Self-Assembly and the Properties of Micro-Mesoporous Carbon

This study introduces a new approach for constructing atomistic models of nanoporous carbon by randomly distributing carbon atoms and pore volumes in a periodic box and then using empirical and ab initio molecular simulation tools to find the suitable energy-minimum structures. The models, consisting of 5000, 8000, 12000, and 64000 atoms, each at mass densities of 0.5, 0.75, and 1 g/cm3, were analyzed to determine their structural characteristics and relaxed pore size distribution. Surface analysis of the pore region revealed that sp atoms exist predominantly on surfaces and act as active sites for oxygen adsorption. We also investigated the electronic and vibrational properties of the models, and localized states near the Fermi level were found to be primarily situated at sp carbon atoms through which electrical conduction may occur. Additionally, the thermal conductivity was calculated using heat flux correlations and the Green-Kubo formula, and its dependence on pore geometry and connectivity was analyzed. The behavior of the mechanical elasticity moduli (Shear, Bulk, and Young's moduli) of nanoporous carbons at the densities of interest was discussed.

Ab Initio Simulation of Amorphous Graphite

An amorphous graphite material has been predicted from molecular dynamics simulation using ab initio methods. Carbon materials reveal a strong proclivity to convert into a sp^{2} network and then layer at temperatures near 3000 K within a density range of ca. 2.2-2.8  g/cm^{3}. Each layer of amorphous graphite is a monolayer of amorphous graphene including pentagons and heptagons in addition to hexagons, and the planes are separated by about 3.1  Å. The layering transition has been studied using various structural and dynamical analyses. The transition is unique as one of partial ordering (long range order of planes and galleries, but topological disorder in the planes). The planes are quite flat, even though monolayer amorphous graphene puckers near pentagonal sites. Interplane cohesion is due partly to non-Van der Waals interactions. The structural disorder has been studied closely, especially the consequences of disorder to electronic transport. It is expected that the transition elucidated here may be salient to other layered materials.

The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts

PARN is one of several deadenylase enzymes present in mammalian cells, and as such the contribution it makes to the regulation of gene expression is unclear. To address this, we performed global mRNA expression and half-life analysis on mouse myoblasts depleted of PARN. PARN knockdown resulted in the stabilization of 40 mRNAs, including that encoding the mRNA decay factor ZFP36L2. Additional experiments demonstrated that PARN knockdown induced an increase in Zfp36l2 poly(A) tail length as well as increased translation. The elements responsible for PARN-dependent regulation lie within the 3′ UTR of the mRNA. Surprisingly, changes in mRNA stability showed an inverse correlation with mRNA abundance; stabilized transcripts showed either no change or a decrease in mRNA abundance. Moreover, we found that stabilized mRNAs had reduced accumulation of pre–mRNA, consistent with lower transcription rates. This presents compelling evidence for the coupling of mRNA decay and transcription to buffer mRNA abundances. Although PARN knockdown altered decay of relatively few mRNAs, there was a much larger effect on global gene expression. Many of the mRNAs whose abundance was reduced by PARN knockdown encode factors required for cell migration and adhesion. The biological relevance of this observation was demonstrated by the fact that PARN KD cells migrate faster in wound-healing assays. Collectively, these data indicate that PARN modulates decay of a defined set of mRNAs in mammalian cells and implicate this deadenylase in coordinating control of genes required for cell movement.

Almost all cellular mRNAs terminate in a 3′ poly(A) tail, the removal of which can induce both translational silencing and mRNA decay. Mammalian cells encode many poly(A)-specific exoribonucleases, but their individual roles are poorly understood. Here, we undertook an analysis of the role of PARN deadenylase in mouse myoblasts using global measurements of mRNA decay rates. Our results reveal that a discrete set of mRNAs exhibit altered mRNA decay as a result of PARN depletion and that stabilization is associated with increased poly(A) tail length and translation efficiency. We determined that stabilization of mRNAs does not generally result in their increased abundance, supporting the idea that mRNA decay is coupled to transcription. Importantly, knockdown of PARN has wide ranging effects on gene expression that specifically impact the extracellular matrix and cell migration.