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At least 271 records · Page 15

Pressure-driven density match nucleates metastable r8 phases from amorphous Si and Ge

The pressure–temperature phase behavior of covalent disordered solids such as amorphous silicon and germanium is complex. Questions remain on possible glass transitions, on polyamorphism via amorphous–amorphous transitions, on connections with liquid–liquid transitions, on structure-behavior relationships, and on their potential as precursor for novel methods for material discovery. Here we demonstrate experimentally the nucleation of a metastable, four-fold coordinated rhombohedral r8 phase from pure amorphous silicon and germanium upon room temperature compression at pressures below 10 GPa. Accompanying theory reveals a strong pressure-driven distortion of the bond angle transforming the starting tetrahedral low-density amorphous network to a distorted four-fold coordinated medium-density state. This state is of lower density than metallic high-density networks, resembles the crystalline r8 phase and initiates its nucleation. Our finding shows that polyamorphism is not the only possible transformation mode for these amorphous solids and that instead nucleation of interesting functional phases at potentially useful pressures is possible. Such novel access modes to metastable structures are critical for future exploitability and could be useful for other tetrahedral materials including carbon, where the related (bc8) post-diamond phase remains elusive. Our observed density match between an amorphous and a metastable crystalline phase clearly allows for a new phase transition pathway, while corresponding theory demonstrates how carefully validated atomistic simulations can guide prediction, discovery and synthesis of novel material structures.

Materials discovery↗

Using molecular simulation to understand the skin barrier

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.

59 BASIC BIOLOGICAL SCIENCES↗

Screw dislocation impingement and slip transfer at fcc-bcc semicoherent interfaces

Understanding of dislocation-interface interactions at the atomistic level could provide useful insights into the mechanisms behind slip transfer, a key information for higher length-scale formulations. Here, a systematic study of screw dislocation impingement on both Fe/Al and Fe/Cu interfaces with Kurdjumov-Sachs orientation relationship has been carried out using atomistic simulations. For the “strong” Fe/Al interface, there is appreciable dislocation delocalization, in which the change in dislocation content provided by Nye tensor analysis. Interestingly, the delocalization is significant enough that large simulation cells must be employed in order to avoid boundary effects. When the impinging dislocations are far away from the boundaries, the large accumulation of shear strains nearby the impinging dislocations at the interface causes dislocation nucleation/emission at these places. While for the “weak” Fe/Cu interface, the dislocation delocalization at the interface is notably long-range, extending more than 20 nm away from where the initial dislocations entered the interface.

36 MATERIALS SCIENCE↗

Enhanced defect annihilation capability of the graphene/copper interface: An in situ study

It is well known that energetic heavy ion irradiations can often induce defects and ultimately lead to material degradations. Interfaces, such as high-angle grain boundaries (HAGBs), are generally used as defect sinks for alleviating the irradiation damage. However, HAGBs are often unstable during radiation. Here we investigate the interfacial irradiation responses of the graphene (Gr)/Cu composites by using in situ Kr ++ ions irradiation under transmission electron microscopy. The results revealed that the Gr/Cu interface exhibits higher defect annihilation capability compared to the HAGBs in Cu. Moreover, the atomistic simulations suggested a slightly higher and larger range of stress field for the Gr/Cu interface, which contributes to the enhanced defects absorption capability. The present findings are essential to understand and design a new class of carbon/metal composites with superior irradiation tolerance.

36 MATERIALS SCIENCE↗

Reduction of vanadium diffusivity within copper grain boundaries due to enhanced binding

We investigate permeation of vanadium (V) through copper (Cu) layers in V/Cu/niobium (Nb) and molybdenum (Mo)/Cu/V tri-layer composites and compare it with the permeation behavior of Nb. Despite their low solubility in single-crystal Cu, both V and Nb permeate readily due to short-circuit transport through Cu grain boundaries (GBs). However, Nb permeates preferentially to V. Atomistic simulations suggest that this difference is due to lower V diffusivity at general GBs in Cu, compared to Nb. Here, the lower V diffusivity, in turn, arises from stronger V binding to the boundary, which manifests as a greater equilibrium GB concentration as well as a higher activation energy for GB diffusion.

