Soft fundamental measure theory functional for the Weeks-Chandler-Andersen repulsive potential.

We introduce a soft fundamental measure theory functional for the purely repulsive Weeks-Chandler-Andersen (WCA) fluid. This classical density functional could serve as a reference fluid for functionals created using thermodynamic perturbation theory instead of the hard-sphere fluid. Our functional incorporates temperature-dependent parameters describing the length scale and effective softness of the particle interaction, and which reproduce the second virial coefficient of the WCA fluid. We find that this approach is comparable in accuracy to the Barker-Henderson approach combined with the White Bear density functional for the hard-sphere fluid.

Flat-histogram method comparison on the two-dimensional Ising model.

We compare the convergence of several flat-histogram methods applied to the two-dimensional Ising model, including the recently introduced stochastic approximation with a dynamic update factor (SAD) method. We compare this method to the Wang-Landau (WL) method, the 1/t variant of the WL method, and standard stochastic approximation Monte Carlo (SAMC). In addition, we consider a procedure WL followed by a "production run" with fixed weights that refines the estimation of the entropy. We find that WL followed by a production run does converge to the true density of states, in contrast to pure WL. Three of the methods converge robustly: SAD, 1/t-WL, and WL followed by a production run. Of these, SAD does not require a priori knowledge of the energy range. This work also shows that WL followed by a production run performs superior to other forms of WL while ensuring both ergodicity and detailed balance.

Statistical Mechanical Model of Gas Adsorption in a Metal-Organic Framework Harboring a Rotaxane Molecular Shuttle.

Metal-organic frameworks (MOFs) are modular and tunable nanoporous materials with applications in gas storage, separations, and sensing. Integrating flexible/dynamic, gas-responsive components into MOFs can give them unique or enhanced adsorption properties. Here, we explore the adsorption properties that could be imparted to a MOF by a rotaxane molecular shuttle (RMS) in its pores. In the unit cell of an RMS-MOF, a macrocyclic wheel is mechanically interlocked with a strut of the MOF scaffold. The wheel shuttles between stations on the strut that are also gas adsorption sites. At a level of abstraction similar to the seminal Langmuir adsorption model, we pose and analyze a simple statistical mechanical model of gas adsorption in an RMS-MOF that accounts for (i) wheel/gas competition for sites on the strut and (ii) gas-induced changes in the configurational entropy of the shuttling wheel. We determine how the amount of gas adsorbed, the position of the wheel, and the differential energy of adsorption depend on temperature, pressure, and the interactions of the gas and wheel with the stations on the strut. Our model reveals that, compared to a rigid, Langmuir material, the chemistry of the RMS-MOF can be tuned to render gas adsorption more or less temperature sensitive and to release more or less heat upon adsorption. The model also uncovers that, if gas-wheel competition for a station is fierce, temperature influences the position of the wheel differently depending on the amount of gas adsorbed.

Stochastic approximation Monte Carlo with a dynamic update factor.

We present a Monte Carlo algorithm based on the stochastic approximation Monte Carlo (SAMC) algorithm for directly calculating the density of states. The proposed method is stochastic approximation with a dynamic update factor (SAD), which dynamically adjusts the update factor γ_{t} during the course of the simulation. We test this method on a square-well fluid and a 31-atom Lennard-Jones cluster and compare the convergence behavior of several related Monte Carlo methods. We find that both the SAD and 1/t-Wang-Landau (1/t-WL) methods rapidly converge to the correct density of states without the need for the user to specify an arbitrary tunable parameter t_{0} as in the case of SAMC. SAD requires as input the temperature range of interest, in contrast with 1/t-WL, which requires that the user identify the interesting range of energies. The convergence of the 1/t-WL method is very sensitive to the energy range chosen for the low-temperature heat capacity of the Lennard-Jones cluster. Thus, SAD is more powerful in the common case in which the range of energies is not known in advance.

Theoretical Prediction of Disrupted Min Oscillation in Flattened Escherichia coli.

The dynamics of the Min-protein system help Escherichia coli regulate the process of cell division by identifying the center of the cell. While this system exhibits robust bipolar oscillations in wild-type cell shapes, recent experiments have shown that when the cells are mechanically deformed into wide, flattened out, irregular shapes, the spatial regularity of these oscillations breaks down. We employ widely used stochastic and deterministic models of the Min system to simulate cells with flattened shapes. The deterministic model predicts strong bipolar oscillations, in contradiction with the experimentally observed behavior, while the stochastic model, which is based on the same reaction-diffusion equations, predicts more spatially irregular oscillations. We further report simulations of flattened but more symmetric shapes, which suggest that the flattening and lateral expansion may contribute as much to the irregular oscillation behavior as the asymmetry of the cell shapes.

Approach to approximating the pair distribution function of inhomogeneous hard-sphere fluids.

We introduce an approximation for the pair distribution function of the inhomogeneous hard sphere fluid. Our approximation makes use of our recently published averaged pair distribution function at contact, which has been shown to accurately reproduce the averaged pair distribution function at contact for inhomogeneous density distributions. This approach achieves greater computational efficiency than previous approaches by enabling the use of exclusively fixed-kernel convolutions and thus allowing an implementation using fast Fourier transforms. We compare results for our pair distribution approximation with two previously published works and Monte Carlo simulation, showing favorable results.

