Rationalizing accurate structure prediction in the meta-GGA SCAN functional

The ability of first-principles computational methods to reproduce ground-state crystal structure selection is key to their application in the discovery of new materials, and yet presents a formidable challenge due to the low-energy scale of the problem and lack of systematic error cancellation. The recently developed Strongly Constrained and Appropriately Normed (SCAN) functional is notable for accurately calculating physical properties such as formation energies and in particular, correctly predicting ground-state structures. Here, we attempt to rationalize the improved structure prediction accuracy in SCAN by investigating the relationship between preferred coordination environments, the description of attractive van der Waals (vdW) interactions, and the overall ground-state prediction in bulk main-group solids. We observe a systematic undercoordination error in the traditional Perdew, Burke, and Ernzerhof (PBE) functional which is not present in SCAN results and find that semiempirical dispersion corrections in the form of PBE+D3 fail to correct this error in a consistent or physical manner. We conclude that the medium-range vdW interaction is correctly parametrized in SCAN and yields meaningful relative energies between coordination environments

Landau-Zener-Stuckelberg interference in a multi-anticrossing system

We propose a universal analytical method to study the dynamics of a multi-anticrossing system subject to driving by one single large-amplitude triangle pulse, within its time scales smaller than the dephasing time. Our approach can explain the main features of the Landau-Zener-Stuckelberg interference patterns recently observed in a tripartite system [Nature Communications 1:51 (2010)]. In particular, we focus on the effects of the size of anticrossings on interference and compare the calculated interference patterns with numerical simulations. In addition, Fourier transform of the patterns can extract information on the energy level spectrum.Comment: 6 pages, 5 figure

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs.

Although recent studies have indicated roles of long non-coding RNAs (lncRNAs) in physiological aspects of cell-type determination and tissue homeostasis, their potential involvement in regulated gene transcription programs remains rather poorly understood. The androgen receptor regulates a large repertoire of genes central to the identity and behaviour of prostate cancer cells, and functions in a ligand-independent fashion in many prostate cancers when they become hormone refractory after initial androgen deprivation therapy. Here we report that two lncRNAs highly overexpressed in aggressive prostate cancer, PRNCR1 (also known as PCAT8) and PCGEM1, bind successively to the androgen receptor and strongly enhance both ligand-dependent and ligand-independent androgen-receptor-mediated gene activation programs and proliferation in prostate cancer cells. Binding of PRNCR1 to the carboxy-terminally acetylated androgen receptor on enhancers and its association with DOT1L appear to be required for recruitment of the second lncRNA, PCGEM1, to the androgen receptor amino terminus that is methylated by DOT1L. Unexpectedly, recognition of specific protein marks by PCGEM1-recruited pygopus 2 PHD domain enhances selective looping of androgen-receptor-bound enhancers to target gene promoters in these cells. In 'resistant' prostate cancer cells, these overexpressed lncRNAs can interact with, and are required for, the robust activation of both truncated and full-length androgen receptor, causing ligand-independent activation of the androgen receptor transcriptional program and cell proliferation. Conditionally expressed short hairpin RNA targeting these lncRNAs in castration-resistant prostate cancer cell lines strongly suppressed tumour xenograft growth in vivo. Together, these results indicate that these overexpressed lncRNAs can potentially serve as a required component of castration-resistance in prostatic tumours

Heavy-ion Physics at a Fixed-Target Experiment Using the LHC Proton and Lead Beams (AFTER@LHC): Feasibility Studies for Quarkonium and Drell-Yan Production

We outline the case for heavy-ion-physics studies using the multi-TeV lead LHC beams in the fixed-target mode. After a brief contextual reminder, we detail the possible contributions of AFTER@LHC to heavy-ion physics with a specific emphasis on quarkonia. We then present performance simulations for a selection of observables. These show that $\Upsilon(nS)$, $J/\psi$ and $\psi(2S)$ production in heavy-ion collisions can be studied in new energy and rapidity domains with the LHCb and ALICE detectors. We also discuss the relevance to analyse the Drell-Yan pair production in asymmetric nucleus-nucleus collisions to study the factorisation of the nuclear modification of partonic densities and of further quarkonia to restore their status of golden probes of the quark-gluon plasma formation.Comment: 18 pages, 7 figure

