987 research outputs found
Bundles of Interacting Strings in Two Dimensions
Bundles of strings which interact via short-ranged pair potentials are
studied in two dimensions. The corresponding transfer matrix problem is solved
analytically for arbitrary string number N by Bethe ansatz methods. Bundles
consisting of N identical strings exhibit a unique unbinding transition. If the
string bundle interacts with a hard wall, the bundle may unbind from the wall
via a unique transition or a sequence of N successive transitions. In all
cases, the critical exponents are independent of N and the density profile of
the strings exhibits a scaling form that approaches a mean-field profile in the
limit of large N.Comment: 8 pages (latex) with two figure
Critical behavior of interacting surfaces with tension
Wetting phenomena, molecular protrusions of lipid bilayers and membrane
stacks under lateral tension provide physical examples for interacting surfaces
with tension. Such surfaces are studied theoretically using functional
renormalization and Monte Carlo simulations. The critical behavior arising from
thermally-excited shape fluctuations is determined both for global quantities
such as the mean separation of these surfaces and for local quantities such as
the probabilities for local contacts.Comment: 13 pages, 17 figures; accepted for publication in The European
Physical Journa
Collective Molecular Dynamics in Proteins and Membranes
The understanding of dynamics and functioning of biological membranes and in
particular of membrane embedded proteins is one of the most fundamental
problems and challenges in modern biology and biophysics. In particular the
impact of membrane composition and properties and of structure and dynamics of
the surrounding hydration water on protein function is an upcoming hot topic,
which can be addressed by modern experimental and computational techniques.
Correlated molecular motions might play a crucial role for the understanding
of, for instance, transport processes and elastic properties, and might be
relevant for protein function. Experimentally that involves determining
dispersion relations for the different molecular components, i.e., the length
scale dependent excitation frequencies and relaxation rates. Only very few
experimental techniques can access dynamical properties in biological materials
on the nanometer scale, and resolve dynamics of lipid molecules, hydration
water molecules and proteins and the interaction between them. In this context,
inelastic neutron scattering turned out to be a very powerful tool to study
dynamics and interactions in biomolecular materials up to relevant nanosecond
time scales and down to the nanometer length scale. We review and discuss
inelastic neutron scattering experiments to study membrane elasticity and
protein-protein interactions of membrane embedded proteins
Segregation of receptor-ligand complexes in cell adhesion zones: Phase diagrams and role of thermal membrane roughness
The adhesion zone of immune cells, the 'immunological synapse', exhibits
characteristic domains of receptor-ligand complexes. The domain formation is
likely caused by a length difference of the receptor-ligand complexes, and has
been investigated in experiments in which T cells adhere to supported membranes
with anchored ligands. For supported membranes with two types of anchored
ligands, MHCp and ICAM1, that bind to the receptors TCR and LFA1 in the cell
membrane, the coexistence of domains of TCR-MHCp and LFA1-ICAM1 complexes in
the cell adhesion zone has been observed for a wide range of ligand
concentrations and affinities. For supported membranes with long and short
ligands that bind to the same cell receptor CD2, in contrast, domain
coexistence has been observed for a rather narrow ratio of ligand
concentrations. In this article, we determine detailed phase diagrams for cells
adhering to supported membranes with a statistical-physical model of cell
adhesion. We find a characteristic difference between the adhesion scenarios in
which two types of ligands in a supported membrane bind (i) to the same cell
receptor or (ii) to two different cell receptors, which helps to explain the
experimental observations. Our phase diagrams fully include thermal shape
fluctuations of the cell membranes on nanometer scales, which lead to a
critical point for the domain formation and to a cooperative binding of the
receptors and ligands.Comment: 23 pages, 6 figure
Large stress asymmetries of lipid bilayers and nanovesicles generate lipid flip-flops and bilayer instabilities
Much effort has been devoted to lipid bilayers and nanovesicles with a compositional asymmetry between the two leaflets of the bilayer membranes. Here, we address another fundamental asymmetry related to lipid densities and membrane tensions. To avoid membrane rupture, the osmotic conditions must be adjusted in such a way that the bilayer membranes are subject to a relatively low bilayer tension. However, even for vanishing bilayer tension, the individual leaflets can still experience significant leaflet tensions if one leaflet is stretched whereas the other leaflet is compressed. Such a stress asymmetry between the two leaflets can be directly controlled in molecular dynamics simulations by the initial assembly of the lipid bilayers. This stress asymmetry is varied here over a wide range to determine the stability and