An Atomistic View of Platinum Cluster Growth on Pristine and Defective Graphene Supports

Density functional theory (DFT) is used to systematically investigate the electronic structure of platinum clusters grown on different graphene substrates. Platinum clusters with 1 to 10 atoms and graphene vacancy defect supports with 0 to 5 missing C atoms are investigated. Calculations show that Pt clusters bind more strongly as the vacancy size increases. For a given defect size, increasing the cluster size leads to more endothermic energy of formation, suggesting a templating effect that limits cluster growth. The opposite trend is observed for defect-free graphene where the formation energy becomes more exothermic with increasing cluster size. Calculations show that oxidation of the defect weakens binding of the Pt cluster, hence it is suggested that oxygen-free graphene supports are critical for successful attachment of Pt to carbon-based substrates. However, once the combined material is formed, oxygen adsorption is more favorable on the cluster than on the support, indicating resistance to oxidative support degradation. Finally, while highly-symmetric defects are found to encourage formation of symmetric Pt clusters, calculations also reveal that cluster stability in this size range mostly depends on the number of and ratio between PtC, PtPt, and PtO bonds; the actual cluster geometry seems secondary.

The Impact of Electron Phonon Scattering, Finite Size and Lateral Electric Field on Transport Properties of Topological Insulators: A First Principles Quantum Transport Study

We study, using non-equilibrium Green's function simulations combined with first-principles density functional theory, the edge-state transport in two-dimensional topological insulators. We explore the impact of electron-phonon coupling on carrier transport through the protected states of two widely known topological insulators with different bulk gaps, namely stanene and bismuthene. We observe that the transport in a topological insulator with a small bulk gap (such as stanene) can be heavily affected by electron-phonon scattering, as the bulk states broaden into the bulk gap. In bismuthene with a larger bulk gap, however, a significantly higher immunity to electron-phonon scattering is observed. To mitigate the negative effects of a small bulk gap, finite-size effects are studied in stanene ribbons. The bulk gap increases in ultra-narrow stanene ribbons, but the transport results revealed no improvement in the dissipative case, as the states in the enlarged bulk gaps aren't sufficiently localized. To investigate an application, we also used topological insulator ribbons as a material for field-effect transistors with side gates imposing a lateral electric field. Our results demonstrate that the lateral electric field could offer another avenue to manipulate the edge states and even open a gap in stanene ribbons, leading to an I_ON/I_OFF of 28 in the ballistic case. These results shed light on the opportunities and challenges in the design of topological insulator field-effect transistors.

A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin

Collagen triple helices are critical in the function of mannan-binding lectin (MBL), an oligomeric recognition molecule in complement activation. The MBL collagen regions form complexes with the serine proteases MASP-1 and MASP-2 in order to activate complement, and mutations lead to common immunodeficiencies. To evaluate their structure-function properties, we studied the solution structures of four MBL-like collagen peptides. The thermal stability of the MBL collagen region was much reduced by the presence of a GQG interruption in the typical (X-Y-Gly)n repeat compared to controls. Experimental solution structural data were collected using analytical ultracentrifugation and small angle X-ray and neutron scattering. As controls, we included two standard Pro-Hyp-Gly collagen peptides (POG)_10-13, as well as three more peptides with diverse (X-Y-Gly)n sequences that represented other collagen features. These data were quantitatively compared with atomistic linear collagen models derived from crystal structures and 12,000 conformations obtained from molecular dynamics simulations. All four MBL peptides were bent to varying degrees up to 85^o in the best-fit molecular dynamics models. The best-fit benchmark peptides (POG)_n were more linear but exhibited a degree of conformational flexibility. The remaining three peptides showed mostly linear solution structures. In conclusion, the collagen helix is not strictly linear, the degree of flexibility in the triple helix depends on its sequence, and the triple helix with the GQG interruption showed a pronounced bend. The bend in MBL GQG peptides resembles the bend in the collagen of complement C1q and may be key for lectin pathway activation.