36 MATERIALS SCIENCE↗

The physical origin of heterogeneous solute clustering and nanoprecipitation at grain boundaries in ultrafine-grained immiscible alloys

Here, grain-boundary segregation effects on heterogeneous solute clustering and nanoprecipitation at low solute concentrations were investigated in sputter-deposited ultrafine-grained Ag-Cu alloy films. X-ray diffraction and scanning transmission electron microscopy revealed extended solubility of Cu in Ag matrix, accompanied by the formation of Cu-rich nanoprecipitates and solute clusters at grain boundaries and their junctions. Atomistic simulations further demonstrated that Cu solutes heterogeneously segregate to Ag GBs and form small clusters that grow into nuclei for Cu nanoprecipitates. These findings provide critical insights into the role of heterogeneous grain-boundary segregation in governing the phase separation pathways of immiscible nanocrystalline and ultrafine-grained alloys.

Heterogeneous segregation↗

Structure-dependent clustering-to-declustering solute segregation transitions near disconnections

Grain-boundary disconnections, characterized by a step and a dislocation, are pervasive interfacial line defects that play a critical role in governing the properties and performance of nanocrystalline alloys. Although segregation of alloying elements is frequently observed at GB disconnections, the underlying mechanisms remain poorly understood, particularly at elevated temperatures and non-dilute conditions. In this study, we employ atomistic simulations to study the segregation behavior of Ag at various faulted disconnections in Cu as a model material system. Our results demonstrate a pronounced size and compactness effect on the segregation behavior: more compact faulted disconnection structures promote the formation of Ag segregation clusters due to a highly localized tensile field, whereas more spread faulted disconnection structures (i.e., with wider partial dislocation spacing) exhibit much weaker clustering tendencies. Furthermore, with increasing temperature, Ag clustering in small disconnections initially intensifies and then disappears, indicating a thermally driven transition from clustering to declustering segregation behavior.

Disconnections↗

Solid solutions limited by grain-boundary solute clustering in ultrafine-grained alloys

Immiscible Ag-Cu alloys exhibit complex behavior due to varying Cu solid solubilities reported under equilibrium and metastable conditions. In ultrafine-grained alloys, these limits are further complicated by a high fraction of grain boundaries, where solute atoms tend to segregate and, in some cases, form clusters. Here, this study investigates the influence of Cu solute segregation and clustering on solid-solution limits in ultrafine-grained Ag-Cu alloys synthesized by magnetron sputtering with varying Cu content. X-ray diffraction peak shifts reveal a solid-solution concentration plateau for Cu contents from 4.9 to 11.7 at %, in contrast to the peak shifts predicted by density-functional theory for Ag-Cu alloys. Scanning transmission electron microscopy further reveals limited solid solubility and the formation of numerous Cu-rich clusters at grain boundaries. Atomistic simulations demonstrate that such limited solubility does not arise from grain boundary segregation alone, but only when strong solute-solute interactions promote the formation of grain-boundary Cu solute clusters.

Density-functional theory↗

Protein Surface Printer for Exploring Protein Domains

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of Water Extraction on Malonamide Aggregation: A Molecular Dynamics and Graph Theoretic Approach

Solution structure in liquid-liquid extraction affects the efficacy of separation; however, even for simplified organic phases, structural characterization and attribution of aggregation to intermolecular interactions are fundamental challenges. We investigate water uptake into organic phases for two malonamides commonly applied to actinide and lanthanide separations. Extracted water induces reorganization of the amphiphilic extractant molecules, although we find this rearrangement is not strongly manifested in small-angle X-ray scattering making it challenging to probe without methods such as atomistic simulation. Using a graph theoretic approach to define hydrogen bonded water/malonamide aggregates from molecular dynamics simulations, we find evidence of a characteristic aggregate size by water number that results from geometric accommodation of the surrounding malonamide molecules. Furthermore, this implies a degree of size selectivity inherent to these water-in-oil aggregates. Conversely, we find no evidence of a characteristic size of the aggregates with respect to their malonamide number. By defining a separate graphical representation of self-association of the amphiphilic malonamides, we quantify how water affects the local and nonlocal topology of the malonamide network, providing a basis for characterization of the structure and impact of polar solutes in increasingly complex organic phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computing Thermodynamic Properties of Fluids Augmented by Nanoconfinement: Application to Pressurized Methane

