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Probing the electrical double layer by operando X‐ray photoelectron spectroscopy through a graphene‐carbon nanotube composite window
Abstract The electrical double layer is known to spontaneously form at the electrode‐electrolyte interface, impacting many important chemical and physical processes as well as applications including electrocatalysis, electroorganic synthesis, nanomaterial preparation, energy storage, and even emulsion stabilization. However, it has been challenging to study this fundamental phenomenon at the molecular level because the electrical double layer is deeply “buried” by the bulk electrolyte solution. Here, we report a quantitative probing of the electrical double layer of ionic liquids from the solid side of a photoelectron‐transparent graphene‐carbon nanotube hybrid membrane electrode using X‐ray photoelectron spectroscopy. The membrane window is ultrathin (1‐1.5 nm), large (~1 cm 2 ), and robust, enabling a tight seal of the electrolyte and quantitative measurement with excellent photoelectron signals. By operando monitoring the population changes of cations and anions in response to the applied electrical potentials, we experimentally resolve the chemical structure and dynamics of the electrical double layer, which corroborate results from molecular dynamics simulations. image
Manipulating Conjugated Polymer Backbone Dynamics through Controlled Thermal Cleavage of Alkyl Side Chains
The morphological stability of an organic photovoltaic (OPV) device is greatly affected by the dynamics of donors and acceptors occurring near the device's operational temperature. These dynamics can be quantified by the glass transition temperature (T g ) of conjugated polymers (CPs). Because flexible side chains possess much faster dynamics, the cleavage of the alkyl side chains will reduce chain dynamics, leading to a higher T g . In this work, the T g s for CPs are systematically studied with controlled side chain cleavage. Isothermal annealing of polythiophenes featuring thermally cleavable side chains at 140 °C, is found to remove more than 95% of alkyl side chains in 24 h, and raise the backbone T g from 23 to 75 °C. Coarse grain molecular dynamics simulations are used to understand the T g dependence on side chain cleavage. X-ray scattering indicates that the relative degree of crystallization remains constantduring isothermal annealing process. The effective conjugation length is not influenced by thermal cleavage; however, the density of chromophore is doubled after the complete removal of alkyl side chains. Here, the combined effect of enhancing T g and conserving crystalline structures during the thermal cleavage process can provide a pathway to improving the stability of optoelectronic properties in future OPV devices.
27 Al NMR diffusometry of Al 13 Keggin nanoclusters
Although nanometer-sized aluminum hydroxide clusters (i.e., ϵ-Al 13 , [Al 13 O 4 (OH) 24 (H 2 O) 12 ] 7+ ) command a central role in aluminum ion speciation and transformations between minerals, measurement of their translational diffusion is often limited to indirect methods. Here, in this work, 27 Al pulsed field gradient stimulated echo nuclear magnetic resonance (PFGSTE NMR) spectroscopy has been applied to the AlO 4 core of the ϵ-Al 13 cluster with complementary theoretical simulations of the diffusion coefficient and corresponding hydrodynamic radii from a boundary element-based calculation. The tetrahedral AlO 4 center of the ϵ-Al 13 cluster is symmetric and exhibits only weak quadrupolar coupling, which results in favorable T 1 and T 2 27 Al NMR relaxation coefficients for 27 Al PFGSTE NMR studies. Stokes–Einstein relationship was used to relate the 27 Al diffusion coefficient of the ϵ-Al 13 cluster to the hydrodynamic radius for comparison with theoretical simulations, dynamic light scattering from literature, and previously published 1 H PFGSTE NMR studies of chelated Keggin clusters. This first-of-its-kind observation proves that 27 Al PFGSTE NMR diffusometry can probe symmetric Al environments in polynuclear clusters of greater molecular weight than previously considered.
