Phase separation of chromatin brush driven by enzymatic reaction dynamics of histone posttranslational modifications

The nuclei of undifferentiated cells show uniform decompacted chromatin while during development nuclei decrease in size and foci of condensed chromatin appear, reminiscent of phase separation. This study is motivated by recent experiments that suggest that the unbinding of enzymes that chemically modify (acetylate) histone tails causes decompaction of condensed chromatin. Here we take into account the enzymatic reactions of histone modifications to predict the phase separation of chromatin in a model system, the chromatin brush, which mimics chromatin at the proximity of a nuclear membrane. The model contains ‘activators’ and ‘silencers’, which change the state of the nucleosomes to (transcriptionally) active or inactive via the Michaelis-Menten kinetics. Our theory predicts that the chromatin brush will phase separate when the brush height is reduced below a threshold height. The phase separation is driven by an anti-correlation: Activators change the state of nucleosomes to the active state suppressing the binding of silencers to these nucleosomes and vice versa.

Morphologies of a polyelectrolyte brush grafted onto a cubic colloid in the presence of trivalent ions

Electrostatic correlation induces the non-monotonic variation of the brush height, multi-scale ordering and abundant lateral separated patterns.

Simulation and modelling of slip flow over surfaces grafted with polymer brushes and glycocalyx fibres

Fabrication of functionalized surfaces using polymer brushes is a relatively simple process and parallels the presence of glycocalyx filaments coating the luminal surface of our vasculature. In this paper, we perform atomistic-like simulations based on dissipative particle dynamics (DPD) to study both polymer brushes and glycocalyx filaments subject to shear flow, and we apply mean-field theory to extract useful scaling arguments on their response. For polymer brushes, a weak shear flow has no effect on the brush density profile or its height, while the slip length is independent of the shear rate and is of the order of the brush mesh size as a result of screening by hydrodynamic interactions. However, for strong shear flow, the polymer brush is penetrated deeper and is deformed, with a corresponding decrease of the brush height and an increase of the slip length. The transition from the weak to the strong shear regime can be described by a simple ‘blob’ argument, leading to the scaling ${\dot {\gamma } }_{0} \propto {\sigma }^{3/ 2} $, where ${\dot {\gamma } }_{0} $ is the critical transition shear rate and $\sigma $ is the grafting density. Furthermore, in the strong shear regime, we observe a cyclic dynamic motion of individual polymers, causing a reversal in the direction of surface flow. To study the glycocalyx layer, we first assume a homogeneous flow that ignores the discrete effects of blood cells, and we simulate microchannel flows at different flow rates. Surprisingly, we find that, at low Reynolds number, the slip length decreases with the mean flow velocity, unlike the behaviour of polymer brushes, for which the slip length remains constant under similar conditions. (The slip length and brush height are measured with respect to polymer mesh size and polymer contour length, respectively.) We also performed additional DPD simulations of blood flow in a tube with walls having a glycocalyx layer and with the deformable red blood cells modelled accurately at the spectrin level. In this case, a plasma cell-free layer is formed, with thickness more than three times the glycocalyx layer. We then find our scaling arguments based on the homogeneous flow assumption to be valid for this physiologically correct case as well. Taken together, our findings point to the opposing roles of conformational entropy and bending rigidity – dominant effects for the brush and glycocalyx, respectively – which, in turn, lead to different flow characteristics, despite the apparent similarity of the two systems.

Effect of Fluctuations in the Brush Conformation on the Interaction Between Polymer Brushes in a Good Solvent

This study presents a novel approach for analyzing the interaction between two parallel surfaces grafted with polymer brushes in a good solvent. In the proposed approach, molecular dynamics simulations are performed to establish the mean brush height and the standard deviation of the brush height distribution for a given value of the surface separation. The corresponding probability density function (PDF) of the brush height is then determined and a statistical technique is applied to compute the corresponding interaction free energy per unit area of the grafted substrates. Finally, the Derjaguin approximation is employed to determine the corresponding value of the interaction force between the two surfaces. At relatively high surface grafting density as well as under low to moderate compressions of these two parallel plates, the interdigitation effect of the brushes is quite weak and is not considered in the present study. The results obtained for the interaction free energy and interaction force are compared with those derived using the Alexander and de Gennes (AdG) model [1977, “Adsorption of Chain Molecules With a Polar Head. A Scaling Approach,” J. Phys. (Paris), 38, pp. 983–989, 1985, “Films of Polymer-Solutions,” C. R. Acad. Sci., 300, pp. 839–843] and the Milner, Witten, and Cates (MWC) model [1988, “Theory of the Grafted Polymer Brush,” Macromolecules, 21, pp. 2610–2619], respectively. The value of the normalized interaction free energy computed using the present method is higher than that obtained from the AdG and MWC models at larger surface separations. However, the three sets of results are in good agreement particularly at smaller values of the surface separation. In addition, the results obtained by the current method for the interaction force are found to be in better agreement with the experimental data than those obtained using the AdG or MWC models. The enhanced performance of the proposed method is attributed primarily to the use of an adaptive non-Gaussian PDF of the brush height to model the effects of fluctuations in the brush conformation at different distances from the grafting plane.

Growth of Advance Regeneration in Response to Residual Overstory Treatment in Northern Idaho

The effects of killing a low-volume residual overstory on growth of advance natural regeneration in North Idaho were assessed. Killing this overstory had little effect on subsequent growth of advance regeneration regardless of the basal area killed. Growth of regeneration following release was affected by competition from other advance regeneration and competition from brush. Height-growth response was negligible when density of either advance regeneration or brush were high. Residual tree killing was associated with improved crown vigor of regeneration where residual overstory basal area was high. Height growth of advance regeneration following residual tree killing was highly correlated with prerelease height growth and current crown vigor of advance regeneration. West. J. Appl. For. 7(3):78-81.