting diffusion coefficients from the model are compared to the diffusion equation for a two-time continuous time random walk. The model is found to have the same frequency dependency. At lower particle velocity amplitude values, the model has a quadratic relation with the particle velocity amplitude as described by the two-time continuous time random walk derived diffusion equation, but at higher amplitudes, the model deviates, and its diffusion coefficient reaches the non-hindered diffusion coefficient. This observation suggests that at higher ultrasound intensities in hydrogels, the non-hindered diffusion coefficient can be used. [ABSTRACT FROM AUTHOR]

Flow-enhanced nucleation (FEN) of n-pentacontahectane (C150) under biaxial extensional flows of varying strain rate ratios is studied using nonequilibrium molecular dynamics simulation. The nucleation rates thus calculated are used to test previously published FEN models based on invariants of the conformation tensor of Kuhn segments and the extra stress tensor. Models based on the conformation tensor provide a more accurate description of FEN observed in biaxial flow simulations than those based on the extra stress tensor. In addition, the formation of nematic domains previously reported to be stabilized by shear or extensional flow is absent in equibiaxial flows. However, such domains do form in non-equibiaxial flows, and nucleation occurs in these domains preferentially. The shape and orientation of nuclei formed under biaxial flows of various strengths and strain rate ratios are also reported. [ABSTRACT FROM AUTHOR]

The granular materials of soft particles (SPs) demonstrate unique viscoelasticity distinct from general colloidal and polymer systems. Exploiting dynamic light scattering measurements, together with molecular dynamics simulations, we study the diffusive dynamics of soft particle clusters (SPCs) with spherical and cylindrical brush topologies, respectively, in the melts of SPs. A topologically constrained relaxation theory is proposed by quantitatively correlating the relaxation time to the topologies of the SPCs, through the mean free space (Va) of tethered SPs in the cluster. The tethered SPs in SPCs are crowded by SPs of the melts to form the cage zones, and the cooperative diffusion of the tether SPs in the zones is required for the diffusive motion of SPCs. The cage zone serves as an entropic barrier for the diffusion of SP clusters, while its strength is determined by Va. Three characteristic modes can be confirmed: localized non-diffusive mode around critical Va, diffusive mode with Va deviating far from the critical value, and a sub-diffusive mode as an interlude between two limits. Our studies raise attention to the emergent physical properties of materials based on SPs via a topological design while opening new avenues for the design of soft structural materials. [ABSTRACT FROM AUTHOR]

Identifying the oxidation structure of two-dimensional interfaces is crucial to improve surface chemistry and electronic properties. Beyond graphene with only phenyl rings, a novel carbon-nitrogen material, C3N, presents an intrinsic heterogeneous surface morphology where each phenyl ring is encircled by six nitrogen atoms, yet its atomistic oxidation structure remains unclear. Here, combining a series of density functional theory calculations and ab initio molecular dynamics simulations, we demonstrate that thermodynamically favorable oxidation loci are confined to the phenyl ring, and kinetic transformations of oxidation structures are feasible along the phenyl ring, whereas those toward nitrogen atoms are proven to be extremely difficult. These results are attributed to the lower barrier of oxygen atom migration along the phenyl ring, while the significantly high barriers toward nitrogen atoms are due to the heterogeneous potential energy surface for oxygen–C3N interaction. This work highlights the significance of surface morphology on the characteristics of oxidation structure, offering insights into tunable electronic properties via confined interfacial oxidation. [ABSTRACT FROM AUTHOR]

The potential energy landscape (PEL) formalism is a tool within statistical mechanics that has been used in the past to calculate the equation of states (EOS) of classical rigid model liquids at low temperatures, where computer simulations may be challenging. In this work, we use classical molecular dynamics (MD) simulations and the PEL formalism to calculate the EOS of the flexible q-TIP4P/F water model. This model exhibits a liquid–liquid critical point (LLCP) in the supercooled regime, at (Pc = 150 MPa, Tc = 190 K, and ρc = 1.04 g/cm3) [using the reaction field technique]. The PEL-EOS of q-TIP4P/F water and the corresponding location of the LLCP are in very good agreement with the MD simulations. We show that the PEL of q-TIP4P/F water is Gaussian, which allows us to calculate the configurational entropy of the system, Sconf. The Sconf of q-TIP4P/F water is surprisingly similar to that reported previously for rigid water models, suggesting that intramolecular flexibility does not necessarily add roughness to the PEL. We also show that the Adam–Gibbs relation, which relates the diffusion coefficient D with Sconf, holds for the flexible q-TIP4P/F water model. Overall, our results indicate that the PEL formalism can be used to study molecular systems that include molecular flexibility, the common case in standard force fields. This is not trivial since the introduction of large bending/stretching mode frequencies is problematic in classical statistical mechanics. For example, as shown previously, we find that such high frequencies lead to unphysical (negative) entropy for q-TIP4P/F water when using classical statistical mechanics (yet, the PEL formalism can be applied successfully). [ABSTRACT FROM AUTHOR]

Thermodynamic and dynamic anomalies of water play a crucial role in supporting life on our planet. The two-state theory attributes these anomalies to a dynamic equilibrium between locally favored tetrahedral structures (LFTSs) and disordered normal liquid structures. This theory provides a straightforward, phenomenological explanation for water's unique thermodynamic and dynamic characteristics. To validate this two-state feature, it is critical to unequivocally identify these structural motifs in a dynamically fluctuating disordered liquid. In this study, we employ a recently introduced structural parameter (θavg) that characterizes the local angular order within the first coordination shell to identify these LFTSs through molecular dynamics simulations. We employ both realistic water models with a liquid–liquid critical point (LLCP) and a coarse-grained water model without an LLCP to study water's anomalies in low-pressure regions below 2 kbar. The two-state theory consistently describes water's thermodynamic anomalies in these models, both with and without an LLCP. This suggests that the anomalies predominantly result from the two-state features rather than criticality, particularly within experimentally accessible temperature–pressure regions. [ABSTRACT FROM AUTHOR]

