1,227 research outputs found
Simple flexible polymers in a spherical cage
We report the results of Monte Carlo simulations investigating the effect of
a spherical confinement within a simple model for a flexible homopolymer. We
use the parallel tempering method combined with multi-histogram reweighting
analysis and multicanonical simulations to investigate thermodynamical
observables over a broad range of temperatures, which enables us to describe
the behavior of the polymer and to locate the freezing and collapse
transitions. We find a strong effect of the spherical confinement on the
location of the collapse transition, whereas the freezing transition is hardly
effected.Comment: 7 pages, 4 figure
A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics
We present a novel multiscale simulation approach for modeling stochasticity
in chemical reaction networks. The approach seamlessly integrates
exact-stochastic and "leaping" methodologies into a single "partitioned
leaping" algorithmic framework. The technique correctly accounts for stochastic
noise at significantly reduced computational cost, requires the definition of
only three model-independent parameters and is particularly well-suited for
simulating systems containing widely disparate species populations. We present
the theoretical foundations of partitioned leaping, discuss various options for
its practical implementation and demonstrate the utility of the method via
illustrative examples.Comment: v4: 12 pages, 5 figures, final accepted version. Error found and
fixed in Appendi
Enhancement of the stability of genetic switches by overlapping upstream regulatory domains
We study genetic switches formed from pairs of mutually repressing operons.
The switch stability is characterised by a well defined lifetime which grows
sub-exponentially with the number of copies of the most-expressed transcription
factor, in the regime accessible by our numerical simulations. The stability
can be markedly enhanced by a suitable choice of overlap between the upstream
regulatory domains. Our results suggest that robustness against biochemical
noise can provide a selection pressure that drives operons, that regulate each
other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX
Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm
There is a great need for accurate and efficient computational approaches
that can account for both the discrete and stochastic nature of chemical
interactions as well as spatial inhomogeneities and diffusion. This is
particularly true in biology and nanoscale materials science, where the common
assumptions of deterministic dynamics and well-mixed reaction volumes often
break down. In this article, we present a spatial version of the
partitioned-leaping algorithm (PLA), a multiscale accelerated-stochastic
simulation approach built upon the tau-leaping framework of Gillespie. We pay
special attention to the details of the implementation, particularly as it
pertains to the time step calculation procedure. We point out conceptual errors
that have been made in this regard in prior implementations of spatial
tau-leaping and illustrate the manifestation of these errors through practical
examples. Finally, we discuss the fundamental difficulties associated with
incorporating efficient exact-stochastic techniques, such as the next-subvolume
method, into a spatial-leaping framework and suggest possible solutions.Comment: 15 pages, 9 figures, 2 table
Monotone Grid Drawings of Planar Graphs
A monotone drawing of a planar graph is a planar straight-line drawing of
where a monotone path exists between every pair of vertices of in some
direction. Recently monotone drawings of planar graphs have been proposed as a
new standard for visualizing graphs. A monotone drawing of a planar graph is a
monotone grid drawing if every vertex in the drawing is drawn on a grid point.
In this paper we study monotone grid drawings of planar graphs in a variable
embedding setting. We show that every connected planar graph of vertices
has a monotone grid drawing on a grid of size , and such a
drawing can be found in O(n) time
Age-Related Changes in the Penile Reflex of Rats
The penile reflex in sexually experienced male rats aged 10 and 44 weeks was observed for 20 min following sheath retraction. All 7 males aged 10 weeks showed erections, cups arid flips, while of 5 males aged 44 weeks only 2 showed erections.Frequencies of the above behaviors in aged males were significantly lower than that in young males. The decrease of penile reflexes with aging was similar to that of copulatory behavior with aging, when paired with receptive females. The presentstudy is the first to clearly establish the pattern of penile reflexes in aged rats
Metallochaperones regulate intracellular copper levels.
Copper (Cu) is an important enzyme co-factor that is also extremely toxic at high intracellular concentrations, making active efflux mechanisms essential for preventing Cu accumulation. Here, we have investigated the mechanistic role of metallochaperones in regulating Cu efflux. We have constructed a computational model of Cu trafficking and efflux based on systems analysis of the Cu stress response of Halobacterium salinarum. We have validated several model predictions via assays of transcriptional dynamics and intracellular Cu levels, discovering a completely novel function for metallochaperones. We demonstrate that in addition to trafficking Cu ions, metallochaperones also function as buffers to modulate the transcriptional responsiveness and efficacy of Cu efflux. This buffering function of metallochaperones ultimately sets the upper limit for intracellular Cu levels and provides a mechanistic explanation for previously observed Cu metallochaperone mutation phenotypes
Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.
The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45
Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.
BackgroundDesulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations.ResultsThe functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells.ConclusionsEven though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion
Selection of chromosomal DNA libraries using a multiplex CRISPR system.
The directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. We developed quantitative gene assembly and DNA library insertion into the Saccharomyces cerevisiae genome by optimizing an efficient single-step and marker-free genome editing system using CRISPR-Cas9. With this Multiplex CRISPR (CRISPRm) system, we selected an improved cellobiose utilization pathway in diploid yeast in a single round of mutagenesis and selection, which increased cellobiose fermentation rates by over 10-fold. Mutations recovered in the best cellodextrin transporters reveal synergy between substrate binding and transporter dynamics, and demonstrate the power of CRISPRm to accelerate selection experiments and discoveries of the molecular determinants that enhance biomolecule function
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