Learn More
The antiviral activity of compounds that bind an internal pocket of picornaviruses is due in part to stabilization of the protein capsid and inhibition of the uncoating process required for virus replication. Information on the basis for this structural stabilization of the virus capsid is important to elucidate the mechanism of antiviral action and provide(More)
In this paper, we explore in detail the way in which quantum decoherence is treated in different mixed quantum-classical molecular dynamics algorithms. The quantum decoherence time proves to be a key ingredient in the production of accurate nonadiabatic dynamics from computer simulations. Based on a short time expansion to a semiclassical golden rule(More)
To better understand the role of surface chemical heterogeneity in natural nanoscale hydration, we study via molecular dynamics simulation the structure and thermodynamics of water confined between two protein-like surfaces. Each surface is constructed to have interactions with water corresponding to those of the putative hydrophobic surface of a melittin(More)
Many biomolecules are characterized by surfaces containing extended nonpolar regions, and the aggregation and subsequent removal of such surfaces from water is believed to play a critical role in the biomolecular assembly in cells. A better understanding of the hydrophobic hydration of biomolecules may therefore yield new insights into intracellular(More)
We investigate the microscopic mechanism of cold and heat denaturation using a 3D lattice model of a hydrated protein in which water is represented explicitly. The water model, which incorporates directional bonding and tetrahedral geometry, captures many aspects of water thermodynamics and properly describes hydrophobic hydration around apolar solutes(More)
Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the(More)
To my wife, Sheryl, for her unending love and support. Acknowledgements Many people have made this dissertation possible, without them none of this would have been achievable. I would like to thank Dr. Isaac Sanchez, whose patience and guidance have been invaluable. I appreciate the opportunity to learn from him. My fellow group members, in 't Veld, have(More)
We perform systematic molecular dynamics simulations of water confined between two nanoscale plates at T = 300K. We investigate the effect of pressure (-0.15 GPa< or = P< or =0.2GPa) and plate separation (0.4 nm < or =d < or =1.6 nm) on the phase behavior of water when the plates are either hydrophobic or hydrophilic. When water is confined between(More)