The extreme ultraviolet (EUV) nanolithography technology is the keystone for developing the next-generation chips. As conventional chemically amplified resists are approaching the resolution limit, metal-containing photoresists, especially tin-oxo clusters, seize the opportunity to embrace this challenge owing to their small sizes, precise atomic structures, and strong EUV absorption. However, atomistic insights into the mechanism for regulating their photolithographic behavior are lacking. Herein, we systematically explored the effects of ligands, counterions, and endohedral doping on the photophysical properties of tin-oxo cage clusters by first-principles calculations combined with molecular dynamics simulations. Photoresists assembled by allyl-protected clusters with small-size OH− or Cl− counterions have a high absorption coefficient at the EUV wavelength of 13.5 nm and a low energy cost for ligand detachment and superior stability to ensure high sensitivity and strong etch resistance, respectively. The photoresist performance can further be improved by endohedral doping of the metal-oxo nanocage with Ag+ and Cd2+ ions, which exhibit superatomic characteristics and are likely to be synthesized in laboratory. These theoretical results provide useful guidance for modification of metal-oxo clusters for high-resolution EUV photolithography. [ABSTRACT FROM AUTHOR]

The compound 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) is a versatile fluorophore widely used in Förster resonance energy transfer (FRET) spectroscopy studies due to its remarkable sensitivity, enabling precise donor–acceptor distance measurements, even for short peptides. Integrating time-resolved and FRET spectroscopies with molecular dynamics simulations provides a robust approach to unravel the structure and dynamics of biopolymers in a solution. This study investigates the structural behavior of three octapeptide variants: Trp-(Gly-Ser)3-Dbo, Trp-(GlyGly)3-Dbo, and Trp-(SerSer)3-Dbo, where Dbo represents the DBO-containing modified aspartic acid, using molecular dynamics simulations. Glycine- and serine-rich amino acid fragments, common in flexible protein regions, play essential roles in functional properties. Results show excellent agreement between end-to-end distances, orientational factors from simulations, and the available experimental and theoretical data, validating the reliability of the GROMOS force field model. The end-to-end distribution, modeled using three Gaussian distributions, reveals a complex shape, confirmed by cluster analysis highlighting a limited number of significant conformations dominating the peptide landscape. All peptides predominantly adopt a disordered state in the solvent, yet exhibit a compact shape, aligning with the model of disordered polypeptide chains in poor solvents. Conformations show marginal dependence on chain composition, with Ser-only chains exhibiting slightly more elongation. This study enhances our understanding of peptide behavior, providing valuable insights into their structural dynamics in solution. [ABSTRACT FROM AUTHOR]

Designing homogeneous networks is considered one typical strategy for solving the problem of strength and toughness conflict of polymer network materials. Experimentalists have proposed the hypothesis of obtaining a structurally homogeneous hydrogel by crosslinking tetra-armed polymers, whose homogeneity was claimed to be verified by scattering characterization and other methods. Nevertheless, it is highly desirable to further evaluate this issue from other perspectives. In this study, a coarse-grained molecular dynamics simulation coupled with a stochastic reaction model is applied to reveal the topological structure of a polymer network synthesized by tetra-armed monomers as precursors. Two different scenarios, distinguished by whether internal cross-linking is allowed, are considered. We introduce the Dijkstra algorithm from graph theory to precisely characterize the network structure. The microscopic features of the network structure, e.g., loop size, dispersity, and size distribution, are obtained via the Dijkstra algorithm. By comparing the two reaction scenarios, Scenario II exhibits an overall more idealized structure. Our results demonstrate the feasibility of the Dijkstra algorithm for precisely characterizing the polymer network structure. We expect this work will provide a new insight for the evaluation and description of gel networks and further help to reveal the dynamic process of network formation. [ABSTRACT FROM AUTHOR]

We present a comprehensive analysis of the structure–property relationship in small molecule non-fullerene acceptors (NFAs) featuring an acceptor–donor–acceptor configuration employing state-of-the-art quantum chemical computational methods. Our focus lies in the strategic functionalization of halogen groups at the terminal positions of NFAs as an effective means to mitigate non-radiative voltage losses and augment photovoltaic and photophysical properties relevant to organic solar cells. Through photophysical studies, we observe a bathochromic shift in the visible region for all halogen-functionalized NFAs, except type-2, compared to the unmodified compound. Most of these functionalized compounds exhibit exciton binding energies below 0.3 eV and ΔLUMO less than 0.3 eV, indicating their potential as promising candidates for organic solar cells. Selected candidate structures undergo an analysis of charge transport properties using the semi-classical Marcus theory based on hopping transport formalism. Molecular dynamics simulations followed by charge transport simulations reveal an ambipolar nature of charge transport in the investigated NFAs, with equivalent hole and electron mobilities compared to the parent compound. Our findings underscore the crucial role of end-group functionalization in enhancing the photovoltaic and photophysical characteristics of NFAs, ultimately improving the overall performance of organic solar cells. This study advances our understanding of the structure–property relationships in NFAs and provides valuable insights into the design and optimization of organic solar cell materials. [ABSTRACT FROM AUTHOR]

We present a detailed assessment of deep neural network potentials developed within the Deep Potential Molecular Dynamics (DeePMD) framework and trained on the MB-pol data-driven many-body potential energy function. Specific focus is directed at the ability of DeePMD-based potentials to correctly reproduce the accuracy of MB-pol across various water systems. Analyses of bulk and interfacial properties as well as many-body interactions characteristic of water elucidate inherent limitations in the transferability and predictive accuracy of DeePMD-based potentials. These limitations can be traced back to an incomplete implementation of the "nearsightedness of electronic matter" principle, which may be common throughout machine learning potentials that do not include a proper representation of self-consistently determined long-range electric fields. These findings provide further support for the "short-blanket dilemma" faced by DeePMD-based potentials, highlighting the challenges in achieving a balance between computational efficiency and a rigorous, physics-based representation of the properties of water. Finally, we believe that our study contributes to the ongoing discourse on the development and application of machine learning models in simulating water systems, offering insights that could guide future improvements in the field. [ABSTRACT FROM AUTHOR]