Electron-Phonon Coupling in a Magic-Angle Twisted-Bilayer Graphene Device from Gate-Dependent Raman Spectroscopy and Atomistic Modeling

The importance of phonons in the strong correlation phenomena observed in twisted-bilayer graphene (TBG) at the so-called magic-angle is under debate. Here we apply gate-dependent micro-Raman spectroscopy to monitor the G band line width in TBG devices of twist angles θ = 0° (Bernal), ∼1.1° (magic-angle), and ∼7° (large-angle). The results show a broad and p-/n-asymmetric doping behavior at the magic angle, in clear contrast to the behavior observed in twist angles above and below this point. Atomistic modeling reproduces the experimental observations in close connection with the joint density of electronic states in the electron-phonon scattering process, revealing how the unique electronic structure of magic-angle TBGs influences the electron-phonon coupling and, consequently, the G band line width. Overall, the value of the G band line width in magic-angle TBG is larger when compared to that of the other samples, in qualitative agreement with our calculations.

Te/CdTe and Al/CdTe Interfacial Energy Band Alignment by Atomistic Modeling

A synergistic approach that incorporates first-principles atomistic modeling with numerical device simulations is used to systematically evaluate the role of heterointerfaces within metal-chalcogenide-based photovoltaic technologies. Two interfaces involving either a tellurium back contact or aluminum back electrode combined with a cadmium telluride absorber layer within cadmium-telluride-based thin-film solar cells are investigated on an atomic scale to determine the mechanisms contributing to variations in device performance. Electronic structures and predicted charge transport behavior with respect to cadmium and tellurium termination of the absorber layer are studied along the polar oriented CdTe{111} facets. The computational methodology reveals a noticeable contrast between the Schottky barrier forming Al/CdTe interface versus the Type I Te/CdTe heterojunction. Greater band bending features are exhibited by the cadmium termination as opposed to the tellurium termination for each interface case. Subsequent device modeling suggests that 3.6% higher photovoltaic conversion efficiency is achievable for the cadmium termination relative to the tellurium termination of the Te/CdTe interface. Based strictly on an idealistic representation, both interface models show the importance of atomic-scale interfacial properties for cadmium telluride solar cell device performance with their bulk properties being validated in comparison to published experimental data. The synergistic approach offers a suitable method to analyze solar cell interfaces through a predictive computational framework for the engineering and optimization of metal-chalcogenide-based thin-film photovoltaic technologies.

Current State and Perspectives of Simulation and Modeling of Aliphatic Isocyanates and Polyisocyanates

Aliphatic isocyanates and polyisocyanates are central molecules in the fabrication of polyurethanes, coatings, and adhesives and, due to their excellent mechanical and stability properties, are continuously investigated in advanced applications; however, despite the growing interest in isocyanate-based systems, atomistic simulations on them have been limited by the lack of accurate parametrizations for these molecular species. In this review, we will first provide an overview of current research on isocyanate systems to highlight their most promising applications, especially in fields far from their typical usage, and to justify the need for further modeling works. Next, we will discuss the state of their modeling, from first-principle studies to atomistic molecular dynamics simulations and coarse-grained approaches, highlighting the recent advances in atomistic modeling. Finally, the most promising lines of research in the modeling of isocyanates are discussed in light of the possibilities opened by novel approaches, such as machine learning.

Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex

Nonspecific binding of crowder proteins with functional proteins is likely prevalent in vivo, yet direct quantitative evidence, let alone residue-specific information, is scarce. Here we present nuclear magnetic resonance (NMR) characterization showing that bovine serum albumin weakly but preferentially interacts with the histidine carrier protein (HPr). Notably, the binding interface overlaps with that for HPr's specific partner protein, EIN, leading to competition. The crowder protein thus decreases the EIN-HPr binding affinity and accelerates the dissociation of the native complex. In contrast, Ficoll-70 stabilizes the native complex and slows its dissociation, as one would expect from excluded-volume and microviscosity effects. Our atomistic modeling of macromolecular crowding rationalizes the experimental data and provides quantitative insights into the energetics of protein-crowder interactions. The integrated NMR and modeling study yields benchmarks for the effects of crowded cellular environments on protein-protein specific interactions, with implications for evolution regarding how nonspecific binding can be minimized or exploited.

