Showing papers by "Abraham D. Stroock published in 2006"

Mass transfer to reactive boundaries from steady three-dimensional flows in microchannels

Abstract: This paper presents a numerical study of the effect of transverse secondary flows on mass transfer to reactive boundaries in microchannels. The geometry considered is relevant to surface catalyzed reactions, fuel cells, biochemical sensors, and other microreactor applications. The 3D flows that we consider approximate flows that are experimentally achievable through topographical patterning of one wall of a microchannel, as in the Staggered Herringbone Mixer (SHM) and similar geometries. We simulate a mass transfer process using passive tracers to model reactive solute molecules in a Stokes flow (Reynolds number, Re=0) over a range of Peclet number, 102⩽Pe⩽105, with instantaneous kinetics at the reactive boundary. Our simulation allows for the evaluation of the local Sherwood number produced by a uniaxial Poiseuille flow and several chaotic and nonchaotic 3D flows. In chaotic flows, the local Sherwood number evolves in a simple manner that shares features with the classic Graetz solution for transfer from...

Protein translocation through a tunnel induces changes in folding kinetics: A lattice model study

Abstract: Compaction of a nascent polypeptide chain inside the ribosomal exit tunnel, before it leaves the ribosome, has been proposed to accelerate the folding of newly synthesized proteins following their release from the ribosome. Thus, we used Kinetic Monte Carlo simulations of a minimalist on-lattice model to explore the effect that polypeptide translocation through a variety of channels has on protein folding kinetics. Our results demonstrate that tunnel confinement promotes faster folding of a well-designed protein relative to its folding in free space by displacing the unfolded state towards more compact structures that are closer to the transition state. Since the tunnel only forbids rarely visited, extended configurations, it has little effect on a "poorly designed" protein whose unfolded state is largely composed of low-energy, compact, misfolded configurations. The beneficial effect of the tunnel depends on its width; for example, a too-narrow tunnel enforces unfolded states with limited or no access to the transition state, while a too-wide tunnel has no effect on the unfolded state entropy. We speculate that such effects are likely to play an important role in the folding of some proteins or protein domains in the cellular environment and might dictate whether a protein folds co-translationally or post-translationally.

Materials for Micro- and Nanofluidics

Abstract: Over the last two decades, our ability to create networks of fluidic channels of submillimeter or even sub-micrometer diameters has led to a wide range of microchemical applications. Whereas early efforts were directed toward the development of microanalysis systems, in more recent times the development of microreactors and tools for biotechnology and basic biological studies has emerged. This issue of MRS Bulletin highlights the many different ways in which material properties are crucial in the fabrication, assembly, and operation of micro- and nanofluidic systems. Choice-of-material considerations range from an assessment of whether a desired channel design can be microfabricated in a certain material to whether the material is compatible with the operating conditions (i.e., pressure, temperature) and the chemical composition (solvent, solutes) of the fluid used. Moreover, in certain cases, specific surface or bulk material properties can be used to the benefit of the application of the device. In the development of today’s wide range of integrated micro- and nanofluidic applications, a common challenge emerges: meeting the often contradictory set of constraints imposed on the physical and chemical properties of materials by the envisioned applications. This issue reviews these challenges and their solutions and provides an outlook on how the ingenious use of existing and new materials can spur the development of ever more sophisticated micro- and nanofluidic systems.