921 research outputs found
Probing molecular free energy landscapes by periodic loading
Single molecule pulling experiments provide information about interactions in
biomolecules that cannot be obtained by any other method. However, the
reconstruction of the molecule's free energy profile from the experimental data
is still a challenge, in particular for the unstable barrier regions. We
propose a new method for obtaining the full profile by introducing a periodic
ramp and using Jarzynski's identity for obtaining equilibrium quantities from
non-equilibrium data. Our simulated experiments show that this method delivers
significant more accurate data than previous methods, under the constraint of
equal experimental effort.Comment: 4 pages, 3 figure
A Connection between Obscuration and Star Formation in Luminous Quasars
We present a measurement of the star formation properties of a uniform sample of mid-IR selected, unobscured and obscured quasars (QSO1s and QSO2s) in the Bo\ otes survey region. We use an spectral energy distribution (SED) analysis for photometric data spanning optical to far-IR wavelengths to decompose AGN and host galaxy components. We find that when compared to a matched sample of QSO1s, the QSO2s have higher far-IR detection fractions, far-IR fluxes and infrared star formation luminosities (LSFIR) by a factor of ∼2. Correspondingly, we show that the AGN obscured fraction rises from 0.3 to 0.7 between 4−40×1011L⊙. We also find evidence associating the absorption in the X-ray emission with the presence of far-IR emitting dust. Overall, these results are consistent with galaxy evolution models in which quasar obscurations can be associated with a dust-enshrouded starburst galaxie
Polymer translocation through a nanopore under an applied external field
We investigate the dynamics of polymer translocation through a nanopore under
an externally applied field using the 2D fluctuating bond model with
single-segment Monte Carlo moves. We concentrate on the influence of the field
strength , length of the chain , and length of the pore on forced
translocation. As our main result, we find a crossover scaling for the
translocation time with the chain length from for
relatively short polymers to for longer chains, where
is the Flory exponent. We demonstrate that this crossover is due to the
change in the dependence of the translocation velocity v on the chain length.
For relatively short chains , which crosses over to for long polymers. The reason for this is that with increasing
there is a high density of segments near the exit of the pore, which slows down
the translocation process due to slow relaxation of the chain. For the case of
a long nanopore for which , the radius of gyration along
the pore, is smaller than the pore length, we find no clear scaling of the
translocation time with the chain length. For large , however, the
asymptotic scaling is recovered. In this regime, is almost independent of . We have previously found that for a polymer,
which is initially placed in the middle of the pore, there is a minimum in the
escape time for . We show here that this minimum
persists for a weak fields such that is less than some critical value,
but vanishes for large values of .Comment: 25 Pages, 10 figures. Submitted to J. Chem. Phys. J. Chem. Phys. 124,
in press (2006
Polymer translocation through a nanopore: a two-dimensional Monte Carlo simulation
We investigate the problem of polymer translocation through a nanopore in the
absence of an external driving force. To this end, we use the two-dimensional
(2D) fluctuating bond model with single-segment Monte Carlo moves. To overcome
the entropic barrier without artificial restrictions, we consider a polymer
which is initially placed in the middle of the pore, and study the escape time
required for the polymer to completely exit the pore on either end. In
particular, we examined the effect of the pore length on the escape time.Comment: 16Pages, 6 figure
Mechanochemical action of the dynamin protein
Dynamin is a ubiquitous GTPase that tubulates lipid bilayers and is
implicated in many membrane severing processes in eukaryotic cells. Setting the
grounds for a better understanding of this biological function, we develop a
generalized hydrodynamics description of the conformational change of large
dynamin-membrane tubes taking into account GTP consumption as a free energy
source. On observable time scales, dissipation is dominated by an effective
dynamin/membrane friction and the deformation field of the tube has a simple
diffusive behavior, which could be tested experimentally. A more involved,
semi-microscopic model yields complete predictions for the dynamics of the tube
and possibly accounts for contradictory experimental results concerning its
change of conformation as well as for plectonemic supercoiling.Comment: 17 pages, 4 figures; typos corrected, reference adde
An affine continuum mechanical model for cross-linked F-actin networks with compliant linker proteins