Atomistic Assessment of Solute-Solute Interactions during Grain Boundary Segregation

Grain boundary solute segregation is becoming increasingly common as a means of stabilizing nanocrystalline alloys. Thermodynamic models for grain boundary segregation have recently revealed the need for spectral information, i.e., the full distribution of environments available at the grain boundary during segregation, in order to capture the essential physics of the problem for complex systems like nanocrystalline materials. However, there has been only one proposed method of extending spectral segregation models beyond the dilute limit, and it is based on simple, fitted parameters that are not atomistically informed. In this work, we present a physically motived atomistic method to measure the full distribution of solute-solute interaction energies at the grain boundaries in a polycrystalline environment. We then cast the results into a simple thermodynamic model, analyze the Al(Mg) system as a case study, and demonstrate strong agreement with physically rigorous hybrid Monte Carlo/molecular statics simulations. This approach provides a means of rapidly measuring key interactions for non-dilute grain boundary segregation for any system with an interatomic potential.

Understanding the Copassivation Effect of Cl and Se for CdTe Grain Boundaries

Chlorine passivation treatment of cadmium telluride (CdTe) solar cells improves device performance by assisting electron-hole carrier separation at CdTe grain boundaries. Further improvement in device efficiency is observed after alloying the CdTe absorber layer with selenium. High-resolution secondary ion mass spectroscopy (NanoSIMS) imaging has been used to determine the distribution of selenium and chlorine at the CdTe grain boundaries in a selenium-graded CdTe device. Atomistic modeling based on density functional theory (DFT-1/2) further reveals that the presence of selenium and chlorine at an exemplar (110)/(100) CdTe grain boundary passivates critical acceptor defects and leads to n-type inversion at the grain boundary. The defect state analysis provides an explanation for the band-bending effects observed in the energy band alignment results, thereby elucidating mechanisms for high efficiencies observed in Se-alloyed and Cl-passivated CdTe solar cells.

The solution structure of the complement deregulator FHR5 reveals a compact dimer and provides new insights into CFHR5 nephropathy

The human complement Factor H-related 5 protein (FHR5) antagonizes the main circulating complement regulator Factor H, resulting in the deregulation of complement activation. FHR5 normally contains nine short complement regulator (SCR) domains, but a FHR5 mutant has been identified with a duplicated N-terminal SCR-1/2 domain pair that causes CFHR5 nephropathy. To understand how this duplication causes disease, we characterized the solution structure of native FHR5 by analytical ultracentrifugation and small-angle X-ray scattering. Sedimentation velocity and X-ray scattering indicated that FHR5 was dimeric, with a radius of gyration (Rg ) of 5.5 ± 0.2 nm and a maximum protein length of 20 nm for its 18 domains. This result indicated that FHR5 was even more compact than the main regulator Factor H, which showed an overall length of 26-29 nm for its 20 SCR domains. Atomistic modeling for FHR5 generated a library of 250,000 physically realistic trial arrangements of SCR domains for scattering curve fits. Only compact domain structures in this library fit well to the scattering data, and these structures readily accommodated the extra SCR-1/2 domain pair present in CFHR5 nephropathy. This model indicated that mutant FHR5 can form oligomers that possess additional binding sites for C3b in FHR5. We conclude that the deregulation of complement regulation by the FHR5 mutant can be rationalized by the enhanced binding of FHR5 oligomers to C3b deposited on host cell surfaces. Our FHR5 structures thus explained key features of the mechanism and pathology of CFHR5 nephropathy.

