I have recently written, for WIREs Computational Molecular Science, a review article on the use of Principal Component Analysis (PCA) in the study of dynamical systems, with a particular focus on molecular dynamics (MD) simulations of biomolecules [1]. The aim of this work is to provide a clear and practical overview of how PCA has become a central tool for extracting meaningful collective motions from high-dimensional simulation data, and how modern methodological extensions continue to expand its capabilities.

Surfactants are everywhere in protein science — from biochemical laboratories to industrial detergents. Among them, sodium dodecyl sulfate (SDS) is perhaps the most famous (or infamous), widely used for its ability to bind, deactivate, and often denature proteins. Despite decades of experimental and theoretical work, the molecular details of how surfactants bind to protein surfaces are still not fully understood. In my recent study, “Binding Dynamics of Linear Alkyl-sulfates of Different Chain Lengths on a Protein Surface” [1], I have explored this problem using molecular dynamics (MD) simulations, focusing on how the length of the surfactant’s hydrocarbon chain influences protein binding.

In a recent molecular dynamics study [1] in collaboration with Prof. K. J. Karki (Department of Physics, Guangdong Technion-Israel Institute of Technology in China), we explored how EthylChlorophyllide a behaves when confined between two silica surfaces — a situation relevant for artificial photosynthesis, nanomaterials, and bio-inspired light-harvesting systems. Chlorophylls are among the most important molecules on Earth. They enable plants, algae, and photosynthetic bacteria to convert sunlight into chemical energy. Yet, outside their natural protein environment, chlorophyll molecules are fragile as they can easily lose their central magnesium ion (demetallation), they degrade under light, and they tend to aggregate uncontrollably in solution.

In natural photosynthetic systems, proteins protect and organize chlorophylls. Reproducing this level of control in artificial systems remains a major challenge. One promising strategy is nanoconfinement — trapping chlorophyll derivatives inside well-defined inorganic structures such as silica nanopores.

Proteins are not always rigid structures. Many of their most important parts — linkers, loops, and disordered regions — are highly flexible, constantly changing shape in solution. To understand how these regions behave, scientists often study short model peptides that capture the essential physics of flexibility. In a new article [1], I have explored the behavior of glycine- and serine-rich octapeptides using molecular dynamics simulations combined with concepts from FRET (Förster Resonance Energy Transfer) spectroscopy (see also my previous post).