This work is part of a prediction challenge that invited theoretical/computational chemists to predict the photochemistry of cyclobutanone in the gas phase, excited at 200 nm by a laser pulse, and the expected signal that will be recorded during a time-resolved megaelectronvolt ultrafast electron diffraction (MeV-UED). We present here our theoretical predictions based on a combination of trajectory surface hopping with XMS-CASPT2 (for the nonadiabatic molecular dynamics) and Born–Oppenheimer molecular dynamics with MP2 (for the athermal ground-state dynamics following internal conversion), coined (NA+BO)MD. The initial conditions were sampled from Born–Oppenheimer molecular dynamics coupled to a quantum thermostat. Our simulations indicate that the main photoproducts after 2 ps of dynamics are CO + cyclopropane (50%), CO + propene (10%), and ethene and ketene (34%). The photoexcited cyclobutanone in its second excited electronic state S 2 can follow two pathways for its nonradiative decay: (i) a ring-opening in S 2 and a subsequent rapid decay to the ground electronic state, where the photoproducts are formed, or (ii) a transfer through a closed-ring conical intersection to S 1 , where cyclobutanone ring opens and then funnels to the ground state. Lifetimes for the photoproduct and electronic populations were determined. We calculated a stationary MeV-UED signal [difference pair distribution function— Δ PDF (r) ] for each (interpolated) pathway as well as a time-resolved signal [ Δ PDF (r , t) and Δ I / I (s , t) ] for the full swarm of (NA+BO)MD trajectories. Furthermore, our analysis provides time-independent basis functions that can be used to fit the time-dependent experimental UED signals [both Δ PDF (r , t) and Δ I / I (s , t) ] and potentially recover the population of photoproducts. We also offer a detailed analysis of the limitations of our model and their potential impact on the predicted experimental signals. [ABSTRACT FROM AUTHOR]

Understanding the structural behavior of solid hydrogen under high pressures is crucial for uncovering its unique properties and potential applications. In this study, starting from the phase I of solid hydrogen—free-rotator hcp structure, we conduct extensive ab initio molecular dynamics calculations to simulate the cooling, heating, and equilibrium processes within a pressure range of 80–260 GPa. Without relying on any structure previously predicted, we identify the high-pressure phase structures of solid hydrogen as P21/c for phase II, P6522 for phase III, and BG1BG2BG3 six-layer structure for phase IV, which are different from those proposed previously using the structure-search method. The reasonability of these structures are validated by Raman spectra and x-ray diffraction patterns by comparison with the experimental results. Our results actually show pronounced changes in the c/a ratio between phases I, III, and IV, which hold no brief for the experimental interpretation of an isostructural hcp transformations for phases I–III–IV. [ABSTRACT FROM AUTHOR]

The photoexcitation dynamics of molecular materials on the 10–100 nm length scale depend on complex interactions between electronic and vibrational degrees of freedom, rendering exact calculations difficult or intractable. The adaptive Hierarchy of Pure States (adHOPS) is a formally exact method that leverages the locality imposed by interactions between thermal environments and electronic excitations to achieve size-invariant scaling calculations for single-excitation processes in systems described by a Frenkel–Holstein Hamiltonian. Here, we extend adHOPS to account for arbitrary couplings between thermal environments and vertical excitation energies, enabling formally exact, size-invariant calculations that involve multiple excitations or states with shared thermal environments. In addition, we introduce a low-temperature correction and an effective integration of the noise to reduce the computational expense of including ultrafast vibrational relaxation in Hierarchy of Pure States (HOPS) simulations. We present these advances in the latest version of the open-source MesoHOPS library and use MesoHOPS to characterize charge separation at a one-dimensional organic heterojunction when both the electron and hole are mobile. [ABSTRACT FROM AUTHOR]

A new multiple-time scale integration method is presented that propagates ab initio path integral molecular dynamics (PIMD). This method uses a large time step to generate an approximate geometrical configuration whose energy and gradient are evaluated at the level of an ab initio method, and then, a more precise integration scheme, e.g., the Bulirsch–Stoer method or velocity Verlet integration with a smaller time step, is used to integrate from the previous step using the computationally efficient interpolated potential energy surface constructed from two consecutive points. This method makes the integration of PIMD more efficient and accurate compared with the velocity Verlet integration. A Nos e ́ –Hoover chain thermostat combined with this new multiple-time scale method has good energy conservation even with a large time step, which is usually challenging in velocity Verlet integration for PIMD due to the very small chain mass when a large number of beads are used. The new method is used to calculate infrared spectra and free energy profiles to demonstrate its accuracy and capabilities. [ABSTRACT FROM AUTHOR]

The crystallization process of methane hydrates in a confined geometry resembling seabed porous silica sedimentary conditions has been studied using molecular dynamics simulations. With this objective in mind, a fully atomistic quartz silica slit pore has been designed, and the temperature stability of a methane hydrate crystalline seed in the presence of water and guest molecule methane has been analyzed. NaCl ion pairs have been added in different concentrations, simulating salinity conditions up to values higher than average oceanic conditions. The structure obtained when the hydrate crystallizes inside the pore is discussed, paying special attention to the presence of ionic doping inside the hydrate and the subsequent induced structural distortion. The shift in the hydrate stability conditions due to the increasing water salinity is discussed and compared with the case of unconfined hydrate, concluding that the influence of the confinement geometry and pore hydrophilicity produces a larger deviation in the confined hydrate phase equilibria. [ABSTRACT FROM AUTHOR]

A frequency-dependent dielectric constant characterizes the dielectric response of a medium and also represents the time scale of system's collective dynamics. Although it is valuable not only academically but also practically for developing advanced devices, getting the value of a solution at the interface with a solid or electrode surface is challenging both experimentally and computationally. Here, we propose a computational method that imitates the dielectric spectroscopy and AC impedance measurement. It combines a time-dependent voltage applied molecular dynamics simulation with an equivalent circuit representation of a system composed of a solution confined between two identical electrodes. It gives the frequency-dependent dielectric constants of the bulk solution and the interface simultaneously. Unlike the conventional method, it does not require computation of a dipole autocorrelation function and its Fourier transformation. Application of the method on a system of water confined between polarizable Pt electrodes gives the static dielectric constant and the relaxation time of the bulk water in good agreement with previous simulation results and experimental values. In addition, it gives a much smaller static dielectric constant at the interface, consistent with previous observations. The outline of the dielectric dispersion curve of the interface seems similar to that of the bulk, but the relaxation time is several times faster. [ABSTRACT FROM AUTHOR]