Machine Learning Interatomic Potentials as Emerging Tools for Materials Science

Atomic-scale modeling and understanding of materials have made remarkable progress, but they are still fundamentally limited by the large computational cost of explicit electronic-structure methods such as density-functional theory. This Progress Report shows how machine learning (ML) is currently enabling a new degree of realism in materials modeling: by "learning" electronic-structure data, ML-based interatomic potentials give access to atomistic simulations that reach similar accuracy levels but are orders of magnitude faster. A brief introduction to the new tools is given, and then, applications to some select problems in materials science are highlighted: phase-change materials for memory devices; nanoparticle catalysts; and carbon-based electrodes for chemical sensing, supercapacitors, and batteries. It is hoped that the present work will inspire the development and wider use of ML-based interatomic potentials in diverse areas of materials research.

Potential energy landscape activations governing plastic flows in glass rheology

While glasses are ubiquitous in natural and manufactured materials, the atomic-level mechanisms governing their deformation and how these mechanisms relate to rheological behavior are still open questions for fundamental understanding. Using atomistic simulations spanning nearly 10 orders of magnitude in the applied strain rate we probe the atomic rearrangements associated with 3 characteristic regimes of homogeneous and heterogeneous shear flow. In the low and high strain-rate limits, simulation results together with theoretical models reveal distinct scaling behavior in flow stress variation with strain rate, signifying a nonlinear coupling between thermally activated diffusion and stress-driven motion. Moreover, we find the emergence of flow heterogeneity is closely correlated with extreme values of local strain bursts that are not readily accommodated by immediate surroundings, acting as origins of shear localization. The atomistic mechanisms underlying the flow regimes are interpreted by analyzing a distance matrix of nonaffine particle displacements, yielding evidence of various barrier-hopping processes on a fractal potential energy landscape (PEL) in which shear transformations and liquid-like regions are triggered by the interplay of thermal and stress activations.

Janus Segregation at the Carbon Nanotube-Catalyst Interface

The contact between a carbon nanotube (CNT) edge and a catalyst is a curvilinear interface of fundamental and practical importance. Here, the first-principles evidence shows that on a rigid/solid catalyst the faceted CNT edge is significantly lower in energy compared to the minimal-length circle, with the interface energy difference decreasing on more compliant surfaces. This universal trend, found for typical monometallic (Ni, Co), bimetallic (Co₇W₆), and metal carbide (WC) catalysts, results in a peculiar edge segregation into one-dimensional Janus (armchair-zigzag) interface. Its lowered energy greatly enhances the nucleation probability of chiral tubes, dramatically affecting their growth kinetics. This offers a richer basis for understanding, modeling, and control of catalytic CNT synthesis.

Transient Kinetic Selectivity in Nanotubes Growth on Solid Co-W Catalyst

Solid Co-W catalysts have been shown to yield single-walled carbon nanotubes (CNT) with high selectivity, simplistically attributed to CNT-catalyst symmetry match for certain chiral indices ( n, m). Here, based on large-scale first-principles calculations combined with kinetic Monte Carlo simulations, we show instead that such selectivity arises from a complex kinetics of growth. The solid Co₇W₆ catalyst strongly favors a restructured, asymmetric CNT edge which entails preferential nucleation of tubes with 2 m < n but much faster growth of chiral tubes with n ⩽ 2 m. We uncover a tendency of interface defects formation that, although rare, drive CNT type change from smaller to larger chiral angles (zigzag to armchair). Being both least prone to defects and fast growing, the (12,6) CNT appears as a transient, kinetics-selected type reaching highest abundance.

Grain Boundaries Softening Thermoelectric Oxide BiCuSeO

Engineering grain boundaries (GBs) are effective in tuning the thermoelectric (TE) properties of TE materials, but the role of GB on mechanical properties, which is important for their commercial applications, remains unexplored. In this paper, we apply ab initio method to examine the ideal shear strength and failure mechanism of GBs in TE oxide BiCuSeO. We find that the ideal shear strength of the GB is much lower than that of the ideal single crystal. The atomic rearrangements accommodating the lattice and neighbor structure mismatch between different grains leads to the much weaker GB stiffness compared with grains. Failure of the GBs arises from either the distortion of the Cu-Se layers or the relative slip between Bi-O and Cu-Se layers. This work is crucial to illustrate the deformation of GBs, laying the basis for the development and design of mechanically robust polycrystalline TE materials.

