Measuring and modeling optical diffraction from subwavelength features

We describe a technique for studying scattering from subwavelength features. A simple scatterometer was developed to measure the scattering from the single-submicrometer, subwavelength features generated with a focused ion beam system. A model that can describe diffraction from subwavelength features with arbitrary profiles is also presented and shown to agree quite well with the experimental measurements. The model is used to demonstrate ways in which the aspect ratios of subwavelength ridges and trenches can be obtained from scattering data and how ridges can be distinguished from trenches over a wide range of aspect ratios. We show that some earlier results of studies on distinguishing pits from particles do not extend to low-aspect-ratio features

Persistent Vascular Collagen Accumulation Alters Hemodynamic Recovery from Chronic Hypoxia

Pulmonary arterial hypertension (PAH) is caused by narrowing and stiffening of the pulmonary arteries that increase pulmonary vascular impedance (PVZ). In particular, small arteries narrow and large arteries stiffen. Large pulmonary artery (PA) stiffness is the best current predictor of mortality from PAH. We have previously shown that collagen accumulation leads to extralobar PA stiffening at high strain (Ooi et al. 2010). We hypothesized that collagen accumulation would increase PVZ, including total pulmonary vascular resistance (Z0), characteristic impedance (ZC), pulse wave velocity (PWV) and index of global wave reflections (Pb/Pf), which contribute to increased right ventricular afterload. We tested this hypothesis by exposing mice unable to degrade type I collagen (Col1a1R/R) to 21 days of hypoxia (hypoxia), some of which were allowed to recover for 42 days (recovery). Littermate wild-type mice (Col1a1+/+) were used as controls. In response to hypoxia, mean PA pressure (mPAP) increased in both mouse genotypes with no changes in cardiac output (CO) or PA inner diameter (ID); as a consequence, Z0 (mPAP/CO) increased by ∼100% in both genotypes (pZC, PWV and Pb/Pf did not change. However, with recovery, ZC and PWV decreased in the Col1a1+/+ mice and remained unchanged in the Col1a1R/R mice. Z0 decreased with recovery in both genotypes. Microcomputed tomography measurements of large PAs did not show evidence of stiffness changes as a function of hypoxia exposure or genotype. We conclude that hypoxia-induced PA collagen accumulation does not affect the pulsatile components of pulmonary hemodynamics but that excessive collagen accumulation does prevent normal hemodynamic recovery, which may have important consequences for right ventricular function

Targeting Liver Cancer: First Steps toward a miRacle?

In a recent issue of Cell, Iliopoulos and colleagues demonstrate a novel and targetable epigenetic amplification loop in hepatocellular carcinoma involving HNF4α, miR-124, IL6-R, Stat3, miR-24, and miR-629. These results establish microRNAs as novel players in early stages of hepatocarcinogenesis and as potential targets for the treatment of hepatocellular carcinoma

Variable-free exploration of stochastic models: a gene regulatory network example

Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these complex systems and (b) characterizing the dynamics of the observables. In a previous paper [13], we assumed that good observables were known a priori, and presented an equation-free approach to approximate coarse-grained quantities (i.e, effective drift and diffusion coefficients) that characterize the long-time behavior of the observables. Here we use diffusion maps [9] to extract appropriate observables ("reduction coordinates") in an automated fashion; these involve the leading eigenvectors of a weighted Laplacian on a graph constructed from network simulation data. We present lifting and restriction procedures for translating between physical variables and these data-based observables. These procedures allow us to perform equation-free coarse-grained, computations characterizing the long-term dynamics through the design and processing of short bursts of stochastic simulation initialized at appropriate values of the data-based observables.Comment: 26 pages, 9 figure

Performance of periodic EOM-CCSD for band gaps of inorganic semiconductors and insulators

We calculate the band gaps of 12 inorganic semiconductors and insulators composed of atoms from the first three rows of the periodic table using periodic equation-of-motion coupled-cluster theory with single and double excitations (EOM-CCSD). Our calculations are performed with atom-centered triple-zeta basis sets and up to 64 $k$-points in the Brillouin zone. We analyze the convergence behavior with respect to number of orbitals and number of $k$-points sampled, using composite corrections and extrapolations to produce our final values. When accounting for electron-phonon corrections to experimental band gaps, we find that EOM-CCSD has a mean signed error of $-0.12$ eV and a mean absolute error of $0.42$ eV; the largest outliers are C (error of $-0.93$ eV), BP ($-1.00$ eV), and LiH ($+0.78$ eV). Surprisingly, we find that the more affordable partitioned EOM-MP2 theory performs as well as EOM-CCSD.Comment: 6 pages, 5 figures, 1 tabl

Unintended Environmental Consequences of a Global Biofuels Program

Abstract and PDF report are also available on the MIT Joint Program on the Science and Policy of Global Change website (http://globalchange.mit.edu/).Biofuels are being promoted as an important part of the global energy mix to meet the climate change challenge. The environmental costs of biofuels produced with current technologies at small scales have been studied, but little research has been done on the consequences of an aggressive global biofuels program with advanced technologies using cellulosic feedstocks. Here, with simulation modeling, we explore two scenarios for cellulosic biofuels production and find that both could contribute substantially to future global-scale energy needs, but with significant unintended environmental consequences. As the land supply is squeezed to make way for vast areas of biofuels crops, the global landscape is defined by either the clearing of large swathes of natural forest, or the intensification of agricultural operations worldwide. The greenhouse gas implications of land-use conversion differ substantially between the two scenarios, but in both, numerous biodiversity hotspots suffer from serious habitat loss. Cellulosic biofuels may yet serve as a crucial wedge in the solution to the climate change problem, but must be deployed with caution so as not to jeopardize biodiversity, compromise ecosystems services, or undermine climate policy.This study received funding from the MIT Joint Program on the Science and Policy of Global Change, which is supported by a onsortium of government, industry and foundation sponsors