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Atomistic simulations are performed to assess how the main characteristics of a pairwise interatomic potential function can affect the occurrence of wear. A Morse-like potential is tailored in its attractive part such as to vary independently the cut-off radius and the maximum value of the attractive (adhesive) force. An ideal numerical experiment is then performed where the interaction between a metal crystal and a probe changes, while their material properties are not affected, to isolate the behavior of the interface. Force functions with larger adhesive force can loosely be interpreted as describing dry contacts while those with smaller adhesive force can be interpreted as describing lubricated contacts. Results demonstrate that the occurrence of wear is strongly dependent on the shape of the interatomic force field, and more specifically on the combination of maximum adhesive force and effective length of the interatomic attraction. Wear can initiate also at small adhesive energy, provided that the maximum adhesive force between atoms is large. When the surface of the crystal is taken to be rough instead of flat, the effect of the interatomic potential function on friction and wear becomes smaller, as the atoms belonging to the roughness are weakly bound to the rest of the crystal and are easily dislodged with any of the force functions we used.

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The dynamic characterization of guest molecules in the metal-organic frameworks (MOFs) can always provide the insightful and inspiring information to facilitate the synthetic design of MOF materials from the bottom-up design of perspective. Herein, we present a series of atomistic molecular dynamics simulation for investigating the bipyridine dicarboxylate (bpydc) linker rotation effect on guest molecule adsorption with and without considering the transition metal (TM) chelation in MOF-253 materials. The simulated PXRD patterns of the various linker orientations present the challenge of distinguishing these structural varieties by the conventional crystalline spectroscopic measurements. The observed short inter-TM stable structure may subsequently lead to the formation of a binuclear TM catalytic site, and a proposed formic acid generation mechanism from CO2 and H2 is derived based upon the density functional theory calculations for the application of CO2 reduction.

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This paper describes the physical modelling of neutron scattering in two polycrystalline inclusion compounds, fully deuterated clathrate hydrate andC60, each with paramagnetic oxygen as guest molecules. For studying the suitability of these materials for neutron moderation to very low energies, the model includes, in addition to the magnetic neutron scattering by the oxygen, the nuclear scattering by all constituents. The theoretical total cross sections are calculated based on the phonon density of states obtained by density functional theory and molecular dynamics simulations. At low temperatures, the developed scattering kernels are in good agreement with experimental neutron scattering data reported in the literature. At 20 K and above, a Lorentzian distribution for the zero-field splitting of the magnetic substates of the spin triplet of the oxygen molecules helps to reproduce magnetic peaks observed in inelastic neutron scattering experiments better than the original theory based on a single-valued splitting constant. Neutron spectra obtained by Monte Carlo simulations in infinite media are presented, highlighting the potential use ofO2-containing fully deuterated clathrate hydrate as a neutron moderator for the production of very cold neutrons.

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Ni is the second most abundant element in the Earth's core. Yet, its effects on the inner core's structure and formation process are usually disregarded because of its electronic and size similarity with Fe. Using ab initio molecular dynamics simulations, we find that the bcc phase can spontaneously crystallize in liquid Ni at temperatures above Fe's melting point at inner core pressures. The melting temperature of Ni is shown to be 700 to 800 K higher than that of Fe at 323 to 360 GPa. hcp, bcc, and liquid phase relations differ for Fe and Ni. Ni can be a bcc stabilizer for Fe at high temperatures and inner core pressures. A small amount of Ni can accelerate Fe's crystallization at core pressures. These results suggest that Ni may substantially impact the structure and formation process of the solid inner core.

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Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties. Molecular simulations of nanoscopic atomistic structures therefore require accurately resolved three-dimensional input structures. If extracted from experiment, these structures often suffer from severe uncertainties, of which the lack of information on hydrogen atoms is a prominent example. Hence, experimental structures require careful review and curation, which is a time-consuming and error-prone process. Here, we present a fast and robust protocol for the automated structure analysis and pH-consistent protonation, in short, ASAP. For biomolecules as a target, the ASAP protocol integrates sequence analysis and error assessment of a given input structure. ASAP allows for p K a prediction from reference data through Gaussian process regression including uncertainty estimation and connects to system-focused atomistic modeling described in Brunken and Reiher (J. Chem. Theory Comput. 16, 2020, 1646). Although focused on biomolecules, ASAP can be extended to other nanoscopic objects, because most of its design elements rely on a general graph-based foundation guaranteeing transferability. The modular character of the underlying pipeline supports different degrees of automation, which allows for (i) efficient feedback loops for human-machine interaction with a low entrance barrier and for (ii) integration into autonomous procedures such as automated force field parametrizations. This facilitates fast switching of the pH-state through on-the-fly system-focused reparametrization during a molecular simulation at virtually no extra computational cost.

