Specific protein-protein binding in many-component mixtures of proteins

Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein, specific binding in many component mixtures is studied. It is found to be a demanding function in the sense that it demands that the binding sites of the proteins be encoded by long sequences of bits, and the requirement for specific binding then strongly constrains these sequences. This is quantified by the capacity of proteins of a given size (sequence length), which is the maximum number of specific-binding interactions possible in a mixture. This calculation of the maximum number possible is in the same spirit as the work of Shannon and others on the maximum rate of communication through noisy channels.Comment: 13 pages, 3 figures (changes for v2 mainly notational - to be more in line with notation in information theory literature

Direct Observation of Site-specific Valence Electronic Structure at Interface: SiO2/Si Interface

Atom specific valence electronic structures at interface are elucidated successfully using soft x-ray absorption and emission spectroscopy. In order to demonstrate the versatility of this method, we investigated SiO2/Si interface as a prototype and directly observed valence electronic states projected at the particular atoms of the SiO2/Si interface; local electronic structure strongly depends on the chemical states of each atom. In addition we compared the experimental results with first-principle calculations, which quantitatively revealed the interfacial properties in atomic-scale.Comment: 4 pages, 3 figure

All Teleportation and Dense Coding Schemes

We establish a one-to-one correspondence between (1) quantum teleportation schemes, (2) dense coding schemes, (3) orthonormal bases of maximally entangled vectors, (4) orthonormal bases of unitary operators with respect to the Hilbert-Schmidt scalar product, and (5) depolarizing operations, whose Kraus operators can be chosen to be unitary. The teleportation and dense coding schemes are assumed to be ``tight'' in the sense that all Hilbert spaces involved have the same finite dimension d, and the classical channel involved distinguishes d^2 signals. A general construction procedure for orthonormal bases of unitaries, involving Latin Squares and complex Hadamard Matrices is also presented.Comment: 21 pages, LaTe

Doppler cooling and trapping on forbidden transitions

Ultracold atoms at temperatures close to the recoil limit have been achieved by extending Doppler cooling to forbidden transitions. A cloud of ^40Ca atoms has been cooled and trapped to a temperature as low as 6 \mu K by operating a magneto-optical trap on the spin-forbidden intercombination transition. Quenching the long-lived excited state with an additional laser enhanced the scattering rate by a factor of 15, while a high selectivity in velocity was preserved. With this method more than 10% of pre-cooled atoms from a standard magneto-optical trap have been transferred to the ultracold trap. Monte-Carlo simulations of the cooling process are in good agreement with the experiments

What's the point of knowing how?

Why is it useful to talk and think about knowledge-how? Using Edward Craig’s discussion of the function of the concepts of knowledge and knowledge-how as a jumping off point, this paper argues that considering this question can offer us new angles on the debate about knowledge-how. We consider two candidate functions for the concept of knowledge-how: pooling capacities, and mutual reliance. Craig makes the case for pooling capacities, which connects knowledge-how to our need to pool practical capacities. I argue that the evidence is much more equivocal. My suggested diagnosis is that the concept of knowledge-how plays both functions, meaning that the concept of knowledge-how is inconsistent, and that the debate about knowledge-how is at least partly a metalinguistic negotiation. In closing, I suggest a way to revise the philosophical concept of knowledge how

Intimin, tir, and Shiga toxin 1 do not influence enteropathogenic responses to Shiga toxin-producing Escherichia coli in bovine ligated intestinal loops

Shiga toxin-producing Escherchia coli (STEC) comprises a group of attaching and effacing (A/E) enteric pathogens of animals and humans. Natural and experimental infection of calves with STEC may result in acute enteritis or subclinical infection, depending on serotype- and host-specific factors. To quantify intestinal secretory and inflammatory responses to STEC in the bovine intestine, serotypes that are associated with human disease (O103:H2 and O157:H7) were introduced into ligated mid-ileal loops in gnotobiotic and conventional calves, and fluid accumulation and recruitment of radiolabeled neutrophils were measured after 12 h. STEC serotype O103:H2, but not serotype O157:H7, elicited strong enteropathogenic responses. To determine if the inflammatory response to STEC O103:H2 in calves requires Shiga toxin 1 or intimate bacterial attachment to the intestinal epithelium, defined mutations were made in the stx1, eae, and tir genes. Our data indicate that some STEC induce intestinal inflammatory responses in calves by a mechanism that is independent of A/E-lesion formation, intimin, or Shiga toxin 1. This may have implications for strategies to reduce STEC carriage in cattle

Application of a stochastic modeling to evaluate tuberculosis onset in patients treated with tumor necrosis factor inhibitors

In this manuscript we apply stochastic modeling to investigate the risk of reactivation of latent mycobacterial infections in patients undergoing treatment with tumor necrosis factor inhibitors. First, we review the perspective proposed by one of the authors in a previous work and which consists in predicting the occurrence of reactivation of latent tuberculosis infection or newly acquired tuberculosis during treatment; this is based on variational procedures on a simple set of parameters (e.g. rate of reactivation of a latent infection). Then, we develop a full analytical study of this approach through a Markov chain analysis and we find an exact solution for the temporal evolution of the number of cases of tuberculosis infection (re)activation. The analytical solution is compared with Monte Carlo simulations and with experimental data, showing overall excellent agreement. The generality of this theoretical framework allows to investigate also the case of non-tuberculous mycobacteria infections; in particular, we show that reactivation in that context plays a minor role. This may suggest that, while the screening for tuberculous is necessary prior to initiating biologics, when considering non-tuberculous mycobacteria only a watchful monitoring during the treatment is recommended. The framework outlined in this paper is quite general and could be extremely promising in further researches on drug-related adverse events.Comment: 26 pages, 7 figure

Spatial coherence and density correlations of trapped Bose gases

We study first and second order coherence of trapped dilute Bose gases using appropriate correlation functions. Special attention is given to the discussion of second order or density correlations. Except for a small region around the surface of a Bose-Einstein condensate the correlations can be accurately described as those of a locally homogeneous gas with a spatially varying chemical potential. The degrees of first and second order coherence are therefore functions of temperature, chemical potential, and position. The second order correlation function is governed both by the tendency of bosonic atoms to cluster and by a strong repulsion at small distances due to atomic interactions. In present experiments both effects are of comparable magnitude. Below the critical temperature the range of the bosonic correlation is affected by the presence of collective quasi-particle excitations. The results of some recent experiments on second and third order coherence are discussed. It is shown that the relation between the measured quantities and the correlation functions is much weaker than previously assumed.Comment: RevTeX, 25 pages with 7 Postscript figure