Simulation of a Dripping Faucet

We present a simulation of a dripping faucet system. A new algorithm based on Lagrangian description is introduced. The shape of drop falling from a faucet obtained by the present algorithm agrees quite well with experimental observations. Long-term behavior of the simulation can reproduce period-one, period-two, intermittent and chaotic oscillations widely observed in experiments. Possible routes to chaos are discussed.Comment: 20 pages, 15 figures, J. Phys. Soc. Jpn. (in press

Effective Lagrangian Approach to the Fermion Mass Problem

An effective theory is proposed, combining the standard gauge group $SU(3)_{C}\otimes SU(2)_{L}\otimes U(1)_{Y}$ with a horizontal discrete symmetry. By assigning appropriate charges under this discrete symmetry to the various fermion fields and to (at least) two Higgs doublets, the broad spread of the fermion mass and mixing angle spectrum can be explained as a result of suppressed, non-renormalisable terms. A particular model is constructed which achieves the above while simultaneously suppressing neutral Higgs-induced flavour-changing processes.Comment: 21 pages, UM-P-93/81, latex file, 1 figure available on reques

Gaia Data Processing Architecture

Gaia is ESA's ambitious space astrometry mission the main objective of which is to astrometrically and spectro-photometrically map 1000 Million celestial objects (mostly in our galaxy) with unprecedented accuracy. The announcement of opportunity for the data processing will be issued by ESA late in 2006. The Gaia Data Processing and Analysis Consortium (DPAC) has been formed recently and is preparing an answer. The satellite will downlink close to 100 TB of raw telemetry data over 5 years. To achieve its required accuracy of a few 10s of Microarcsecond astrometry, a highly involved processing of this data is required. In addition to the main astrometric instrument Gaia will host a Radial Velocity instrument, two low-resolution dispersers for multi-color photometry and two Star Mappers. Gaia is a flying Giga Pixel camera. The various instruments each require relatively complex processing while at the same time being interdependent. We describe the overall composition of the DPAC and the envisaged overall architecture of the Gaia data processing system. We shall delve further into the core processing - one of the nine, so-called, coordination units comprising the Gaia processing system.Comment: 10 Pages, 2 figures. To appear in ADASS XVI Proceeding

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA

Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monodisperse suspensions, small crowding particles increase the stability of compact structures to a greater extent than larger crowders. If the sizes of crowders in a binary mixture are smaller than the unfolded RNA, the increase in melting temperature due to the two components is additive. In a ternary mixture of crowders that are larger than the unfolded RNA, which mimics the composition of ribosome, large enzyme complexes and proteins in E. coli, the marginal increase in stability is entirely determined by the smallest component. We predict that crowding can restore partially telomerase activity in mutants, which dramatically decrease the PK stability.Comment: File "JACS_MAIN_archive_PDF_from_DOC.pdf" (PDF created from DOC) contains the main text of the paper File JACS_SI_archive.tex + 7 figures are the supplementary inf

Pathway to the PiezoElectronic Transduction Logic Device

The information age challenges computer technology to process an exponentially increasing computational load on a limited energy budget - a requirement that demands an exponential reduction in energy per operation. In digital logic circuits, the switching energy of present FET devices is intimately connected with the switching voltage, and can no longer be lowered sufficiently, limiting the ability of current technology to address the challenge. Quantum computing offers a leap forward in capability, but a clear advantage requires algorithms presently developed for only a small set of applications. Therefore, a new, general purpose, classical technology based on a different paradigm is needed to meet the ever increasing demand for data processing.Comment: in Nano Letters (2015

On the selection and design of proteins and peptide derivatives for the production of photoluminescent, red-emitting gold quantum clusters

Novel pathways of the synthesis of photoluminescent gold quantum clusters (AuQCs) using biomolecules as reactants provide biocompatible products for biological imaging techniques. In order to rationalize the rules for the preparation of red-emitting AuQCs in aqueous phase using proteins or peptides, the role of different organic structural units was investigated. Three systems were studied: proteins, peptides, and amino acid mixtures, respectively. We have found that cysteine and tyrosine are indispensable residues. The SH/S-S ratio in a single molecule is not a critical factor in the synthesis, but on the other hand, the stoichiometry of cysteine residues and the gold precursor is crucial. These observations indicate the importance of proper chemical behavior of all species in a wide size range extending from the atomic distances (in the AuI-S semi ring) to nanometer distances covering the larger sizes of proteins assuring the hierarchical structure of the whole self-assembled system

Gene expression drives the evolution of dominance.