With large-scale non-equilibrium molecular dynamics simulations and in situ x-ray diffraction analysis, we conducted a systematic investigation into the effects of pre-existing shear strain (γ x y ) on the shock response of single crystal iron. Our findings reveal significant effects of γ x y on the deformation of the crystal structure during shock loading, leading to noticeable alterations in the propagation of shock waves. Specifically, during the elastic stage, the presence of γ x y results in a reduction of shock strength, consequently diminishing the magnitude of elastic lattice strain (ε e ). In the plastic stage, γ x y stimulates the α – ε phase transformation, and structure deformation undergoes a transition from the sequential activity of dislocation-to-transformation to the synchronous activity of dislocation and transformation. This transition inhibits the propagation of plastic waves and consequently broadens the elastic regime. Additionally, the introduction of γ x y activates different slip systems, as it alters the corresponding resolved shear stress. Concurrently, the presence of γ x y triggers the activation of different high-pressure phase variants. Our investigation sheds light on the fundamental physics of iron under shock compression and the influence of pre-existing shear strain on its behavior. [ABSTRACT FROM AUTHOR]

We simulate an alloy of HfNbTaTi mixed in six different proportions and also of the equiatomic system under uniaxial tensile loading at 300 K. Molecular dynamics simulation trajectories are analyzed using radial distribution functions, OVITO, bond-orientational order parameters, and coordination numbers. Equiatomic and the two other alloys (Hf 0.31 Nb 0.23 Ta 0.23 Ti 0.23 and Hf 0.23 Nb 0.31 Ta 0.23 Ti 0.23 ) containing comparable fraction of elements deform similarly through the formation of an amorphous state. Two alloys rich in Nb (Hf 0.17 Nb 0.50 Ta 0.16 Ti 0.17 ) and Ta (Hf 0.17 Nb 0.16 Ta 0.50 Ti 0.17 ) deform similarly resulting in the formation of bcc atoms, which transform to fcc at higher loading. Finally, alloys rich in Hf (Hf 0.50 Nb 0.16 Ta 0.17 Ti 0.17 ) and Ti (Hf 0.17 Nb 0.16 Ta 0.17 Ti 0.50 ) deform resulting in high dislocation densities and hcp atoms. These two hcp-rich alloys also undergo strain hardening. In each mixture during loading, local orientational order of all the different elements changes similarly. Atoms prefer to pair with other atoms than to themselves during tensile loading. [ABSTRACT FROM AUTHOR]

PtS2, a member of the group 10 transition metal dichalcogenides (TMDs), has received extensive attention because of its excellent electrical properties and air stability. However, there are few reports on the preparation of single-crystal PtS2 in the literature, and the growth mechanism of single crystal PtS2 is not well elucidated. In this work, we proposed a method of preparation that combines magnetron sputtering and chemical vapor transport to obtain monocrystalline PtS2 on a SiO2/Si substrate. By controlling the growth temperature and time, we have synthesized a single crystalline PtS2 of hexagonal shape and size of 1–2 μm on a silicon substrate. Combining the molecular dynamics simulation, the growth mechanism of single crystal PtS2 was investigated both experimentally and theoretically. The synthesis method has a short production cycle and low cost, which opens the door for the fabrication of other TMDs single crystals. [ABSTRACT FROM AUTHOR]

The moisture with salt ions adsorbed on the mineral soil surface is crucial to the cohesion process when the media is exposed to marine or coastal environments. However, the impact of salinity on the cohesion of soils is not well studied at the nanoscale. In this study, the salinity effect was investigated by studying the wettability and capillary force of NaCl solutions on quartz substrates via a molecular dynamics-based approach. Besides, a new visualization method was proposed to measure the contact angle of liquid droplets from the aspect of nanoscale. The results indicated that salt ions can weaken the wettability of the liquid on the quartz surface and inhibit the capillary force. Compared with water, the liquid with a 10% NaCl solution can achieve a capillary force reduction of around 70%, resulting in a detrimental effect on the cohesion of soils. Overall, this study enhanced the understanding of the nanoscale salinity effect on the cohesion process and provided insights into the modification of the mechanical properties of soils from the aspect of nanoscale. [ABSTRACT FROM AUTHOR]

We evaluate depletion forces in molecular dynamics simulation of a binary mixture of spheres (depleted particles) and rods (depletant particles) for a wide range of densities for both species. This evaluation was carried out using a recently proposed least squares fitting algorithm. We found that the restriction of the rods' rotational degrees of freedom, when the distance between two spheres is less than the rods length, creates a shallow, and apparently linear, attractive force ramp. For intersphere distances smaller than the rods' diameter, a much stronger attractive force is found, and a large repulsive barrier appears between these aforementioned regimes, roughly at the distance of the rods' thickness. The evaluated forces are validated via a comparison of the pairwise correlation functions obtained from molecular dynamics simulation of a mono-disperse sphere fluid, using the evaluated effective forces, against the original (full system) pairwise correlation functions. Agreement is excellent. We also record the angular pairwise correlation function, using the P2(x) Legendre polynomial, and find that for high densities of both species, a local nematic ordering starts to appear. This nematic order may be a factor in the small differences found between original and effective pairwise correlation functions at high densities of rods. [ABSTRACT FROM AUTHOR]

Shale gas reservoirs generally have ultra-low water saturation, and the water in reservoirs is closely bound to the walls of inorganic nanopores, forming a water film structure on the hydrophilic surface. When shale gas enters the inorganic nanopores, the water films in the inorganic pores will be removed by evaporation instead of being driven away by the gas, which increases the difficulty of predicting production during shale gas extraction. Based on molecular dynamics simulations, a water film evaporation model is proposed, considering the evaporation of water films during shale gas transport and the influence of water film evaporation on the shale gas transport mechanism. The Green–Kubo method is employed to calculate the viscosity of the water film. The evaporation flux of the water film under the influence of viscosity is discussed in the evaporation model. The transport mechanisms of shale gas in nanopores and the effect of water film evaporation on shale gas transport mechanisms are analyzed in detail. The result indicates that the water films in the inorganic nanopores are constrained on the hydrophilic surface, and the viscosity normal to the surface of the water film of 4 Å is 0.005 26 Pa⋅S, which is 6.12 times the reference value of viscosity at 298 K. In the process of water film evaporation, the evaporation flux of the water film is influenced by viscosity. In the study of the shale gas transport mechanism, water films in inorganic nanopores can hinder the surface diffusion of the methane molecules adsorbed on boundary and significantly reduce the mass flux of shale gas. [ABSTRACT FROM AUTHOR]

