Enhanced tracer transport by the spiral defect chaos state of a convecting fluid

To understand how spatiotemporal chaos may modify material transport, we use direct numerical simulations of the three-dimensional Boussinesq equations and of an advection-diffusion equation to study the transport of a passive tracer by the spiral defect chaos state of a convecting fluid. The simulations show that the transport is diffusive and is enhanced by the spatiotemporal chaos. The enhancement in tracer diffusivity follows two regimes. For large Peclet numbers (that is, small molecular diffusivities of the tracer), we find that the enhancement is proportional to the Peclet number. For small Peclet numbers, the enhancement is proportional to the square root of the Peclet number. We explain the presence of these two regimes in terms of how the local transport depends on the local wave numbers of the convection rolls. For large Peclet numbers, we further find that defects cause the tracer diffusivity to be enhanced locally in the direction orthogonal to the local wave vector but suppressed in the direction of the local wave vector.Comment: 11 pages, 12 figure

Ultralow thermal conductivity of single crystalline porous silicon nanowires

Porous materials provide a large surface to volume ratio, thereby providing a knob to alter fundamental properties in unprecedented ways. In thermal transport, porous nanomaterials can reduce thermal conductivity by not only enhancing phonon scattering from the boundaries of the pores and therefore decreasing the phonon mean free path, but also by reducing the phonon group velocity. Here we establish a structure-property relationship by measuring the porosity and thermal conductivity of individual electrolessly etched single crystalline silicon nanowires using a novel electron beam heating technique. Such porous silicon nanowires exhibit extremely low diffusive thermal conductivity (as low as 0.33 Wm-1K-1 at 300K for 43% porosity), even lower than that of amorphous silicon. The origin of such ultralow thermal conductivity is understood as a reduction in the phonon group velocity, experimentally verified by measuring the Young modulus, as well as the smallest structural size ever reported in crystalline Silicon (less than 5nm). Molecular dynamics simulations support the observation of a drastic reduction in thermal conductivity of silicon nanowires as a function of porosity. Such porous materials provide an intriguing platform to tune phonon transport, which can be useful in the design of functional materials towards electronics and nano-electromechanical systems

Serum outperforms plasma in small extracellular vesicle microRNA biomarker studies of adenocarcinoma of the esophagus

Background: To compare computed tomography coronary angiography (CTCA) with intravascular ultrasound (IVUS) in quantitative and qualitative plaque assessment. Methods: Patients who underwent IVUS and CTCA within 3 months for suspected coronary artery disease were retrospectively studied. Plaque volumes on CTCA were quantified manually and with automated-software and were compared to IVUS. High-risk plaque features were compared between CTCA and IVUS. Results: There were 769 slices in 32 vessels (27 patients). Manual plaque quantification on CTCA was comparable to IVUS per slice (mean difference of 0.06 ± 0.07, p = 0.44; Bland-Altman 95% limits of agreement -2.19–2.08 mm3, bias of -0.06 mm3) and per vessel (3.1 mm3 ± -2.85 mm3, p = 0.92). In contrast, there was significant difference between automated-software and IVUS per slice (2.3 ± 0.09mm3, p < 0.001; 95% LoA -6.78 to 2.25 mm3, bias of -2.2 mm3) and per vessel (33.04 ± 10.3 mm3, p < 0.01). The sensitivity, specificity, positive and negative predictive value of CTCA to detect plaques that had features of echo-attenuation on IVUS was 93.3%, 99.6%, 93.3% and 99.6% respectively. The association of ≥2 high-risk plaque features on CTCA with echo attenuation (EA) plaque features on IVUS was excellent (86.7%, 99.6%, 92.9% and 99.2%). In comparison, the association of high-risk plaque features on CTCA and plaques with echo-lucency on IVUS was only modest. Conclusion: Plaque volume quantification by manual CTCA method is accurate when compared to IVUS. The presence of at least two high-risk plaque features on CTCA is associated with plaque features of echo attenuation on IVUS.Ravi Kiran Munnur, Jordan Andrews ... Dorothy Keefe ... Lorelle Smith ... Joanne Bowen ... Sarah Thompson ... et al

