Identity, energetics, dynamics and environment of interfacial water molecules in a micellar solution

The structure and energetics of interfacial water molecules in the aqueous micelle of cesium perfluorooctanoate have been investigated, using large-scale atomistic molecular dynamics simulations, with the primary objective of classifying them. The simulations show that the water molecules at the interface fall into two broad classes: bound and free, present in a ratio of 9:1. The bound water molecules can be further categorized on the basis of the number of hydrogen bonds (one or two) that they form with the surfactant headgroups. The hydrogen bonds of the doubly hydrogen-bonded species are found to be, on the average, slightly weaker than those in the singly bonded species. The environment around interfacial water molecules is more ordered than that in the bulk. The surface water molecules have substantially lower potential energy, because of interaction with the micelle. In particular, both forms of bound water have energies that are lower by �2.5-4.0 kcal/ mol. Entropy is found to play an important role in determining the relative concentration of the species.

Study of the dynamics of protein folding through minimalistic models

Starting with the Levinthal paradox, a brief introduction to the protein folding problem is presented. The existing theories of protein folding, including the folding funnel scenario, are discussed. After briefly discussing different simulation studies of model proteins, we discuss our recent work on the dynamics of folding of the model HP-36 (the chicken villin headpiece) protein by using a simplified hydropathy scale. Special attention has been paid to the statics and dynamics of contact formation among the hydrophobic residues. The results obtained from this simple model appear to be surprisingly similar to several features observed in the folding of real proteins. The account concludes with a discussion of future problems.

Two-Stage Extended Kalman Filters with Derivative-Free Local Linearizations

This paper proposes a derivative-free two-stage extended Kalman filter (2-EKF) especially suited for state and parameter identification of mechanical oscillators under Gaussian white noise. Two sources of modeling uncertainties are considered: (1) errors in linearization, and (2) an inadequate system model. The state vector is presently composed of the original dynamical/parameter states plus the so-called bias states accounting for the unmodeled dynamics. An extended Kalman estimation concept is applied within a framework predicated on explicit and derivative-free local linearizations (DLL) of nonlinear drift terms in the governing stochastic differential equations (SDEs). The original and bias states are estimated by two separate filters; the bias filter improves the estimates of the original states. Measurements are artificially generated by corrupting the numerical solutions of the SDEs with noise through an implicit form of a higher-order linearization. Numerical illustrations are provided for a few single- and multidegree-of-freedom nonlinear oscillators, demonstrating the remarkable promise that 2-EKF holds over its more conventional EKF-based counterparts. DOI: 10.1061/(ASCE)EM.1943-7889.0000255. (C) 2011 American Society of Civil Engineers.

Vortex dynamics and upper critical fields in ultrathin Bi films

Current-voltage (I-V) characteristics of quench condensed, superconducting, ultrathin Bi films in a magnetic field are reported. These I-V's show hysteresis for all films, grown both with and without thin Ge underlayers. Films on Ge underlayers, close to superconductor-insulator transition, show a peak in the critical current, indicating a structural transformation of the vortex solid. These underlayers, used to make the films more homogeneous, are found to be more effective in pinning the vortices. The upper critical fields (B-c2) of these films are determined from the resistive transitions in perpendicular magnetic field. The temperature dependence of the upper critical field is found to differ significantly from Ginzburg-Landau theory, after modifications for disorder.

Dynamics of pulled desorption with effects of excluded-volume interaction: The p-Laplacian diffusion equation and its exact solution

We analyze the dynamics of desorption of a polymer molecule which is pulled at one of its ends with force f, trying to desorb it. We assume a monomer to desorb when the pulling force on it exceeds a critical value f(c). We formulate an equation for the average position of the n-th monomer, which takes into account excluded-volume interaction through the blob-picture of a polymer under external constraints. The approach leads to a diffusion equation with a p-Laplacian for the propagation of the stretching along the chain. This has to be solved subject to a moving boundary condition. Interestingly, within this approach, the problem can be solved exactly in the trumpet, stem-flower and stem regimes. In the trumpet regime, we get tau = tau(0)n(d)(2), where n(d) is the number of monomers that have desorbed at the time tau. tau(0) is known only numerically, but for f close to f(c), it is found to be tau(0) similar to f(c)/(f(2/3) - f(c)(2/3)) If one used simple Rouse dynamics, this result would change to tau similar to f(c)n(d)(2)/(f - f(c)). In the other regimes too, one can find exact solution, and interestingly, in all regimes tau similar to n(d)(2). Copyright (C) EPLA, 2011

