Stability of a microwave heated fluid Layer

When a time harmonic electromagnetic wave impinges on a slaba certain portion of the wave creates heat within the slab throughdipolar and ohmic heating. The electrical and thermal propertiesof the material dictate the dynamical nature of the heatingprocess, as well as the steady-state temperature profile. Thematerial considered here is a slab of fluid. We consider thecase where the fluid is bounded by thin rigid layers of transparentmaterial. The steady-state heating profile governs the typesof convective motions that can occur and also affects the stabilitycharacteristics of temperature, pressure and velocity perturbationsintroduced in the slab. The main objective here is to examinesuch stability characteristics, initially in the linear regime.Both rigid-rigid and rigid-free configurations are considered.     

Development and use of an atomistic CHARMM‐based forcefield for peptoid simulation

Peptoids are positional isomers of peptides: peptoid sidechains are attached to backbone nitrogens rather than α‐carbons. Peptoids constitute a class of sequence‐specific polymers resistant to biological degradation and potentially as diverse, structurally and functionally, as proteins. While molecular simulation of proteins is commonplace, relatively few tools are available for peptoid simulation. Here, we present a first‐generation atomistic forcefield for peptoids. Our forcefield is based on the peptide forcefield CHARMM22, with key parameters tuned to match both experimental data and quantum mechanical calculations for two model peptoids (dimethylacetamide and a sarcosine dipeptoid). We used this forcefield to demonstrate that solvation of a dipeptoid substantially modifies the conformations it can access. We also simulated a crystal structure of a peptoid homotrimer, H‐(N‐2‐phenylethyl glycine)₃‐OH, and we show that experimentally observed structural and dynamical features of the crystal are accurately described by our forcefield. The forcefield presented here provides a starting point for future development of peptoid‐specific simulation methods within CHARMM. © 2013 Wiley Periodicals, Inc.     

A new perspective on the coarse-grained dynamics of fluids

A computational methodology is presented that is designed to model, at a coarse-grained level, the mesoscale dynamics of fluids and potentially other forms of soft matter. Within a molecular dynamics simulation, "ghost" particles of a specific size, corresponding to the fundamental length-scale of coarse-graining, are used as micro-probes designed to respond to local mesoscale fluid flows and stress gradients. A subsequent coarse-grained model is then developed that incorporates both the coarse-grained mesoscale dynamics and isothermal compressibility of the original microscopic system. The method is applied to water and methanol. A contrast with dissipative particle dynamics (DPD) is also presented.