Understanding the mechanisms of amorphous creep through molecular simulation

Molecular processes of creep in metallic glass thin films are simulated at experimental timescales using a metadynamics-based atomistic method. Space-time evolutions of the atomic strains and nonaffine atom displacements are analyzed to reveal details of the atomic-level deformation and flow processes of amorphous creep in response to stress and thermal activations. From the simulation results, resolved spatially on the nanoscale and temporally over time increments of fractions of a second, we derive a mechanistic explanation of the well-known variation of creep rate with stress. We also construct a deformation map delineating the predominant regimes of diffusional creep at low stress and high temperature and deformational creep at high stress. Our findings validate the relevance of two original models of the mechanisms of amorphous plasticity: one focusing on atomic diffusion via free volume and the other focusing on stress-induced shear deformation. These processes are found to be nonlinearly coupled through dynamically heterogeneous fluctuations that characterize the slow dynamics of systems out of equilibrium.

Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 Provides Insight on Lectin Pathway Activation

The lectin pathway of complement is activated by complexes comprising a recognition component (mannose-binding lectin, serum ficolins, collectin-LK or collectin-K1) and a serine protease (MASP-1 or MASP-2). MASP-1 activates MASP-2, and MASP-2 cleaves C4 and C4b-bound C2. To clarify activation, new crystal structures of Ca²⁺-bound MASP dimers were determined, together with their solution structures from X-ray scattering, analytical ultracentrifugation, and atomistic modeling. Solution structures of the CUB1-EGF-CUB2 dimer of each MASP indicate that the two CUB2 domains were tilted by as much as 90° compared with the crystal structures, indicating considerable flexibility at the EGF-CUB2 junction. Solution structures of the full-length MASP dimers in their zymogen and activated forms revealed similar structures that were much more bent than anticipated from crystal structures. We conclude that MASP-1 and MASP-2 are flexible at multiple sites and that this flexibility may permit both intra- and inter-complex activation.

About the Compatibility between High Voltage Spinel Cathode Materials and Solid Oxide Electrolytes as a Function of Temperature

The reactivity of mixtures of high voltage spinel cathode materials Li₂NiMn₃O₈, Li₂FeMn₃O₈, and LiCoMnO₄ cosintered with Li_1.5Al_0.5Ti_1.5(PO₄)₃ and Li_6.6La₃Zr_1.6Ta_0.4O₁₂ electrolytes is studied by thermal analysis using X-ray-diffraction and differential thermoanalysis and thermogravimetry coupled with mass spectrometry. The results are compared with predicted decomposition reactions from first-principles calculations. Decomposition of the mixtures begins at 600 °C, significantly lower than the decomposition temperature of any component, especially the electrolytes. For the cathode + Li_6.6La₃Zr_1.6Ta_0.4O₁₂ mixtures, lithium and oxygen from the electrolyte react with the cathodes to form highly stable Li₂MnO₃ and then decompose to form stable and often insulating phases such as La₂Zr₂O₇, La₂O₃, La₃TaO₇, TiO₂, and LaMnO₃ which are likely to increase the interfacial impedance of a cathode composite. The decomposition reactions are identified with high fidelity by first-principles calculations. For the cathode + Li_1.5Al_0.5Ti_1.5(PO₄)₃ mixtures, the Mn tends to oxidize to MnO₂ or Mn₂O₃, supplying lithium to the electrolyte for the formation of Li₃PO₄ and metal phosphates such as AlPO₄ and LiMPO₄ (M = Mn, Ni). The results indicate that high temperature cosintering to form dense cathode composites between spinel cathodes and oxide electrolytes will produce high impedance interfacial products, complicating solid state battery manufacturing.

