Good + Bad = Ugly, and other pitfalls to avoid when calculating free energies

Molecular simulation is an experiment performed on a system defined by a molecular model. In recent years much of the effort to advance molecular simulation has been put toward improving the quality and quantity of information that it provides. These efforts have been very successful, and perhaps have improved the utility of molecular simulation even more than advances in raw computing power occurring over the same period. One important application of molecular simulation is the calculation of free-energy differences, which are required for analyses of phase and reaction equilibria, solvation, binding affinity, stability, kinetics, and so on. Some of the most popular approaches to calculating the free energy are highly prone to systematic errors, and simple countermeasures designed to remedy these inaccuracies often do not improve the outcome. We show that the key consideration influencing the accuracy is the overlap of the important regions of phase space for the systems of interest. We are developing measures to quantify this overlap and we examine the connection between them and the performance of the calculations. We use these ideas to formulate simple variants of the basic technique that can be applied to increase the likelihood of obtaining a good result

Questions, Questions: Using Problem-Based Learning to Infuse Disability Studies into an Introductory Secondary Special Education Course

This essay describes how an introductory special education course for future high school general education teachers became disability studies friendly through problem-based learning. Course structure and content are described, including opportunities for introducing disability studies concepts. Instructional challenges related to problem-based learning and maintaining a dual content focus are considered

Effect of monovacancies on the relative stability of fcc and hcp hard-sphere crystals

The effect of monovacancies on the free energy difference of close-packed hard-sphere crystals was examined. The monovacancy free energy and concentration were obtained via Monte Carlo simulations with a biased insertion method interpreted in a grand-canonical formalism. The difference in the effect of the vacancies to the difference between the free energies of the defect-free crystalline phases was compared. It was observed that the relative stability of stress-free fcc and hcp crystals is not affected by the presence of monovacancies, and fcc remaines the more stable phase over all solid-phase densities.open5

Fabrication, Characterization, and Chemical Modification of Plasmonic Devices

Metallic structures with feature sizes on the order of the wavelength of light show numerous optical phenomena which have been attributed to excitation of surface plasmons upon the structures. The ability to prepare and characterize metallic nanostructures has resulted in a host of novel applications ranging from biosensing to optoelectronics, both for devices integrated on chips and small nanoparticles in solution. In order to fully realize the potential of such plasmonic devices a better understanding of the fundamental physical processes responsible for the observed phenomena is essential. This dissertation explores the underlying process of the extraordinary optical transmission (EOT) mechanism in nanoaperture array plasmonic devices. The first part of this work explores how surface plasmon polaritons influence the EOT in two dimensional annular aperture arrays. This study is followed by an analysis of the geometrical factors of the nanoaperture in the array and how they impact the observed transmission. From these data, the role of localized surface plasmons, which are supported by the central disk of the annular aperture, are found to have significant effects on the device performance. These findings were demonstrated further by designing devices composed of a nanoparticle nested in a nanoslit in which the only mechanism for observed EOT is through localized plasmon resonances on the nanoparticles. Lastly, a novel method for conducting seedless anisotropic synthesis upon both Au nanoapertures and substrate bound Au nanoparticles is described, and control of the resultant nanostructures through alteration of either the surface chemistry or the growth solution conditions is demonstrated. The topics covered here should enable a deeper understanding of EOT in nanoaperture arrays as well as establish new pathways for making plasmonic devices

Accurate simulation estimates of phase behaviour in ternary mixtures with prescribed composition

This paper describes an isobaric semi-grand canonical ensemble Monte Carlo scheme for the accurate study of phase behaviour in ternary fluid mixtures under the experimentally relevant conditions of prescribed pressure, temperature and overall composition. It is shown how to tune the relative chemical potentials of the individual components to target some requisite overall composition and how, in regions of phase coexistence, to extract accurate estimates for the compositions and phase fractions of individual coexisting phases. The method is illustrated by tracking a path through the composition space of a model ternary Lennard-Jones mixture.Comment: 6 pages, 3 figure

Melting of Polydisperse Hard Disks

The melting of a polydisperse hard disk system is investigated by Monte Carlo simulations in the semigrand canonical ensemble. This is done in the context of possible continuous melting by a dislocation unbinding mechanism, as an extension of the 2D hard disk melting problem. We find that while there is pronounced fractionation in polydispersity, the apparent density-polydispersity gap does not increase in width, contrary to 3D polydisperse hard spheres. The point where the Young's modulus is low enough for the dislocation unbinding to occur moves with the apparent melting point, but stays within the density gap, just like for the monodisperse hard disk system. Additionally, we find that throughout the accessible polydispersity range, the bound dislocation-pair concentration is high enough to affect the dislocation unbinding melting as predicted by Kosterlitz, Thouless, Halperin, Nelson and Young.Comment: 6 pages, 6 figure

