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Transportof single molecules in nanochannels or nanoslits mightbe used to identify them via their transit (flight) times. In thispaper, we present molecular dynamics simulations of transport of singledeoxynucleotide 5′-monophoshates (dNMP) in aqueous solutionunder pressure-driven flow, to average velocities between 0.4 and1.0 m/s, in 3 nm wide slits with hydrophobic walls. The simulationresults show that, while moving along the slit, the mononucleotidesare adsorbed and desorbed from the walls multiple times. For the simulations,the estimated minimum slit length required for separation of the dNMPflight time distributions is about 5.9 μm, and the minimum analysistime per dNMP is about 10 μs. These are determined by the natureof the nucleotide–wall interactions, channel width, and bythe flow characteristics. A simple analysis using realistic dNMP velocitiesshows that, in order to reduce the effects of diffusional broadeningand keep the analysis time per dNMP reasonably small, the nucleotidevelocity should be relatively high. Tailored surface chemistry couldlead to further reduction of the analysis time toward its minimumvalue for a given driving force. [ABSTRACT FROM AUTHOR]

The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ∼45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg2ATP, a monomer with bound Mg2ATP, and a homodimer with bound Mg2ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg2ATP. For the dimer with Mg2ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg2ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg2ATP is only approximately 2 kBT higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg2ATP are much smaller than the overall reaction time, which is on the order of seconds. Proteins 2011. © 2010 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Using grain growth in nanocrystalline palladium as a simple case study, we demonstrate how a novel mesoscale approach for simulating microstructural evolution in polycrystalline materials can be validated directly against atomic-level simulations of the same system. We first describe molecular dynamics simulations of grain growth in a columnar model microstructure. The atomic-level insights into the grain-growth mechanism gained from these simulations, particularly in the role of grain rotations, are captured theoretically for incorporation into the mesoscale approach, in which the objects evolving in space and time are the grain boundaries and grain junctions rather than the atoms. With all the input parameters to the mesoscale being physically well defined and obtained directly from the atomic-level simulations, the mesoscale simulations are fully prescribed. We find that the morphology of the mesoscale system evolves in an almost identical manner with that of the molecular dynamics simulation, demonstrating that the length- and time-scale linking has been performed correctly. When applied to systems containing large numbers of grains, the now validated mesoscale simulation approach allows the growth topology and long-time growth kinetics to be determined. As an outlook, we describe how the effects of applied stress can be incorporated. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulations, we investigate the surface stress induced structural transformations and pseudoelastic behaviors in palladium nanowires. For wires with a <100> initial orientation, the simulations indicate that when the cross-sectional area is less than 2.18 ×2.18 nm2, the nanowire undergoes spontaneous reversible phase transformation from fcc to body-centered tetragonal structure. In wires with larger cross-sectional areas, the structural transformation is achieved via spontaneous reversible lattice reorientation. In both cases, under tensile loading and unloading, Pd nanowires reverse between the corresponding transformed structure and the original structure, exhibiting pseudoelastic behaviors characterized by fully recoverable strains of up to 50%. [ABSTRACT FROM AUTHOR]