Indentation Tests Reveal Geometry-Regulated Stiffening of Nanotube Junctions

Here we report a unique method to locally determine the mechanical response of individual covalent junctions between carbon nanotubes (CNTs), in various configurations such as "X", "Y", and "Λ"-like. The setup is based on in situ indentation using a picoindenter integrated within a scanning electron microscope. This allows for precise mapping between junction geometry and mechanical behavior and uncovers geometry-regulated junction stiffening. Molecular dynamics simulations reveal that the dominant contribution to the nanoindentation response is due to the CNT walls stretching at the junction. Targeted synthesis of desired junction geometries can therefore provide a "structural alphabet" for construction of macroscopic CNT networks with tunable mechanical response.

Segregation of In to dislocations in InGaN

Dislocations are one-dimensional topological defects that occur frequently in functional thin film materials and that are known to degrade the performance of InxGa1-xN-based optoelectronic devices. Here, we show that large local deviations in alloy composition and atomic structure are expected to occur in and around dislocation cores in InxGa(1-x)N alloy thin films. We present energy-dispersive X-ray spectroscopy data supporting this result. The methods presented here are also widely applicable for predicting composition fluctuations associated with strain fields in other inorganic functional material thin films.

A tight-binding study of single-atom transistors

A detailed theoretical study of the electronic and transport properties of a single atom transistor, where a single phosphorus atom is embedded within a single crystal transistor architecture, is presented. Using a recently reported deterministic single-atom transistor as a reference, the electronic structure of the device is represented atomistically with a tight-binding model, and the channel modulation is simulated self-consistently with a Thomas-Fermi method. The multi-scale modeling approach used allows confirmation of the charging energy of the one-electron donor charge state and explains how the electrostatic environments of the device electrodes affects the donor confinement potential and hence extent in gate voltage of the two-electron charge state. Importantly, whilst devices are relatively insensitive to dopant ordering in the highly doped leads, a ∼1% variation of the charging energy is observed when a dopant is moved just one lattice spacing within the device. The multi-scale modeling method presented here lays a strong foundation for the understanding of single-atom device structures: essential for both classical and quantum information processing.

Atomistic study on dopant-distributions in realistically sized, highly P-doped Si nanowires

The dependency of dopant-distributions on channel diameters in realistically sized, highly phosphorus-doped silicon nanowires is investigated with an atomistic tight-binding approach coupled to self-consistent Schrödinger-Poisson simulations. By overcoming the limit in channel sizes and doping densities of previous studies, this work examines electronic structures and electrostatics of free-standing circular silicon nanowires that are phosphorus-doped with a high density of ∼ 2 × 10(19) cm(-3) and have 12 nm-28 nm cross-sections. Results of analysis on the channel energy indicate that the uniformly distributed dopant profile would be hardly obtained when the nanowire cross-section is smaller than 20 nm. Insufficient room to screen donor ions and shallower impurity bands are the primary reasons of the nonuniform dopant-distributions in smaller nanowires. Being firmly connected to the recent experimental study (Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 15254-15258), this work establishes the first theoretical framework for understanding dopant-distributions in over-10 nm highly doped silicon nanowires.

Al-Air Batteries: Fundamental Thermodynamic Limitations from First-Principles Theory

The Al-air battery possesses high theoretical specific energy (4140 W h/kg) and is therefore an attractive candidate for vehicle propulsion. However, the experimentally observed open-circuit potential is much lower than what bulk thermodynamics predicts, and this potential loss is typically attributed to corrosion. Similarly, large Tafel slopes associated with the battery are assumed to be due to film formation. We present a detailed thermodynamic study of the Al-air battery using density functional theory. The results suggest that the maximum open-circuit potential of the Al anode is only -1.87 V versus the standard hydrogen electrode at pH 14.6 instead of the traditionally assumed -2.34 V and that large Tafel slopes are inherent in the electrochemistry. These deviations from the bulk thermodynamics are intrinsic to the electrochemical surface processes that define Al anodic dissolution. This has contributions from both asymmetry in multielectron transfers and, more importantly, a large chemical stabilization inherent to the formation of bulk Al(OH)3 from surface intermediates. These are fundamental limitations that cannot be improved even if corrosion and film effects are completely suppressed.