Nanoconfined fluids exhibit remarkably different thermodynamic behavior compared to the bulk phase. These confinement effects render predictions of thermodynamic quantities of nanoconfined fluids challenging. In particular, confinement creates a spatially varying density profile near the wall that is primarily responsible for adsorption and capillary condensation behavior. Significant fluctuations in thermodynamic quantities, inherent in such nanoscale systems, coupled to strong fluid–wall interactions give rise to this near-wall density profile. Empirical models have been proposed to explain and model these effects, yet no first-principles based formulation has been developed. We present a statistical mechanics framework that embeds such a coupling to describe the effect of the fluid–wall interaction in amplifying the near-wall density behavior for compressible gases at elevated pressures such as pressurized methane in confinement. We show that the proposed theory predicts accurately the adsorbed layer thickness as obtained with small-angle neutron scattering measurements. Furthermore, the predictions of density under confinement from the proposed theory are shown to be in excellent agreement with available experimental and atomistic simulations data for a range of temperatures for nanoconfined methane. While the framework is presented for evaluating the near-wall density, owing to its rigorous foundation in statistical mechanics, the proposed theory can also be generalized for predicting phase-transition and nonequilibrium transport of nanoconfined fluids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Specific Ion and Electric Field Controlled Diverse Ion Distribution and Electroosmotic Transport in a Polyelectrolyte Brush Grafted Nanochannel

Controlling ion distribution inside a charged nanochannel is central to using such channels in diverse applications. Here, we show the possibility of using a charged polyelectrolyte (PE) brush grafted nanochannel for triggering diverse nanoscopic ion distribution and nanofluidic electroosmotic transport by controlling the valence and size of the counterions (that screen the charges of the PE brushes) and the strength of an externally applied axial electric field. We atomistically simulate separate cases of fully charged Polyacrylic acid (PAA) brush functionalized nanochannels with Na + , Cs + , Ca 2+ , Ba 2+ , and Y 3+ counterions screening the PE charges. Four key findings emerge from our simulations. First, we find that the counterions with a greater valence and a smaller size prefer to remain localized inside the brush layer. Second, for the case where there is an added chloride salt with the same cation (as the screening counterions), there are more coions (Cl - ions) in the brush-free bulk than counterions (for counterions Na + , Ca 2+ , Ba 2+ , Y 3+ ): this is a manifestation of the overscreening (OS) of the PE brush layer. Contrastingly, the number of Cs + ions remain higher than the Cl - ions inside the brush-free bulk, ensuring that there is no OS effect for this case. Third, large applied electric field enables a few Na + , Cs + , and Ba 2+ counterions to leave the brush layer and to go to the bulk: this makes the OS of the PE brush layer disappear for the cases of PE brushes being screened by the Na+ and Ba 2+ ions. On the other hand, no such electric-field-mediated disappearance of OS is observed for the cases of Ca 2+ and Y 3+ screening counterions; we attribute this to the firm attachment of these counterions to the negatively charged monomers. Free energy associated to a counterion binding to a PE chain corroborates this diversity in the counterion-specific response to the applied electric field. Lastly, we demonstrate that such diverse ion distributions, along with specific electric-field-strength-dependent ion properties, lead to (1) EOS transport in nanochannels grafted with PAA brushes screened with Cs + ions to be always counterion dominated, (2) EOS transport in nanochannels grafted with PAA brushes screened with Ca 2+ and Y 3+ ions to be always coion dominated, and (3) EOS transport in nanochannels grafted with PAA brushes screened with Na + and Ba 2+ ions to be coion dominated for smaller electric fields and counterion dominated for larger electric fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure–Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca)

