Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?

Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory---a framework that can treat thousands of atoms on firm theoretical ground---can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent work utilizing these methods to study biologically-relevant systems will be highlighted, and a vision for the future of density functional theory within molecular biology will be discussed

Sterile neutrino dark matter in warped extra dimensions

We consider a (long-lived) sterile neutrino dark matter scenario in a five dimensional (5D) warped extra dimension model where the fields can live in the bulk, which is partly motivated from the absence of the absolutely stable particles in a simple Randall-Sundrum model. The dominant production of the sterile neutrino can come from the decay of the radion (the scalar field representing the brane separation) around the electroweak scale. The suppressions of the 4D parameters due to the warp factor and the small wave function overlaps in the extra dimension help alleviate the exceeding fine-tunings typical for a sterile neutrino dark matter scenario in a 4D setup.Comment: Typos corrected and references adde

Cosmic Acceleration from Causal Backreaction with Recursive Nonlinearities

We revisit the causal backreaction paradigm, in which the need for Dark Energy is eliminated via the generation of an apparent cosmic acceleration from the causal flow of inhomogeneity information coming in towards each observer from distant structure-forming regions. This second-generation formalism incorporates "recursive nonlinearities": the process by which already-established metric perturbations will then act to slow down all future flows of inhomogeneity information. Here, the long-range effects of causal backreaction are now damped, weakening its impact for models that were previously best-fit cosmologies. Nevertheless, we find that causal backreaction can be recovered as a replacement for Dark Energy via the adoption of larger values for the dimensionless `strength' of the clustering evolution functions being modeled -- a change justified by the hierarchical nature of clustering and virialization in the universe, occurring on multiple cosmic length scales simultaneously. With this, and with one new model parameter representing the slowdown of clustering due to astrophysical feedback processes, an alternative cosmic concordance can once again be achieved for a matter-only universe in which the apparent acceleration is generated entirely by causal backreaction effects. One drawback is a new degeneracy which broadens our predicted range for the observed jerk parameter $j_{0}^{\mathrm{Obs}}$, thus removing what had appeared to be a clear signature for distinguishing causal backreaction from Cosmological Constant $\Lambda$CDM. As for the long-term fate of the universe, incorporating recursive nonlinearities appears to make the possibility of an `eternal' acceleration due to causal backreaction far less likely; though this does not take into account gravitational nonlinearities or the large-scale breakdown of cosmological isotropy, effects not easily modeled within this formalism.Comment: 53 pages, 7 figures, 3 tables. This paper is an advancement of previous research on Causal Backreaction; the earlier work is available at arXiv:1109.4686 and arXiv:1109.515

Jaw Rotation in Dysarthria Measured With a Single Electromagnetic Articulography Sensor

Purpose This study evaluated a novel method for characterizing jaw rotation using orientation data from a single electromagnetic articulography sensor. This method was optimized for clinical application, and a preliminary examination of clinical feasibility and value was undertaken. Method The computational adequacy of the single-sensor orientation method was evaluated through comparisons of jaw-rotation histories calculated from dual-sensor positional data for 16 typical talkers. The clinical feasibility and potential value of single-sensor jaw rotation were assessed through comparisons of 7 talkers with dysarthria and 19 typical talkers in connected speech. Results The single-sensor orientation method allowed faster and safer participant preparation, required lower data-acquisition costs, and generated less high-frequency artifact than the dual-sensor positional approach. All talkers with dysarthria, regardless of severity, demonstrated jaw-rotation histories with more numerous changes in movement direction and reduced smoothness compared with typical talkers. Conclusions Results suggest that the single-sensor orientation method for calculating jaw rotation during speech is clinically feasible. Given the preliminary nature of this study and the small participant pool, the clinical value of such measures remains an open question. Further work must address the potential confound of reduced speaking rate on movement smoothness

The small mixing angle θ13\theta_{13} and the lepton asymmetry

We present the correlation of low energy CP phases, both Dirac and Majorana, and the lepton asymmetry for the baryon asymmetry in the universe, with a certain class of Yukawa matrices that consist of two right-handed neutrinos and include one texture zero in themselves. For cases in which the amount of the lepton asymmetry $Y_L$ turns out to be proportional to $\theta_{13}^2$, we consider the relation between two types of CP phases and the relation of $Y_L$ versus the Jarlskog invariant or the amplitude of neutrinoless double beta decay as $\theta_{13}$ varies.Comment: 17 pages, 14 figures, information for figures added, version published in PR

v4: A small, but sensitive observable for heavy ion collisions

Higher order Fourier coefficients of the azimuthally dependent single particle spectra resulting from noncentral heavy ion collisions are investigated. For intermediate to large transverse momenta, these anisotropies are expected to become as large as 5 %, and should be clearly measurable. The physics content of these observables is discussed from two different extreme but complementary viewpoints, hydrodynamics and the geometric limit with extreme energy loss.Comment: as published: typos corrected, Fig. 3 slightly improved in numerics and presentatio

Transverse flow and hadro-chemistry in Au+Au collisions at \sqrt{s_{NN}}=200 GeV

We present a hydrodynamic assessment of preliminary particle spectra observed in Au+Au collisions at \sqrt{s_{NN}}=200 GeV. The hadronic part of the underlying equation of state is based on explicit conservation of (measured) particle ratios throughout the resonance gas stage after chemical freezeout by employing chemical potentials for stable mesons, nucleons and anti-nucleons. We find that under these conditions the data (in particular the proton spectra) favor a low freeze-out temperature of around 100 MeV. Furthermore we show that through inclusion of a moderate pre-hydrodynamic transverse flow field the shape of the spectra improves with respect to the data. The effect of the initial transverse boost on elliptic flow and the freeze-out geometry of the system is also elucidated.Comment: as published: more data included in Fig. 1, discussions throughout the text improved, 6 pages, 4 figure

Statistical mechanics of soft-boson phase transitions

The existence of structure on large (100 Mpc) scales, and limits to anisotropies in the cosmic microwave background radiation (CMBR), have imperiled models of structure formation based solely upon the standard cold dark matter scenario. Novel scenarios, which may be compatible with large scale structure and small CMBR anisotropies, invoke nonlinear fluctuations in the density appearing after recombination, accomplished via the use of late time phase transitions involving ultralow mass scalar bosons. Herein, the statistical mechanics are studied of such phase transitions in several models involving naturally ultralow mass pseudo-Nambu-Goldstone bosons (pNGB's). These models can exhibit several interesting effects at high temperature, which is believed to be the most general possibilities for pNGB's