Electrospun nanosized cellulose fibers using ionic liquids at room temperature

Aiming at replacing the noxious solvents commonly employed, ionic-liquid-based solvents have been recently explored as novel non-volatile and non-flammable media for the electrospinning of polymers. In this work, nanosized and biodegradable cellulose fibers were obtained by electrospinning at room temperature using a pure ionic liquid or a binary mixture of two selected ionic liquids. The electrospinning of 8 wt% cellulose in 1-ethyl-3-methylimidazolium acetate medium (a low viscosity and room temperature ionic liquid capable of efficiently dissolving cellulose) showed to produce electrospun fibers with average diameters within (470 ± 110) nm. With the goal of tailoring the surface tension of the spinning dope, a surface active ionic liquid was further added in a 0.10 : 0.90 mole fraction ratio. Electrospun cellulose fibers from the binary mixture composed of 1-ethyl-3-methylimidazolium acetate and 1-decyl-3-methylimidazolium chloride ionic liquids presented average diameters within (120 ± 55) nm. Scanning electron microscopy, X-ray diffraction analysis, nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, and thermogravimetric assays were used as core methods to evaluate the structural integrity, morphology and crystallinity of the raw, electrospun, and regenerated samples of cellulose. Moreover, the photoluminescence spectra of both raw and electrospun fibers were acquired, and compared, indicating that the cellulose emitting centers are not affected by the dissolution of cellulose in ionic liquids. Finally, the use of non-volatile solvents in electrospinning coupled to a water coagulation bath allows the recovery of the ionic fluid, and represents a step forward into the search of environmentally friendly alternatives to the conventional approaches

Random attractors for degenerate stochastic partial differential equations

We prove the existence of random attractors for a large class of degenerate stochastic partial differential equations (SPDE) perturbed by joint additive Wiener noise and real, linear multiplicative Brownian noise, assuming only the standard assumptions of the variational approach to SPDE with compact embeddings in the associated Gelfand triple. This allows spatially much rougher noise than in known results. The approach is based on a construction of strictly stationary solutions to related strongly monotone SPDE. Applications include stochastic generalized porous media equations, stochastic generalized degenerate p-Laplace equations and stochastic reaction diffusion equations. For perturbed, degenerate p-Laplace equations we prove that the deterministic, infinite dimensional attractor collapses to a single random point if enough noise is added.Comment: 34 pages; The final publication is available at http://link.springer.com/article/10.1007%2Fs10884-013-9294-

Green functions for generalized point interactions in 1D: A scattering approach

Recently, general point interactions in one dimension has been used to model a large number of different phenomena in quantum mechanics. Such potentials, however, requires some sort of regularization to lead to meaningful results. The usual ways to do so rely on technicalities which may hide important physical aspects of the problem. In this work we present a new method to calculate the exact Green functions for general point interactions in 1D. Our approach differs from previous ones because it is based only on physical quantities, namely, the scattering coefficients, $R$ and $T$, to construct $G$. Renormalization or particular mathematical prescriptions are not invoked. The simple formulation of the method makes it easy to extend to more general contexts, such as for lattices of $N$ general point interactions; on a line; on a half-line; under periodic boundary conditions; and confined in a box.Comment: Revtex, 9 pages, 3 EPS figures. To be published in PR

Terahertz underdamped vibrational motion governs protein-ligand binding in solution

Low-frequency collective vibrational modes in proteins have been proposed as being responsible for efficiently directing biochemical reactions and biological energy transport. However, evidence of the existence of delocalized vibrational modes is scarce and proof of their involvement in biological function absent. Here we apply extremely sensitive femtosecond optical Kerr-effect spectroscopy to study the depolarized Raman spectra of lysozyme and its complex with the inhibitor triacetylchitotriose in solution. Underdamped delocalized vibrational modes in the terahertz frequency domain are identified and shown to blue-shift and strengthen upon inhibitor binding. This demonstrates that the ligand-binding coordinate in proteins is underdamped and not simply solvent-controlled as previously assumed. The presence of such underdamped delocalized modes in proteins may have significant implications for the understanding of the efficiency of ligand binding and protein–molecule interactions, and has wider implications for biochemical reactivity and biological function