Biofilms are the predominant mode of microbial life on Earth, and so a deep understanding of microbial communities-and their impacts on environmental processes-requires a firm understanding of biofilm properties. Because of the importance of biofilms to their microbial inhabitants, microbes have evolved different ways of engineering and reconfiguring the matrix of extracellular polymeric substances (EPS) that constitute the main non-living component of biofilms. This ability makes it difficult to distinguish between the biotic and abiotic origins of biofilm properties. An important route toward establishing this distinction has been the study of simplified models of the EPS matrix. This study builds on such efforts by using atomistic simulations to predict the nanoscale (≤10 nm scale) structure of a model EPS matrix and the sensitivity of this structure to interpolymer interactions and water content. To accomplish this, we use replica exchange molecular dynamics (REMD) simulations to generate all-atom configurations of ten 3.4 kDa alginate polymers at a range of water contents and Ca–Na ratios. Simulated systems are solvated with explicitly modeled water molecules, which allows us to capture the discrete structure of the hydrating water and to examine the thermodynamic stability of water in the gels as they are progressively dehydrated. Our primary findings are that (i) the structure of the hydrogels is highly sensitive to the identity of the charge-compensating cations, (ii) the thermodynamics of water within the gels (specific enthalpy and free energy) are, surprisingly, only weakly sensitive to cation identity, and (iii) predictions of the differential enthalpy and free energy of hydration include a short-ranged enthalpic term that promotes hydration and a longer-ranged (presumably entropic) term that promotes dehydration, where short and long ranges refer to distances shorter or longer than ~0.6 nm between alginate strands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of Normal and Lateral Electric Fields on Membrane Mechanical Properties

As a core component of biological and synthetic membranes, lipid bilayers are key to compartmentalizing chemical processes. Bilayer morphology and mechanical properties are heavily influenced by electric fields such as those caused by biological ion concentration gradients. We present atomistic simulations exploring the effects of electric fields applied normally and laterally to lipid bilayers. We find that normal fields decrease membrane tension, while lateral fields increase it. Free energy perturbation calculations indicate the importance of dipole-dipole interactions to these tension changes, especially for lateral fields. We additionally show that membrane area compressibilities can be related to their cohesive energies, allowing us to estimate changes in membrane bending rigidity under applied fields. We find that normal fields decrease bending rigidity, while lateral fields increase it. Furthermore, these results point to the use of directed electric fields to locally control membrane stiffness, thereby modulating associated cellular processes.

Chemistry↗

Structural Implications of Interfacial Hydrogen Bonding in Hydrated Wyoming-Montmorillonite Clay

Montmorillonite (MMT) clay - a layered porous nanomaterial used as seals in engineered waste containment barriers for spent nuclear fuel - adopts discrete hydration/swelling states depending upon surrounding water and ion activities and confining pressure. The structure of nanoconfined water and charge-balancing counterions in the clay mineral interlayers dictate the swelling and mechanical behavior of MMT, so a molecular model for this clay with high structural fidelity is required to accurately predict the reliability of long-term nuclear waste storage. Here, we present a molecular model for MMT that is based on high resolution transmission electron microscopy of Wyoming-MMT single crystals. Imaging data unambiguously show a cis-vacant arrangement of structural hydroxyl groups in the octahedral sheet, whereas existing molecular models assume a centrosymmetric trans-vacant configuration for MMT. Furthermore, using atomistic simulations, we find that the cis-vacant arrangement of structural hydroxyl groups significantly affects the structure of adsorbed water yielding a larger population of hydrogen bonds with bridging oxygens on the tetrahedral sheet and weak hydrogen bonding between the hydroxyl groups in the octahedral sheet and water in the clay mineral interlayers. As a result, water adsorbed in the interlayer is more "ice-like", with stronger ordering and lower density, although the diffusivity of the interlayer species is not significantly diminished. Our improved structural model for MMT provides insight into the energetics of water adsorption, which ultimately dictates its pore- to macro-scale swelling, transport, and fracture properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-Adiabatic Excited State Molecular Dynamics Methodologies: comparison and convergence

