Polyethylene under tensile load: strain energy storage and breaking of linear and knotted alkanes probed by first-principles molecular dynamics calculations

The mechanical resistance of a polyethylene strand subject to tension and the way its properties are affected by the presence of a knot is studied using first-principles molecular dynamics calculations. The distribution of strain energy for the knotted chains has a well-defined shape that is very different from the one found in the linear case. The presence of a knot significantly weakens the chain in which it is tied. Chain rupture invariably occurs just outside the entrance to the knot, as is the case for a macroscopic rope.Comment: 8 pages, 11 figures, to appear on J. Chem. Phy

Transcriptional inhibition of type I collagen gene expression in scleroderma fibroblasts by the antineoplastic drug ecteinascidin 743.

We previously showed that COL1A1 expression is up-regulated at the transcriptional level in systemic sclerosis (SSc) fibroblasts and that the CCAAT-binding factor (CBF) is involved in this increased expression. Ecteinascidin 743 (ET-743) is a chemotherapeutic agent that binds with sequence specificity to the minor groove of DNA and inhibits CBF-mediated transcriptional activation of numerous genes. Therefore, we examined the effects of ET-743 on the increased COL1A1 expression in SSc fibroblasts. The drug caused a potent and dose-dependent inhibition of type I collagen biosynthesis, which reached 70-90% at 700 pM without affecting cell viability. The same drug concentration caused 60-80% reduction in COL1A1 mRNA levels. The stability of the corresponding transcripts was not affected. In vitro nuclear transcription assays demonstrated a 54% down-regulation of COL1A1 transcription. Transient transfections with COL1A1 promoter constructs containing the specific CBF binding sequence into SSc cells previously treated with 700 pM ET-743 failed to show an effect on COL1A1 promoter activity. Furthermore, ET-743 did not affect the binding of CBF or Sp1 transcription factors to their cognate COL1A1 elements. However, treatment with 700 pM ET-743 of stably transfected NIH 3T3 cells expressing a human type II procollagen gene under the control of the human COL1A1 promoter caused a greater than 50% reduction in the production of type II procollagen and a similar decrease in the corresponding type II procollagen transcripts. These results indicate that ET-743 is a potent inhibitor of COL1A1 transcription. However, this effect cannot be explained by a direct effect on CBF binding to the COL1A1 promoter. Although the exact mechanisms responsible for the transcriptional inhibition of COL1A1 by ET-743 are not apparent, our observations suggest that the drug may be an effective agent to decrease collagen overproduction in SSc and other fibrotic diseases

Entropy-based measure of structural order in water

We analyze the nature of the structural order established in liquid TIP4P water in the framework provided by the multi-particle correlation expansion of the statistical entropy. Different regimes are mapped onto the phase diagram of the model upon resolving the pair entropy into its translational and orientational components. These parameters are used to quantify the relative amounts of positional and angular order in a given thermodynamic state, thus allowing a structurally unbiased definition of low-density and high-density water. As a result, the structurally anomalous region within which both types of order are simultaneously disrupted by an increase of pressure at constant temperature is clearly identified through extensive molecular-dynamics simulations.Comment: 5 pages, 2 figures, to appear in Phys. Rev. E (Rapid Communication

Effects of disorder on the optical gap of (Zn,Mg)(S,Se)

The electronic properties and optical gap of (Zn,Mg)(S,Se) wide-gap solid solutions are studied using ab initio techniques and starting from the previously determined atomistic structure of the alloy. Compositional disorder is shown to close the gap substantially with respect to the predictions of the virtual-crystal approximation. The bowing of the fundamental gap versus composition predicted by our calculations is in very good agreement with experiments available for the Zn(S,Se) pseudobinary alloy. At temperatures typical of molecular-beam epitaxy growth, the quaternary alloy displays a rather large amount of short-range order whose effect is to slightly but unmistakably open the gap. Our results agree well with recent experimental data for the quaternary alloy. (C) 1999 American Institute of Physics. [S0003-6951(99)02044-6]

Structure and stability of graphene nanoribbons in oxygen, carbon dioxide, water, and ammonia

We determine, by means of density functional theory, the stability and the structure of graphene nanoribbon (GNR) edges in presence of molecules such as oxygen, water, ammonia, and carbon dioxide. As in the case of hydrogen-terminated nanoribbons, we find that the most stable armchair and zigzag configurations are characterized by a non-metallic/non-magnetic nature, and are compatible with Clar's sextet rules, well known in organic chemistry. In particular, we predict that, at thermodynamic equilibrium, neutral GNRs in oxygen-rich atmosphere should preferentially be along the armchair direction, while water-saturated GNRs should present zigzag edges. Our results promise to be particularly useful to GNRs synthesis, since the most recent and advanced experimental routes are most effective in water and/or ammonia-containing solutions.Comment: accepted for publication in PR