Functional renormalization group in the broken symmetry phase: momentum dependence and two-parameter scaling of the self-energy

We include spontaneous symmetry breaking into the functional renormalization group (RG) equations for the irreducible vertices of Ginzburg-Landau theories by augmenting these equations by a flow equation for the order parameter, which is determined from the requirement that at each RG step the vertex with one external leg vanishes identically. Using this strategy, we propose a simple truncation of the coupled RG flow equations for the vertices in the broken symmetry phase of the Ising universality class in D dimensions. Our truncation yields the full momentum dependence of the self-energy Sigma (k) and interpolates between lowest order perturbation theory at large momenta k and the critical scaling regime for small k. Close to the critical point, our method yields the self-energy in the scaling form Sigma (k) = k_c^2 sigma^{-} (k | xi, k / k_c), where xi is the order parameter correlation length, k_c is the Ginzburg scale, and sigma^{-} (x, y) is a dimensionless two-parameter scaling function for the broken symmetry phase which we explicitly calculate within our truncation.Comment: 9 pages, 4 figures, puplished versio

Non-perturbative renormalization-group approach to zero-temperature Bose systems

We use a non-perturbative renormalization-group technique to study interacting bosons at zero temperature. Our approach reveals the instability of the Bogoliubov fixed point when $d\leq 3$ and yields the exact infrared behavior in all dimensions $d>1$ within a rather simple theoretical framework. It also enables to compute the low-energy properties in terms of the parameters of a microscopic model. In one-dimension and for not too strong interactions, it yields a good picture of the Luttinger-liquid behavior of the superfluid phase.Comment: v1) 6 pages, 8 figures; v2) added references; v3) corrected typo

Infrared behavior of interacting bosons at zero temperature

We review the infrared behavior of interacting bosons at zero temperature. After a brief discussion of the Bogoliubov approximation and the breakdown of perturbation theory due to infrared divergences, we present two approaches that are free of infrared divergences -- Popov's hydrodynamic theory and the non-perturbative renormalization group -- and allow us to obtain the exact infrared behavior of the correlation functions. We also point out the connection between the infrared behavior in the superfluid phase and the critical behavior at the superfluid--Mott-insulator transition in the Bose-Hubbard model.Comment: 8 pages, 4 figures. Proceedings of the 19th International Laser Physics Workshop, LPHYS'10 (Foz do Iguacu, Brazil, July 5-9, 2010

Native structure-based modeling and simulation of biomolecular systems per mouse click

Background Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization. Results Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins. Conclusions We present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research

The scope of language contact as a constraint factor in language change: The periphrasis haber de plus infinitive in a corpus of language immediacy in modern Spanish

In this work an empirical study grounded in the principles and methods of the comparative variationist framework is conducted to measure the scope of language contact as a factor constraining some potentially diverging uses of a Spanish verbal periphrasis that has undergone a sharp decline over the last century (haber de plus infinitive). The analysis is based on three independent samples of text that correspond to three dialectal areas of peninsular Spanish (monolingual zones, Catalan-speaking linguistic territories and the north-western linguistic area). These samples, extracted from a corpus made up of texts of communicative immediacy from the 19th and the first half of the 20th centuries, confirm the existence of a certain linguistic convergence in the expressive habits of the speakers in the bilingual communities. In each region, however, the outcomes are different, due to parallel differences in the structural position of the periphrasis in each language. However, a thorough analysis of the variable context that surrounds the periphrasis shows that the observed differences do not affect the essence of the underlying grammar of this variant, whose decline (which favours tener que plus infinitive and becomes faster as the 20th century advances) is constrained by identical linguistic and extralinguistic conditioning factors in all the dialectal areas

Detection of peptide-based nanoparticles in blood plasma by ELISA

Aims: The aim of the current study was to develop a method to detect peptide-linked nanoparticles in blood plasma. Materials & Methods: A convenient enzyme linked immunosorbent assay (ELISA) was developed for the detection of peptides functionalized with biotin and fluorescein groups. As a proof of principle, polymerized pentafluorophenyl methacrylate nanoparticles linked to biotin-carboxyfluorescein labeled peptides were intravenously injected in Wistar rats. Serial blood plasma samples were analyzed by ELISA and by liquid chromatography mass spectrometry (LC/MS) technology. Results: The ELISA based method for the detection of FITC labeled peptides had a detection limit of 1 ng/mL. We were able to accurately measure peptides bound to pentafluorophenyl meth-acrylate nanoparticles in blood plasma of rats, and similar results were obtained by LC/MS. Conclusions: We detected FITC-labeled peptides on pentafluorophenyl methacrylate nanoparticles after injection in vivo. This method can be extended to detect nanoparticles with different chemical compositions

Gene-gene Interaction Analyses for Atrial Fibrillation

Atrial fibrillation (AF) is a heritable disease that affects more than thirty million individuals worldwide. Extensive efforts have been devoted to the study of genetic determinants of AF. The objective of our study is to examine the effect of gene-gene interaction on AF susceptibility. We performed a large-scale association analysis of gene-gene interactions with AF in 8,173 AF cases, and 65,237 AF-free referents collected from 15 studies for discovery. We examined putative interactions between genome-wide SNPs and 17 known AF-related SNPs. The top interactions were then tested for association in a

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death. Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups. To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery

Potential for pancreatic maturation of differentiating human embryonic stem cells is sensitive to the specific pathway of definitive endoderm commitment

This study provides a detailed experimental and mathematical analysis of the impact of the initial pathway of definitive endoderm (DE) induction on later stages of pancreatic maturation. Human embryonic stem cells (hESCs) were induced to insulin-producing cells following a directed-differentiation approach. DE was induced following four alternative pathway modulations. DE derivatives obtained from these alternate pathways were subjected to pancreatic progenitor (PP) induction and maturation and analyzed at each stage. Results indicate that late stage maturation is influenced by the initial pathway of DE commitment. Detailed quantitative analysis revealed WNT3A and FGF2 induced DE cells showed highest expression of insulin, are closely aligned in gene expression patterning and have a closer resemblance to pancreatic organogenesis. Conversely, BMP4 at DE induction gave most divergent differentiation dynamics with lowest insulin upregulation, but highest glucagon upregulation. Additionally, we have concluded that early analysis of PP markers is indicative of its potential for pancreatic maturation. © 2014 Jaramillo et al