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The intrinsic dynamics of most proteins are central to their function. Protein tyrosine kinases such as Abl1 undergo significant conformational changes that modulate their activity in response to different stimuli. These conformational…
The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the…
Bacteria often traverse confined spaces to perform critical functions in symbiosis, infection, drug delivery, and soil bioremediation. While the canonical run-and-tumble strategy enables exploration, its reliance on constant sensing and…
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…
Increased Atmospheric CO2 to over 400 ppm has prompted global climate irregularities. Reducing the released CO2 from biotechnological processes could remediate these phenomena. In this study, we sought to find a solution to reduce the…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Accurate drug-target interaction (DTI) prediction is essential for computational drug discovery, yet existing models often rely on single-modality predefined molecular descriptors or sequence-based embeddings with limited…
The design of antibacterial-releasing coatings or wrapping materials with controlled drug release capability is a promising strategy to minimise risks of infection and medical device failure in vivo. Collagen fibres have been employed as…
Microorganisms navigating through narrow spaces encounter significant hydrodynamic challenges. To overcome these constraints and sustain efficient motion, they employ adaptive strategies, including adaptive oscillatory body deformations.…
As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of…
Recently, Antimicrobial peptides (AMPs) have been an area of interest in the researches, as the first line of defense against the bacteria. They are raising attention as an efficient way of fighting multidrug resistance. Discovering and…
Human telomeric G-quadruplex DNA structures are attractive anticancer drug targets, but the target's polymorphism complicates the drug design: different ligands prefer different folds, and very few complexes have been solved at high…
In this paper, we investigate the dynamics of hepatitis B virus infection taking into account the implementation of combination therapy through mathematical modeling. This model is established considering the interplay between uninfected…
Multidrug resistance consists of a series of genetic and epigenetic alternations that involve multifactorial and complex processes, which are a challenge to successful cancer treatments. Accompanied by advances in biotechnology and…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
The adaptive immune system constantly remodels its lymphocyte repertoire for better protection against future pathogens. Its ability to improve antigen recognition on the fly relies on somatic mutation and selective expansion of B…
Despite recent advances in our ability to detect adaptive evolution involving the cis-regulation of gene expression, our knowledge of the molecular mechanisms underlying these adaptations has lagged far behind. Across all model organisms…
Targeted protein degradation (TPD) is a rapidly growing field in modern drug discovery that aims to regulate the intracellular levels of proteins by harnessing the cell's innate degradation pathways to selectively target and degrade…
Despite its high prevalence and impact on the lives of those affected, a complete understanding of the cause of inflammatory bowel disease (IBD) is lacking. In this paper, we investigate a novel mechanism which proposes that mutant…
Antimicrobial Resistance (AMR) is a rapidly escalating global health crisis. While genomic sequencing enables rapid prediction of resistance phenotypes, current computational methods have limitations. Standard machine learning models treat…