Martin McCullagh

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Coarse-grained (CG) models provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms correlated over distance scales of many covalent bond lengths and long time scales. Variational methods based on information from simulations of finer-grained (e.g., all-atom) models, for example the(More)
Actin performs its myriad cellular functions by the growth and disassembly of its filamentous form. The hydrolysis of ATP in the actin filament has been shown to modulate properties of the filament, thus making it a pivotal regulator of the actin life cycle. Actin has evolved to selectively hydrolyze ATP in the filamentous form, F-actin, with an(More)
An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the(More)
· Developing multiscale and coarse-grain methods for treatment of large biomolecular systems. · Investigating ATP hydrolysis in actin using QM/MM and enhanced sampling techniques. · Performing large-scale all-atom molecular dynamics simulations of helicase proteins to gain an understanding of the function of these motor proteins. · Determined mechanism for(More)
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