Synthesizing realistic sand assemblies with denoising diffusion in latent space
Abstract The shapes and morphological features of grains in sand assemblies have far‐reaching implications in many engineering applications, such as geotechnical engineering, computer animations, petroleum engineering, and concentrated solar power. Yet, our understanding of the influence of grain geometries on macroscopic response is often only qualitative, due to the limited availability of high‐quality 3D grain geometry data. In this paper, we introduce a denoising diffusion algorithm that uses a set of point clouds collected from the surface of individual sand grains to generate grains in the latent space. By employing a point cloud autoencoder, the three‐dimensional point cloud structures of sand grains are first encoded into a lower‐dimensional latent space. A generative denoising diffusion probabilistic model is trained to produce synthetic sand that maximizes the log‐likelihood of the generated samples belonging to the original data distribution measured by a Kullback‐Leibler divergence. Numerical experiments suggest that the proposed method is capable of generating realistic grains with morphology, shapes and sizes consistent with the training data inferred from an F50 sand database. We then use a rigid contact dynamic simulator to pour the synthetic sand in a confined volume to form granular assemblies in a static equilibrium state with targeted distribution properties. To ensure third‐party validation, 50,000 synthetic sand grains and the 1542 real synchrotron microcomputed tomography (SMT) scans of the F50 sand, as well as the granular assemblies composed of synthetic sand grains are made available in an open‐source repository.
A Fundamentally New Coupled Approach to Contact Mechanics via the Dirichlet‐Neumann Schwarz Alternating Method
Contact phenomena are crucial for understanding the behavior of mechanical systems. However, existing computational approaches for simulating mechanical contact often face numerical challenges, such as inaccurate physical predictions, energy conservation errors, and unwanted oscillations. Here, we introduce an alternative technique for simulating dynamic contact based on the non‐overlapping Schwarz alternating method, originally developed for domain decomposition. In multibody contact scenarios, this method treats each body as a separate, non‐overlapping domain and prevents interpenetration using an alternating Dirichlet–Neumann iterative process. This approach has a strong theoretical foundation, eliminates the need for contact constraints, and offers flexibility, making it ideal for multiscale and multiphysics applications. We conducted a numerical comparison between the Schwarz method and traditional methods, such as the Lagrange multiplier and penalty methods, focusing on a benchmark impact problem. Our results indicate that the Schwarz alternating method outperforms traditional methods in several key areas: it provides more accurate predictions for various measurable quantities and demonstrates exceptional energy conservation capabilities. To address unwanted oscillations in contact velocities and forces, we explored various algorithms and stabilization techniques, ultimately opting for the naïve‐stabilized Newmark scheme for its simplicity and effectiveness. Additionally, we validated the efficiency of the Schwarz method in a three‐dimensional impact problem, highlighting its inherent capacity to accommodate different mesh topologies, time‐integration schemes, and time steps for each interacting body.
Structure preserving and energy dissipative contact approaches for implicit dynamics
In this work, several structure preserving and energy dissipative contact approaches are proposed and evaluated. The time integration schemes considered are general with regard to the version of constraint type, but here the emphasis was on mortar contact. The proposed mortar contact approach conserves both linear and angular momentum for mortar contact in a novel way. The proposed time integration scheme can conserve energy or provide strict contact dissipation. In addition, the proposed scheme enforces both gap constraints and gap velocity constraints (i.e., persistency). Using a midstep time integrator often causes energy dissipation during initial impact, here this energy can be recovered in a novel way. Enforcing the gap velocity constraint mitigates the contact chatter of the contact pressure and nodes in many problems. Whereas some approaches enforce the persistency condition and gap constraints simultaneously during the solution of the equations of motion (EOM) requiring multipliers for both constraints included in the equation set, here the gap constraint is solved through the equations of motion and the persistency condition is satisfied in the time integration scheme by the velocity update after the equations of motion. It is shown that this approach is strictly dissipative in that a plastic contact condition can be achieved. Analogous to a coefficient of restitution for rigid bodies, any dissipated energy can then be returned upon release if energy conservation is desired. Structure preserving methods are good for long-time dynamics simulations and energy conserving and strictly dissipative methods can overcome stability issues associated with standard time integration algorithms such as the Newmark method.
Thermal Gradient Effects on Local Hotspot Ignition in 1,3,5,7‐Tetranitro‐1,3,5,7‐tetrazocane (HMX)
Understanding hotspot ignition, growth, and criticality, as well as the timescales of each, is crucial for parameterizing mesoscale and continuum‐level models that rely on a statistical understanding of hotspots. However, these models often consider hotspots to have uniform temperatures or for hotspots of a given temperature and size to always behave the same. Therefore, using molecular dynamics simulations, we assess the influence of thermal distribution effects on hotspot local ignition and time to ignition in 1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocane (HMX) nanoscale hotspots. Finally, by assessing hotspots with a gradient driven from an initial two‐temperature core–shell setup, we show that small increases in the core temperature under a constant average temperature can lead to order‐of‐magnitude effects on reaction and local ignition timescales.
