1,258 research outputs found
Extensions and block decompositions for finite-dimensional representations of equivariant map algebras
Suppose a finite group acts on a scheme and a finite-dimensional Lie
algebra . The associated equivariant map algebra is the Lie
algebra of equivariant regular maps from to . The irreducible
finite-dimensional representations of these algebras were classified in
previous work with P. Senesi, where it was shown that they are all tensor
products of evaluation representations and one-dimensional representations. In
the current paper, we describe the extensions between irreducible
finite-dimensional representations of an equivariant map algebra in the case
that is an affine scheme of finite type and is reductive.
This allows us to also describe explicitly the blocks of the category of
finite-dimensional representations in terms of spectral characters, whose
definition we extend to this general setting. Applying our results to the case
of generalized current algebras (the case where the group acting is trivial),
we recover known results but with very different proofs. For (twisted) loop
algebras, we recover known results on block decompositions (again with very
different proofs) and new explicit formulas for extensions. Finally,
specializing our results to the case of (twisted) multiloop algebras and
generalized Onsager algebras yields previously unknown results on both
extensions and block decompositions.Comment: 41 pages; v2: minor corrections, formatting changed to match
published versio
Visualizing and quantifying structural diversity around mobile resistance genes.
Understanding the evolution of mobile genes is important for understanding the spread of antimicrobial resistance (AMR). Many clinically important AMR genes have been mobilized by mobile genetic elements (MGEs) on the kilobase scale, such as integrons and transposons, which can integrate into both chromosomes and plasmids and lead to rapid spread of the gene through bacterial populations. Looking at the flanking regions of these mobile genes in diverse genomes can highlight common structures and reveal patterns of MGE spread. However, historically this has been a largely descriptive process, relying on gene annotation and expert knowledge. Here we describe a general method to visualize and quantify the structural diversity around genes using pangraph to find blocks of homologous sequence. We apply this method to a set of 12 clinically important beta-lactamase genes and provide interactive visualizations of their flanking regions at https://liampshaw.github.io/flanking-regions. We show that nucleotide-level variation in the mobile gene itself generally correlates with increased structural diversity in its flanking regions, demonstrating a relationship between rates of mutational evolution and rates of structural evolution, and find a bias for greater structural diversity upstream. Our framework is a starting point to investigate general rules that apply to the horizontal spread of new genes through bacterial populations
Target search on a dynamic DNA molecule
We study a protein-DNA target search model with explicit DNA dynamics
applicable to in vitro experiments. We show that the DNA dynamics plays a
crucial role for the effectiveness of protein "jumps" between sites distant
along the DNA contour but close in 3D space. A strongly binding protein that
searches by 1D sliding and jumping alone, explores the search space less
redundantly when the DNA dynamics is fast on the timescale of protein jumps
than in the opposite "frozen DNA" limit. We characterize the crossover between
these limits using simulations and scaling theory. We also rationalize the slow
exploration in the frozen limit as a subtle interplay between long jumps and
long trapping times of the protein in "islands" within random DNA
configurations in solution.Comment: manuscript and supplementary material combined into a single documen
Ozone Depletion from Nearby Supernovae
Estimates made in the 1970's indicated that a supernova occurring within tens
of parsecs of Earth could have significant effects on the ozone layer. Since
that time, improved tools for detailed modeling of atmospheric chemistry have
been developed to calculate ozone depletion, and advances have been made in
theoretical modeling of supernovae and of the resultant gamma-ray spectra. In
addition, one now has better knowledge of the occurrence rate of supernovae in
the galaxy, and of the spatial distribution of progenitors to core-collapse
supernovae. We report here the results of two-dimensional atmospheric model
calculations that take as input the spectral energy distribution of a
supernova, adopting various distances from Earth and various latitude impact
angles. In separate simulations we calculate the ozone depletion due to both
gamma-rays and cosmic rays. We find that for the combined ozone depletion
roughly to double the ``biologically active'' UV flux received at the surface
of the Earth, the supernova must occur at <8 pc. Based on the latest data, the
time-averaged galactic rate of core-collapse supernovae occurring within 8 pc
is ~1.5/Gyr. In comparing our calculated ozone depletions with those of
previous studies, we find them to be significantly less severe than found by
Ruderman (1974), and consistent with Whitten et al. (1976). In summary, given
the amplitude of the effect, the rate of nearby supernovae, and the ~Gyr time
scale for multicellular organisms on Earth, this particular pathway for mass
extinctions may be less important than previously thought.Comment: 24 pages, 4 Postscript figures, to appear in The Astrophysical
Journal, 2003 March 10, vol. 58
