Search results for "nuclei"

tbg - a new file format for genomic data

2021

AbstractMotivationThe question of determining whether a Single-Nucleotide Polymorphism (SNP) or a variant in general leads to a change in the amino acid sequence of a protein coding gene is often a laborious and time-consuming challenge. Here, we introduce the tbg file format for storing genomic data and tbg-tools, a user-friendly toolbox for the faster analysis of SNPs. The file format stores information for each nucleotide in each gene, allowing to predict which change in the amino acid sequence will be caused by a variant in the nucleotide sequence. Our new tool therefore has the potential to make biological sense of the unprecedented amount of genome-wide genetic variation that research…

Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems

2018

DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled…

2015

Abstract. A recent parcel model study (Reutter et al., 2009) showed three deterministic regimes of initial cloud droplet formation, characterized by different ratios of aerosol concentrations (NCN) to updraft velocities. This analysis, however, did not reveal how these regimes evolve during the subsequent cloud development. To address this issue, we employed the Active Tracer High Resolution Atmospheric Model (ATHAM) with full microphysics and extended the model simulation from the cloud base to the entire column of a single pyro-convective mixed-phase cloud. A series of 2-D simulations (over 1000) were performed over a wide range of NCN and dynamic conditions. The integrated concentration …

A Theoretical Study of the Wet Removal of Atmospheric Pollutants. Part III: The Uptake, Redistribution, and Deposition of (NH4)2SO4Particles by a Con…

1988

Abstract Our model for the scavenging of aerosol particles has been coupled with the two-dimensional form of the convective cloud model of Clark and Collaborators. The combined model was then used to simulate a convective warm cloud for the meteorological situation which existed at 1100 LST 12 July 1985 over Hawaii; assuming an aerosol size distribution of maritime number concentration and of mixed composition with (NH4)2SO4 as the soluble compound. A shallow model cloud developed 26 min after the onset of convection leading to moderate rain which began after 45 min and ended after 60 min. Various parameters which characterize the dynamics and micophysics of the cloud, as well as the scaven…

Comparing parameterized versus measured microphysical properties of tropical convective cloud bases during the ACRIDICON–CHUVA campaign

2017

The objective of this study is to validate parameterizations that were recently developed for satellite retrievals of cloud condensation nuclei supersaturation spectra, NCCN(S), at cloud base alongside more traditional parameterizations connecting NCCN(S) with cloud base updrafts and drop concentrations. This was based on the HALO aircraft measurements during the ACRIDICON–CHUVA campaign over the Amazon region, which took place in September 2014. The properties of convective clouds were measured with a cloud combination probe (CCP), a cloud and aerosol spectrometer (CAS-DPOL), and a CCN counter onboard the HALO aircraft. An intercomparison of the cloud drop size distributions (DSDs) and the…

Impacts of Varying Concentrations of Cloud Condensation Nuclei on Deep Convective Cloud Updrafts—A Multimodel Assessment

2021

AbstractThis study presents results from a model intercomparison project, focusing on the range of responses in deep convective cloud updrafts to varying cloud condensation nuclei (CCN) concentrations among seven state-of-the-art cloud-resolving models. Simulations of scattered convective clouds near Houston, Texas, are conducted, after being initialized with both relatively low and high CCN concentrations. Deep convective updrafts are identified, and trends in the updraft intensity and frequency are assessed. The factors contributing to the vertical velocity tendencies are examined to identify the physical processes associated with the CCN-induced updraft changes. The models show several c…

Structural variability of 3C 111 on parsec scales

2011

We discuss the parsec-scale structural variability of the extragalactic jet 3C 111 related to a major radio flux density outburst in 2007. The data analyzed were taken within the scope of the MOJAVE, UMRAO, and F-GAMMA programs, which monitor a large sample of the radio brightest compact extragalactic jets with the VLBA, the University of Michigan 26 m, the Effelsberg 100 m, and the IRAM 30 m radio telescopes. The analysis of the VLBA data is performed by fitting Gaussian model components in the visibility domain. We associate the ejection of bright features in the radio jet with a major flux-density outburst in 2007. The evolution of these features suggests the formation of a leading compo…

Structure of low-lying states in 140Sm studied by Coulomb excitation

2016

The electromagnetic structure of 140Sm was studied in a low-energy Coulomb excitation experiment with a radioactive ion beam from the REX-ISOLDE facility at CERN. The 2+ and 4+ states of the ground-state band and a second 2+ state were populated by multistep excitation. The analysis of the differential Coulomb excitation cross sections yielded reduced transition probabilities between all observed states and the spectroscopic quadrupole moment for the 2+ 1 state. The experimental results are compared to large-scale shell model calculations and beyond-mean-field calculations based on the Gogny D1S interaction with a five-dimensional collective Hamiltonian formalism. Simpler geometric and alge…

Role of Disorder on the Dynamics of a Nonlinear Model for DNA Thermal Denaturation

1992

The dynamics of thermal denaturation of DNA is a good example in which nonlinearity coexits with disorder. The amplitude of the motions is so high that bonds break and the base sequence is inhomogeneous since it contains the genetic code. Using a simple nonlinear model, we study the role of local inhomogeneities or of extended disorder on the dynamics of the localized excitations and on the denaturation rate by numerical simulations at constrained temperature. Approximate analytical results are obtained for the trapping of the breatherlike excitations by isolated defects and the statistical mechanics of the disordered molecule.

New enveloped dsRNA phage from freshwater habitat.

2015

Cystoviridae is a family of bacteriophages with a tri-segmented dsRNA genome enclosed in a tri-layered virion structure. Here, we present a new putative member of the Cystoviridae family, bacteriophage ϕNN. ϕNN was isolated from a Finnish lake in contrast to the previously identified cystoviruses, which originate from various legume samples collected in the USA. The nucleotide sequence of the virus reveals a strong genetic similarity (~80 % for the L-segments, ~55 % for the M-segments and ~84 % for the S-segments) to Pseudomonas phage ϕ6, the type member of the virus family. However, the relationship between ϕNN and other cystoviruses is more distant. In general, proteins located in the int…