Puja Adhikari

Refractory-based high-entropy alloys (RHEAs) are compelling materials for super-high-temperature (1500–2000 K) applications, such as jet-engines, gas turbines, and nuclear powerplants.

SARS-CoV-2 remains a severe threat to worldwide public health, particularly as the virus continues to evolve and diversify into variants of concern (VOCs). Among these VOCs, Omicron variants exhibit unique phenotypic traits, such as immune evasion, transmissibility, and severity, due to numerous spike protein mutations and the rapid subvariant evolution. These Omicron subvariants have more than 15 mutations in the receptor-binding domain (RBD), a region of the SARS-CoV-2 spike protein that is important for recognition and binding with the angiotensin-converting enzyme 2 (ACE2) human receptor. To address the impact of these high numbers of Omicron mutations on the binding process, we have developed a novel method to precisely quantify amino acid interactions via the amino acid–amino acid bond pair (AABP). We applied this concept to investigate the interface interactions of the RBD–ACE2 complex in four Omicron Variants (BA.1, BA.2, BA.5, and XBB.1.16) with its Wild Type counterpart. Based on the AABP analysis, we have identified all the sites that are affected by mutation and have provided evidence that unmutated sites are also impacted by mutation. We have calculated that the binding between RBD and ACE2 is strongest in OV BA.1, followed by OV BA.2, WT, OV BA.5, and OV XBB.1.16. We also present the partial charge values for all 311 residues across these five models. Our analysis provides a detailed understanding of changes caused by mutation in each Omicron interface complex.

The mechanical properties of proteins/peptides play an essential role in their functionalities and implications, as well as their structure and dynamic properties. Understanding mechanical properties is pivotal to our knowledge of protein folding and the molecular basis of diverse cellular processes. Herein, we present a computational approach using ab initio quantum mechanical calculations to determine the mechanical properties—such as bulk modulus, shear modulus, Young’s modulus, and Poisson’s ratio—of a solvated Arg-Gly-Asp (RGD) peptide model. Since this peptide serves as the RGD-directed integrin recognition site and may participate in cellular adhesion, it is considered a promising small peptide for medicinal applications. This successful approach paves the way for investigating larger and more complex biomolecules.

The massive amount of wasted heat energy from industry has pushed the development of thermoelectric (TE) materials that directly convert heat into electricity to a new level of concern. Recently, multicomponent alloys such as GeTe-based and PbSe-based high-entropy (HE) chalcogenides have attracted a great deal of attention due to their potential application as TE materials. The nature of the interatomic bonding, lattice distortion (LD), and the electronic structure in this class of materials is not fully understood. Herein, we report a comprehensive computational investigation of nine GeTe-based HE alloys with eight metallic elements (Ag, Pb, Sb, Bi, Cu, Cd, Mn, and Sn) with large supercells of 1080 atoms each; seven PbSe-based HE solid solutions: Pb0.99−ySb0.012SnySe1−2xTexSx (x = 0.1, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, with y = 0) with supercells of 1000 atoms each; and five Pb0.99−ySb0.012SnySe1−2xTexSx (y = 0.05, 0.1, 0.15, 0.2, 0.25 with x = 0.25) solid solutions with supercells of 1000 atoms each. All these HE models are theoretically investigated for the first time. The electronic structure, interatomic bonding, charge transfer, and lattice distortion (LD) are investigated by first-principles calculations based on density functional theory. Multicomponent HE alloys can cause a significant LD, which affects their mechanical, thermal, and TE properties. The calculations for the GeTe-based HE chalcogenides showed that they are semiconductors with a narrow bandgap, except for m8, which has a semi-metallic characteristic, and this makes them good candidates for TE applications. For most of these models, the Fermi level shifts upward and locates deeply in the conduction bands, resulting in the enhancement of the electrical conductivity (σ). The bonding properties showed that most bonds in m5 are more dispersed, indicating highest LD and lower lattice thermal conductivity. For PbSe-based HE solid solutions, the LD calculations showed that the models Pb0.99Sb0.012Se0.5Te0.25S0.25 and Pb0.89Sb0.012Sn0.1Se0.5Te0.25S0.25 have the higher LD, and thus a lower lattice thermal conductivity. Such investigations are in high demand since it enables us to design new HE chalcogenides for TE applications. We use the novel concept of total bond order density as a single quantum mechanical metric to characterize the internal cohesion of these HE alloys and correlate with calculated properties, especially the mechanical properties. This work provides a solid database for HE chalcogenides and a road map for many potential applications. Moreover, the computational procedure we developed can be used to design new HE chalcogenides for specific TE applications.