Cross-linked actin networks are important building blocks of the cytoskeleton. In order to gain deeper insight into the interpretation of experimental data on actin networks, adequate models are required. In this paper we introduce an affine constitutive network model for cross-linked F-actin networks based on nonlinear continuum mechanics, and specialize it in order to reproduce the experimental behavior of in vitro reconstituted model networks. The model is based on the elastic properties of single filaments embedded in an isotropic matrix such that the overall properties of the composite are described by a free-energy function. In particular, we are able to obtain the experimentally determined shear and normal stress responses of cross-linked actin networks typically observed in rheometer tests. In the present study an extensive analysis is performed by applying the proposed model network to a simple shear deformation. The single filament model is then extended by incorporating the compliance of cross-linker proteins and further extended by including viscoelasticity. All that is needed for the finite element implementation is the constitutive model for the filaments, the linkers and the matrix, and the associated elasticity tensor in either the Lagrangian or Eulerian formulation. The model facilitates parameter studies of experimental setups such as micropipette aspiration experiments and we present such studies to illustrate the efficacy of this modeling approach
Molecular Spiders in One Dimension
Molecular spiders are synthetic bio-molecular systems which have "legs" made
of short single-stranded segments of DNA. Spiders move on a surface covered
with single-stranded DNA segments complementary to legs. Different mappings are
established between various models of spiders and simple exclusion processes.
For spiders with simple gait and varying number of legs we compute the
diffusion coefficient; when the hopping is biased we also compute their
velocity.Comment: 14 pages, 2 figure
Stochastic Eulerian Lagrangian Methods for Fluid-Structure Interactions with Thermal Fluctuations
We present approaches for the study of fluid-structure interactions subject
to thermal fluctuations. A mixed mechanical description is utilized combining
Eulerian and Lagrangian reference frames. We establish general conditions for
operators coupling these descriptions. Stochastic driving fields for the
formalism are derived using principles from statistical mechanics. The
stochastic differential equations of the formalism are found to exhibit
significant stiffness in some physical regimes. To cope with this issue, we
derive reduced stochastic differential equations for several physical regimes.
We also present stochastic numerical methods for each regime to approximate the
fluid-structure dynamics and to generate efficiently the required stochastic
driving fields. To validate the methodology in each regime, we perform analysis
of the invariant probability distribution of the stochastic dynamics of the
fluid-structure formalism. We compare this analysis with results from
statistical mechanics. To further demonstrate the applicability of the
methodology, we perform computational studies for spherical particles having
translational and rotational degrees of freedom. We compare these studies with
results from fluid mechanics. The presented approach provides for
fluid-structure systems a set of rather general computational methods for
treating consistently structure mechanics, hydrodynamic coupling, and thermal
fluctuations.Comment: 24 pages, 3 figure
The influence of gene expression time delays on Gierer-Meinhardt pattern formation systems
There are numerous examples of morphogen gradients controlling long range signalling in developmental and cellular systems. The prospect of two such interacting morphogens instigating long range self-organisation in biological systems via a Turing bifurcation has been explored, postulated, or implicated in the context of numerous developmental processes. However, modelling investigations of cellular systems typically neglect the influence of gene expression on such dynamics, even though transcription and translation are observed to be important in morphogenetic systems. In particular, the influence of gene expression on a large class of Turing bifurcation models, namely those with pure kinetics such as the Gierer–Meinhardt system, is unexplored. Our investigations demonstrate that the behaviour of the Gierer–Meinhardt model profoundly changes on the inclusion of gene expression dynamics and is sensitive to the sub-cellular details of gene expression. Features such as concentration blow up, morphogen oscillations and radical sensitivities to the duration of gene expression are observed and, at best, severely restrict the possible parameter spaces for feasible biological behaviour. These results also indicate that the behaviour of Turing pattern formation systems on the inclusion of gene expression time delays may provide a means of distinguishing between possible forms of interaction kinetics. Finally, this study also emphasises that sub-cellular and gene expression dynamics should not be simply neglected in models of long range biological pattern formation via morphogens
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