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Alumina surface coatings are commonly applied to layered oxide cathode particles for lithium-ion battery applications. Atomic layer deposition (ALD) is one such surface coating technique, and ultrathin alumina ALD films (<2 nm) are shown to improve the electrochemical performance of LiNixMnyCo1-x-yO2 materials, with groups hypothesizing that a beneficial Li-Al-O product is being formed during the alumina ALD process. However, the atomic structure of these films is still not well understood, and quantifying the interface of ultrathin (∼1 nm) ALD films is an arduous experimental task. Here, we perform molecular dynamics simulations of amorphous alumina films of varying thickness in contact with the (0001) LiCoO2 (LCO) surface to quantify the film nanostructure. We calculate elemental mass density profiles through the films and observe that the Li-Al-O interphase extends ∼2 nm from the LCO surface. Additionally, we observe layering of Al and O atoms at the LCO-film interface that extends for ∼1.5 nm. To access the short-range order of the amorphous film, we calculated the Al coordination numbers through the film. We find that while [4]Al is the prevailing coordination environment, significant amounts of [6]Al exist at the interface between the LiCoO2 surface and the film. Taken together, these principal findings point to a pseudomorphic Li-Al-O overlayer that approximates the underlying layered LiCoO2 lattice but does not exactly replicate it. Additionally, with sufficient thickness, the Li-Al-O film transitions to an amorphous alumina structure. We anticipate that our findings on the ALD-like, Li-Al-O film nanostructure can be applied to other layered LiNixMnyCo1-x-yO2 materials because of their shared crystal structure with LiCoO2. This work provides insight into the nanostructure of amorphous ALD alumina films to help inform their use as protective coatings for Li-ion battery cathode active materials.

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In Type 2 diabetes, increased insulin sensitivity is induced by thiazolidinedione activation of the peroxisome proliferator-activated receptor gamma (PPARγ). Recent data indicate a relationship between SNPs in PPARγ and poor drug response. Therefore, understanding the pathogenic consequences of mutations in PPARγ-mediated protein-drug interactions will be prima-facie for establishing personalized medicine. The PPARG gene has 197 missense SNPs, 22 of which were determined to be both deleterious and destabilizing, employing in silico approaches. Molecular docking analysis suggested that the mutation influenced the binding energy of at least seven of the variants. The mutant R316H was identified as the most damaging and deleterious from the observed results. For a better understanding of the dynamic variation upon mutation at the atomic level, molecular dynamics simulations of the wild-type and R316H mutant PPARγ structure were performed. The analysis indicates that the mutation increased protein structural compactness while decreasing flexibility. The reduced dynamics in the mutant structure was further validated by principal component analysis. This mechanistic evaluation of the PPARγ protein variants provides insight into the relationship between genetic variation and interindividual variability of drug responsiveness and will facilitate the future studies for the development of tailored treatment regime for precision medicine.

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Mg3(Sb1-xBix)2 alloy has been extensively studied in the last 5 years due to its exceptional thermoelectric (TE) performance. The absence of accurate force field for inorganic alloy compounds presents great challenges for computational studies. Here, we explore the atomic microstructure, thermal, and elastic properties of the Mg3(Sb1-xBix)2 alloy at different solution concentrations through atomic simulations with a highly accurate machine learning interatomic potential (ML-IAP). We find atomic local ordering in the optimized structure with the Bi-Bi pair inclined to join adjacent layers and Sb-Sb pair preferring to stay within the same layer. The thermal conductivity changes with the solution concentrations can be correctly predicted through ML-IAP-based molecular dynamics simulations. Spectral thermal conductance analysis shows that the continuous movement of low-frequency peak to high frequency is responsible for the reduction of the thermal conductivity upon alloying. Elastic calculations reveal that similar to the thermal conductivity, solid solution alloying can reduce the overall elastic properties at both Mg3Sb2 and Mg3Bi2 ends, while anisotropic behavior is clearly observed with linear interpolation relationship upon alloying along the interlayer direction and nonlinearity along the intralayer direction. Although the atomic local ordering shows little effects on the properties of the Mg3(Sb1-xBix)2 alloy with only two alloying elements, it possesses potential important impacts on multiprincipal element inorganic TE alloys. This work provides a recipe for computational studies on the TE alloy systems and thus can accelerate the discovery and optimization of TE materials with high TE performance.

