8,318 research outputs found
From imagery to ecology: Leveraging time series of all available Landsat observations to map and monitor ecosystem state and dynamics
https://zslpublications.onlinelibrary.wiley.com/doi/full/10.1002/rse2.24Published versio
Self-consistent analytic solution for the current and the access resistance in open ion channels.
A self-consistent analytic approach is introduced for the estimation of the access resistance and the current through an open ion channel for an arbitrary number of species. For an ion current flowing radially inward from infinity to the channel mouth, the Poisson-Boltzmann-Nernst-Planck equations are solved analytically in the bulk with spherical symmetry in three dimensions, by linearization. Within the channel, the Poisson-Nernst-Planck equation is solved analytically in a one-dimensional approximation. An iterative procedure is used to match the two solutions together at the channel mouth in a self-consistent way. It is shown that the currentvoltage characteristics obtained are in good quantitative agreement with experimental measurements
Energetics of discrete selectivity bands and mutation-induced transitions in the calcium-sodium ion channels family
We use Brownian dynamics (BD) simulations to study the ionic conduction and valence selectivity of a generic electrostatic model of a biological ion channel as functions of the fixed charge Qf at its selectivity filter. We are thus able to reconcile the discrete calcium conduction bands recently revealed in our BD simulations, M0 (Qf = 1e), M1 (3e), M2 (5e), with a set of sodium conduction bands L0 (0.5e), L1 (1.5e), thereby obtaining a completed pattern of conduction and selectivity bands vs Qf for the sodium-calcium channels family. An increase of Qf leads to an increase of calcium selectivity: L0 (sodium-selective, nonblocking channel) → M0 (nonselective channel) → L1 (sodium-selective channel with divalent block) → M1 (calcium-selective channel exhibiting the anomalous mole fraction effect). We create a consistent identification scheme where the L0 band is putatively identified with the eukaryotic sodium channel The scheme created is able to account for the experimentally observed mutation-induced transformations between nonselective channels, sodium selective channels, and calcium-selective channels, which we interpret as transitions between different rows of the identification table. By considering the potential energy changes during permeation, we show explicitly that the multi-ion conduction bands of calcium and sodium channels arise as the result of resonant barrierless conduction. The pattern of periodic conduction bands is explained on the basis of sequential neutralization taking account of self-energy, as Qf (z,i) = ze(1/2 + i), where i is the order of the band and z is the valence of the ion. Our results confirm the crucial influence of electrostatic interactions on conduction and on the Ca2+/Na+ valence selectivity of calcium and sodium ion channels. The model and results could be also applicable to biomimetic nanopores with charged walls
Stochastic dynamics of remote knock-on permeation in biological ion channels
Brownian dynamics simulations provide evidence for a remote knock-on mechanism facilitating the permeation of a biological ion channel by an ion that is initially trapped at the selectivity filter (SF). Unlike the case of conventional direct knock-on, the second ion that instigates permeation does not need to enter the channel. Nor does it necessarily take the place of the permeating ion at the SF, and it can even be of a different ionic species. The study is based on the simultaneous, self-consistent, solution of the coupled Poisson and Langevin equations for a simple generic model, taking account of all the charges present. The new permeation mechanism involves electrostatic amplification attributable to the permittivity mismatch between water and protein: the arrival of the instigating ion at the channel entrance reduces the exit barrier for the ion trapped at the SF, facilitating escape
Self-organized enhancement of conductivity in biological ion channels
We discuss an example of self-organization in a biological system. It arises from long-range ion–ion interactions, and it leads us to propose a new kind of enhanced conduction in ion channels. The underlying mechanism involves charge fluctuations near the channel mouth, amplified by the mismatch between the relative permittivities of water and the protein of the channel walls. We use Brownian dynamics simulations to show that, as in conventional 'knock on' permeation, these interactions can strongly enhance the channel current; but unlike the conventional mechanism, the enhancement occurs without the instigating bath ion entering the channel. The transition between these two mechanisms is clearly demonstrated, emphasizing their distinction. A simple model accurately reproduces the observed phenomena. We point out that electrolyte plus protein of low relative permittivity are universal in living systems, so that long-range ion–ion correlations of the kind considered must be common
Faster k-Medoids Clustering: Improving the PAM, CLARA, and CLARANS Algorithms
Clustering non-Euclidean data is difficult, and one of the most used
algorithms besides hierarchical clustering is the popular algorithm
Partitioning Around Medoids (PAM), also simply referred to as k-medoids. In
Euclidean geometry the mean-as used in k-means-is a good estimator for the
cluster center, but this does not hold for arbitrary dissimilarities. PAM uses
the medoid instead, the object with the smallest dissimilarity to all others in
the cluster. This notion of centrality can be used with any (dis-)similarity,
and thus is of high relevance to many domains such as biology that require the
use of Jaccard, Gower, or more complex distances.