Tumorigenic p53 mutants undergo common structural disruptions including conversion to α‐sheet structure
Abstract The p53 protein is a commonly studied cancer target because of its role in tumor suppression. Unfortunately, it is susceptible to mutation‐associated loss of function; approximately 50% of cancers are associated with mutations to p53, the majority of which are located in the central DNA‐binding domain. Here, we report molecular dynamics simulations of wild‐type (WT) p53 and 20 different mutants, including a stabilized pseudo‐WT mutant. Our findings indicate that p53 mutants tend to exacerbate latent structural‐disruption tendencies, or vulnerabilities, already present in the WT protein, suggesting that it may be possible to develop cancer therapies by targeting a relatively small set of structural‐disruption motifs rather than a multitude of effects specific to each mutant. In addition, α‐sheet secondary structure formed in almost all of the proteins. α‐Sheet has been hypothesized and recently demonstrated to play a role in amyloidogenesis, and its presence in the reported p53 simulations coincides with the recent re‐consideration of cancer as an amyloid disease.
Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum
Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.
3D Printing of Supramolecular Polymer Hydrogels with Hierarchical Structure
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Long‐Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires
Abstract The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano‐ and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein‐protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.
Counterintuitive Trend of Intrusion Pressure with Temperature in the Hydrophobic Cu 2 (tebpz) MOF
Liquid porosimetry experiments reveal a peculiar trend of the intrusion pressure of water in hydrophobic Cu 2 (3,3',5,5'-tetraethyl-4,4'-bipyrazolate) MOF. At lower temperature (T) range, the intrusion pressure (P i ) increases with T. For higher T values, P i first reaches a maximum and then decreases. This is at odds with the Young–Laplace law, which for systems showing a continuous decrease of contact angle with T predicts a corresponding reduction of the intrusion pressure. Though the Young–Laplace law is not expected to provide quantitative predictions at the subnanoscale of Cu 2 (tebpz) pores, the physical intuition suggests that to a reduction of their hydrophobicity corresponds a reduction of the P i . Molecular dynamics simulations and sychrothron experiments allowed to clarify the mechanism of the peculiar trend of P i with T. At increasing temperatures the vapor density within the MOF’ pores grows significantly, bringing the corresponding partial pressure to ≈5 MPa. This pressure, which is consistent with the shift of P i observed in liquid porosimetry, represents a threshold to be overcame before intrusion takes place. Beyond some value of temperature, the phenomenon of reduction of hydrophobicity (and water surface tension) dominated over the opposite effect of increase of vapor pressure and P i inverts its trend with T.
Self‐Lubricating Tribo‐Catalytic Activity of 2D High Entropy Alloy Nanoflakes
High Entropy Alloys (HEAs) have garnered attention due to their remarkable tribological attributes. Predominantly, failure mechanisms in HEAs emanate from stress‐induced dislocations, culminating in crack propagation and film delamination. In this study, we report on the synthesis of 2D HEA of (MoWNbTaV) 0.2 S 2 which facilitates shear‐induced energy dissipation at sliding interfaces. The ball‐on‐disk tribological investigations demonstrate unprecedentedly low average coefficients of friction (0.076) and wear rates (10 −9 mm 3 (N∙m) −1 ) under high contact pressures (0.936 GPa) within ambient conditions. Employing multi‐scale characterizations alongside molecular dynamic simulations, we elucidate that the presence of the HEA triggers tribocatalytic activity under high contact pressures emerging as a pivotal factor in extending lubricant lifespan during tribological tests. The resilient lubriciousness coupled with the facile spray coating methodology of (MoWNbTaV) 0.2 S 2 in ambient environments paves the way for the development of a new class of solid lubricants based on 2D HEA.