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Chemical growth of two-dimensional (2D) materials with controlled morphology is critical to bring their tantalizing properties to fruition. However, the growth must be on a substrate, which involves either intrinsic or intentionally introduced undulation, at a scale significantly larger than the materials thickness. Recent theory and experiments showed that 2D materials grown on a curved feature on substrates can incur a variety of topological defects and grain boundaries. Using a Monte Carlo method, we herein show that 2D materials growing on periodically undulated substrates with nonzero Gaussian curvature of practical relevance follow three distinct modes: defect-free conformal, defect-free suspension and defective conformal modes. The growth on the non-Euclidean surface can accumulate tensile stress that gradually lifts the materials from substrates and progressively turns the conformal mode into a suspension mode with increasing the undulation amplitude. Further enhancing the undulation can trigger Asaro-Tiller-Grinfield growth instability in the materials, manifested as discretely distributed topological defects due to strong stress concentration. We rationalize these results by model analyses and establish a "phase" diagram for guiding the control of growth morphology via substrate patterning. The undulation-induced suspension of 2D materials can help understand the formation of overlapping grain boundaries, spotted quite often in experiments, and guide how to avoid them.

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Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.

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Tribological properties depend strongly on environmental conditions such as temperature, humidity, and operation liquid. However, the origin of the liquid effect on friction remains largely unexplored. Herein, taking molybdenum disulfide (MoS2) as a model system, we explored the nanoscale friction of MoS2 in polar (water) and nonpolar (dodecane) liquids through friction force microscopy. The friction force exhibits a similar layer-dependent behavior in liquids as in air; i.e., thinner samples have a larger friction force. Interestingly, friction is significantly influenced by the polarity of the liquid, and it is larger in polar water than in nonpolar dodecane. Atomically resolved friction images together with atomistic simulations reveal that the polarity of the liquid has a substantial effect on friction behavior, where liquid molecule arrangement and hydrogen-bond formation lead to a higher resistance in polar water in comparison to that in nonpolar dodecane. This work provides insights into the friction on two-dimensional layered materials in liquids and holds great promise for future low-friction technologies.

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Short peptide sequences and bolaamphiphiles derived from natural proteins are gaining importance due to their ability to form unique nanoscale architectures for a variety of biological applications. In this work, we have designed six short peptides (triplet or monomeric forms) and two peptide bolaamphiphiles that either incorporate the bioactive collagen motif (Gly-X-Y) or sequences where Gly, Pro, or hydroxyproline (Hyp) are replaced by Ala or His. For the bolaamphiphiles, a malate moiety was used as the aliphatic linker for connecting His with Hyp to create collagen mimics. Stability of the assemblies was assessed through molecular dynamics simulations and results indicated that (Pro-Ala-His)3 and (Ala-His-Hyp)3 formed the most stable structures, while the amphiphiles and the monomers showed some disintegration over the course of the 200 ns simulation, though most regained structural integrity and formed fibrillar structures, and micelles by the end of the simulation, likely due to the formation of more thermodynamically stable conformations. Multiple replica simulations (REMD) were also conducted where the sequences were simulated at different temperatures. Our results showed excellent convergence in most cases compared to constant temperature molecular dynamics simulation. Furthermore, molecular docking and MD simulations of the sequences bound to collagen triple helix structure revealed that several of the sequences had a high binding affinity and formed stable complexes, particularly (Pro-Ala-His)3 and (Ala-His-Hyp)3. Thus, we have designed new hybrid-peptide-based sequences which may be developed for potential applications as biomaterials for tissue engineering or drug delivery.

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Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.

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The influence of the indenter angle on the deformation mechanisms of single-crystal Si was analyzed via molecular dynamics simulations of the nanoindentation process. Three different types of diamond conical indenters with semi-angles of 45°, 60°, and 70° were used. The load-indentation depth curves were obtained by varying the indenter angles, and the structural phase transformations of single-crystal Si were observed from an atomistic view. In addition, the hardness and elastic modulus with varying indenter angles were evaluated based on the Oliver-Pharr method and Sneddon's solution. The simulation results showed that the indenter angle had a significant effect on the load-indentation depth curves, which resulted from the strong dependence of the elastic and plastic deformation ratios on the indenter angle during indentations.

