Consistent Modeling of Rotational Nonequilibrium in a Hybrid Particle-Continuum Method

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106474/1/AIAA2013-3145.pd

Rotational Correlation Functions of Single Molecules

Single molecule rotational correlation functions are analyzed for several reorientation geometries. Even for the simplest model of isotropic rotational diffusion our findings predict non-exponential correlation functions to be observed by polarization sensitive single molecule fluorescence microscopy. This may have a deep impact on interpreting the results of molecular reorientation measurements in heterogeneous environments.Comment: 5 pages, 4 figure

Analysis of Diffusion of Ras2 in Saccharomyces cerevisiae Using Fluorescence Recovery after Photobleaching

Binding, lateral diffusion and exchange are fundamental dynamic processes involved in protein association with cellular membranes. In this study, we developed numerical simulations of lateral diffusion and exchange of fluorophores in membranes with arbitrary bleach geometry and exchange of the membrane localized fluorophore with the cytosol during Fluorescence Recovery after Photobleaching (FRAP) experiments. The model simulations were used to design FRAP experiments with varying bleach region sizes on plasma-membrane localized wild type GFP-Ras2 with a dual lipid anchor and mutant GFP-Ras2C318S with a single lipid anchor in live yeast cells to investigate diffusional mobility and the presence of any exchange processes operating in the time scale of our experiments. Model parameters estimated using data from FRAP experiments with a 1 micron x 1 micron bleach region-of-interest (ROI) and a 0.5 micron x 0.5 micron bleach ROI showed that GFP-Ras2, single or dual lipid modified, diffuses as single species with no evidence of exchange with a cytoplasmic pool. This is the first report of Ras2 mobility in yeast plasma membrane. The methods developed in this study are generally applicable for studying diffusion and exchange of membrane associated fluorophores using FRAP on commercial confocal laser scanning microscopes.Comment: Accepted for publication in Physical Biology (2010). 28 pages, 7 figures, 3 table

On the use of fractional Brownian motion simulations to determine the 3D statistical properties of interstellar gas

Based on fractional Brownian motion (fBm) simulations of 3D gas density and velocity fields, we present a study of the statistical properties of spectro-imagery observations (channel maps, integrated emission, and line centroid velocity) in the case of an optically thin medium at various temperatures. The power spectral index gamma_W of the integrated emission is identified with that of the 3D density field (gamma_n) provided the medium's depth is at least of the order of the largest transverse scale in the image, and the power spectrum of the centroid velocity map is found to have the same index gamma_C as that of the velocity field (gamma_v). Further tests with non-fBm density and velocity fields show that this last result holds, and is not modified either by the effects of density-velocity correlations. A comparison is made with the theoretical predictions of Lazarian & Pogosyan (2000).Comment: 28 pages, 14 figures, accepted for publication in ApJ. For preprint with higher-resolution figures, see http://www.cita.utoronto.ca/~mamd/miville_fbm2003.pd

Excitation lines and the breakdown of Stokes-Einstein relations in supercooled liquids

By applying the concept of dynamical facilitation and analyzing the excitation lines that result from this facilitation, we investigate the origin of decoupling of transport coefficients in supercooled liquids. We illustrate our approach with two classes of models. One depicts diffusion in a strong glass former, and the other in a fragile glass former. At low temperatures, both models exhibit violation of the Stokes-Einstein relation, $D\sim\tau^{-1}$, where $D$ is the self diffusion constant and $\tau$ is the structural relaxation time. In the strong case, the violation is sensitive to dimensionality $d$, going as $D\sim\tau^{-2/3}$ for $d=1$, and as $D\sim \tau^{-0.95}$ for $d=3$. In the fragile case, however, we argue that dimensionality dependence is weak, and show that for $d=1$, $D \sim \tau^{-0.73}$. This scaling for the fragile case compares favorably with the results of a recent experimental study for a three-dimensional fragile glass former.Comment: 7 pages, 7 figures, submitted to Phys. Rev.

Structure and Colors of Diffuse Emission in the Spitzer Galactic First Look Survey

We investigate the density structure of the interstellar medium using new high-resolution maps of the 8 micron, 24 micron, and 70 micron surface brightness towards a molecular cloud in the Gum Nebula, made as part of the Spitzer Space Telescope Galactic First Look Survey. The maps are correlated with 100 micron images measured with IRAS. At 24 and 70 micron, the spatial power spectrum of surface brightness follows a power law with spectral index -3.5. At 24 micron, the power law behavior is remarkably consistent from the 0.2 degree size of our maps down to the 5 arcsecond spatial resolution. Thus, the structure of the 24 micron emission is self-similar even at milliparsec scales. The combined power spectrum produced from Spitzer 24 micron and IRAS 25 micron images is consistent with a change in the power law exponent from -2.6 to -3.5. The decrease may be due to the transition from a two-dimensional to three-dimensional structure. Under this hypothesis, we estimate the thickness of the emitting medium to be 0.3 pc.Comment: 13 Pages, 3 Figures, to be published in Astrophysical Journal Supplement Series (Spitzer Special Issue), volume 154. Uses aastex v5.

Achieving Acetylcholine Receptor Clustering in Tissue-Engineered Skeletal Muscle Constructs In vitro through a Materials-Directed Agrin Delivery Approach

Volumetric muscle loss (VML) can result from trauma, infection, congenital anomalies, or surgery, and produce permanent functional and cosmetic deficits. There are no effective treatment options for VML injuries, and recent advances toward development of muscle constructs lack the ability to achieve innervation necessary for long-term function. We sought to develop a proof-of-concept biomaterial construct that could achieve acetylcholine receptor (AChR) clustering on muscle-derived cells (MDCs) in vitro. The approach consisted of the presentation of neural (Z+) agrin from the surface of microspheres embedded with a fibrin hydrogel to muscle cells (C2C12 cell line or primary rat MDCs). AChR clustering was spatially restricted to areas of cell (C2C12)-microsphere contact when the microspheres were delivered in suspension or when they were incorporated into a thin (2D) fibrin hydrogel. AChR clusters were observed from 16 to 72 h after treatment when Z+ agrin was adsorbed to the microspheres, and for greater than 120 h when agrin was covalently coupled to the microspheres. Little to no AChR clustering was observed when agrin-coated microspheres were delivered from specially designed 3D fibrin constructs. However, cyclic stretch in combination with agrin-presenting microspheres led to dramatic enhancement of AChR clustering in cells cultured on these 3D fibrin constructs, suggesting a synergistic effect between mechanical strain and agrin stimulation of AChR clustering in vitro. These studies highlight a strategy for maintaining a physiological phenotype characterized by motor endplates of muscle cells used in tissue engineering strategies for muscle regeneration. As such, these observations may provide an important first step toward improving function of tissue-engineered constructs for treatment of VML injuries