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Performing SELEX experiments in silico.
J Chem Phys
November 2017
Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.
Due to the sequence-dependent nature of the elasticity of DNA, many protein-DNA complexes and other systems in which DNA molecules must be deformed have preferences for the type of DNA sequence they interact with. SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments and similar sequence selection experiments have been used extensively to examine the (indirect readout) sequence preferences of, e.g.
View Article and Find Full Text PDFde Sitter vacua via consistent terms.
Phys Rev Lett
December 2005
Dipartimento di Fisica, Università di Roma La Sapienza and INFN, Sezione di Roma, P.le Aldo Moro 2, I-00185 Rome, Italy.
We introduce a new mechanism for producing locally stable de Sitter or Minkowski vacua, with spontaneously broken N = 1 supersymmetry and no massless scalars, applicable to superstring and M-theory compactifications with fluxes. We illustrate the mechanism with a simple N = 1 supergravity model that provides parametric control on the sign and the size of the vacuum energy. The crucial ingredient is a gauged U(1) that involves both an axionic shift and an R symmetry, and severely constrains the F- and D-term contributions to the potential.
View Article and Find Full Text PDFModels of coral growth: spontaneous branching, compactification and the Laplacian growth assumption.
J Theor Biol
September 2003
Section Computational Science, Faculty of Science, University of Amsterdam, Kruislaan 403, 1098 SJ, Amsterdam, The Netherlands.
In stony corals it is often observed that specimens collected from a sheltered growth site have more open and more thinly branched growth forms than specimens of the same species from more exposed growth sites, where stronger water currents are found. This observation was explained using an abiotic computational model inspired by coral growth, in which the growth velocity depended locally on the absorption of a resource dispersed by advection and diffusion (Kaandorp and Sloot, J. Theor.
View Article and Find Full Text PDFMorphological diversity of DNA-colloidal self-assembly.
Phys Rev Lett
September 2002
Department of Physics, University of Michigan, 500 E. University Avenue, Ann Arbor, Michigan 48109, USA.
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft-core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which both the repulsion and the attraction may be induced by DNA solution. The system is shown to exhibit surprisingly diverse and unusual morphologies.
View Article and Find Full Text PDFGeneralized symmetry breaking on orbifolds.
Phys Rev Lett
March 2002
Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA.
We reconsider the phenomenon of mass generation via coordinate-dependent compactifications of higher-dimensional theories on orbifolds. For definiteness, we study a generic five-dimensional theory compactified on S(1)/Z(2). We show that the presence of fixed points, where the fields or their derivatives may be discontinuous, permits new realizations of the Scherk-Schwarz mechanism where, for example, the mass terms are localized at the orbifold fixed points.
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