PanGraph: scalable bacterial pan-genome graph construction
The genomic diversity of microbes is commonly parameterized as SNPs relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome, the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the widespread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. In addition to pangenomic approaches that focus on the variation in the sets of genes present in different genomes, complete assemblies allow investigations of the evolution of genome structure and gene order. This latter problem, however, is computationally demanding with few tools available that shed light on these dynamics. Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as a path along vertices, which in turn encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into several common formats for either downstream analysis or immediate visualization
On the action potential as a propagating density pulse and the role of anesthetics
The Hodgkin-Huxley model of nerve pulse propagation relies on ion currents
through specific resistors called ion channels. We discuss a number of
classical thermodynamic findings on nerves that are not contained in this
classical theory. Particularly striking is the finding of reversible heat
changes, thickness and phase changes of the membrane during the action
potential. Data on various nerves rather suggest that a reversible density
pulse accompanies the action potential of nerves. Here, we attempted to explain
these phenomena by propagating solitons that depend on the presence of
cooperative phase transitions in the nerve membrane. These transitions are,
however, strongly influenced by the presence of anesthetics. Therefore, the
thermodynamic theory of nerve pulses suggests a explanation for the famous
Meyer-Overton rule that states that the critical anesthetic dose is linearly
related to the solubility of the drug in the membranes.Comment: 13 pages, 8 figure
Effect of anisotropy and destructuration on behavior of Haarajoki test embankment
This paper investigates the influence of anisotropy and destructuration on the behavior of Haarajoki test embankment, which was built by the Finnish National Road Administration as a noise barrier in 1997 on a soft clay deposit. Half of the embankment is constructed on an area improved with prefabricated vertical drains, while the other half is constructed on the natural deposit without any ground improvement. The construction and consolidation of the embankment is analyzed with the finite-element method using three different constitutive models to represent the soft clay. Two recently proposed constitutive models, namely S-CLAY1 which accounts for initial and plastic strain induced anisotropy, and its extension, called S-CLAY1S which accounts, additionally, for interparticle bonding and degradation of bonds, were used in the analysis. For comparison, the problem is also analyzed with the isotropic modified cam clay model. The results of the numerical analyses are compared with the field measurements. The simulations reveal the influence that anisotropy and destructuration have on the behavior of an embankment on soft clay
Relating a calcium indicator signal to the unperturbed calcium concentration time-course
BACKGROUND: Optical indicators of cytosolic calcium levels have become important experimental tools in systems and cellular neuroscience. Indicators are known to interfere with intracellular calcium levels by acting as additional buffers, and this may strongly alter the time-course of various dynamical variables to be measured. RESULTS: By investigating the underlying reaction kinetics, we show that in some ranges of kinetic parameters one can explicitly link the time dependent indicator signal to the time-course of the calcium influx, and thus, to the unperturbed calcium level had there been no indicator in the cell
Simulation-based reachability analysis for nonlinear systems using componentwise contraction properties
A shortcoming of existing reachability approaches for nonlinear systems is
the poor scalability with the number of continuous state variables. To mitigate
this problem we present a simulation-based approach where we first sample a
number of trajectories of the system and next establish bounds on the
convergence or divergence between the samples and neighboring trajectories. We
compute these bounds using contraction theory and reduce the conservatism by
partitioning the state vector into several components and analyzing contraction
properties separately in each direction. Among other benefits this allows us to
analyze the effect of constant but uncertain parameters by treating them as
state variables and partitioning them into a separate direction. We next
present a numerical procedure to search for weighted norms that yield a
prescribed contraction rate, which can be incorporated in the reachability
algorithm to adjust the weights to minimize the growth of the reachable set
On multigraded generalizations of Kirillov-Reshetikhin modules
We study the category of Z^l-graded modules with finite-dimensional graded
pieces for certain Z+^l-graded Lie algebras. We also consider certain Serre
subcategories with finitely many isomorphism classes of simple objects. We
construct projective resolutions for the simple modules in these categories and
compute the Ext groups between simple modules. We show that the projective
covers of the simple modules in these Serre subcategories can be regarded as
multigraded generalizations of Kirillov-Reshetikhin modules and give a
recursive formula for computing their graded characters
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