Structural and vibrational properties of aqueous solutions of alkali hydroxides (LiOH, NaOH, and KOH) are computed using quantum molecular dynamics simulations for solute concentrations ranging between 1 and 10M. Element-resolved partial radial distribution functions, neutron and x-ray structure factors, and angular distribution functions are computed for the three hydroxide solutions as a function of concentration. The vibrational spectra and frequency-dependent conductivity are computed from the Fourier transforms of velocity autocorrelation and current autocorrelation functions. Our results for the structure are validated with the available neutron data for 17M concentration of NaOH in water [Semrouni et al., Phys. Chem. Chem. Phys. 21, 6828 (2019)]. We found that the larger ionic radius [ r L i + < r N a + < r K + ] and higher concentration disturb the hydrogen-bond network of water, resulting in more disordered cationic hydration shell. Our ab initio simulation data for solute concentrations ranging between 1 and 10M can be used to guide future elastic and inelastic neutron-scattering experiments. [ABSTRACT FROM AUTHOR]

Intragenic translational heterogeneity describes the variation in translation at the level of transcripts for an individual gene. A factor that contributes to this source of variation is the mRNA structure. Both the composition of the thermodynamic ensemble, i.e., the stationary distribution of mRNA structures, and the switching dynamics between those play a role. The effect of the switching dynamics on intragenic translational heterogeneity remains poorly understood. We present a stochastic translation model that accounts for mRNA structure switching and is derived from a Markov model via approximate stochastic filtering. We assess the approximation on various timescales and provide a method to quantify how mRNA structure dynamics contributes to translational heterogeneity. With our approach, we allow quantitative information on mRNA switching from biophysical experiments or coarse-grain molecular dynamics simulations of mRNA structures to be included in gene regulatory chemical reaction network models without an increase in the number of species. Thereby, our model bridges a gap between mRNA structure kinetics and gene expression models, which we hope will further improve our understanding of gene regulatory networks and facilitate genetic circuit design. [ABSTRACT FROM AUTHOR]

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman's path integral formalism of quantum mechanics. The flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients. [ABSTRACT FROM AUTHOR]

The lattice thermal conductivity stands as a pivotal thermos-physical parameter of high-entropy alloys; nonetheless, achieving precise predictions of the lattice thermal conductivity for high-entropy alloys poses a formidable challenge due to their complex composition and structure. In this study, machine learning models were built to predict the lattice thermal conductivity of AlCoCrNiFe high-entropy alloy based on molecular dynamic simulations. Our model shows high accuracy with R2, mean absolute percentage error, and root mean square error of the test set is 0.91, 0.031, and 1.128 W m−1 k−1, respectively. In addition, a high-entropy alloy with low a lattice thermal conductivity of 2.06 W m−1 k−1 (Al8Cr30Co19Ni20Fe23) and with a high lattice thermal conductivity of 5.29 W m−1 k−1 (Al0.5Cr28.5Co25Ni25.5Fe20.5) was successfully predicted, which shows good agreement with the results from molecular dynamics simulations. The mechanisms of the thermal conductivity divergence are further explained through their phonon density of states and elastic modulus. The established model provides a powerful tool for developing high-entropy alloys with the desired properties. [ABSTRACT FROM AUTHOR]

Alzheimer's disease is a detrimental neurological disorder caused by the formation of amyloid fibrils due to the aggregation of amyloid-β peptide. The primary therapeutic approaches for treating Alzheimer's disease are targeted to prevent this amyloid fibril formation using potential inhibitor molecules. The discovery of such inhibitor molecules poses a formidable challenge to the design of anti-amyloid drugs. This study investigates the effect of caffeine on dimer formation of the full-length amyloid-β using a combined approach of all-atom, explicit water molecular dynamics simulations and the three-dimensional reference interaction site model theory. The change in the hydration free energy of amyloid-β dimer, with and without the inhibitor molecules, is calculated with respect to the monomeric amyloid-β, where the hydration free energy is decomposed into energetic and entropic components, respectively. Dimerization is accompanied by a positive change in the partial molar volume. Dimer formation is spontaneous, which implies a decrease in the hydration free energy. However, a reverse trend is observed for the dimer with inhibitor molecules. It is observed that the negatively charged residues primarily contribute for the formation of the amyloid-β dimer. A residue-wise decomposition reveals that hydration/dehydration of the side-chain atoms of the charged amino acid residues primarily contribute to dimerization. [ABSTRACT FROM AUTHOR]

The rates and pathways of chemical reactions at metal surfaces can be strongly influenced by energy dissipation due to the nonadiabatic excitation of metallic conduction electrons. The introduction of frictional forces to account for this dissipation has been quite successful in situations for which the nonadiabatic coupling is weak. However, in cases where nonadiabatic coupling is strong, such as when electron transfer occurs, the friction model is likely to break down. Ryabinkin and Izmaylov have proposed 2-state and 3-state alternatives to the friction model for introducing electronic dissipation in molecular dynamics simulations. Here, we examine their 2-state model using some simple examples of atom–surface scattering. We find that, with the addition of decoherence, the 2-state model can produce quite promising results. [ABSTRACT FROM AUTHOR]

As typical representatives of group III chalcogenides, InSe, α-In2Se3, and β′-In2Se3 have drawn considerable interest in the domain of photoelectrochemistry. However, the microscopic mechanisms of carrier dynamics in these systems remain largely unexplored. In this work, we first reveal that hot electrons in the three systems have different cooling rate stages and long-lived hot electrons, through the utilization of density functional theory calculations and nonadiabatic molecular dynamics simulations. Furthermore, the ferroelectric polarization of α-In2Se3 weakens the nonadiabatic coupling of the nonradioactive recombination, successfully competing with the narrow bandgap and slow dephasing process, and achieving both high optical absorption efficiency and long carrier lifetime. In addition, we demonstrate that the ferroelectric polarization of α-In2Se3 not only enables the formation of the double type-II band alignment in the InSe/α-In2Se3/InSe heterostructure, with the top and bottom InSe sublayers acting as acceptors and donors, respectively, but also eliminates the hindrance of the built-in electric field at the interface, facilitating an ultrafast interlayer carrier transfer in the heterojunction. This work establishes an atomic mechanism of carrier dynamics in InSe, α-In2Se3, and β′-In2Se3 and the regulatory role of the ferroelectric polarization on the charge carrier dynamics, providing a guideline for the design of photoelectronic materials. [ABSTRACT FROM AUTHOR]