Measuring benefits and patients' satisfaction when glasses are not needed after cataract and presbyopia surgery: scoring and psychometric validation of the Freedom from Glasses Value Scale (FGVS©)

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to reduce the number of items, create a scoring method and assess the psychometric properties of the Freedom from Glasses Value Scale (FGVS), which measures benefits of freedom from glasses perceived by cataract and presbyopic patients after multifocal intraocular lens (IOL) surgery.</p> <p>Methods</p> <p>The 21-item FGVS, developed simultaneously in French and Spanish, was administered by phone during an observational study to 152 French and 152 Spanish patients who had undergone cataract or presbyopia surgery at least 1 year before the study. Reduction of items and creation of the scoring method employed statistical methods (principal component analysis, multitrait analysis) and content analysis. Psychometric properties (validation of the structure, internal consistency reliability, and known-group validity) of the resulting version were assessed in the pooled population and per country.</p> <p>Results</p> <p>One item was deleted and 3 were kept but not aggregated in a dimension. The other 17 items were grouped into 2 dimensions ('global evaluation', 9 items; 'advantages', 8 items) and divided into 5 sub-dimensions, with higher scores indicating higher benefit of surgery. The structure was validated (good item convergent and discriminant validity). Internal consistency reliability was good for all dimensions and sub-dimensions (Cronbach's alphas above 0.70). The FGVS was able to discriminate between patients wearing glasses or not after surgery (higher scores for patients not wearing glasses). FGVS scores were significantly higher in Spain than France; however, the measure had similar psychometric performances in both countries.</p> <p>Conclusions</p> <p>The FGVS is a valid and reliable instrument measuring benefits of freedom from glasses perceived by cataract and presbyopic patients after multifocal IOL surgery.</p

Numerical study of chemical reaction effects in magnetohydrodynamic Oldroyd B oblique stagnation flow with a non-Fourier heat flux model

Reactive magnetohydrodynamic (MHD) flows arise in many areas of nuclear reactor transport. Working fluids in such systems may be either Newtonian or non-Newtonian. Motivated by these applications, in the current study, a mathematical model is developed for electrically-conducting viscoelastic oblique flow impinging on stretching wall under transverse magnetic field. A non-Fourier Cattaneo-Christov model is employed to simulate thermal relaxation effects which cannot be simulated with the classical Fourier heat conduction approach. The Oldroyd-B non-Newtonian model is employed which allows relaxation and retardation effects to be included. A convective boundary condition is imposed at the wall invoking Biot number effects. The fluid is assumed to be chemically reactive and both homogeneous-heterogeneous reactions are studied. The conservation equations for mass, momentum, energy and species (concentration) are altered with applicable similarity variables and the emerging strongly coupled, nonlinear non-dimensional boundary value problem is solved with robust well-tested Runge-Kutta-Fehlberg numerical quadrature and a shooting technique with tolerance level of 10−4. Validation with the Adomian decomposition method (ADM) is included. The influence of selected thermal (Biot number, Prandtl number), viscoelastic hydrodynamic (Deborah relaxation number), Schmidt number, magnetic parameter and chemical reaction parameters, on velocity, temperature and concentration distributions are plotted for fixed values of geometric (stretching rate, obliqueness) and thermal relaxation parameter. Wall heat transfer rate (local heat flux) and wall species transfer rate (local mass flux) are also computed and it is observed that local mass flux increases with strength of heterogeneous reactions whereas it decreases with strength of homogeneous reactions. The results provide interesting insights into certain nuclear reactor transport phenomena and furthermore a benchmark for more general CFD simulations

Multi-Scale Stochastic Simulation of Diffusion-Coupled Agents and Its Application to Cell Culture Simulation

