544 research outputs found
A two-state model for helicase translocation and unwinding of nucleic acids
Helicases are molecular motors that unwind double-stranded nucleic acids
(dsNA), such as DNA and RNA). Typically a helicase translocates along one of
the NA single strands while unwinding and uses adenosine triphosphate (ATP)
hydrolysis as an energy source. Here we model of a helicase motor that can
switch between two states, which could represent two different points in the
ATP hydrolysis cycle. Our model is an extension of the earlier
Betterton-J\"ulicher model of helicases to incorporate switching between two
states. The main predictions of the model are the speed of unwinding of the
dsNA and fluctuations around the average unwinding velocity. Motivated by a
recent claim that the NS3 helicase of Hepatitis C virus follows a flashing
ratchet mechanism, we have compared the experimental results for the NS3
helicase with a special limit of our model which corresponds to the flashing
ratchet scenario. Our model accounts for one key feature of the experimental
data on NS3 helicase. However, contradictory observations in experiments
carried out under different conditions limit the ability to compare the model
to experiments.Comment: minor modification
The temperature dependence of the isothermal bulk modulus at 1 bar pressure
It is well established that the product of the volume coefficient of thermal
expansion and the bulk modulus is nearly constant at temperatures higher than
the Debye temperature. Using this approximation allows predicting the values of
the bulk modulus. The derived analytical solution for the temperature
dependence of the isothermal bulk modulus has been applied to ten substances.
The good correlations to the experiments indicate that the expression may be
useful for substances for which bulk modulus data are lacking
Metal-Organic Frameworks in Germany: from Synthesis to Function
Metal-organic frameworks (MOFs) are constructed from a combination of
inorganic and organic units to produce materials which display high porosity,
among other unique and exciting properties. MOFs have shown promise in many
wide-ranging applications, such as catalysis and gas separations. In this
review, we highlight MOF research conducted by Germany-based research groups.
Specifically, we feature approaches for the synthesis of new MOFs,
high-throughput MOF production, advanced characterization methods and examples
of advanced functions and properties
Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding
Ribosome is a molecular machine that polymerizes a protein where the sequence
of the amino acid residues, the monomers of the protein, is dictated by the
sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that
serves as the template. The ribosome is a molecular motor that utilizes the
template mRNA strand also as the track. Thus, in each step the ribosome moves
forward by one codon and, simultaneously, elongates the protein by one amino
acid. We present a theoretical model that captures most of the main steps in
the mechano-chemical cycle of a ribosome. The stochastic movement of the
ribosome consists of an alternating sequence of pause and translocation; the
sum of the durations of a pause and the following translocation is the time of
dwell of the ribosome at the corresponding codon. We derive the analytical
expression for the distribution of the dwell times of a ribosome in our model.
Whereever experimental data are available, our theoretical predictions are
consistent with those results. We suggest appropriate experiments to test the
new predictions of our model, particularly, the effects of the quality control
mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article
accepted for publication in Physical Biology. IOP Publishing Ltd is not
responsible for any errors or omissions in this version of the manuscript or
any version derived from it. The definitive publisher authenticated version
is available online at DOI:10.1088/1478-3975/8/2/02600
Stochastic Description of a Bistable Frustrated Unit
Mixed positive and negative feedback loops are often found in biological
systems which support oscillations. In this work we consider a prototype of
such systems, which has been recently found at the core of many genetic
circuits showing oscillatory behaviour. Our model consists of two interacting
species A and B, where A activates not only its own production, but also that
of its repressor B. While the self-activation of A leads already to a bistable
unit, the coupling with a negative feedback loop via B makes the unit
frustrated. In the deterministic limit of infinitely many molecules, such a
bistable frustrated unit is known to show excitable and oscillatory dynamics,
depending on the maximum production rate of A which acts as a control
parameter. We study this model in its fully stochastic version and we find
oscillations even for parameters which in the deterministic limit are deeply in
the fixed-point regime. The deeper we go into this regime, the more irregular
these oscillations are, becoming finally random excitations whenever
fluctuations allow the system to overcome the barrier for a large excursion in
phase space. The fluctuations can no longer be fully treated as a perturbation.
The smaller the system size (the number of molecules), the more frequent are
these excitations. Therefore, stochasticity caused by demographic noise makes
this unit even more flexible with respect to its oscillatory behaviour.Comment: 28 pages, 17 figure
Change in Migration and Pasture Utilization by Brokpa Pastoral Nomads: A Sustainable Adaptation Strategy for Climate Sensitive Arunachal Pradesh!?
The north-eastern states of India specially Arunachal Pradesh, one of the bio-diversity hotspot, is expected to be greatly affected by climate change. Climate change will not only adversely impact the biodiversity of Arunachal Pradesh, but also affect the livelihood of local communities as they fully dependent on the natural resources. The Monpa is a primitive tribe inhabiting parts of West Kameng and Tawang district of Arunachal Pradesh. The pastoral nomad of the Monpa tribe is popularly known as Brokpa. Transhumance system of livestock mainly yak (Poephagus grunniens L.) rearing is their main source of livelihood. In recent past, challenges of the Brokpa pastoral community transform into threat due to synergistic effect of impending climate change. But, this nomad has their own mechanism to cope up with adverse impact of climate change. Therefore, a systematic study was carried out to document and analyze these coping mechanisms
Diagnosing the Clumpy Protoplanetary Disk of the UXor Type Young Star GM Cephei
UX Orionis stars (UXors) are Herbig Ae/Be or T Tauri stars exhibiting
sporadic occultation of stellar light by circumstellar dust. GM\,Cephei is such
a UXor in the young (~Myr) open cluster Trumpler\,37, showing prominent
infrared excess, emission-line spectra, and flare activity. Our photometric
monitoring (2008--2018) detects (1)~an 3.43~day period, likely arising
from rotational modulation by surface starspots, (2)~sporadic brightening on
time scales of days due to accretion, (3)~irregular minor flux drops due to
circumstellar dust extinction, and (4)~major flux drops, each lasting for a
couple of months with a recurrence time, though not exactly periodic, of about
two years. The star experiences normal reddening by large grains, i.e., redder
when dimmer, but exhibits an unusual "blueing" phenomenon in that the star
turns blue near brightness minima. The maximum extinction during relatively
short (lasting ~days) events, is proportional to the duration, a
consequence of varying clump sizes. For longer events, the extinction is
independent of duration, suggestive of a transverse string distribution of
clumps. Polarization monitoring indicates an optical polarization varying
--8, with the level anticorrelated with the slow brightness
change. Temporal variation of the unpolarized and polarized light sets
constraints on the size and orbital distance of the circumstellar clumps in the
interplay with the young star and scattering envelope. These transiting clumps
are edge-on manifestations of the ring- or spiral-like structures found
recently in young stars with imaging in infrared of scattered light, or in
submillimeter of thermalized dust emission.Comment: 20 pages, 9 figure
The changing face of AU Mic b: stellar spots, spin-orbit commensurability, and transit timing variations as seen by CHEOPS and TESS
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