Procedural aspects of modeling the dynamics of a three wheeled vehicle using ADAMS-CAR

We describe in some detail the process of development of a dynamic model of a three wheeled vehicle using ADAMS-CAR. We first describe the rigid body model, and then the modeling of structural flexibilities. The aim of this report is to document procedural details of such modeling, with a view to presenting more research and development oriented investigations in the future. The contents of this report may also be of interest to practicing engineers engaged in multi-body dynamics modeling of wheeled vehicles.

Modeling of nonreacting and reacting turbulent spray jets using a fully stochastic separated flow approach

Numerical modeling of several turbulent nonreacting and reacting spray jets is carried out using a fully stochastic separated flow (FSSF) approach. As is widely used, the carrier-phase is considered in an Eulerian framework, while the dispersed phase is tracked in a Lagrangian framework following the stochastic separated flow (SSF) model. Various interactions between the two phases are taken into account by means of two-way coupling. Spray evaporation is described using a thermal model with an infinite conductivity in the liquid phase. The gas-phase turbulence terms are closed using the k-epsilon model. A novel mixture fraction based approach is used to stochastically model the fluctuating temperature and composition in the gas phase and these are then used to refine the estimates of the heat and mass transfer rates between the droplets and the surrounding gas-phase. In classical SSF (CSSF) methods, stochastic fluctuations of only the gas-phase velocity are modeled. Successful implementation of the FSSF approach to turbulent nonreacting and reacting spray jets is demonstrated. Results are compared against experimental measurements as well as with predictions using the CSSF approach for both nonreacting and reacting spray jets. The FSSF approach shows little difference from the CSSF predictions for nonreacting spray jets but differences are significant for reacting spray jets. In general, the FSSF approach gives good predictions of the flame length and structure but further improvements in modeling may be needed to improve the accuracy of some details of the Predictions. (C) 2011 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Doubly spectral stochastic finite element method (DSSFEM) for random field problems

Uncertainties in complex dynamic systems play an important role in the prediction of a dynamic response in the mid- and high-frequency ranges. For distributed parameter systems, parametric uncertainties can be represented by random fields leading to stochastic partial differential equations. Over the past two decades, the spectral stochastic finite-element method has been developed to discretize the random fields and solve such problems. On the other hand, for deterministic distributed parameter linear dynamic systems, the spectral finite-element method has been developed to efficiently solve the problem in the frequency domain. In spite of the fact that both approaches use spectral decomposition (one for the random fields and the other for the dynamic displacement fields), very little overlap between them has been reported in literature. In this paper, these two spectral techniques are unified with the aim that the unified approach would outperform any of the spectral methods considered on their own. An exponential autocorrelation function for the random fields, a frequency-dependent stochastic element stiffness, and mass matrices are derived for the axial and bending vibration of rods. Closed-form exact expressions are derived by using the Karhunen-Loève expansion. Numerical examples are given to illustrate the unified spectral approach.

Fluid dynamics study of a new vacuum degassing process

Recently, the demand of the steel having superior chemical and physical properties has increased for which the content of carbon must be in ultra low range. There are many processes which can produce low carbon steel such as Tank degasser and RH (Rheinstahl-Heraeus) processes. It has been claimed that using a new process, called REDA (Revolutionary Degassing Activator), one can achieve the carbon content below 10ppm in less time. REDA process in terms of installment cost is in between tank degasser and RH processes. As such, REDA process has not been studied thoroughly. Fluid flow phenomena affect the decarburization rate the most besides the chemical reaction rate. Therefore, momentum balance equations along with k-ε turbulent model have been solved for gas and liquid phases in two-dimension (2D) for REDA process. The fluid flow phenomena have been studied in details for this process by varying gas flow rate, depth of immersed snorkel in the steel, diameter of the snorkel and change in vacuum pressure. It is found that design of snorkel affects the mixing process of the bath significantly.