instability regimes of the asymmetric bilayers. The stability regime shrinks with decreasing size and increasing membrane curvature of the nanovesicle. In the instability regimes, the lipids undergo stress-induced flip-flops with a flip-flop rate that increases with increasing stress asymmetry. The onset of flip-flops can be characterized by a cumulative distribution function that is well-fitted by an exponential function for planar bilayers but has a sigmoidal shape for nanovesicles. In addition, the bilayer membranes form transient non-bilayer structures that relax back towards ordered bilayers with a reduced stress asymmetry. Our study reveals intrinsic limits for the possible magnitude of the transbilayer stress asymmetry and shows that the leaflet tensions represent key parameters for the flip-flop rates
Molecular motor traffic in a half-open tube
The traffic of molecular motors which interact through mutual exclusion is
studied theoretically for half-open tube-like compartments. These half-open
tubes mimic the shapes of axons. The mutual exclusion leads to traffic jams or
density plateaus on the filaments. A phase transition is obtained when the
motor velocity changes sign. We identify the relevant length scales and
characterize the jamming behavior using both analytical approximations and
Monte Carlo simulations of lattice models.Comment: 14 pages, 5 postscript figure
Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks
We investigate the role of degradation of mRNA on protein synthesis using the totally asymmetric simple exclusion process (TASEP) as the underlying model for ribosome dynamics. mRNA degradation has a strong effect on the lifetime distribution of the mRNA, which in turn affects polysome statistics such as the number of ribosomes present on an mRNA strand of a given size. An average over mRNA of all ages is equivalent to an average over possible configurations of the corresponding TASEP-both before steady state and in steady state. To evaluate the relevant quantities for the translation problem, we first study the approach towards steady state of the TASEP, starting with an empty lattice representing an unloaded mRNA. When approaching the high density phase, the system shows two distinct phases with the entry and exit boundaries taking control of the density at their respective ends in the second phase. The approach towards the maximal current phase exhibits the surprising property that the ribosome entry flux can exceed the maximum possible steady state value. In all phases, the averaging over the mRNA age distribution shows a decrease in the average ribosome density profile as a function of distance from the entry boundary. For entry/exit parameters corresponding to the high density phase of TASEP, the average ribosome density profile also has a maximum near the exit end
Cooperative slowdown of water rotation near densely charged ions is intense but short-ranged
Accepted manuscript versionWe investigate the reorientation dynamics of water at 300 K in solutions of magnesium
sulfate and cesium chloride from classical atomistic molecular dynamics simulations
using the “simple water model with four sites and negative Drude polarizability”
(SWM4-NDP) and accompanying ion models; for SO2− 4 , we derive SWM4-NDPcompatible
parameters. Results indicate that pairs of ions have a cooperative effect on
water rotation, but do not support the model based on experiment whereby ion cooperativity
increases the number of very slow water molecules well beyond the ions’ first
hydration shell. Instead, we find that cooperative slowdown beyond the first hydration
shell is weak. Intense cooperative slowdown is limited to the first hydration shells, the
magnitude of the slowdown being stronger for the multivalent ions. Cooperative effects
for different salts differ in both the magnitude of rotational slowdown and the spatial
range of the affected water subpopulations
From supported membranes to tethered vesicles: lipid bilayers destabilisation at the main transition
We report results concerning the destabilisation of supported phospholipid
bilayers in a well-defined geometry. When heating up supported phospholipid
membranes deposited on highly hydrophilic glass slides from room temperature
(i.e. with lipids in the gel phase), unbinding was observed around the main gel
to fluid transition temperature of the lipids. It lead to the formation of
relatively monodisperse vesicles, of which most remained tethered to the
supported bilayer. We interpret these observations in terms of a sharp decrease
of the bending rigidity modulus in the transition region, combined
with a weak initial adhesion energy. On the basis of scaling arguments, we show
that our experimental findings are consistent with this hypothesis.Comment: 11 pages, 3 figure
Hydrodynamic lift on bound vesicles
Bound vesicles subject to lateral forces such as arising from shear flow are
investigated theoretically by combining a lubrication analysis of the bound
part with a scaling approach to the global motion. A minor inclination of the
bound part leads to significant lift due to the additive effects of lateral and
tank-treading motions. With increasing shear rate, the vesicle unbinds from the
substrate at a critical value. Estimates are in agreement with recent
experimental data.Comment: 9 pages, one figur
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