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At least 55 records · Page 3

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗

Graphite Lithiation under Fast Charging Conditions: Atomistic Modeling Insights

The charging of lithium ion batteries in a fast and safe manner is critical for promoting the mass adoption of electric vehicles. Li intercalation in graphite electrodes is known to be one of the bottlenecks during the fast charging process. The mechanism of Li diffusion in highly polarized graphite anode at high current rates remains, however, not well understood. In this work, Density Functional Theory (DFT) calculations are used to gain insights into the Li diffusion process in graphite when it is far from equilibrium under fast charging conditions. The effect of uncompensated charges on Li mobility is determined in the highly polarized regions of the anode close to the interfaces. The extra charge was found to increase the interlayer spacing in the diffusion layer and adjacent channels, increasing the diffusivity and promoting the formation of Li clusters. A concerted diffusion mechanism at the edge of high-concentration Li domains is proposed to enhance the diffusion of Li.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Heavy boron doping effects on biaxially tensile strained germanium (>1.5%) investigated via structural characterization, effective lifetime assessment and atomistic modeling

Highly tensile strained germanium (ε-Ge) represents an essential material system for emerging electronic and photonics applications. Moreover, adjusting the doping levels to moderate or high concentrations can effectively tailor the properties of ε-Ge for specific applications. This article combines experimental characterization with a theoretical framework to examine the effects of heavy elemental boron (B) doping on pseudomorphic sub-50 nm ε-Ge. High resolution X-ray diffractometry is used to validate tensile strain levels of 1.53% and 1.68% in Ge epilayers, surpassing the indirect-to-direct band gap crossover point at ∼1.5% biaxial tensile strain. Cross-sectional transmission electron microscopy revealed visual evidence of stacking faults and surface roughening in 1.68% ε-Ge, although a coherent and abrupt Ge/III–V heterointerface is observed, devoid of interfacial misfit dislocations. Effective lifetime measurements demonstrated approximately twofold enhancement in 1.53% B-doped ε-Ge (N B ∼7 × 10 19 cm −3 ) compared to its unstrained B-doped counterpart, while no such improvement was observed in 1.68% B-doped ε-Ge. This lack of enhancement is attributed to the presence of stacking faults and surface roughness within the ε-Ge epilayer. Through density functional theory calculations, we independently demonstrate that substitutional B atoms induce local deformation of Ge–Ge bonds in both unstrained Ge and ε-Ge epilayers, resulting in an additive tensile strain. This phenomenon could potentially lead to dynamic reduction and overcoming of the critical layer thickness for the system, facilitating the nucleation and subsequent glide of 90° leading Shockley partial dislocations, thereby generating stacking faults. In essence, these findings establish an upper limit on the B-doping concentration that can be achieved in highly ε-Ge epilayers, and collectively, offer valuable insights into the significance of heavy doping in Ge-based heterostructures. As such, this study delineates a fundamental constraint for integrating heavily doped ε-Ge in high-performance optoelectronic systems, necessitating precise strain-doping co-optimization to avoid performance degradation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Atomistic models of In and Ga diffusion in Cu(In,Ga)Se 2

To improve the performance of Cu(In,Ga)Se 2 thin-film photovoltaic devices, a robust understanding of the dominant diffusion pathways of the alloy species In and Ga is needed. Here, the most probable defect complexes and mechanisms for In and Ga diffusion are identified with the aid of density functional theory. The binding energies and migration barriers for these complexes are calculated in bulk CuInSe 2 and CuGaSe 2 . Analytic models and kinetic lattice Monte Carlo simulations are employed to predict the diffusivity of In and Ga under variations in composition and temperature. Here, we find that a model based on coulombic interactions between group III antisites and vacancies on the Cu-sublattice produces results that match well with experiment.

