Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.Comment: 17 pages, 8 figure

Hyperglycaemia does not increase perfusion deficits after focal cerebral ischaemia in male Wistar rats

Background: Hyperglycaemia is associated with a worse outcome in acute ischaemic stroke patients; yet the pathophysiological mechanisms of hyperglycaemia-induced damage are poorly understood. We hypothesised that hyperglycaemia at the time of stroke onset exacerbates ischaemic brain damage by increasing the severity of the blood flow deficit. Methods: Adult, male Wistar rats were randomly assigned to receive vehicle or glucose solutions prior to permanent middle cerebral artery occlusion. Cerebral blood flow was assessed semi-quantitatively either 1 h after middle cerebral artery occlusion using 99mTc-D, L-hexamethylpropyleneamine oxime (99mTc-HMPAO) autoradiography or, in a separate study, using quantitative pseudo-continuous arterial spin labelling for 4 h after middle cerebral artery occlusion. Diffusion weighted imaging was performed alongside pseudo-continuous arterial spin labelling and acute lesion volumes calculated from apparent diffusion coefficient maps. Infarct volume was measured at 24 h using rapid acquisition with refocused echoes T2-weighted magnetic resonance imaging. Results: Glucose administration had no effect on the severity of ischaemia when assessed by either 99mTc-HMPAO autoradiography or pseudo-continuous arterial spin labelling perfusion imaging. In comparison to the vehicle group, apparent diffusion coefficient–derived lesion volume 2–4 h post-middle cerebral artery occlusion and infarct volume 24 h post-middle cerebral artery occlusion were significantly greater in the glucose group. Conclusions: Hyperglycaemia increased acute lesion and infarct volumes but there was no evidence that the acute blood flow deficit was exacerbated. The data reinforce the conclusion that the detrimental effects of hyperglycaemia are rapid, and that treatment of post-stroke hyperglycaemia in the acute period is essential but the mechanisms of hyperglycaemia-induced harm remain unclear

Strong "quantum" chaos in the global ballooning mode spectrum of three-dimensional plasmas

The spectrum of ideal magnetohydrodynamic (MHD) pressure-driven (ballooning) modes in strongly nonaxisymmetric toroidal systems is difficult to analyze numerically owing to the singular nature of ideal MHD caused by lack of an inherent scale length. In this paper, ideal MHD is regularized by using a $k$-space cutoff, making the ray tracing for the WKB ballooning formalism a chaotic Hamiltonian billiard problem. The minimum width of the toroidal Fourier spectrum needed for resolving toroidally localized ballooning modes with a global eigenvalue code is estimated from the Weyl formula. This phase-space-volume estimation method is applied to two stellarator cases.Comment: 4 pages typeset, including 2 figures. Paper accepted for publication in Phys. Rev. Letter

Boosting Long-term Memory via Wakeful Rest: Intentional Rehearsal is not Necessary, Automatic Consolidation is Sufficient.

<div><p>People perform better on tests of delayed free recall if learning is followed immediately by a short wakeful rest than by a short period of sensory stimulation. Animal and human work suggests that wakeful resting provides optimal conditions for the consolidation of recently acquired memories. However, an alternative account cannot be ruled out, namely that wakeful resting provides optimal conditions for intentional rehearsal of recently acquired memories, thus driving superior memory. Here we utilised non-recallable words to examine whether wakeful rest boosts long-term memory, even when new memories could not be rehearsed intentionally during the wakeful rest delay. The probing of non-recallable words requires a recognition paradigm. Therefore, we first established, via Experiment 1, that the rest-induced boost in memory observed via free recall can be replicated in a recognition paradigm, using concrete nouns. In Experiment 2, participants heard 30 non-recallable non-words, presented as ‘foreign names in a bridge club abroad’ and then either rested wakefully or played a visual spot-the-difference game for 10 minutes. Retention was probed via recognition at two time points, 15 minutes and 7 days after presentation. As in Experiment 1, wakeful rest boosted recognition significantly, and this boost was maintained for at least 7 days. Our results indicate that the enhancement of memory via wakeful rest is <i>not</i> dependent upon intentional rehearsal of learned material during the rest period. We thus conclude that consolidation is <i>sufficient</i> for this rest-induced memory boost to emerge. We propose that wakeful resting allows for superior memory consolidation, resulting in stronger and/or more veridical representations of experienced events which can be detected via tests of free recall and recognition.</p></div

Electronic Correlations in Oligo-acene and -thiophene Organic Molecular Crystals

From first principles calculations we determine the Coulomb interaction between two holes on oligo-acene and -thiophene molecules in a crystal, as a function of the oligomer length. The relaxation of the molecular geometry in the presence of holes is found to be small. In contrast, the electronic polarization of the molecules that surround the charged oligomer, reduces the bare Coulomb repulsion between the holes by approximately a factor of two. In all cases the effective hole-hole repulsion is much larger than the calculated valence bandwidth, which implies that at high doping levels the properties of these organic semiconductors are determined by electron-electron correlations.Comment: 5 pages, 3 figure

Nonequilibrium statistical mechanics of shear flow: invariant quantities and current relations

In modeling nonequilibrium systems one usually starts with a definition of the microscopic dynamics, e.g., in terms of transition rates, and then derives the resulting macroscopic behavior. We address the inverse question for a class of steady state systems, namely complex fluids under continuous shear flow: how does an externally imposed shear current affect the microscopic dynamics of the fluid? The answer can be formulated in the form of invariant quantities, exact relations for the transition rates in the nonequilibrium steady state, as discussed in a recent letter [A. Baule and R. M. L. Evans, Phys. Rev. Lett. 101, 240601 (2008)]. Here, we present a more pedagogical account of the invariant quantities and the theory underlying them, known as the nonequilibrium counterpart to detailed balance (NCDB). Furthermore, we investigate the relationship between the transition rates and the shear current in the steady state. We show that a fluctuation relation of the Gallavotti-Cohen type holds for systems satisfying NCDB.Comment: 24 pages, 11 figure

Lattice-gas model for alkali-metal fullerides: face-centered-cubic structure

A lattice-gas model is suggested for describing the ordering phenomena in alkali-metal fullerides of face-centered-cubic structure assuming the electric charge of alkali ions residing in either octahedral or tetrahedral interstitial sites is completely screened by the first-neighbor C_60 molecules. This approximation allows us to derive an effective ion-ion interaction. The van der Waals interaction between the ion and C_60 molecule is characterized by introducing an additional energy at the tetrahedral sites. This model is investigated by using a three-sublattice mean-field approximation and a simple cluster-variation method. The analysis shows a large variety of phase diagrams when changing the site energy parameter.Comment: 10 twocolumn pages (REVTEX) including 12 PS figure