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Log-normal distribution of single molecule fluorescence bursts in micro/nano-fluidic channels Appl. The role of excitations statistic and nonlinearity in energy harvesting from random impulsive excitations Appl. Thermodynamic and structural properties of the high density Gaussian core model A new Monte Carlo simulation procedure is developed which is(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)
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)
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)
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)
We examine by molecular dynamics simulation the solubility of small apolar solutes in a solvent whose particles interact via the Jagla potential, a spherically symmetric ramp potential with two characteristic lengths: an impenetrable hard core and a penetrable soft core. The Jagla fluid has been recently shown to possess water-like structural, dynamic, and(More)
We present results from molecular dynamics simulations of water confined by two parallel atomically detailed hydrophobic walls. Simulations are performed at T = 300 K and wall-wall separation d = 0.6-1.6 nm. At 0.7 < or = d < or = 0.9 nm, a first order transition occurs between a bilayer liquid (BL) and a trilayer heterogeneous fluid (THF) as water density(More)
We investigate the properties of a two-dimensional lattice heteropolymer model for a protein in which water is explicitly represented. The model protein distinguishes between hydrophobic and polar monomers through the effect of the hydrophobic monomers on the entropy and enthalpy of the hydrogen bonding of solvation shell water molecules. As experimentally(More)