Improved association in a classical density functional theory for water.

We present a modification to our recently published statistical associating fluid theory-based classical density functional theory for water. We have recently developed and tested a functional for the averaged radial distribution function at contact of the hard-sphere fluid that is dramatically more accurate at interfaces than earlier approximations. We now incorporate this improved functional into the association term of our free energy functional for water, improving its description of hydrogen bonding. We examine the effect of this improvement by studying two hard solutes (a hard hydrophobic rod and a hard sphere) and a Lennard-Jones approximation of a krypton atom solute. The improved functional leads to a moderate change in the density profile and a large decrease in the number of hydrogen bonds broken in the vicinity of the hard solutes. We find an improvement of the partial radial distribution for a krypton atom in water when compared with experiment.

A classical density-functional theory for describing water interfaces.

We develop a classical density functional for water which combines the White Bear fundamental-measure theory (FMT) functional for the hard sphere fluid with attractive interactions based on the statistical associating fluid theory variable range (SAFT-VR). This functional reproduces the properties of water at both long and short length scales over a wide range of temperatures and is computationally efficient, comparable to the cost of FMT itself. We demonstrate our functional by applying it to systems composed of two hard rods, four hard rods arranged in a square, and hard spheres in water.

Using fundamental measure theory to treat the correlation function of the inhomogeneous hard-sphere fluid.

We investigate the value of the correlation function of an inhomogeneous hard-sphere fluid at contact. This quantity plays a critical role in statistical associating fluid theory, which is the basis of a number of recently developed classical density functionals. We define two averaged values for the correlation function at contact and derive formulas for each of them from the White Bear version of the fundamental measure theory functional, using an assumption of thermodynamic consistency. We test these formulas, as well as two existing formulas, against Monte Carlo simulations and find excellent agreement between the Monte Carlo data and one of our averaged correlation functions.

Improving accuracy by subpixel smoothing in the finite-difference time domain.

Finite-difference time-domain (FDTD) methods suffer from reduced accuracy when modeling discontinuous dielectric materials, due to the inhererent discretization (pixelization). We show that accuracy can be significantly improved by using a subpixel smoothing of the dielectric function, but only if the smoothing scheme is properly designed. We develop such a scheme based on a simple criterion taken from perturbation theory and compare it with other published FDTD smoothing methods. In addition to consistently achieving the smallest errors, our scheme is the only one that attains quadratic convergence with resolution for arbitrarily sloped interfaces. Finally, we discuss additional difficulties that arise for sharp dielectric corners.

Microcavity confinement based on an anomalous zero group-velocity waveguide mode.

We propose and demonstrate a mechanism for small-modal-volume high-Q cavities based on an anomalous uniform waveguide mode that has zero group velocity at a nonzero wave vector. In a short piece of a uniform waveguide with a specially designed cross section, light is confined longitudinally by small group-velocity propagation and transversely by a reflective cladding. The quality factor Q is greatly enhanced by the small group velocity for a set of cavity lengths that are separated by approximately pi/k0, where k0 is the longitudinal wave vector for which the group velocity is zero.

A tunable carbon nanotube electromechanical oscillator.

Nanoelectromechanical systems (NEMS) hold promise for a number of scientific and technological applications. In particular, NEMS oscillators have been proposed for use in ultrasensitive mass detection, radio-frequency signal processing, and as a model system for exploring quantum phenomena in macroscopic systems. Perhaps the ultimate material for these applications is a carbon nanotube. They are the stiffest material known, have low density, ultrasmall cross-sections and can be defect-free. Equally important, a nanotube can act as a transistor and thus may be able to sense its own motion. In spite of this great promise, a room-temperature, self-detecting nanotube oscillator has not been realized, although some progress has been made. Here we report the electrical actuation and detection of the guitar-string-like oscillation modes of doubly clamped nanotube oscillators. We show that the resonance frequency can be widely tuned and that the devices can be used to transduce very small forces.

The origin of the anomalous superconducting properties of MgB(2).

Magnesium diboride differs from ordinary metallic superconductors in several important ways, including the failure of conventional models to predict accurately its unusually high transition temperature, the effects of isotope substitution on the critical transition temperature, and its anomalous specific heat. A detailed examination of the energy associated with the formation of charge-carrying pairs, referred to as the 'superconducting energy gap', should clarify why MgB(2) is different. Some early experimental studies have indicated that MgB(2) has multiple gaps, but past theoretical studies have not explained from first principles the origin of these gaps and their effects. Here we report an ab initio calculation of the superconducting gaps in MgB(2) and their effects on measurable quantities. An important feature is that the electronic states dominated by orbitals in the boron plane couple strongly to specific phonon modes, making pair formation favourable. This explains the high transition temperature, the anomalous structure in the specific heat, and the existence of multiple gaps in this material. Our analysis suggests comparable or higher transition temperatures may result in layered materials based on B, C and N with partially filled planar orbitals.