A key issue with PAM is its high run time cost. We propose modifications to
the PAM algorithm to achieve an O(k)-fold speedup in the second SWAP phase of
the algorithm, but will still find the same results as the original PAM
algorithm. If we slightly relax the choice of swaps performed (at comparable
quality), we can further accelerate the algorithm by performing up to k swaps
in each iteration. With the substantially faster SWAP, we can now also explore
alternative strategies for choosing the initial medoids. We also show how the
CLARA and CLARANS algorithms benefit from these modifications. It can easily be
combined with earlier approaches to use PAM and CLARA on big data (some of
which use PAM as a subroutine, hence can immediately benefit from these
improvements), where the performance with high k becomes increasingly
important.
In experiments on real data with k=100, we observed a 200-fold speedup
compared to the original PAM SWAP algorithm, making PAM applicable to larger
data sets as long as we can afford to compute a distance matrix, and in
particular to higher k (at k=2, the new SWAP was only 1.5 times faster, as the
speedup is expected to increase with k)
Infrared Emission from the Radio Supernebula in NGC 5253: A Proto-Globular Cluster?
Hidden from optical view in the starburst region of the dwarf galaxy NGC 5253
lies an intense radio source with an unusual spectrum which could be
interpreted variously as nebular gas ionized by a young stellar cluster or
nonthermal emission from a radio supernova or an AGN. We have obtained 11.7 and
18.7 micron images of this region at the Keck Telescope and find that it is an
extremely strong mid-infrared emitter. The infrared to radio flux ratio rules
out a supernova and is consistent with an HII region excited by a dense cluster
of young stars. This "super nebula" provides at least 15% of the total
bolometric luminosity of the galaxy. Its excitation requires 10^5-10^6 stars,
giving it the total mass and size (1-2 pc diameter) of a globular cluster.
However, its high obscuration, small size, and high gas density all argue that
it is very young, no more than a few hundred thousand years old. This may be
the youngest globular cluster yet observed.Comment: 6 pages, 2 color figures, Submitted to the ApJL, Revised 4/6/01 based
on referee's comment
Coulomb blockade model of permeation and selectivity in biological ion channels
Biological ion channels are protein nanotubes embedded in, and passing through, the bilipid membranes of cells. Physiologically, they are of crucial importance in that they allow ions to pass into and out of cells, fast and efficiently, though in a highly selective way. Here we show that the conduction and selectivity of calcium/sodium ion channels can be described in terms of ionic Coulomb blockade in a simplified electrostatic and Brownian dynamics model of the channel. The Coulomb blockade phenomenon arises from the discreteness of electrical charge, the strong electrostatic interaction, and an electrostatic exclusion principle. The model predicts a periodic pattern of Ca2+ conduction versus the fixed charge Qf at the selectivity filter (conduction bands) with a period equal to the ionic charge. It thus provides provisional explanations of some observed and modelled conduction and valence selectivity phenomena, including the anomalous mole fraction effect and the calcium conduction bands. Ionic Coulomb blockade and resonant conduction are similar to electronic Coulomb blockade and resonant tunnelling in quantum dots. The same considerations may also be applicable to other kinds of channel, as well as to charged artificial nanopores
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