3,666 research outputs found
Lateral phase separation of confined membranes
We consider membranes interacting via short, intermediate and long stickers.
The effects of the intermediate stickers on the lateral phase separation of the
membranes are studied via mean-field approximation. The critical potential
depth of the stickers increases in the presence of the intermediate sticker.
The lateral phase separation of the membrane thus suppressed by the
intermediate stickers. Considering membranes interacting with short and long
stickers, the effect of confinement on the phase behavior of the membranes is
also investigated analytically
Molecular Electroporation and the Transduction of Oligoarginines
Certain short polycations, such as TAT and polyarginine, rapidly pass through
the plasma membranes of mammalian cells by an unknown mechanism called
transduction as well as by endocytosis and macropinocytosis. These
cell-penetrating peptides (CPPs) promise to be medically useful when fused to
biologically active peptides. I offer a simple model in which one or more CPPs
and the phosphatidylserines of the inner leaflet form a kind of capacitor with
a voltage in excess of 180 mV, high enough to create a molecular electropore.
The model is consistent with an empirical upper limit on the cargo peptide of
40--60 amino acids and with experimental data on how the transduction of a
polyarginine-fluorophore into mouse C2C12 myoblasts depends on the number of
arginines in the CPP and on the CPP concentration. The model makes three
testable predictions.Comment: 15 pages, 5 figure
Cooperativity and Frustration in Protein-Mediated Parallel Actin Bundles
We examine the mechanism of bundling of cytoskeletal actin filaments by two
representative bundling proteins, fascin and espin. Small-angle X-ray studies
show that increased binding from linkers drives a systematic \textit{overtwist}
of actin filaments from their native state, which occurs in a linker-dependent
fashion. Fascin bundles actin into a continuous spectrum of intermediate twist
states, while espin only allows for untwisted actin filaments and
fully-overtwisted bundles. Based on a coarse-grained, statistical model of
protein binding, we show that the interplay between binding geometry and the
intrinsic \textit{flexibility} of linkers mediates cooperative binding in the
bundle. We attribute the respective continuous/discontinous bundling mechanisms
of fascin/espin to differences in the stiffness of linker bonds themselves.Comment: 5 pages, 3 figures, figure file has been corrected in v
Elastic Correlations in Nucleosomal DNA Structure
The structure of DNA in the nucleosome core particle is studied using an
elastic model that incorporates anisotropy in the bending energetics and
twist-bend coupling. Using the experimentally determined structure of
nucleosomal DNA [T.J. Richmond and C.A. Davey, Nature {\bf 423}, 145 (2003)],
it is shown that elastic correlations exist between twist, roll, tilt, and
stretching of DNA, as well as the distance between phosphate groups. The
twist-bend coupling term is shown to be able to capture these correlations to a
large extent, and a fit to the experimental data yields a new estimate of G=25
nm for the value of the twist-bend coupling constant
Comparison of Simulator Wear Measured by Gravimetric vs Optical Surface Methods for Two Million Cycles
Understanding wear mechanisms are key for better implants
Critical to the success of the simulation
Small amount of metal wear can have catastrophic effects in the patient such as heavy metal poisoning or deterioration of the bone/implant interface leading to implant failure
Difficult to measure in heavy hard-on-hard implants (metal-on-metal or ceramic-on-ceramic)
May have only fractions of a milligram of wear on a 200 g component
At the limit of detection of even high-end balances when the component is 200 g and the change in weight is on the order of 0.000 1 grams
Here we compare the standard gravimetric wear estimate with
A non-contact 3D optical profiling method at each weighing stop
A coordinate measuring machine (CMM) at the beginning and end of the ru
Wrapping Transition and Wrapping-Mediated Interactions for Discrete Binding along an Elastic Filament: An Exact Solution
The wrapping equilibria of one and two adsorbing cylinders are studied along
a semi-flexible filament (polymer) due to the interplay between elastic
rigidity and short-range adhesive energy between the cylinder and the filament.
We show that statistical mechanics of the system can be solved exactly using a
path integral formalism which gives access to the full effect of thermal
fluctuations, going thus beyond the usual Gaussian approximations which take
into account only the contributions from the minimal energy configuration and
small fluctuations about this minimal energy solution. We obtain the free
energy of the wrapping-unwrapping transition of the filament around the
cylinders as well as the effective interaction between two wrapped cylinders
due to thermal fluctuations of the elastic filament. A change of entropy due to
wrapping of the filament around the adsorbing cylinders as they move closer
together is identified as an additional source of interactions between them.
Such entropic wrapping effects should be distinguished from the usual entropic
configuration effects in semi-flexible polymers. Our results may be applicable
to the problem of adsorption of proteins as well as synthetic nano-particles on
semi-flexible polymers such as DNA.Comment: 24 pages, 12 figure
Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops
The equilibrium three dimensional shape of relatively short loops of DNA is
studied using an elastic model that takes into account anisotropy in bending
rigidities. Using a reasonable estimate for the anisotropy, it is found that
cyclized DNA with lengths that are not integer multiples of the pitch take on
nontrivial shapes that involve bending out of planes and formation of kinks.
The effect of sequence inhomogeneity on the shape of DNA is addressed, and
shown to enhance the geometrical features. These findings could shed some light
on the role of DNA conformation in protein--DNA interactions
Exact solution of a linear molecular motor model driven by two-step fluctuations and subject to protein friction
We investigate by analytical means the stochastic equations of motion of a
linear molecular motor model based on the concept of protein friction. Solving
the coupled Langevin equations originally proposed by Mogilner et al. (A.
Mogilner et al., Phys. Lett. {\bf 237}, 297 (1998)), and averaging over both
the two-step internal conformational fluctuations and the thermal noise, we
present explicit, analytical expressions for the average motion and the
velocity-force relationship. Our results allow for a direct interpretation of
details of this motor model which are not readily accessible from numerical
solutions. In particular, we find that the model is able to predict
physiologically reasonable values for the load-free motor velocity and the
motor mobility.Comment: 12 pages revtex, 6 eps-figure
Specific protein-protein binding in many-component mixtures of proteins
Proteins must bind to specific other proteins in vivo in order to function.
The proteins must bind only to one or a few other proteins of the of order a
thousand proteins typically present in vivo. Using a simple model of a protein,
specific binding in many component mixtures is studied. It is found to be a
demanding function in the sense that it demands that the binding sites of the
proteins be encoded by long sequences of bits, and the requirement for specific
binding then strongly constrains these sequences. This is quantified by the
capacity of proteins of a given size (sequence length), which is the maximum
number of specific-binding interactions possible in a mixture. This calculation
of the maximum number possible is in the same spirit as the work of Shannon and
others on the maximum rate of communication through noisy channels.Comment: 13 pages, 3 figures (changes for v2 mainly notational - to be more in
line with notation in information theory literature
Twirling Elastica: Kinks, Viscous Drag, and Torsional Stress
Biological filaments such as DNA or bacterial flagella are typically curved
in their natural states. To elucidate the interplay of viscous drag, twisting,
and bending in the overdamped dynamics of such filaments, we compute the
steady-state torsional stress and shape of a rotating rod with a kink. Drag
deforms the rod, ultimately extending or folding it depending on the kink
angle. For certain kink angles and kink locations, both states are possible at
high rotation rates. The agreement between our macroscopic experiments and the
theory is good, with no adjustable parameters.Comment: 4 pages, 4 figure
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