Biomedical subjects

Kristen A Fichthorn

Publications and source records attributed to Kristen A Fichthorn.

7 recordsLinked to original sources

PubMed2006

Accelerated molecular dynamics simulation of the thermal desorption of n-alkanes from the basal plane of graphite.

We utilize accelerated molecular dynamics to simulate alkane desorption from the basal plane of graphite. Eight different molecules, ranging from n-pentane to n-hexadecane, are studied in the low coverage limit. Acceleration of the molecular dynamics simulations is achieved using two different methods: temperature acceleration and a compensating potential scheme. We find that the activation energy for desorption increases with increasing chain length. The desorption prefactor increases with chain length for molecules ranging from pentane to decane. This increase subsides and the value of the preexponential factor fluctuates about an apparently constant value for decane, dodecane, tetradecane, and hexadecane. These trends are consistent with data obtained in experimental temperature-programed desorption (TPD) studies. We explain the dependence of the preexponential factor on alkane chain length by examining conformational changes within the alkane molecules. For the shorter molecules, torsional motion is not activated over experimental temperature ranges. These molecules can be treated as rigid rods and their partial loss in translational and rotational entropies upon adsorption increases as chain length increases, leading to an increasing preexponential factor. At their typical TPD peak temperatures, torsions are activated in the longer adsorbed chain molecules to a significant extent which increases with increasing chain length, increasing the entropy of the adsorbed molecule. This increase counteracts the decrease in entropy due to a loss of translation and rotation, leading to a virtually constant prefactor.

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PubMed2006

Molecular dynamics simulation of nanodroplet spreading enhanced by linear surfactants.

We utilize molecular dynamics simulations to probe the surfactant-mediated spreading of a Lennard-Jones liquid droplet on a solid surface. The surfactants are linear hexamers that are insoluble in the liquid and reduce the surface tension of the liquid-vapor interface. We study how the interaction of the surfactant hexamers with the solid substrate influences spreading, as well as the dependence of spreading on surfactant concentration. We find that the spreading speed is strongly influenced by the attraction of the hydrophobic surfactant tail to the solid surface. When this attraction is sufficiently strong, surfactant molecules partition to the liquid-solid interface and facilitate spreading. This partitioning can lead to an inhomogeneous distribution of surfactant over the liquid-vapor interface, which could drive the Marangoni convection. We also observe that the surfactant molecules can assemble into micelles on the solid surface. The repulsion between micelles at the liquid-solid interface can lead to break-off and migration of the micelles from the liquid-solid to the gas-solid interface and spreading is facilitated in this way. Our model system contains features that are believed to underlie superspreading in experimental studies of droplet spreading.

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PubMed2006

Solvophobic solvation at large and intermediate length scales: Size, shape, and solvent effects.

We report the results of molecular-dynamics simulations of solvophobic nanoparticles in n -decane solvent. We observe that solvent ordering in the interparticle gap and solvation forces depend on the particle size and shape. Analogous to hydrophobic hydration, we observe dewetting of the interparticle region when the nanoparticle separation becomes smaller than a critical value of delta(c). We observe that delta(c) exhibits a nonmonotonic dependence on nanoparticle size, in contrast to what is expected from studies of water. While studies of hydrophobic hydration indicate that two solute length scales govern hydrophobic interactions, our studies indicate that a third length scale can be important in the more general phenomenon of solvophobic solvation.

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PubMed2006

Solvation forces between colloidal nanoparticles: directed alignment.

We study the solvation forces between colloidal nanoparticles in Lennard-Jones liquids using molecular-dynamics simulations. We find that due to the interplay between solvent ordering and surface structure, the solvation forces between two nanoparticles can vary between attraction and repulsion as the particles are rotated relative to one another at a fixed separation. These solvent-mediated forces tend to align the nanoparticles so that they rotate to approach one another in a solution via preferred pathways. This directed alignment could play a role in the assembly of macromolecules and nanoparticles in solution.

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PubMed2005

Molecular dynamics simulation of amphiphilic dimers at a liquid-vapor interface.

Molecular dynamics simulations are utilized to simulate a model liquid-vapor-amphiphile system. Amphiphilic surfactant molecules are modeled as dimers composed of a hydrophilic head and a hydrophobic tail. Three dimer models with three different head sizes and two different head-to-tail size ratios are studied. The surfactant molecules distribute preferentially at the interfaces at low concentrations and form micelles in the bulk liquid phase as the concentration increases. We find that the surface tension decreases as molecular concentration increases, with a reduction in the rate of decrease after micellization occurs. The extent to which a surfactant can reduce the surface tension at a given concentration is found to depend on the head size. Furthermore, the head size and concentration dependence of the surfactant tilt-angle distribution is studied and compared to experimental data.

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PubMed2004

Multiple-time scale accelerated molecular dynamics: addressing the small-barrier problem.

We present a method for accelerated molecular-dynamics simulation in systems with rare-event dynamics that span a wide range of time scales. Using a variant of hyperdynamics, we detect, on the fly, groups of recurrent states connected by small energy barriers and we modify the potential-energy surface locally to consolidate them into large, coarse states. In this way, fast motion between recurrent states is treated within an equilibrium formalism and dynamics can be simulated over the longer time scale of the slow events. We apply the method to simulate cluster diffusion and the initial growth of Co on Cu(001),where time scales spanning more than 6 orders of magnitude are present, and show that the method correctly follows the slow events, so that much larger times can be simulated than with accelerated molecular dynamics alone.

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PubMed2002

Thermal desorption of large molecules from solid surfaces.

We use molecular-dynamics simulations and importance sampling to obtain transition-state-theory rate constants for thermal desorption of an n-alkane series from Au(111). We find that the binding of a large molecule to a solid surface involves different types of local minima. The preexponential factors increase with increasing chain length and can be substantially larger than typical estimates for small molecules. Our results match recent experimental studies and indicate that a proper treatment of conformational isomerism and entropy, heretofore not found in coarse-grained models, is essential to quantitatively describe the thermal desorption of large molecules from solid surfaces.

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