Dominance is a fundamental concept in molecular genetics and has implications for understanding patterns of genetic variation, evolution, and complex traits. However, despite its importance, the degree of dominance in natural populations is poorly quantified. Here, we leverage multiple mating systems in natural populations of Arabidopsis to co-estimate the distribution of fitness effects and dominance coefficients of new amino acid changing mutations. We find that more deleterious mutations are more likely to be recessive than less deleterious mutations. Further, this pattern holds across gene categories, but varies with the connectivity and expression patterns of genes. Our work argues that dominance arises as a consequence of the functional importance of genes and their optimal expression levels

Dripping Faucet Dynamics Clarified by an Improved Mass-Spring Model

An improved mass-spring model for a dripping faucet is presented. The model is constructed based on the numerical results which we recently obtained from fluid dynamical calculations. Both the fluid dynamical calculations and the present mass-spring model exhibit a variety of complex behavior including transition to chaos in good agreement with experiments. Further, the mass-spring model reveals fundamental dynamics inherent in the dripping faucet system.Comment: 17 pages, 17 figure

Relaxation time for a dimer covering with height representation

This paper considers the Monte Carlo dynamics of random dimer coverings of the square lattice, which can be mapped to a rough interface model. Two kinds of slow modes are identified, associated respectively with long-wavelength fluctuations of the interface height, and with slow drift (in time) of the system-wide mean height. Within a continuum theory, the longest relaxation time for either kind of mode scales as the system size N. For the real, discrete model, an exact lower bound of O(N) is placed on the relaxation time, using variational eigenfunctions corresponding to the two kinds of continuum modes.Comment: 12 pages, LaTeX; 1 figure in PostScript file; to appear, J. Stat. Phys. Sections and subsections were reshuffled to improve presentation, some text added on quantum-dimer model, fully-frustrated Ising model, and application to general class of "height" model

The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin

Since 1989, human immunodeficiency virus type 1 (HIV-1) has spread explosively through the heterosexual population in Thailand. This epidemic is caused primarily by viruses classified as "subtype E", which, on the basis of limited sequence comparisons, appear to represent hybrids of subtypes A (gag) and E (env). However, the true evolutionary origins of "subtype E" viruses are still obscure since no complete genomes have been analyzed, and only one full-length subtype A sequence has been available for phylogenetic comparison. In this study, we determined full-length proviral sequences for "subtype E" viruses from Thailand (93TH253) and the Central African Republic (90CR402) and for a subtype A virus from Uganda (92UG037). We also sequenced the long terminal repeat (LTR) regions from 16 virus strains representing clades A, C, E, F, and G. Detailed phylogenetic analyses of these sequences indicated that "subtype E" viruses do indeed represent A/E recombinants with multiple points of crossover along their genomes. The extracellular portion of env, parts of vif and vpr, as well as most of the LTR are of subtype E origin, whereas the remainder of the genome is of subtype A origin. The possibility that the discordant phylogenetic positions of "subtype E" viruses in gag- and env-derived trees are the result of unusual rates or patterns of evolution was also considered but was ruled out on the basis of two lines of evidence: (i) phylogenetic trees constructed for synonymous and nonsynonymous substitutions yielded the same discordant branching orders for "subtype E" gag and env gene sequences, thus excluding selection-driven evolution, and (ii) multiple crossovers in the viral genome are most consistent with the copy choice model of recombination and have been observed in other documented examples of HIV-1 intersubtype recombination. Thai and CAR "subtype E" viruses exhibited the same pattern of A/E mosaicism, indicating that the recombination event occurred in Africa prior to the spread of virus to Asia. Finally, all "subtype E" viruses were found to contain a distinctive two-nucleotide bulge in their transactivation response (TAR) elements. This feature was present only in viruses which also contained a subtype A 5' pol region (i.e., subtype A viruses or A/D and A/E recombinants), raising the possibility of a functional linkage between the TAR region and the polymerase. The implications of epidemic spread of a recombinant HIV-1 strain to viral natural history and vaccine development are discussed