Direct atomistic simulation of nonadiabatic molecular dynamics is a challenging goal that allows important insights into fundamental physical phenomena. A variety of frameworks, ranging from fully quantum treatment of nuclei to semiclassical and mixed quantum–classical approaches, were developed. These algorithms are then coupled to specific electronic structure techniques. Such diversity and lack of standardized implementation make it difficult to compare the performance of different methodologies when treating realistic systems. Here, we compare three popular methods for large chromophores: Ehrenfest, surface hopping, and multiconfigurational Ehrenfest with ab initio multiple cloning (MCE-AIMC). These approaches are implemented in the NEXMD software, which features a common computational chemistry model. The resulting comparisons reveal the method performance for population relaxation and coherent vibronic dynamics. Finally, we study the numerical convergence of MCE-AIMC algorithms by considering the number of trajectories, cloning thresholds, and Gaussian wavepacket width. Our results provide helpful reference data for selecting an optimal methodology for simulating excited-state molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Disconnection-Mediated Transition in Segregation Structures at Twin Boundaries

Twin boundaries play an important role in the thermodynamics, stability, and mechanical properties of nanocrystalline metals. Understanding their structure and chemistry at the atomic scale is key to guide strategies for fabricating nanocrystalline materials with improved properties. In this work, we report an unusual segregation phenomenon at gold-doped platinum twin boundaries, which is arbitrated by the presence of disconnections, a type of interfacial line defect. By using atomistic simulations, we show that disconnections containing a stacking fault can induce an unexpected transition in the interfacial-segregation structure at the atomic scale, from a bilayer, alternating-segregation structure to a trilayer, segregation-only structure. This behavior is found for faulted disconnections of varying step heights and dislocation characters. Supported by a structural analysis and the classical Langmuir–McLean segregation model, we reveal that this phenomenon is driven by a structurally induced drop of the local pressure across the faulted disconnection accompanied by an increase in the segregation volume.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction and Experimental Verification of Electrolyte Solvation Structure from an OMol25-Trained Interatomic Potential

A molecular-level understanding of electrolyte solvation structure and ion–ion correlations is critical to developing next-generation battery chemistries. Atomistic simulation capabilities with sufficient accuracy, speed, and transferability to deliver reliable structural insights while avoiding arduous system-specific reparameterization are thus highly desirable. Machine learning interatomic potentials (MLIPs) trained on large, chemically diverse data sets are revolutionizing computational chemistry, enabling molecular dynamics simulations of battery electrolytes with near-DFT accuracy over 10,000× faster than DFT. While previous MLIP training data sets with suitable elemental coverage for electrolytes have been based on inorganic materials, the Open Molecules 2025 (OMol25) data set provides large-scale molecular DFT MLIP training data with broad elemental coverage and specifically samples tens of millions of electrolyte configurations. Here, we integrate computational modeling with experimental validation to systematically assess the ability of large-scale MLIPs pretrained on materials data or on OMol25 to accurately resolve nanoscale structural organization and ion-solvation characteristics in Na-ion battery electrolytes across diverse physicochemical conditions and compositional regimes. We find that the OMol25-trained Universal Model of Atoms (UMA-OMol) predicts experimentally measured densities and X-ray structure factors in substantially better agreement compared to state-of-the-art models trained only on inorganic materials data. Using UMA-OMol, we further analyze systematic trends in solvation structure as a function of cation identity, anion chemistry, salt concentration, and solvent topology. We observe that increasing system temperature amplifies the heterogeneity within the solvation environment, perturbing cation–solvent interactions and promoting the formation of contact ion pairs (CIPs). Moreover, subtle variations in the solvent topology of glyme-based electrolytes cause pronounced changes in ion correlations and solvation structure. The experimental agreement and microscopic insights shown here position OMol25-trained MLIPs as a practical route to predictive, high-throughput electrolyte simulations beyond the limits of classical force fields and direct DFT molecular dynamics, serving as a powerful tool for accelerating the design of next-generation Na-ion battery electrolytes and beyond.

MLIPs↗