Delineating the Impact of Diluent on High-Concentration Electrolytes for Developing High-Voltage LiNi 0.5 Mn 1.5 O 4 Spinel Cathode
LiNi 0.5 Mn 1.5 O 4 (LNMO) is a high-voltage spinel cathode with low nickel content, making it an attractive candidate for next-generation lithium-ion batteries (LIBs). However, its application is limited by interfacial instability with conventional carbonate-based electrolytes at high voltages. In this work, a localized saturated electrolyte (LSE) capable of stably operating up to 4.85 V is investigated. Molecular dynamics simulations and Fourier transform infrared spectroscopy reveal that adding “non-solvating” 1,1,2,2-tetrafluoroethyl-2,2,3,3-tetrafluoropropyl ether diluent in the saturated electrolyte, more PF 6 − anions are present in the first solvation shell of Li + , at the expense of solvent molecules. This tailored solvation environment promotes the formation of a robust, LiF-rich cathode-electrolyte interphase that mitigates transition metal dissolution and parasitic side reactions. The optimized LSE enables excellent cycling performance, with 95% capacity retention in Li|LNMO half-cells after 100 cycles and 94% retention in Li 4 Ti 5 O 12 |LNMO full cells after 250 cycles, even at a practically relevant LNMO cathode loading of ≈15 mg cm −2 . In conclusion, these results highlight the benefits of electrolyte engineering and solvation structure control in advancing high-voltage LIB technologies.
Supercooling of Alaskan Beetle Larvae as a Winter Survival Strategy
Insects are able to survive subfreezing temperatures by either limiting ice crystal formation in their bodies or through freeze avoidance. Beetle larvae are able to avoid freezing in winter by dehydrating in the fall months and replacing their body water content with high concentrations of glycerol. This enables the body fluid of the insect to supercool, and even vitrify, recovering unharmed when the temperature warms in the spring. Using nondestructive, high‐energy X‐ray synchrotron diffraction experiments, direct insight into how cryopreservation occurs at the atomic level within the beetle larvae has been obtained. The results shed light on the molecular‐level interactions associated with the mechanism responsible for surviving freezing temperatures. The molecular models of severely dehydrated Alaskan beetle larvae, based on glycerol‐water mixtures, yield a total of 4.2 ± 1.2 intermolecular hydrogen bonds per glycerol molecule at 275 K, in good agreement with existing molecular dynamics simulations. Most importantly, they show that if just over half the body fluid content is water, the water clusters are too small to form ice crystals that cause cellular damage.
The FMO-DFTB Method
Although the fragment molecular orbital (FMO) method enables electronic structure calculations with near-linear scaling behavior with respect to system size, the computational cost of ab initio methods typically employed in conjunction with FMO is still prohibitive for routine calculations of very large systems or long timescale molecular dynamics simulations. We, therefore, combined the FMO and density-functional tight-binding (DFTB) method, which is one of the emerging semi-empirical quantum chemical methods, and have demonstrated that FMO-DFTB is capable of performing geometry optimizations for systems containing up to one million atoms using limited computational resources. In this chapter, we will review the basics of the DFTB method first before introducing FMO-DFTB, focusing on the relationship with density functional theory and other FMO methodologies. We also demonstrate the latest scalings of FMO-DFTB2 and DFTB3 using three-dimensional water clusters, showing that the most favorable scaling is O(N1.16). Applications of FMO-DFTB to various systems are briefly summarized, and an outlook to future applications is provided.
Speciation and diffusive dynamics in hydrated grain boundaries of complex oxide Gd2Ti2O7
Abstract Grain boundaries in polycrystalline materials significantly affect their properties, such as ionic transport, corrosion, and chemical durability. The pyrochlore compound (Gd 2 Ti 2 O 7 ) is employed as a model for complex oxides and is known for its diverse applications, including nuclear waste immobilization. Density functional theory-based first-principles molecular dynamics simulations were performed at different temperatures on the hydrated grain boundary system. The results show extensive transformations within the grain boundaries among hydrous water species (OH − , H 2 O, and H 3 O + ). The temperature dependence of self-diffusion coefficients follows Arrhenius behavior, with an activation energy of 35.9 kJ/mol for hydrogen and 46.3 kJ/mol for oxygen. The lifetime of OH − is about three to four times longer than that of H 2 O at temperatures from 800 to 2100 K, suggesting the greater stability of OH − over H 2 O, a unique characteristic of the grain boundaries. The estimated lifetime of the hydrous species decreases as the temperature increases, with an activation energy of 9.9 kJ/mol for OH − and 13.4 kJ/mol for H 2 O. While Gd 3 + is more mobile than Ti 4+ , both the Gd 3 + and Ti 4+ cations are orders of magnitude less mobile than the water species. The results suggest that water species are much more mobile within grain boundaries than in the bulk crystal and have the potential to penetrate deep into polycrystalline materials through grain boundaries, leading to grain boundary degradation and dissolution. The different mobilities of cations in complex oxides can lead to leaching of certain cations and incongruent dissolution during the chemical weathering of Earth and industrial materials.