14 SOLAR ENERGY↗

Exploring dielectric properties in atomistic models of amorphous boron nitride

Abstract We report a theoretical study of dielectric properties of models of amorphous Boron Nitride, using interatomic potentials generated by machine learning. We first perform first-principles simulations on small (about 100 atoms in the periodic cell) sample sizes to explore the emergence of mid-gap states and its correlation with structural features. Next, by using a simplified tight-binding electronic model, we analyse the dielectric functions for complex three dimensional models (containing about 10.000 atoms) embedding varying concentrations of sp 1 , sp 2 and sp 3 bonds between B and N atoms. Within the limits of these methodologies, the resulting value of the zero-frequency dielectric constant is shown to be influenced by the population density of such mid-gap states and their localization characteristics. We observe nontrivial correlations between the structure-induced electronic fluctuations and the resulting dielectric constant values. Our findings are however just a first step in the quest of accessing fully accurate dielectric properties of as-grown amorphous BN of relevance for interconnect technologies and beyond.

Materials Science↗

Atomistic modeling of lanthanide diffusion in refractory body-centered cubic molybdenum

Lanthanide fission products can strongly interact with candidate cladding alloys, but their transport properties in refractory metals remain poorly understood. Here, in this work, we investigate the atomic-scale diffusion behavior of La, Ce, Pr, and Nd in body-centered cubic (bcc) molybdenum, a potential candidate for advanced nuclear cladding. Self-consistent mean-field transport modeling is performed to evaluate the fission product transport and vacancy mobility, informed by first-principles and nudged elastic band calculations of vacancy formation energies, migration barriers, and solute–vacancy binding characteristics. Compared with bcc Fe, lanthanide solutes in bcc Mo exhibit slower tracer diffusion due to higher vacancy formation and migration energies. Furthermore, the calculations reveal that the influence of fission products on migration barriers in bcc Mo are not as extensive in range compared to bcc Fe. Among the studied lanthanides, La exhibits the strongest vacancy binding while also being the fastest diffuser in Mo. These findings highlight how refractory bcc alloys can reduce fission product infiltration, offering valuable insight into the development of durable cladding systems for advanced reactors.

36 - MATERIALS SCIENCE↗

Atomistic modeling of LiF microstructure ionic conductivity and its influence on nucleation and plating

We report the formation and degradation of the solid electrolyte interphase (SEI) and its underlying transport properties play an essential role in the overall performance of lithium-ion batteries. This paper presents classical molecular dynamics studies on polycrystalline inorganic lithium fluoride (LiF) layers to model and predict the SEI transport properties. The ionic conductivity is obtained from the lithium-ion diffusivity in polycrystalline structures of LiF using the Nernst-Einstein relation. The predicted molecular dynamics data are used in a continuum scale phase-field model to evaluate the plating kinetics under fast charging conditions. The analysis emphasizes that the SEI ionic conductivity properties impact the plating dynamics, where SEI's low ion conductivity value is prone to large plating and subsequent capacity degradation. The combination of atomic and continuum scale studies shown herein lays a foundation to tune in SEI transport properties to decrease the amount of lithium plating and improve the performance of fast-charging batteries.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Atomistic Modeling of the Interphase Structure between Alumina and Al12Fe2Cr Quasicrystal Approximant

Molecular dynamics simulations are performed to study the stability of an fcc metallic interlayer phase between an iron aluminide quasicrystal approximant (QCA) phase (84.2 Al, 5.7 Fe, 5.4 Ni, and 4.7 at.% Cr) and aluminum oxides (α-Al 2 O 3 and γ-Al 2 O 3 ). The presence of the interlayer phase was experimentally observed in some regions of the inner diameter surface of a TPBAR cladding tube. The simulations employed existing many-body (MEAM and EAM) interatomic potentials to describe atomic interactions in the interlayer and QCA phases, and Buckingham+Coulomb pair interactions for the alumina and between the alumina and the QCA (or fcc). Interface systems of QCA/alumina, fec/alumina, and QCA/fcc are modeled and the fracture energy of the interfaces is calculated. Based on the fracture energies, for the γ-Al 2 O 3 , both MEAM and EAM suggest that the fcc interlayer phase would not form. For the α-Al 2 O 3 , the MEAM predicts that the fcc phase would form, however, the EAM predicts that it forms only if the α-Al 2 O 3 is Al-terminated at the interface. For the O-terminated α-Al 2 O 3 , the EAM predicts the fcc phase would not form, consistent with the results for γ-Al 2 O 3 .

36 MATERIALS SCIENCE↗