Nanoscale Surface Plasmonics Sensor With Nanofluidic Control

Conventional quantitative protein assays of bodily fluids typically involve multiple steps to obtain desired measurements. Such methods are not well suited for fast and accurate assay measurements in austere environments such as spaceflight and in the aftermath of disasters. Consequently, there is a need for a protein assay technology capable of routinely monitoring proteins in austere environments. For example, there is an immediate need for a urine protein assay to assess astronaut renal health during spaceflight. The disclosed nanoscale surface plasmonics sensor provides a core detection method that can be integrated to a lab-on-chip device that satisfies the unmet need for such a protein assay technology. Assays based upon combinations of nanoholes, nanorings, and nanoslits with transmission surface plasmon resonance (SPR) are used for assays requiring extreme sensitivity, and are capable of detecting specific analytes at concentrations as low as picomole to femtomole level in well-controlled environments. The device operates in a transmission mode configuration in which light is directed at one planar surface of the array, which functions as an optical aperture. The incident light induces surface plasmon light transmission from the opposite surface of the array. The presence of a target analyte is detected by changes in the spectrum of light transmitted by the array when a target analyte induces a change in the refractive index of the fluid within the nanochannels. This occurs, for example, when a target analyte binds to a receptor fixed to the walls of the nanochannels in the array. Independent fluid handling capability for individual nanoarrays on a nanofluidic chip containing a plurality of nanochannel arrays allows each array to be used to sense a different target analyte and/or for paired arrays to analyze control and test samples simultaneously in parallel. The present invention incorporates transmission mode nanoplasmonics and nanofluidics into a single, microfluidically controlled device. The device comprises one or more arrays of aligned nanochannels that are in fluid communication with inflowing and outflowing fluid handling manifolds that control the flow of fluid through the arrays. The array acts as an aperture in a plasmonic sensor. Fluid, in the form of a liquid or a gas and comprising a sample for analysis, is moved from an inlet manifold through the nanochannel array, and out through an exit manifold. The fluid may also contain a reagent used to modify the interior surfaces of the nanochannels, and/or a reagent required for the detection of an analyte

Polydisperse hard spheres at a hard wall

The structural properties of polydisperse hard spheres in the presence of a hard wall are investigated via Monte Carlo simulation and density functional theory (DFT). Attention is focussed on the local density distribution $\rho(\sigma,z)$, measuring the number density of particles of diameter $\sigma$ at a distance $z$ from the wall. The form of $\rho(\sigma,z)$ is obtained for bulk volume fractions $\eta_b=0.2$ and $\eta_b=0.4$ for two choices of the bulk parent distribution: a top-hat form, which we study for degrees of polydispersity $\delta=11.5$ and $\delta=40.4$, and a truncated Schulz form having $\delta=40.7$. Excellent overall agreement is found between the DFT and simulation results, particularly at $\eta_b=0.2$. A detailed analysis of $\rho(\sigma,z)$ confirms the presence of oscillatory size segregation effects observed in a previous DFT study (Pagonabarraga {\em et al.}, Phys. Rev. Lett. {\bf 84}, 911 (2000)). For large $\delta$, the character of these oscillation is observed to depend strongly on the shape of the parent distribution. In the vicinity of the wall, attractive $\sigma$-dependent depletion interactions are found to greatly enhance the density of the largest particles. The local degree of polydispersity $\delta(z)$ is suppressed in this region, while further from the wall it exhibits oscillations.Comment: 12 pages revte

Adjusting the melting point of a model system via Gibbs-Duhem integration: application to a model of Aluminum

Model interaction potentials for real materials are generally optimized with respect to only those experimental properties that are easily evaluated as mechanical averages (e.g., elastic constants (at T=0 K), static lattice energies and liquid structure). For such potentials, agreement with experiment for the non-mechanical properties, such as the melting point, is not guaranteed and such values can deviate significantly from experiment. We present a method for re-parameterizing any model interaction potential of a real material to adjust its melting temperature to a value that is closer to its experimental melting temperature. This is done without significantly affecting the mechanical properties for which the potential was modeled. This method is an application of Gibbs-Duhem integration [D. Kofke, Mol. Phys.78, 1331 (1993)]. As a test we apply the method to an embedded atom model of aluminum [J. Mei and J.W. Davenport, Phys. Rev. B 46, 21 (1992)] for which the melting temperature for the thermodynamic limit is 826.4 +/- 1.3K - somewhat below the experimental value of 933K. After re-parameterization, the melting temperature of the modified potential is found to be 931.5K +/- 1.5K.Comment: 9 pages, 5 figures, 4 table