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Metal oxide ZrO2has been widely explored for resistive switching application due to excellent properties like high ON/OFF ratio, superior data retention, and low operating voltage. However, the conduction mechanism at the atomistic level is still under debate. Therefore, we have performed comprehensive insights into the role of neutral and charged oxygen vacancies in conduction filament (CF) formation and rupture, which are demonstrated using the atomistic simulation based on density functional theory (DFT). Formation energy demonstrated that the fourfold coordinated oxygen vacancy is more stable. In addition, the electronic properties of the defect included supercell confirm the improvement in electrical conductivity due to the presence of additional energy states near Fermi energy. The CF formation and rupture using threefold and fourfold oxygen vacancies are demonstrated through cohesive energy, electron localization function, and band structure. Cohesive energy analysis confirms the cohesive nature of neutral oxygen vacancies while the isolated behavior for +2 charged oxygen vacancies in the CF. In addition, nudged elastic band calculation is also performed to analyze the oxygen vacancy diffusion energy under different paths. Moreover, we have computed the diffusion coefficient and drift velocity of oxygen vacancies to understand the CF. This DFT study described detailed insight into filamentary type resistive switching observed in the experimentally fabricated device. Therefore, this fundamental study provides the platform to explore the switching mechanism of other oxide materials used for memristor device application.

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Biocementation is a ground improvement technique that involves precipitating a mineral (commonly calcium carbonate, CaCO3) in the soil pore space to bind soil particles, in turn increasing the strength and reducing the permeability of the soil. Ureolysis (i.e. hydrolysis of urea) is the most researched calcium carbonate precipitation mechanism, which can be induced through either a microbial (MICP) or enzymatic (EICP) process. While laboratory tests and field trials have provided strong evidence of the efficacy of biocementation in strengthening granular materials, the role of the precipitate-grain interface and the surface chemistry of soil grains in biocementation are largely unknown. This study aims to address this gap. To this end, two geotechnically similar sand samples differing considerably in the amount of iron oxide and iron sulfate on grain surface are biocemented via EICP and tested for unconfined compressive strength (UCS). The biocemented sample containing a high concentration of iron oxide and iron sulfate exhibits almost 50% lower UCS than the other sample. To investigate whether surface chemistry can explain this considerable difference, interactions of CaCO3 with quartz (SiO2), hematite (Fe2O3), and marcasite (FeS2) as polymorphs of silicon dioxide, iron oxide, and iron sulfide, respectively, are simulated using molecular dynamics. The influence of water content at the precipitate-grain interface is also considered. Simulation results indicate that in dry conditions, CaCO3 has almost two times stronger affinity for SiO2 than Fe2O3 and FeS2, suggesting that biocementation is most effective for clean sands. It is also shown that water reduces the precipitate-grain adhesion.

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We investigate the effect of low temperature (cryogenic) thermal cycling on a generic model glass and observe signature of rejuvenation in terms of per-particle potential energy distributions. Most importantly, these distributions become broader and its average values successively increase when applying consecutive thermal cycles. We show that linear dimension plays a key role for these effects to become visible, since we do only observe a weak effect for a cubic system of roughly one hundred particle diameter but observe strong changes for a rule-type geometry with the longest length being two thousand particle diameters. A consistent interpretation of this new finding is provided in terms of a competition between relaxation processes, which are inherent to glassy systems, and excitation due to thermal treatment. In line with our previous report (Bruns et al., PRR 3, 013234 (2021)), it is shown that, depending on the parameters of thermal cycling, rejuvenation can be either too weak to be detected or strong enough for a clear observation.

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We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions.

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Molecular dynamics (MD) simulations are applied to study solute drag by curvature-driven grain boundaries (GBs) in Cu-Ag solid solution. Although lattice diffusion is frozen on the MD timescale, the GB significantly accelerates the solute diffusion and alters the state of short-range order in lattice regions swept by its motion. The accelerated diffusion produces a nonuniform redistribution of the solute atoms in the form of GB clusters enhancing the solute drag by the Zener pinning mechanism. This finding points to an important role of lateral GB diffusion in the solute drag effect. A 1.5 at.%Ag alloying reduces the GB free energy by 10-20% while reducing the GB mobility coefficients by more than an order of magnitude. Given the greater impact of alloying on the GB mobility than on the capillary driving force, kinetic stabilization of nanomaterials against grain growth is likely to be more effective than thermodynamic stabilization aiming to reduce the GB free energy.

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In this study, tensile tests on aluminum/silicon vertically cracked nanofilm/substrate systems were performed using atomistic simulations. Various crystallographic orientations and thicknesses of the aluminum nanofilms were considered to analyze the effects of these factors on the reliability of the nanofilm/substrate systems. The results show that systems with some specific crystallographic orientations have lower reliability compared to the other orientations because of the penetration of the vertical crack into the silicon substrate. This penetration phenomenon occurring in a specific model is related to a high coincidence of atomic matching between the interfaces in the model. This high coincidence leads to a tendency of the interface to maintain a coherent form in which the outermost silicon atoms of the substrate that are bonded to the aluminum nanofilm tend to stick with the aluminum atoms under tensile loads. This phenomenon was verified by interface energy calculations in the simulation models.