Human immunodeficiency virus type 1 (HIV-1) remains a challenging target for vaccine development due to its remarkable genetic diversity. Across viral clades, variations in the HIV-1 Envelope (Env) protein can substantially affect antibody recognition and binding. However, broadly neutralising antibodies (bNAbs) isolated from HIV-1-infected individuals can recognise conserved regions of Env across diverse viral strains. These antibodies, therefore, provide molecular templates for designing immunogens capable of generating broad and effective immune responses.

 To understand how bNAbs recognise genetically diverse HIV-1 variants, experimentally resolved bNAb-HIV-1 Env protein-protein complexes were examined at the molecular level. Structural and energetic properties of the bNAb-Env interfaces were extracted and used as descriptors to train machine-learning models. The goal was to predict two key measures of antibody binding, the binding free energy (ΔG) and the dissociation constant (KD), and to determine how these interactions vary across HIV-1 clades and bNAb classes.

One of the reasons Mycobacterium tuberculosis remains so resilient is its waxy, lipid-rich cell wall, built largely from mycolic acids (MAs). Our molecular simulations reveal how these long lipid molecules self-assemble, fold, and pack together to form a dense protective barrier. We found that different MA types adopt distinct conformations, influencing membrane thickness, flexibility, and packing density. Among them, alpha-mycolic acid forms the most tightly packed structures, creating a highly ordered shield that may hinder drug penetration. These insights help explain how the bacterial cell envelope maintains its remarkable impermeability and could guide the development of strategies to overcome drug resistance.

Uranium contamination poses a growing threat to ecosystems and human health. To tackle this challenge, we explored how PAMAM dendrimers, combined with graphene and carbon nanotubes (CNTs), can serve as powerful uranium-capturing materials. Using molecular simulations and experimental validation, we found that these nanocomposites efficiently attract and bind uranyl ions, with CNT-based materials showing exceptional performance due to their curved surfaces and abundant binding sites. As the dendrimer size increased, so did the adsorption capacity, highlighting a promising strategy for designing next-generation materials for uranium recovery and water remediation.

Small interfering RNA (siRNA) has the potential to silence disease-causing genes, but its success depends on the development of safe and efficient delivery vehicles. Using molecular dynamics simulations, we explored how galactose-functionalized PAMAM and PETIM dendrimers interact with siRNA under different pH conditions. While both carriers formed stable complexes, Gal-PETIM demonstrated a unique balance of strong binding and efficient gene release, making it particularly attractive for delivery at physiological conditions. These findings advance our understanding of dendrimer-based gene carriers and support the development of next-generation RNA therapeutics.

HIV protects itself with a dense layer of sugars, known as glycans, that can hide vulnerable regions from the immune system. Using advanced molecular simulations, we mapped this "glycan shield" across major HIV-1 clades and examined how broadly neutralizing antibodies (bNAbs) navigate this complex landscape. Our study revealed that glycan coverage, flexibility, and antibody accessibility vary significantly between clades, shaping the effectiveness of antibody recognition. These atomistic insights provide a foundation for designing more effective HIV vaccines and antibody-based therapies.

Two water-soluble polymers, poly(acrylic acid) (PAA) and poly(ethylene oxide) (PEO), can unexpectedly form stable complexes when exposed to salt-rich environments. Using atomistic molecular dynamics simulations, we discovered that increasing salt concentration alters the surrounding water environment, causing the polymer chains to shrink and move closer together. Strong hydrogen bonds form between the polymers, replacing their interactions with water and driving the formation of compact, thermodynamically stable assemblies. These findings provide molecular-level insight into polymer complexation and help guide the design of responsive materials for biomedical and industrial applications.

Small changes in molecular architecture can dramatically alter how polymers behave in solution. Using atomistic molecular dynamics simulations, we explored how the stereochemistry of poly(acrylic acid) controls its structure and interactions in water. We discovered that isotactic PAA naturally adopts a compact helical shape, while syndiotactic PAA remains more extended. This difference arises from stronger counter-ion condensation around isotactic chains, which stabilizes their helical conformation. By revealing how molecular arrangement governs polymer structure, our work provides valuable insights for designing advanced materials with applications ranging from drug delivery to gene therapy.