(Bio)molecular recognition and signalling

(Bio)molecular recognition and signaling are essential processes where proteins interact with specific molecules to regulate cellular functions. Molecular dynamics (MD) simulations provide an atomic-level, time-resolved view of these interactions, revealing how proteins recognize and bind to their targets through complementary shape, charge, and hydrophobicity. In signaling, MD simulations track how binding events trigger conformational changes that propagate through the protein, leading to a biological response. These simulations are invaluable for understanding the dynamics of protein function, aiding in drug design by revealing key interaction mechanisms and potential targets for modulation.

Recent Publications:

• https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.206104

Properties of interfacial and confined water

Water plays a fundamental role in biological and chemical processes, and its behavior at interfaces or in confined environments differs significantly from that in bulk. Interfacial water refers to the water molecules in proximity to a surface, while confined water is enclosed within nanoscale spaces, such as biological membranes, pores, or protein cavities. These environments alter the structural and dynamic properties of water, influencing its hydrogen-bond network, dielectric constant, and phase behavior. The unique properties of interfacial and confined water are critical in various biological and technological contexts. In biological systems, water near biomolecular surfaces modulates protein folding, stability, and interactions. In materials science, confined water affects the performance of nanomaterials and energy storage devices. Understanding how water behaves under these conditions is essential for advancing fields like drug delivery, catalysis, and biomaterials design. Computational approaches, including molecular dynamics simulations and ab initio methods, are instrumental in probing the molecular-level properties of interfacial and confined water. These techniques allow researchers to explore water's structure, dynamics, and thermodynamics, revealing how confinement and surface interactions reshape its behavior. By elucidating these properties, computational studies provide critical insights into the role of water in biological processes and technological applications, facilitating the design of systems that harness or control interfacial water behavior.

Recent Publications:

• https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.206104

Protein misfolding and aggregation

Proteins are essential macromolecules responsible for a wide array of biological functions, ranging from catalyzing biochemical reactions to providing structural support. To perform these functions, proteins must fold into precise three-dimensional conformations. However, this folding process is inherently complex and prone to errors. Misfolded proteins can lose their biological activity and, under certain conditions, aggregate into insoluble fibrils or amorphous deposits. Protein misfolding and aggregation are implicated in numerous neurodegenerative and systemic diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis (ALS). In these conditions, the accumulation of misfolded proteins disrupts cellular homeostasis, leading to toxicity and cell death. Understanding the molecular mechanisms underlying misfolding and aggregation is crucial for developing therapeutic strategies to mitigate these pathologies. From a computational perspective, studying protein misfolding involves employing molecular dynamics simulations, structural bioinformatics, and machine learning techniques to model folding pathways, identify aggregation-prone regions, and predict the effects of mutations. These computational approaches offer powerful insights into the thermodynamic and kinetic factors governing misfolding, providing a deeper understanding of the transition from a functional protein to pathogenic aggregates. This knowledge is pivotal in designing interventions to prevent or reverse protein aggregation-related diseases.

Recent Publications:

• https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.206104

• https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.206104

• https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.206104