Generating and probing a two-photon Fock state with a single atom in a cavity

A two-photon Fock state is prepared in a cavity sustaining a "source mode " and a "target mode", with a single circular Rydberg atom. In a third-order Raman process, the atom emits a photon in the target while scattering one photon from the source into the target. The final two-photon state is probed by measuring by Ramsey interferometry the cavity light shifts induced by the target field on the same atom. Extensions to other multi-photon processes and to a new type of micromaser are briefly discussed

Accelerating Cosmologies from Exponential Potentials

An exponential potential of the form $V\sim \exp(-2c \phi/M_p)$ arising from the hyperbolic or flux compactification of higher-dimensional theories is of interest for getting short periods of accelerated cosmological expansions. Using a similar potential but derived for the combined case of hyperbolic-flux compactification, we study the four-dimensional flat (and open) FLRW cosmologies and give analytic (and numerical) solutions with exponential behavior of scale factors. We show that, for the M-theory motivated potentials, the cosmic acceleration of the universe can be eternal if the spatial curvature of the 4d spacetime is negative, while the acceleration is only transient for a spatially flat universe. We also comment on the size of the internal space and its associated geometric bounds on massive Kaluza-Klein excitations.Comment: 17 pages, 6 figures; minor typos fixe

Quinto ciclo de seleção recorrente na população de milho sintético Elite NT em solos com baixo nível de nitrogênio.

Os programas de melhoramento, de modo geral, têm selecionado sob condições ótimas, mas, esta parece ser a estratégia ideal no desenvolvimento de cultivares para áreas sob estresses. O objetivo deste trabalho foi avaliar o quinto ciclo de seleção recorrente na população Sintético Elite NT e efetuar as estimativas de parâmetros genéticos sob duas condições ambientais:com estresse (N-) e sem estresse de nitrogênio (N+). Foram avaliadas em Sete Lagoas-MG, 64 famílias de meios irmãos tendo-se utilizado o delineamento em látice simples 8x8 e uma testemunha intercalar (BR106), selecionada sempre em condiçoes ótimas. Os resultados da análise individual e conjunta de variância mostraram diferenças altamente significativas para tratamento (P<0.001) e para a interação tratamentos x ambientes. A redução de produtividade de N+ para N-foi de 75% para a testemunha intercalar e 62%para as famílias selecionadas. A estimativa da variância genética aditiva no ambiente N- foi 5,5 vezes mais baixa que no ambiente N+ e o coeficiente de herdabilidade ao nível de médias foi 2,5 vezes mais alto que ao nível de plantas individuais. O ganho genético estimado em N-foi de 9,66g/planta enquanto que em N+ foi de 35,03 g/planta. Apesar das estimativas dos parâmetros genéticos serem mais baixas em N-, há suficiente variabilidade genética para continuidade com o programa de melhoramento.Made available in DSpace on 2018-06-06T01:08:39Z (GMT). No. of bitstreams: 1 Quintociclo.pdf: 5065935 bytes, checksum: 6625bb5fdd87301ddd3192a96aea13e9 (MD5) Previous issue date: 2003-09-10bitstream/item/54961/1/Quinto-ciclo.pd

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

Observing Supermassive Black Holes across cosmic time: from phenomenology to physics

In the last decade, a combination of high sensitivity, high spatial resolution observations and of coordinated multi-wavelength surveys has revolutionized our view of extra-galactic black hole (BH) astrophysics. We now know that supermassive black holes reside in the nuclei of almost every galaxy, grow over cosmological times by accreting matter, interact and merge with each other, and in the process liberate enormous amounts of energy that influence dramatically the evolution of the surrounding gas and stars, providing a powerful self-regulatory mechanism for galaxy formation. The different energetic phenomena associated to growing black holes and Active Galactic Nuclei (AGN), their cosmological evolution and the observational techniques used to unveil them, are the subject of this chapter. In particular, I will focus my attention on the connection between the theory of high-energy astrophysical processes giving rise to the observed emission in AGN, the observable imprints they leave at different wavelengths, and the methods used to uncover them in a statistically robust way. I will show how such a combined effort of theorists and observers have led us to unveil most of the SMBH growth over a large fraction of the age of the Universe, but that nagging uncertainties remain, preventing us from fully understating the exact role of black holes in the complex process of galaxy and large-scale structure formation, assembly and evolution.Comment: 46 pages, 21 figures. This review article appears as a chapter in the book: "Astrophysical Black Holes", Haardt, F., Gorini, V., Moschella, U and Treves A. (Eds), 2015, Springer International Publishing AG, Cha

Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study

The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt pathway. In this chapter we use the Wnt pathway to showcase current mathematical and statistical techniques that enable modelers to gain insight into (models of) gene regulation, and generate testable predictions. We introduce a range of modeling frameworks, but focus on ordinary differential equation (ODE) models since they remain the most widely used approach in systems biology and medicine and continue to offer great potential. We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine.Comment: Submitted to 'Systems Medicine' as a book chapte

Quinto ciclo de seleção recorrente na população de milho sintético Eite NT em solos com baixo nível de nitrogênio.

