Structure of Polymer Brushes in Cylindrical Tubes: A Molecular Dynamics Simulation

Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide range and the crossover from ``mushroom'' to ``brush'' behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $\sigma$ for large enough pore diameter where the brush height in the pore exceeds the brush height on the flat substrate, while for large enough $N$ and $\sigma$ (and small enough pore diameters) the opposite behavior occurs, i.e. the brush is compressed by confinement. These findings are used to discuss the corresponding theories on polymer brushes at concave substrates.Comment: 11 figure

Monte Carlo simulations reveal the straightening up of an end-grafted flexible chain with a rigid side chain

We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we observe a considerable straightening of the flexible backbone as quantified via the gyration tensor. For $b=N$, i.e. when attaching the side chain to the free end of the flexible backbone, the effect was strongest

Structural Properties of Two-Dimensional Polymers

We present structural properties of two-dimensional polymers as far as they can be described by percolation theory. The percolation threshold, critical exponents and fractal dimensions of clusters are determined by computer simulation and compared to the results of percolation theory. We also describe the dependence of the typical cluster structures on the reaction rate.Comment: 7 pages, LaTeX with RevTeX and epsf styles and PostScript figures included (uuencoded shell archive), TVP-93051

Survival and some physiological aspects of tissue cultured cells from Douglas-fir (Pseudotsuga menziesii Mirb. (Franco)) and a poplar hybrid after freezing to liquid nitrogen temperature

Cell aggregate size in both Douglas-fir and poplar suspension cultures was reduced by the addition of the chelator compounds EDTA and CDTA at concentrations under 100 ppm. Reduced cell aggregate size increased growth efficiency of suspension cultures of both species. Cell aggregates 550 j.z. or smaller in size were used in the cryogenic studies. At room temperature, the cryoprotectants dimethyl sulfoxide (DMSO) and glycerol at concentrations above 5% were toxic to cell survival; however when these were washed out with fresh media, the growth rate of both Douglas-fir and poplar suspension cultures was increased. The optimum cryoprotectant concentration was about 1.0%. At concentrations above 5% repeated washing with fresh media did not reduce the cellular cryoprotectant concentration and cellular injury or death may have resulted solely from the presence of cryoprotectants, even in the absence of freezing. Cryoprotectant influences observed were thought to be due to cell membrane changes allowing increased nutrient flow in the case of cell death. Cold conditioning or chilling callus at +4°C allowed higher concentrations of cryoprotectants to be added without killing cells. Suspension cultures showed that Douglas-fir entered the log phase of growth 7 days and poplar 3 days after innoculation. Cells were small and densely cytoplasmic during this time. For both species slow freezing of log-growth-phase cells at 1°C/mm was better than fast freezing; a two-step freezing protocol, cooling first to -40°C and then immersion into liquid nitrogen was successful; cooling to -40°C was more effective than cooling to higher temperatures; and fast thawing to +40°C was more effective than slow thawing in air. The cryoprotectants DMSO, glycerol and sucrose are effective alone and in combination. Most effective was a combination of all three; DMSO 5%/glycerol 1%/sucrose 4% for Douglas-fir and DMSO 5%/glycerol 5%/sucrose 4% for poplar. Douglas-fir and poplar cultures on thawing were tested for viability-by assessing ability to reduce tetrazolium salts and ability to continue growth. Poplar cultures resumed growth after approximately 5 weeks post-thaw culture, whereas for Douglas-fir over 80 days was required. Thawed and recultured poplar callus differentiated into shoots and roots. Cold conditioned callus Of both Douglas-fir and poplar produced high TTC reduction values directly after thawing. Cold conditioned poplar callus frozen without cryoprotectantS or liquid responded better on thawing than when frozen with cryoprotectants in liquid media. Douglas-fir buds obtained from field trees in August or seedlings cold conditioned at +4°C for 8 weeks were frozen under various conditions, but no buds survived the freezing process. The development of techniques for successful freeze preservation requires a detailed empirical examination of; prefreezing culture conditions, physiological state and size of cells, cryoprotectant type and concentration used, freezing rate and temperature frozen to, and thaw rate and post-thaw culture conditions

Large-scale Simulation of the Two-dimensional Kinetic Ising Model

We present Monte Carlo simulation results for the dynamical critical exponent $z$ of the two-dimensional kinetic Ising model using a lattice of size $10^6 \times 10^6$ spins. We used Glauber as well as Metropolis dynamics. The $z$-value of $2.16\pm 0.005$ was calculated from the magnetization and energy relaxation from an ordered state towards the equilibrium state at $T_c$.Comment: 6 pages + 2 figures as separate uuencoded compressed tar file, Postscipt also available at http://wwwcp.tphys.uni-heidelberg.de/papers

Dynamical temperature study for classical planar spin systems

In this micro-canonical simulation the temperature and also the specific heat are determined as averages of expressions easy to implement. The XY-chain is studied for a test. The second order transition on a cubic lattice and the first order transition on an fcc lattice are analyzed in greater detail to have a more severe test about the feasibility of this micro-canonical method.Comment: 9 pages in Latex(revtex), 7 PS-figure

The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin

We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$ between the in and outgoing DNA strands. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the vertical distance $d$ has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded volume borderline or missing H1 histones which can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values

Superdiffusion in a Model for Diffusion in a Molecularly Crowded Environment

We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous diffusion at intermediate times. The effective exponents for square distance versus time usually are below one at these intermediate times, but can be also larger than one for high barrier concentrations. Thus we observe sub- as well as super-diffusion in a crowded environment.Comment: 8 pages including 4 figure