2,627 research outputs found
Density fields for branching, stiff networks in rigid confining regions
We develop a formalism to describe the equilibrium distributions for segments
of confined branched networks consisting of stiff filaments. This is applicable
to certain situations of cytoskeleton in cells, such as for example actin
filaments with branching due to the Arp2/3 complex. We develop a grand ensemble
formalism that enables the computation of segment density and polarisation
profiles within the confines of the cell. This is expressed in terms of the
solution to nonlinear integral equations for auxiliary functions. We find three
specific classes of behaviour depending on filament length, degree of branching
and the ratio of persistence length to the dimensions of the geometry. Our
method allows a numerical approach for semi-flexible filaments that are
networked.Comment: 15 pages, revise
Entropic competition in polymeric systems under geometrical confinement
Using molecular dynamics simulation, we investigate the effect of confinement
on a system that comprises several stiff segmented polymer chains where each
chain has similar segments, but length and stiffness of the segments vary among
the chains which makes the system inhomogeneous. The translational and
orientational entropy loss due to the confinement plays a crucial role in
organizing the chains which can be considered as an entropy-driven segregation
mechanism to differentiate the components of the system. Due to the
inhomogeneity, both weak and strong confinement regimes show the competition in
the system and we see segregation of chains as the confining volume is
decreased. In the case of strong spherical confinement, a chain at the
periphery shows higher angular mobility than other chains, despite being more
radially constrained.Comment: 16 pages, 11 figure
Total N difference method and 15N isotope dilution methode - A comparative study on N-fixation
In the study, the 15N fixation of a number of green manure crops were studied using either the 15N dilution technique, or the simple total N difference method. The results of the two methods were not very different, and the total N difference method seemed to give as good results as the more complicated and expencive 15N dillution method
Catch Crops in Organic Farming Systems without Livestock Husbandry - Simulations with the DAISY model
This paper presents simulations of the soil-plant-atmosphere model DAISY based on an organic crop rotation with incorporation of different catch crops following pea as a leguminous cash crop. Special emphasise was put on the simulation of N-mineralisation/-immobilisation and of soil microbial biomass N. The DAISY model was able to simulate soil mineral N and soil microbial biomass N after soil incorporation of catch crop plant residues to some extend. Several processes need further attention and may be integrated into the DAISY model: (1) soil tillage induced mobilisation of organic material including considerable amounts of organic N, (2) winter killing of sensitive plant species and varieties, (3) decomposition of plant residues at the soil surface as occurring after winter killing, (4) decomposition of easily decomposable plant residues at low temperatures, (5) soil microbial residues as an organic pool temporarily protected against turnover. Furthermore, reliable criteria for the subdivision of green plant residues into an easily decomposable pool and a more recalcitrant pool have to be developed
Field-theoretical approach to a dense polymer with an ideal binary mixture of clustering centers
We propose a field-theoretical approach to a polymer system immersed in an
ideal mixture of clustering centers. The system contains several species of
these clustering centers with different functionality, each of which connects a
fixed number segments of the chain to each other. The field-theory is solved
using the saddle point approximation and evaluated for dense polymer melts
using the Random Phase Approximation. We find a short-ranged effective
inter-segment interaction with strength dependent on the average segment
density and discuss the structure factor within this approximation. We also
determine the fractions of linkers of the different functionalities.Comment: 27 pages, 9 figures, accepted on Phys. Rev.
Collective Dynamics of Random Polyampholytes
We consider the Langevin dynamics of a semi-dilute system of chains which are
random polyampholytes of average monomer charge and with a fluctuations in
this charge of the size and with freely floating counter-ions in the
surrounding. We cast the dynamics into the functional integral formalism and
average over the quenched charge distribution in order to compute the dynamic
structure factor and the effective collective potential matrix. The results are
given for small charge fluctuations. In the limit of finite we then find
that the scattering approaches the limit of polyelectrolyte solutions.Comment: 13 pages including 6 figures, submitted J. Chem. Phy
Motor-driven Dynamics of Cytoskeletal FIlaments in Motility Assays
We model analytically the dynamics of a cytoskeletal filament in a motility
assay. The filament is described as rigid rod free to slide in two dimensions.
The motor proteins consist of polymeric tails tethered to the plane and modeled
as linear springs and motor heads that bind to the filament. As in related
models of rigid and soft two-state motors, the binding/unbinding dynamics of
the motor heads and the dependence of the transition rates on the load exerted
by the motor tails play a crucial role in controlling the filament's dynamics.
Our work shows that the filament effectively behaves as a self-propelled rod at
long times, but with non-Markovian noise sources arising from the coupling to
the motor binding/unbinding dynamics. The effective propulsion force of the
filament and the active renormalization of the various friction and diffusion
constants are calculated in terms of microscopic motor and filament parameters.
These quantities could be probed by optical force microscopy.Comment: 13 pages, 8 figures, 1 Tabl
Adsorption studies of DNA origami on silicon dioxide
Self-assembled DNA nanostructures promise low-cost ways to create nanoscale shapes. DNA nanostructures can also be used to position particles with nanometer precision. Yet, reliable and low-cost ways of integrating the structures with MEMS technology still have to be developed and innovations are of great interest to the field. We have examined in detail the adherence of DNA origami tiles on silicon oxide surfaces of wafers in dependence on pH-value and magnesium ion concentration. The results of this work will help to pursue new strategies of positioning DNA nanostruc-tures on SiO2. Precise control over the strength of structure-surface adhesion is a prerequisite of relia-ble processes
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