Os programas de melhoramento, de modo geral, têm selecionado sob condições ótimas, mas, esta parece ser a estratégia ideal no desenvolvimento de cultivares para áreas sob estresses. O objetivo deste trabalho foi avaliar o quinto ciclo de seleção recorrente na população Sintético Elite NT e efetuar as estimativas de parâmetros genéticos sob duas condições ambientais:com estresse (N-) e sem estresse de nitrogênio (N+). Foram avaliadas em Sete Lagoas-MG, 64 famílias de meios irmãos tendo-se utilizado o delineamento em látice simples 8x8 e uma testemunha intercalar (BR106), selecionada sempre em condiçoes ótimas. Os resultados da análise individual e conjunta de variância mostraram diferenças altamente significativas para tratamento (P<0.001) e para a interação tratamentos x ambientes. A redução de produtividade de N+ para N-foi de 75% para a testemunha intercalar e 62%para as famílias selecionadas. A estimativa da variância genética aditiva no ambiente N- foi 5,5 vezes mais baixa que no ambiente N+ e o coeficiente de herdabilidade ao nível de médias foi 2,5 vezes mais alto que ao nível de plantas individuais. O ganho genético estimado em N-foi de 9,66g/planta enquanto que em N+ foi de 35,03 g/planta. Apesar das estimativas dos parâmetros genéticos serem mais baixas em N-, há suficiente variabilidade genética para continuidade com o programa de melhoramento

Cystinosin, MPDU1, SWEETs and KDELR Belong to a Well-Defined Protein Family with Putative Function of Cargo Receptors Involved in Vesicle Trafficking

Classification of proteins into families based on remote homology often helps prediction of their biological function. Here we describe prediction of protein cargo receptors involved in vesicle formation and protein trafficking. Hidden Markov model profile-to-profile searches in protein databases using endoplasmic reticulum lumen protein retaining receptors (KDEL, Erd2) as query reveal a large and diverse family of proteins with seven transmembrane helices and common topology and, most likely, similar function. Their coding genes exist in all eukaryota and in several prokaryota. Some are responsible for metabolic diseases (cystinosis, congenital disorder of glycosylation), others are candidate genes for genetic disorders (cleft lip and palate, certain forms of cancer) or solute uptake and efflux (SWEETs) and many have not yet been assigned a function. Comparison with the properties of KDEL receptors suggests that the family members could be involved in protein trafficking and serve as cargo receptors. This prediction sheds new light on a range of biologically, medically and agronomically important proteins and could open the way to discovering the function of many genes not yet annotated. Experimental testing is suggested

Glucose Availability and AMP-Activated Protein Kinase Link Energy Metabolism and Innate Immunity in the Bovine Endometrium

Defences against the bacteria that usually infect the endometrium of postpartum cattle are impaired when there is metabolic energy stress, leading to endometritis and infertility. The endometrial response to bacteria depends on innate immunity, with recognition of pathogen-associated molecular patterns stimulating inflammation, characterised by secretion of interleukin (IL)-1β, IL-6 and IL-8. How metabolic stress impacts tissue responses to pathogens is unclear, but integration of energy metabolism and innate immunity means that stressing one system might affect the other. Here we tested the hypothesis that homeostatic pathways integrate energy metabolism and innate immunity in bovine endometrial tissue. Glucose deprivation reduced the secretion of IL-1β, IL-6 and IL-8 from ex vivo organ cultures of bovine endometrium challenged with the pathogen-associated molecular patterns lipopolysaccharide and bacterial lipopeptide. Endometrial inflammatory responses to lipopolysaccharide were also reduced by small molecules that activate or inhibit the intracellular sensor of energy, AMP-activated protein kinase (AMPK). However, inhibition of mammalian target of rapamycin, which is a more global metabolic sensor than AMPK, had little effect on inflammation. Similarly, endometrial inflammatory responses to lipopolysaccharide were not affected by insulin-like growth factor-1, which is an endocrine regulator of metabolism. Interestingly, the inflammatory responses to lipopolysaccharide increased endometrial glucose consumption and induced the Warburg effect, which could exacerbate deficits in glucose availability in the tissue. In conclusion, metabolic energy stress perturbed inflammatory responses to pathogen-associated molecular patterns in bovine endometrial tissue, and the most fundamental regulators of cellular energy, glucose availability and AMPK, had the greatest impact on innate immunity