The increasing presence of 1,1,1,2-tetrafluoroethane (CF3CH2F) in the atmosphere has prompted detailed studies into its complex photodissociation behavior. Experiments focusing on CF3CH2F irradiation have unveiled an array of ions, with the persistent observation of the rearrangement product CHF2+ not yet fully understood. In this work, we combine density functional theory, coupled-cluster calculations with a complete basis set formalism, and atom-centered density matrix propagation molecular dynamics to investigate the energetics and dynamics of different potential pathways leading to CHF2+. We found that the two-body dissociation pathway involving an HF rearrangement, which was previously considered complex for CHF2+ formation, is actually straightforward but not likely due to the facile loss of HF. In contrast, our calculations reveal that the H elimination pathway, once thought of as a potential route to CHF2+, is not only comparably disadvantageous from both thermodynamic and kinetic points of view but also does not align with experimental data, particularly the lack of a rebound peak at m/z 101–102. We establish that the formation of CHF2+ is predominantly via the HF elimination channel, a conclusion experimentally corroborated by studies involving the trifluoroethylene cation CF2CHF+, a key intermediate in this process. [ABSTRACT FROM AUTHOR]

Protein conformational changes play crucial roles in their biological functions. In recent years, the Markov State Model (MSM) constructed from extensive Molecular Dynamics (MD) simulations has emerged as a powerful tool for modeling complex protein conformational changes. In MSMs, dynamics are modeled as a sequence of Markovian transitions among metastable conformational states at discrete time intervals (called lag time). A major challenge for MSMs is that the lag time must be long enough to allow transitions among states to become memoryless (or Markovian). However, this lag time is constrained by the length of individual MD simulations available to track these transitions. To address this challenge, we have recently developed Generalized Master Equation (GME)-based approaches, encoding non-Markovian dynamics using a time-dependent memory kernel. In this Tutorial, we introduce the theory behind two recently developed GME-based non-Markovian dynamic models: the quasi-Markov State Model (qMSM) and the Integrative Generalized Master Equation (IGME). We subsequently outline the procedures for constructing these models and provide a step-by-step tutorial on applying qMSM and IGME to study two peptide systems: alanine dipeptide and villin headpiece. This Tutorial is available at https://github.com/xuhuihuang/GME%5ftutorials. The protocols detailed in this Tutorial aim to be accessible for non-experts interested in studying the biomolecular dynamics using these non-Markovian dynamic models. [ABSTRACT FROM AUTHOR]

The crystal orientation and the temperature of the substrate are crucial factors that influence clusters deposition and, consequently, the properties of thin films. In this study, the molecular dynamics simulation method was employed to investigate the deposition of Cu55 clusters on Fe(001), Fe(011), and Fe(111) substrates with varying crystal orientations. The incident energies used ranged from 0.1 to 20.0 eV/atom, and the substrates were maintained at temperatures of 300, 500, and 800 K. Analysis of cluster and substrate atom snapshots, along with the physical properties of clusters, revealed how the crystal orientation of Fe substrates affects the morphology and structure of the cluster at different temperatures. Additionally, specific microscopic mechanisms responsible for these effects were identified. The simulation results demonstrate that the crystal orientation of Fe substrate significantly influences the deposition of Cu55 clusters. The structures of the clusters on the three crystal substrates undergo similar changes as the substrate temperature increases, with the Cu55 clusters on the Fe(111) substrate exhibiting the most significant changes in response to the temperature rise. [ABSTRACT FROM AUTHOR]

Protein–calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding. [ABSTRACT FROM AUTHOR]

We present a detailed computational study on the temperature effect of the dynamics and the interfacial width of unentangled cis-1,4 polybutadiene linear chains confined between strongly attractive alumina layers via long, several μs, atomistic molecular dynamics simulations for a wide range of temperatures (143–473 K). We examine the spatial gradient of the translational segmental dynamics and of an effective local glass temperature ( T g L ). The latter is found to be much higher than the bulk Tg for the adsorbed layer. It gradually reduces to the bulk Tg at about 2 nm away from the substrate. For distant regions (more than ≈ 1.2 n m), a bulk-like behavior is observed; relaxation times follow a typical Vogel–Fulcher–Tammann dependence for temperatures higher than Tg and an Arrhenius dependence for temperatures below the bulk Tg. On the contrary, the polymer chains at the vicinity of the substrate follow piecewise Arrhenius processes. For temperatures below about the adsorbed layer's T g L , the translational dynamics follows a bulk-like (same activation energy) Arrhenius process. At higher temperatures, there is a low activation energy Arrhenius process, caused by high interfacial friction forces. Finally, we compute the interfacial width, based on both structural and dynamical definitions, as a function of temperature. The absolute value of the interfacial width depends on the actual definition, but, regardless, the qualitative behavior is consistent. The interfacial width peaks around the bulk Tg and contracts for lower and higher temperatures. At bulk Tg, the estimated length of the interfacial width, computed via the various definitions, ranges between 1.0 and 2.7 nm. [ABSTRACT FROM AUTHOR]

We use molecular dynamics simulations to unravel the physics underpinning the light-induced density changes caused by the dynamic trans–cis–trans isomerization cycles of azo-mesogens embedded in a liquid crystal polymer network, an intriguing experimental observation reported in the literature. We employ two approaches, cyclic and probabilistic switching of isomers, to simulate dynamic isomerization. The cyclic switching of isomers confirms that dynamic isomerization can lead to density changes at specific switch-time intervals. The probabilistic switching approach further deciphers the physics behind the non-monotonous relation between density reduction and light intensities observed in experiments. Light intensity variations in experiments are accounted for in simulations by varying the trans–cis and cis–trans isomerization probabilities. The simulations show that an optimal combination of these two probabilities results in a maximum density reduction, corroborating the experimental observations. At such an optimal combination of probabilities, the dynamic trans–cis–trans isomerization cycles occur at a specific frequency, causing significant distortion in the polymer network, resulting in a maximum density reduction. [ABSTRACT FROM AUTHOR]

