Correlation effects and orbital magnetism of Co clusters

Recent experiments on isolated Co clusters have shown huge orbital magnetic moments in comparison with their bulk and surface counterparts. These clusters hence provide the unique possibility to study the evolution of the orbital magnetic moment with respect to the cluster size and how competing interactions contribute to the quenching of orbital magnetism. We investigate here different theoretical methods to calculate the spin and orbital moments of Co clusters, and assess the performances of the methods in comparison with experiments. It is shown that density functional theory in conventional local density or generalized gradient approximations, or even with a hybrid functional, severely underestimates the orbital moment. As natural extensions/corrections we considered the orbital polarization correction, the LDA+U approximation as well as the LDA+DMFT method. Our theory shows that of the considered methods, only the LDA+DMFT method provides orbital moments in agreement with experiment, thus emphasizing the importance of dynamic correlations effects for determining fundamental magnetic properties of magnets in the nano-size regime

The structure of preserved information in quantum processes

We introduce a general operational characterization of information-preserving structures (IPS) -- encompassing noiseless subsystems, decoherence-free subspaces, pointer bases, and error-correcting codes -- by demonstrating that they are isometric to fixed points of unital quantum processes. Using this, we show that every IPS is a matrix algebra. We further establish a structure theorem for the fixed states and observables of an arbitrary process, which unifies the Schrodinger and Heisenberg pictures, places restrictions on physically allowed kinds of information, and provides an efficient algorithm for finding all noiseless and unitarily noiseless subsystems of the process

Autoregulation of yeast ribosomal proteins discovered by efficient search for feedback regulation

Post-transcriptional autoregulation of gene expression is common in bacteria but many fewer examples are known in eukaryotes. We used the yeast collection of genes fused to GFP as a rapid screen for examples of feedback regulation in ribosomal proteins by overexpressing a non-regulatable version of a gene and observing the effects on the expression of the GFP-fused version. We tested 95 ribosomal protein genes and found a wide continuum of effects, with 30% showing at least a 3-fold reduction in expression. Two genes, RPS22B and RPL1B, showed over a 10-fold repression. In both cases the cis-regulatory segment resides in the 5\u27 UTR of the gene as shown by placing that segment of the mRNA upstream of GFP alone and demonstrating it is sufficient to cause repression of GFP when the protein is over-expressed. Further analyses showed that the intron in the 5\u27 UTR of RPS22B is required for regulation, presumably because the protein inhibits splicing that is necessary for translation. The 5\u27 UTR of RPL1B contains a sequence and structure motif that is conserved in the binding sites of Rpl1 orthologs from bacteria to mammals, and mutations within the motif eliminate repression

Information preserving structures: A general framework for quantum zero-error information

Quantum systems carry information. Quantum theory supports at least two distinct kinds of information (classical and quantum), and a variety of different ways to encode and preserve information in physical systems. A system's ability to carry information is constrained and defined by the noise in its dynamics. This paper introduces an operational framework, using information-preserving structures to classify all the kinds of information that can be perfectly (i.e., with zero error) preserved by quantum dynamics. We prove that every perfectly preserved code has the same structure as a matrix algebra, and that preserved information can always be corrected. We also classify distinct operational criteria for preservation (e.g., "noiseless", "unitarily correctible", etc.) and introduce two new and natural criteria for measurement-stabilized and unconditionally preserved codes. Finally, for several of these operational critera, we present efficient (polynomial in the state-space dimension) algorithms to find all of a channel's information-preserving structures.Comment: 29 pages, 19 examples. Contains complete proofs for all the theorems in arXiv:0705.428

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells

In embryonic stem cells (ESCs), a core transcription factor (TF) network establishes the gene expression program necessary for pluripotency. To address how interactions between four key TFs contribute t

On the computation of zone and double zone diagrams

Classical objects in computational geometry are defined by explicit relations. Several years ago the pioneering works of T. Asano, J. Matousek and T. Tokuyama introduced "implicit computational geometry", in which the geometric objects are defined by implicit relations involving sets. An important member in this family is called "a zone diagram". The implicit nature of zone diagrams implies, as already observed in the original works, that their computation is a challenging task. In a continuous setting this task has been addressed (briefly) only by these authors in the Euclidean plane with point sites. We discuss the possibility to compute zone diagrams in a wide class of spaces and also shed new light on their computation in the original setting. The class of spaces, which is introduced here, includes, in particular, Euclidean spheres and finite dimensional strictly convex normed spaces. Sites of a general form are allowed and it is shown that a generalization of the iterative method suggested by Asano, Matousek and Tokuyama converges to a double zone diagram, another implicit geometric object whose existence is known in general. Occasionally a zone diagram can be obtained from this procedure. The actual (approximate) computation of the iterations is based on a simple algorithm which enables the approximate computation of Voronoi diagrams in a general setting. Our analysis also yields a few byproducts of independent interest, such as certain topological properties of Voronoi cells (e.g., that in the considered setting their boundaries cannot be "fat").Comment: Very slight improvements (mainly correction of a few typos); add DOI; Ref [51] points to a freely available computer application which implements the algorithms; to appear in Discrete & Computational Geometry (available online

Global entrainment of transcriptional systems to periodic inputs

This paper addresses the problem of giving conditions for transcriptional systems to be globally entrained to external periodic inputs. By using contraction theory, a powerful tool from dynamical systems theory, it is shown that certain systems driven by external periodic signals have the property that all solutions converge to a fixed limit cycle. General results are proved, and the properties are verified in the specific case of some models of transcriptional systems. The basic mathematical results needed from contraction theory are proved in the paper, making it self-contained

A proof of the Mazur-Orlicz theorem via the Markov-Kakutani common fixed point theorem, and vice versa

In this paper, we present a new proof of the Mazur-Orlicz theorem, which uses the Markov-Kakutani common fixed point theorem, and a new proof of the Markov-Kakutani common fixed point theorem, which uses the Mazur-Orlicz theorem

Interpolating orientation fields : an axiomatic approach

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