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With the advent of enhanced computational power, molecular dynamics (MD)
simulations has emerged as an indispensable tool to probe the thermodynamic and
kinetic underpinnings of ‘soft matter’ behaviour. In particular, the myriad
superposition of short- and long- ranged interactions that underlie complex
biomolecular phenomena such as folding, stability, self-assembly, and surface
interactions manifest themselves in the sampled phase space, and can be analyzed to
elicit information that may often be compared directly to experimental data. In this
talk, I will highlight some of our recent efforts to understand the early self-assembly
of an intrinsically disordered protein, Amyloid beta (A β ), which is intricately
associated with the onset and prognosis of the neurodegenerative Alzheimer’s disease
(AD). Understanding the detailed mechanisms behind A β self-assembly may help in
the design of novel therapeutics for AD. Our work on modulation of this protein’s
self-assembly with carbon nanomaterials has further demonstrated how surface
topography is likely to play a role in general protein stability and adsorption. Finally,
I will discuss the anomalous phenomenon of protein cold denaturation, and how our
MD simulations elicit the asymmetry between early cold and heat denaturation
processes in a small globular protein. |