Entropy scaling is applied to the shear viscosity, self-diffusion coefficient, and thermal conductivity of simple monatomic fluids. An extensive molecular dynamics simulation series is performed to obtain these transport properties and the residual entropy of three potential model classes with variable repulsive exponents: n, 6 Mie (n = 9, 12, 15, and 18), Buckingham's exponential-six (α = 12, 14, 18, and 30), and Tang–Toennies (αT = 4.051, 4.275, and 4.600). A wide range of liquid and supercritical gas- and liquid-like states is covered with a total of 1120 state points. Comparisons to equations of state, literature data, and transport property correlations are made. Although the absolute transport property values within a given potential model class may strongly depend on the repulsive exponent, it is found that the repulsive steepness plays a negligible role when entropy scaling is applied. Hence, the plus-scaled transport properties of n, 6 Mie, exponential-six, and Tang–Toennies fluids lie basically on one master curve, which closely corresponds with entropy scaling correlations for the Lennard-Jones fluid. This trend is confirmed by literature data of n, 6 Mie, and exponential-six fluids. Furthermore, entropy scaling holds for state points where the Pearson correlation coefficient R is well below 0.9. The condition R > 0.9 for strongly correlating liquids is thus not necessary for the successful application of entropy scaling, pointing out that isomorph theory may be a part of a more general framework that is behind the success of entropy scaling. Density scaling reveals a strong influence of the repulsive exponent on this particular approach. [ABSTRACT FROM AUTHOR]

In this study, we use molecular dynamics simulations of liquid water to investigate how shear thinning affects the viscosity of liquid water by structural changes of the hydrogen bond network. The effect of shear on viscosity can be divided into two parts: shear-induced destruction of the hydrogen bond network and the influence of the water structure on shear viscosity. First, strong shear destroys tetrahedral structures and thus reduces the connectivity of the hydrogen bond network. It is mainly because shear deformation, characterized by compression and expansion axes, respectively, triggers the destruction and formation of hydrogen bonds, resulting in anisotropic effects on water structures. At the same time, shear destroys large clusters and enhances the formation of small ones, resulting in a decrease in average cluster sizes. Second, the change of viscosity obeys a power law relationship with the change of hydrogen bond structures, highlighting a one-to-one correspondence between structure and property. Meanwhile, in order to explain why the structure affects viscosity, we define hydrogen-bond viscosity and find that the cooperative motion of the water structures can promote momentum transfer in the form of aggregations. Hydrogen-bond viscosity accounts for 5%–50% of the total viscosity. Our results elucidate that water structures are the important structural units to explain the change of water properties. [ABSTRACT FROM AUTHOR]

Estimating the rate of rare conformational changes in molecular systems is one of the goals of molecular dynamics simulations. In the past few decades, a lot of progress has been done in data-based approaches toward this problem. In contrast, model-based methods, such as the Square Root Approximation (SqRA), directly derive these quantities from the potential energy functions. In this article, we demonstrate how the SqRA formalism naturally blends with the tensor structure obtained by coupling multiple systems, resulting in the tensor-based Square Root Approximation (tSqRA). It enables efficient treatment of high-dimensional systems using the SqRA and provides an algebraic expression of the impact of coupling energies between molecular subsystems. Based on the tSqRA, we also develop the projected rate estimation, a hybrid data-model-based algorithm that efficiently estimates the slowest rates for coupled systems. In addition, we investigate the possibility of integrating low-rank approximations within this framework to maximize the potential of the tSqRA. [ABSTRACT FROM AUTHOR]

Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to millisecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work, we present a comparison of five computational methods that permit the joint analysis of MD simulations and NMR relaxation experiments. We discuss their relative strengths and areas of applicability and demonstrate how they may be utilized to interpret the dynamics in MD simulations with the small protein ubiquitin as a test system. We focus on the aliphatic side chains given the rigidity of the backbone of this protein. We find encouraging agreement between experiment, Markov state models built in the χ1/χ2 rotamer space of isoleucine residues, explicit rotamer jump models, and a decomposition of the motion using ROMANCE. These methods allow us to ascribe the dynamics to specific rotamer jumps. Simulations with eight different combinations of force field and water model highlight how the different metrics may be employed to pinpoint force field deficiencies. Furthermore, the presented comparison offers a perspective on the utility of NMR relaxation to serve as validation data for the prediction of kinetics by state-of-the-art biomolecular force fields. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism. [ABSTRACT FROM AUTHOR]

In order to prepare highly heat-resistant packaging insulation materials, in this paper, bismaleimide/epoxy resin (BMI/EP55) composites with different contents of BMI were prepared by melt blending BMI into amino tetrafunctional and phenolic epoxy resin (at a ratio of 5:5). The microstructures and thermal and electrical properties of the composites were tested. The electrostatic potential distribution, energy level distribution, and molecular orbitals of BMI were calculated using Gaussian. The results showed that the carbonyl group in BMI is highly electronegative, implying that the carbonyl group has a strong electron trapping ability. The thermal decomposition temperature of the composites gradually increased with the increase of BMI content, and the 20% BMI/EP55 composites had the highest heat-resistance index, along with a glass transition temperature (Tg) of >250 °C. At different test temperatures, with increase in the BMI content, the conductivity of epoxy resin composites showed a tendency to first decrease and then increase, the breakdown field strength showed a tendency to first increase and then decrease, and the dielectric constant was gradually decreased. Two trap centers were present simultaneously in the composites, where the shallow trap energy level is the deepest in 20% BMI/EP composites and the deep trap energy level is the deepest in 10% BMI/EP55 composites. Correspondingly, the 10% BMI/EP55 composite had a slower charge decay rate, while the 20% BMI/EP55 had a faster charge decay rate. In summary, the BMI/EP55 composites with high heat resistance and insulating properties were prepared in this study, which provided ideas for preparing high-temperature packaging insulating materials. [ABSTRACT FROM AUTHOR]