Many biological systems consist of multiple cells that interact by secretion and binding of diffusing molecules, thus coordinating responses across cells. Techniques for simulating systems coupling extracellular and intracellular processes are very limited. Here we present an efficient method to stochastically simulate diffusion processes, which at the same time allows synchronization between internal and external cellular conditions through a modification of Gillespie's chemical reaction algorithm. Individual cells are simulated as independent agents, and each cell accurately reacts to changes in its local environment affected by diffusing molecules. Such a simulation provides time-scale separation between the intra-cellular and extra-cellular processes. We use our methodology to study how human monocyte-derived dendritic cells alert neighboring cells about viral infection using diffusing interferon molecules. A subpopulation of the infected cells reacts early to the infection and secretes interferon into the extra-cellular medium, which helps activate other cells. Findings predicted by our simulation and confirmed by experimental results suggest that the early activation is largely independent of the fraction of infected cells and is thus both sensitive and robust. The concordance with the experimental results supports the value of our method for overcoming the challenges of accurately simulating multiscale biological signaling systems

Combined Simulation and Experimental Study of Large Deformation of Red Blood Cells in Microfluidic Systems

Author manuscript; available in PMC 2012 March 1.We investigate the biophysical characteristics of healthy human red blood cells (RBCs) traversing microfluidic channels with cross-sectional areas as small as 2.7 × 3 μm. We combine single RBC optical tweezers and flow experiments with corresponding simulations based on dissipative particle dynamics (DPD), and upon validation of the DPD model, predictive simulations and companion experiments are performed in order to quantify cell deformation and pressure–velocity relationships for different channel sizes and physiologically relevant temperatures. We discuss conditions associated with the shape transitions of RBCs along with the relative effects of membrane and cytosol viscosity, plasma environments, and geometry on flow through microfluidic systems at physiological temperatures. In particular, we identify a cross-sectional area threshold below which the RBC membrane properties begin to dominate its flow behavior at room temperature; at physiological temperatures this effect is less profound.Singapore-MIT Alliance for Research and TechnologyUnited States. National Institutes of Health (National Heart, Lung, and Blood Institute Award R01HL094270

Towards a matrix mechanics framework for dynamic protein network

Protein–protein interaction networks are currently visualized by software generated interaction webs based upon static experimental data. Current state is limited to static, mostly non-compartmental network and non time resolved protein interactions. A satisfactory mathematical foundation for particle interactions within a viscous liquid state (situation within the cytoplasm) does not exist nor do current computer programs enable building dynamic interaction networks for time resolved interactions. Building mathematical foundation for intracellular protein interactions can be achieved in two increments (a) trigger and capture the dynamic molecular changes for a select subset of proteins using several model systems and high throughput time resolved proteomics and, (b) use this information to build the mathematical foundation and computational algorithm for a compartmentalized and dynamic protein interaction network. Such a foundation is expected to provide benefit in at least two spheres: (a) understanding physiology enabling explanation of phenomenon such as incomplete penetrance in genetic disorders and (b) enabling several fold increase in biopharmaceutical production using impure starting materials

Evaluation of a range of mammalian and mosquito cell lines for use in Chikungunya virus research

Chikungunya virus (CHIKV) is becoming an increasing global health issue which has spread across the globe and as far north as southern Europe. There is currently no vaccine or anti-viral treatment available. Although there has been a recent increase in CHIKV research, many of these in vitro studies have used a wide range of cell lines which are not physiologically relevant to CHIKV infection in vivo. In this study, we aimed to evaluate a panel of cell lines to identify a subset that would be both representative of the infectious cycle of CHIKV in vivo, and amenable to in vitro applications such as transfection, luciferase assays, immunofluorescence, western blotting and virus infection. Based on these parameters we selected four mammalian and two mosquito cell lines, and further characterised these as potential tools in CHIKV research