Evaluating force field accuracy with long-time simulations of a tryptophan zipper peptide

We have combined a custom implementation of the fast multiple-time-stepping LN integrator with parallel tempering to explore folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this algorithm to the synthetic {\beta}-hairpin trpzip2 and one of its sequence variants W2W9. Each simulation consisted of over 12 {\mu}s of aggregated virtual time. Several measures of folding behavior showed convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the electrostatic interaction of tryptophan sidechains is responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 {\phi} and {\psi} dihedral energies and implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.Comment: 10 pages, 11 figures, submitted to the Journal of Chemical Physics on June 28, 201

FMRI Clustering and False Positive Rates

Recently, Eklund et al. (2016) analyzed clustering methods in standard FMRI packages: AFNI (which we maintain), FSL, and SPM [1]. They claimed: 1) false positive rates (FPRs) in traditional approaches are greatly inflated, questioning the validity of "countless published fMRI studies"; 2) nonparametric methods produce valid, but slightly conservative, FPRs; 3) a common flawed assumption is that the spatial autocorrelation function (ACF) of FMRI noise is Gaussian-shaped; and 4) a 15-year-old bug in AFNI's 3dClustSim significantly contributed to producing "particularly high" FPRs compared to other software. We repeated simulations from [1] (Beijing-Zang data [2], see [3]), and comment on each point briefly.Comment: 3 pages, 1 figure. A Letter accepted in PNA

Reply to ``Comment on `Insulating Behavior of λ\lambda-DNA on the Micron Scale' "

In our experiment, we found that the resistance of vacuum-dried $\lambda$-DNA exceeds $10^{14} \Omega$ at 295 K. Bechhoefer and Sen have raised a number of objections to our conclusion. We provide counter arguments to support our original conclusion.Comment: 1 page reply to comment, 1 figur

Experimental Evaluation of Psychophysical Distortion Metrics for JPEG-Encoded Images

Two experiments for evaluating psychophysical distortion metrics for JPEG-encoded images are described. The first is a threshold experiment, in which subjects determined the bit rate or level of distortion at which distortion was just noticeable. The second is a suprathreshold experiment in which subjects ranked image blocks according to perceived distortion. The results of these experiments were used to determine the predictive value of a number of computer image distortion metrics. It was found that mean-square-error is not a good predictor of distortion thresholds or suprathreshold perceived distortion. Some simple pointwise measures were in good agreement with psychophysical data; other more computationally intensive metrics involving spatial properties of the human visual system gave mixed results. It was determined that mean intensity, which is not accounted for in the JPEG algorithm, plays a significant role in perceived distortion

Small Energy Scale for Mixed-Valent Uranium Materials

We investigate a two-channel Anderson impurity model with a $5f^1$ magnetic and a $5f^2$ quadrupolar ground doublet, and a $5f^2$ excited triplet. Using the numerical renormalization group method, we find a crossover to a non-Fermi liquid state below a temperature $T^*$ varying as the $5f^2$ triplet-doublet splitting to the 7/2 power. To within numerical accuracy, the non-linear magnetic susceptibility and the $5f^1$ contribution to the linear susceptibility are given by universal one-parameter scaling functions. These results may explain UBe$_{13}$ as mixed valent with a small crossover scale $T^*$.Comment: 4 pages, 3 figures, REVTeX, to appear in Phys. Rev. Let

Unlinked Mendelian inheritance of red and black pigmentation in snakes: Implications for Batesian mimicry

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/1/evo12902_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/2/evo12902.pd

Petrogenesis of plagiogranites in the Muslim Bagh Ophiolite, Pakistan: implications for the generation of Archaean continental crust

High-SiO2 rocks referred to as oceanic plagiogranites are common within the crustal sequences of ophiolites; however, their mode of petrogenesis is controversial with both late-stage fractional crystallization and partial melting models being proposed. Here, we present new whole-rock data from plagiogranitic dyke-like bodies and lenses from the lower and middle sections of the sheeted dyke complex of the Cretaceous Muslim Bagh Ophiolite, northwestern Pakistan. The plagiogranites have similar geochemical signatures that are inconsistent with them being the fractionation products of the mafic units of the Muslim Bagh Ophiolite. However, the plagiogranites all display very low TiO2 contents (<0.4 wt%), implying that they formed by partial melting of mafic rocks. Melt modelling of a crustal gabbro from the Muslim Bagh Ophiolite shows that the trace-element signature of the plagiogranites can be replicated by 5–10% melting of a crustal hornblende gabbro with amphibole as a residual phase, resulting in a concave-up middle rare Earth element pattern. Compositional similarities between the Muslim Bagh Ophiolite plagiogranites and Archaean TTG (trondhjemite–tonalite–granodiorite) has implications for the generation of juvenile Archaean continental crust. As the Muslim Bagh Ophiolite was derived in a supra-subduction zone, it is suggested that some Archaean TTG may have been derived from melting of mafic upper crust in early subduction-like settings. However, due to the small volume of Muslim Bagh Ophiolite plagiogranites, it is inferred that they can be instructive on the petrogenesis of some, but not all, Archaean TTG

Enhancing the management of anorexia of ageing to counteract malnutrition : are physical activity guidelines optimal?

Funding Information: NJC and SERL receive funding from by The National Institute for Health Research (NIHR). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.Peer reviewedPublisher PD