2,839 research outputs found
Cooperative protein transport in cellular organelles
Compartmentalization into biochemically distinct organelles constantly
exchanging material is one of the hallmarks of eukaryotic cells. In the most
naive picture of inter-organelle transport driven by concentration gradients,
concentration differences between organelles should relax. We determine the
conditions under which cooperative transport, i.e. based on molecular
recognition, allows for the existence and maintenance of distinct organelle
identities. Cooperative transport is also shown to control the flux of material
transiting through a compartmentalized system, dramatically increasing the
transit time under high incoming flux. By including chemical processing of the
transported species, we show that this property provides a strong functional
advantage to a system responsible for protein maturation and sorting.Comment: 9 pages, 5 figure
An "All Possible Steps" Approach to the Accelerated Use of Gillespie's Algorithm
Many physical and biological processes are stochastic in nature.
Computational models and simulations of such processes are a mathematical and
computational challenge. The basic stochastic simulation algorithm was
published by D. Gillespie about three decades ago [D.T. Gillespie, J. Phys.
Chem. {\bf 81}, 2340, (1977)]. Since then, intensive work has been done to make
the algorithm more efficient in terms of running time. All accelerated versions
of the algorithm are aimed at minimizing the running time required to produce a
stochastic trajectory in state space. In these simulations, a necessary
condition for reliable statistics is averaging over a large number of
simulations. In this study I present a new accelerating approach which does not
alter the stochastic algorithm, but reduces the number of required runs. By
analysis of collected data I demonstrate high precision levels with fewer
simulations. Moreover, the suggested approach provides a good estimation of
statistical error, which may serve as a tool for determining the number of
required runs.Comment: Accepted for publication at the Journal of Chemical Physics. 19
pages, including 2 Tables and 4 Figure
Relaxation of finite perturbations: Beyond the Fluctuation-Response relation
We study the response of dynamical systems to finite amplitude perturbation.
A generalized Fluctuation-Response relation is derived, which links the average
relaxation toward equilibrium to the invariant measure of the system and points
out the relevance of the amplitude of the initial perturbation. Numerical
computations on systems with many characteristic times show the relevance of
the above relation in realistic cases.Comment: 7 pages, 5 figure
Waiting time distribution for electron transport in a molecular junction with electron-vibration interaction
On the elementary level, electronic current consists of individual electron
tunnelling events that are separated by random time intervals. The waiting time
distribution is a probability to observe the electron transfer in the detector
electrode at time given that an electron was detected in the same
electrode at earlier time . We study waiting time distribution for quantum
transport in a vibrating molecular junction. By treating the electron-vibration
interaction exactly and molecule-electrode coupling perturbatively, we obtain
master equation and compute the distribution of waiting times for electron
transport. The details of waiting time distributions are used to elucidate
microscopic mechanism of electron transport and the role of electron-vibration
interactions. We find that as nonequilibrium develops in molecular junction,
the skewness and dispersion of the waiting time distribution experience
stepwise drops with the increase of the electric current. These steps are
associated with the excitations of vibrational states by tunnelling electrons.
In the strong electron-vibration coupling regime, the dispersion decrease
dominates over all other changes in the waiting time distribution as the
molecular junction departs far away from the equilibrium
Bistability of cell-matrix adhesions resulting from non-linear receptor-ligand dynamics
Bistability is a major mechanism for cellular decision making and usually
results from positive feedback in biochemical control systems. Here we show
theoretically that bistability between unbound and bound states of adhesion
clusters results from positive feedback mediated by structural rather than
biochemical processes, namely by receptor-ligand dissociation and association
dynamics which depend non-linearly on mechanical force and receptor-ligand
separation. For small cell-matrix adhesions, we find rapid switching between
unbound and bound states, which in the initial stages of adhesion allows the
cell to explore its environment through many transient adhesions.Comment: Revtex, 3 pages, 3 postscript figures included, to appear in
Biophysical Journal as Biophysical Lette
Sub-Poissonian atom number fluctuations by three-body loss in mesoscopic ensembles
We show that three-body loss of trapped atoms leads to sub-Poissonian atom
number fluctuations. We prepare hundreds of dense ultracold ensembles in an
array of magnetic microtraps which undergo rapid three-body decay. The
shot-to-shot fluctuations of the number of atoms per trap are sub-Poissonian,
for ensembles comprising 50--300 atoms. The measured relative variance or Fano
factor agrees very well with the prediction by an analytic
theory () and numerical calculations. These results will facilitate
studies of quantum information science with mesoscopic ensembles.Comment: 4 pages, 3 figure
Vlasov Equation In Magnetic Field
The linearized Vlasov equation for a plasma system in a uniform magnetic
field and the corresponding linear Vlasov operator are studied. The spectrum
and the corresponding eigenfunctions of the Vlasov operator are found. The
spectrum of this operator consists of two parts: one is continuous and real;
the other is discrete and complex. Interestingly, the real eigenvalues are
infinitely degenerate, which causes difficulty solving this initial value
problem by using the conventional eigenfunction expansion method. Finally, the
Vlasov equation is solved by the resolvent method.Comment: 15 page
A quantitative comparison of sRNA-based and protein-based gene regulation
Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in
prokaryotes. sRNAs act post-transcriptionally via complementary pairing with
target mRNAs to regulate protein expression. We use a quantitative approach to
compare and contrast sRNAs with conventional transcription factors (TFs) to
better understand the advantages of each form of regulation. In particular, we
calculate the steady-state behavior, noise properties, frequency-dependent gain
(amplification), and dynamical response to large input signals of both forms of
regulation. While the mean steady-state behavior of sRNA-regulated proteins
exhibits a distinctive tunable threshold-linear behavior, our analysis shows
that transcriptional bursting leads to significantly higher intrinsic noise in
sRNA-based regulation than in TF-based regulation in a large range of
expression levels and limits the ability of sRNAs to perform quantitative
signaling. Nonetheless, we find that sRNAs are better than TFs at filtering
noise in input signals. Additionally, we find that sRNAs allow cells to respond
rapidly to large changes in input signals. These features suggest a niche for
sRNAs in allowing cells to transition quickly yet reliably between distinct
states. This functional niche is consistent with the widespread appearance of
sRNAs in stress-response and quasi-developmental networks in prokaryotes.Comment: 26 pages, 8 figures; accepted for publication in Molecular Systems
Biolog
Fluctuation spectrum of quasispherical membranes with force-dipole activity
The fluctuation spectrum of a quasi-spherical vesicle with active membrane
proteins is calculated. The activity of the proteins is modeled as the proteins
pushing on their surroundings giving rise to non-local force distributions.
Both the contributions from the thermal fluctuations of the active protein
densities and the temporal noise in the individual active force distributions
of the proteins are taken into account. The noise in the individual force
distributions is found to become significant at short wavelengths.Comment: 9 pages, 2 figures, minor changes and addition
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