The rapid evolution in materials science has resulted in a significant interest in high-entropy alloys (HEAs) for their unique properties. This study focuses on understanding both quaternary and quinary body-centered cubic (BCC) of 12 refractory-based HEAs, and on analysis of their electronic structures, lattice distortions, mechanical, and thermal properties. A comprehensive assessment is undertaken by means of density functional theory (DFT)-based first principles calculations. It is well known that multiple constituents lead to notable lattice distortions, especially in quinary HEAs. This distortion, in turn, has significant implications on the electronic structure that ultimately affect mechanical and thermal behaviors of these alloys such as ductility, lattice thermal conductivity, and toughness. Our in-depth analysis of their electronic structures revealed the role of valence electron concentration and its correlation with bond order and mechanical properties. Local lattice distortion (LD) was investigated for these 12 HEA models. M1 (WTiVZrHf), M7 (TiZrHfW), and M12 (TiZrHfVNb) have the highest LD whereas the models M3 (MoTaTiV), M5 (WTaCrV), M6 (MoNbTaW), and M9 (NbTaTiV) have the less LD. Furthermore, we investigated the thermal properties focusing on Debye temperature (Θ_D), thermal conductivity (κ), Grüneisen parameter (γ_α), and dominant phonon wavelength (λ_dom). The NbTaTiV(M9) and TiVNbHf(M10) models have significantly reduced lattice thermal conductivities (κ_L). This reduction is due to the mass increase and strain fluctuations, which in turn signify lattice distortion. The findings not only provide an understanding of these promising materials but also offer guidance for the design of next-generation HEAs with properties tailored for potential specific applications.

Montmorillonite clay (MMT) has been widely used in engineering and environmental applications as a landfill barrier and toxic waste repository due to its unique property as an expandable clay mineral that can absorb water easily. This absorption process rendered MMT to be highly exothermic due to electrostatic interactions among molecules and hydrogen bonds between surface atoms. A detailed study of a large supercell model of structural clay enables us to predict long-term nuclear waste storage. Herein, a large solvent MMT model with 4071 atoms is studied using ab initio density functional theory. The DFT calculation and analysis clarify the important issues, such as bond strength, solvation effect, elasticity, and seismic wave velocities. These results are compared to our previous study on crystalline MMT (dry). The solvated MMT has reduced shear modulus (G), bulk modulus (K), and Young’s modulus (E). We observe that the conduction band (CB) in the density of states (DOS) of solvated MMT model has a single, conspicuous peak at −8.5 eV. Moreover, the atom-resolved partial density of states (PDOS) summarizes the roles played by each atom in the DOS. These findings illuminate numerous potential sophisticated applications of MMT clay.

The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid–amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.

The emergence of Omicron SARS-CoV-2 subvariants (BA.1, BA.2, BA.4, and BA.5) with an unprecedented number of mutations in their receptor-binding domain (RBD) of the spike-protein has fueled a new surge of COVID-19 infections, posing a major challenge to the efficacy of existing vaccines and monoclonal antibody (mAb) therapeutics. Here, a thorough and systematic molecular dynamics (MD) simulation study is conducted to investigate how the RBD mutations on these subvariants affect the interactions with broad mAbs including AstraZeneca (COV2-2196 and COV2-2130), Brii Biosciences (BRII-196), Celltrion (CT-P59), Eli Lilly (LY-CoV555 and LY-CoV016), Regeneron (REGN10933 and REGN10987), Vir Biotechnology (S309), and S2X259. Our results show a complete loss of binding for COV2-2196, BRII-196, CT-P59, and LY-CoV555 with all Omicron RBDs. REGN10987 also loses its binding against BA.1 but partially retains against BA.2 and BA.4/5. The reduction in binding is either significant for LY-CoV016 and REGN10933 or moderate for COV2-2130. S309 and S2X259 retain their binding strength against BA.1 but decrease against others. We introduce a mutational escape map for each mAb to identify the key RBD sites and critical mutation. Overall, our findings suggest that majority of therapeutic mAbs have diminished or lost their activity against Omicron subvariants, indicating the urgent need for a new therapeutic mAb, modifying current ones with a better mAb design, or seeking an alternative approach.

The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2′) cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid–amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2’ cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants.