5,599 research outputs found
Bilayer Membrane in Confined Geometry: Interlayer Slide and Steric Repulsion
We derived free energy functional of a bilayer lipid membrane from the first
principles of elasticity theory. The model explicitly includes
position-dependent mutual slide of monolayers and bending deformation. Our free
energy functional of liquid-crystalline membrane allows for incompressibility
of the membrane and vanishing of the in-plane shear modulus and obeys
reflectional and rotational symmetries of the flat bilayer. Interlayer slide at
the mid-plane of the membrane results in local difference of surface densities
of the monolayers. The slide amplitude directly enters free energy via the
strain tensor. For small bending deformations the ratio between bending modulus
and area compression coefficient, Kb/KA, is proportional to the square of
monolayer thickness, h. Using the functional we performed self-consistent
calculation of steric potential acting on bilayer between parallel confining
walls separated by distance 2d. We found that temperature-dependent curvature
at the minimum of confining potential is enhanced four times for a bilayer with
slide as compared with a unit bilayer. We also calculate viscous modes of
bilayer membrane between confining walls. Pure bending of the membrane is
investigated, which is decoupled from area dilation at small amplitudes. Three
sources of viscous dissipation are considered: water and membrane viscosities
and interlayer drag. Dispersion has two branches. Confinement between the walls
modifies the bending mode with respect to membrane in bulk solution.
Simultaneously, inter-layer slipping mode, damped by viscous drag, remains
unchanged by confinement.Comment: 23 pages,3 figures, pd
Giant vesicles at the prolate-oblate transition: A macroscopic bistable system
Giant phospholipid vesicles are shown to exhibit thermally activated
transitions between a prolate and an oblate shape on a time scale of several
seconds. From the fluctuating contour of such a vesicle we extract ellipticity
as an effective reaction coordinate whose temporal probability distribution is
bimodal. We then reconstruct the effective potential from which we derive an
activation energy of the order of in agreement with theoretical
calculations. The dynamics of this transition is well described within a
Kramers model of overdamped diffusion in a bistable potential. Thus, this
system can serve as a model for macroscopic bistability.Comment: 10 pages, LaTeX, epsfig, 4 eps figures included, to appear in
Europhys. Let
Opening the random forest black box by the analysis of the mutual impact of features
Random forest is a popular machine learning approach for the analysis of
high-dimensional data because it is flexible and provides variable importance
measures for the selection of relevant features. However, the complex
relationships between the features are usually not considered for the selection
and thus also neglected for the characterization of the analysed samples. Here
we propose two novel approaches that focus on the mutual impact of features in
random forests. Mutual forest impact (MFI) is a relation parameter that
evaluates the mutual association of the featurs to the outcome and, hence, goes
beyond the analysis of correlation coefficients. Mutual impurity reduction
(MIR) is an importance measure that combines this relation parameter with the
importance of the individual features. MIR and MFI are implemented together
with testing procedures that generate p-values for the selection of related and
important features. Applications to various simulated data sets and the
comparison to other methods for feature selection and relation analysis show
that MFI and MIR are very promising to shed light on the complex relationships
between features and outcome. In addition, they are not affected by common
biases, e.g. that features with many possible splits or high minor allele
frequencies are prefered
An Allosteric Signaling Pathway of Human 3-Phosphoglycerate Kinase from Force Distribution Analysis
3-Phosphogycerate kinase (PGK) is a two domain enzyme, which transfers a phosphate group between its two substrates, 1,3-bisphosphoglycerate bound to the N-domain and ADP bound to the C-domain. Indispensable for the phosphoryl transfer reaction is a large conformational change from an inactive open to an active closed conformation via a hinge motion that should bring substrates into close proximity. The allosteric pathway resulting in the active closed conformation has only been partially uncovered. Using Molecular Dynamics simulations combined with Force Distribution Analysis (FDA), we describe an allosteric pathway, which connects the substrate binding sites to the interdomain hinge region. Glu192 of alpha-helix 7 and Gly394 of loop L14 act as hinge points, at which these two secondary structure elements straighten, thereby moving the substrate-binding domains towards each other. The long-range allosteric pathway regulating hPGK catalytic activity, which is partially validated and can be further tested by mutagenesis, highlights the virtue of monitoring internal forces to reveal signal propagation, even if only minor conformational distortions, such as helix bending, initiate the large functional rearrangement of the macromolecule. © 2014 Palmai et al
Tagged particle in a sheared suspension: effective temperature determines density distribution in a slowly varying external potential beyond linear response
We consider a sheared colloidal suspension under the influence of an external
potential that varies slowly in space in the plane perpendicular to the flow
and acts on one selected (tagged) particle of the suspension. Using a
Chapman-Enskog type expansion we derive a steady state equation for the tagged
particle density distribution. We show that for potentials varying along one
direction only, the tagged particle distribution is the same as the equilibrium
distribution with the temperature equal to the effective temperature obtained
from the violation of the Einstein relation between the self-diffusion and
tagged particle mobility coefficients. We thus prove the usefulness of this
effective temperature for the description of the tagged particle behavior
beyond the realm of linear response. We illustrate our theoretical predictions
with Brownian dynamics computer simulations.Comment: Accepted for publication in Europhys. Let
An analytical analysis of vesicle tumbling under a shear flow
Vesicles under a shear flow exhibit a tank-treading motion of their membrane,
while their long axis points with an angle < 45 degrees with respect to the
shear stress if the viscosity contrast between the interior and the exterior is
not large enough. Above a certain viscosity contrast, the vesicle undergoes a
tumbling bifurcation, a bifurcation which is known for red blood cells. We have
recently presented the full numerical analysis of this transition. In this
paper, we introduce an analytical model that has the advantage of being both
simple enough and capturing the essential features found numerically. The model
is based on general considerations and does not resort to the explicit
computation of the full hydrodynamic field inside and outside the vesicle.Comment: 19 pages, 9 figures, to be published in Phys. Rev.
Elastic deformation of a fluid membrane upon colloid binding
When a colloidal particle adheres to a fluid membrane, it induces elastic
deformations in the membrane which oppose its own binding. The structural and
energetic aspects of this balance are theoretically studied within the
framework of a Helfrich Hamiltonian. Based on the full nonlinear shape
equations for the membrane profile, a line of continuous binding transitions
and a second line of discontinuous envelopment transitions are found, which
meet at an unusual triple point. The regime of low tension is studied
analytically using a small gradient expansion, while in the limit of large
tension scaling arguments are derived which quantify the asymptotic behavior of
phase boundary, degree of wrapping, and energy barrier. The maturation of
animal viruses by budding is discussed as a biological example of such
colloid-membrane interaction events.Comment: 14 pages, 9 figures, REVTeX style, follow-up on cond-mat/021242
Probing active forces via a fluctuation-dissipation relation: Application to living cells
We derive a new fluctuation-dissipation relation for non-equilibrium systems
with long-term memory. We show how this relation allows one to access new
experimental information regarding active forces in living cells that cannot
otherwise be accessed. For a silica bead attached to the wall of a living cell,
we identify a crossover time between thermally controlled fluctuations and
those produced by the active forces. We show that the probe position is
eventually slaved to the underlying random drive produced by the so-called
active forces.Comment: 5 page
Stabilized High Power Laser for Advanced Gravitational Wave Detectors
Second generation gravitational wave detectors require high power lasers with several 100W of output power and with very low temporal and spatial fluctuations. In this paper we discuss possible setups to achieve high laser power and describe a 200W prestabilized laser system (PSL). The PSL noise requirements for advanced gravitational wave detectors will be discussed in general and the stabilization scheme proposed for the Advanced LIGO PSL will be described. Special emphasis will be given to the most demanding power stabilization requiremets and new results (RIN ≤ 4×10-9/surdHz) will be presented
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