A method for characterizing the topological fluctuations in liquids is proposed. This approach exploits the concept of the weighted gyration tensor of a collection of particles and permits the definition of a local configurational unit (LCU). The first principal axis of the gyration tensor serves as the director of the LCU, which can be tracked and analyzed by molecular dynamics simulations. Analysis of moderately supercooled Kob–Andersen mixtures suggests that orientational relaxation of the LCU closely follows viscoelastic relaxation and exhibits a two-stage behavior. The slow relaxing component of the LCU corresponds to the structural, Maxwellian mechanical relaxation. Additionally, it is found that the mean curvature of the LCUs is approximately zero at the Maxwell relaxation time with the Gaussian curvature being negative. This observation implies that structural relaxation occurs when the configurationally stable and destabilized regions interpenetrate each other in a bicontinuous manner. Finally, the mean and Gaussian curvatures of the LCUs can serve as reduced variables for the shear stress correlation, providing a compelling proof of the close connection between viscoelastic relaxation and topological fluctuations in glass-forming liquids. [ABSTRACT FROM AUTHOR]

The large discrepancy among the nucleation kinetics extracted from experimental measurements and computer simulations and the prediction of the classical nucleation theory (CNT) has stimulated intense arguments about its origin in the past decades, which is crucially relevant to the validity of the CNT. In this paper, we investigate the atomistic mechanism of the nucleation in liquid Al in contact with amorphous substrates with atomic-level smooth/rough surfaces, using molecular dynamics (MD) simulations. This study reveals that the slightly distorted local fcc/hcp structures in amorphous substrates with smooth surfaces can promote heterogeneous nucleation through a structural templating mechanism, and on the other hand, homogeneous nucleation will occur at a larger undercooling through a fluctuation mechanism if the surface is rough. Thus, some impurities, previously thought to be impotent, could be activated in the homogeneous nucleation experiments. We further find that the initial growth of the nucleus on smooth surfaces of amorphous substrates is one order of magnitude faster than that in homogeneous nucleation. Both these factors could significantly contribute to the discrepancy in the nucleation kinetics. This study is also supported by a recent study of the synthesis of high-entropy alloy nanoparticles assisted with the liquid metal Ga [Cao et al., Nature 619, 73 (2023)]. In this study, we established that the boundary existed between homogeneous and heterogeneous nucleation, i.e., the structural templating is a general mechanism for heterogeneous nucleation, and in its absence, homogeneous nucleation will occur through the fluctuation mechanism. This study provides an in-depth understanding of the nucleation theory and experiments. [ABSTRACT FROM AUTHOR]

Understanding the ignition and dynamic processes for the combustion of hydrate is crucial for efficient energy utilization. Through reactive force field molecular dynamics simulations, we studied the high-temperature decomposition and combustion processes of methane hydrates in a pure oxygen environment. We found that at an ignition temperature of 2800 K, hydrates decomposed from the interface to the interior, but the layer-by-layer manner was no longer strictly satisfied. At the beginning of combustion, water molecules reacted first to generate OH•, followed by methane oxidation. The combustion pathway of methane is C H 4 → CH 3 • → C H 3 O • → C H 2 O → H C • O → HCO O • → CO (C O 2 ). During the combustion process, a liquid water layer was formed between melted methane and oxygen, which hindered the reaction's progress. When there is no heat resistance, oxygen will transform into radicals such as OH• and O•, which have faster diffusion rates, allowing oxygen to conveniently cross the mass transfer barrier of the liquid water layer and participate in the combustion process. Increasing the amount of OH• may cause a surge in the reaction. On the other hand, when significant heat resistance exists, OH• is difficult to react with low-temperature hydrate components, but it can transform into O• to trigger the oxidation of methane. The H• generated has a sufficient lifetime to contact high-temperature oxygen molecules, converting oxygen into radicals that easily cross the water layer to achieve mass transfer. Therefore, finding ways to convert oxygen into various radicals is the key to solving the incomplete combustion of hydrates. Finally, the reaction pathways and microscopic reaction mechanisms of each species are proposed. [ABSTRACT FROM AUTHOR]

Current models to understand the reactivity of metal/aqueous interfaces in electrochemistry, e.g., volcano plots, are based on the adsorption free energies of reactants and products, which are often small hydrophobic molecules (such as in CO2 and N2 reduction). Calculations played a major role in the quantification and comprehension of these free energies in terms of the interactions that the reactive species form with the surface. However, solvation free energies also come into play in two ways: (i) by modulating the adsorption free energy together with solute–surface interactions, as the solute has to penetrate the water adlayer in contact with the surface and get partially desolvated (which costs free energy); (ii) by regulating transport across the interface, i.e., the free energy profile from the bulk to the interface, which is strongly non-monotonic due to the unique nature of metal/aqueous interfaces. Here, we use constant potential molecular dynamics to study the solvation contributions, and we uncover huge effects of the shape and orientation (on top of the already known size effect) of small hydrophobic and amphiphilic solutes on their adsorption free energy. We propose a minimal theoretical model, the S.O.S. model, that accounts for size, orientation, and shape effects. These novel aspects are rationalized by recasting the concepts at the base of the Lum–Chandler–Weeks theory of hydrophobic solvation (for small solutes in the so-called volume-dominated regime) into a layer-by-layer form, where the properties of each interfacial region close to the metal are explicitly taken into account. [ABSTRACT FROM AUTHOR]

Metal–organic frameworks (MOFs), with their unique porous structures and versatile functionality, have emerged as promising materials for the adsorption, separation, and storage of diverse molecular species. In this study, we investigate water adsorption in MOF-808, a prototypical MOF that shares the same secondary building unit (SBU) as UiO-66, and elucidate how differences in topology and connectivity between the two MOFs influence the adsorption mechanism. To this end, molecular dynamics simulations were performed to calculate several thermodynamic and dynamical properties of water in MOF-808 as a function of relative humidity (RH), from the initial adsorption step to full pore filling. At low RH, the μ3-OH groups of the SBUs form hydrogen bonds with the initial water molecules entering the pores, which triggers the filling of these pores before the μ3-OH groups in other pores become engaged in hydrogen bonding with water molecules. Our analyses indicate that the pores of MOF-808 become filled by water sequentially as the RH increases. A similar mechanism has been reported for water adsorption in UiO-66. Despite this similarity, our study highlights distinct thermodynamic properties and framework characteristics that influence the adsorption process differently in MOF-808 and UiO-66. [ABSTRACT FROM AUTHOR]