Dušan Račko

Segregation of semiflexible macromolecules in nanochannel.

Investigation of segregation of polymer coils in open channel was extended relative to previous studies from flexible chains to semiflexible chains. Our results are based on simulation of confinement free energy of a chain in channel and on direct simulation of coil segregation process. For confinement free energy, we confirm the predicted opposite trend with increasing chain stiffness for the weak and for strong confinement regimes. Results of two different approaches are consistent, in agreement with theoretical analysis and indicate a stronger segregation tendency of flexible chains in channel relative to semiflexible chains both in its extent and dynamics.

The free volume of poly(vinyl methylether) as computed in a wide temperature range and at length scales up to the nanoregion.

In the present work, we focus on the free volume evaluations from different points of view, including the aspect of probe sizes, temperature, and cavity threshold. The free volume structure is analyzed on structures of poly(vinyl methylether) prepared by fully atomistic molecular dynamics. At first, the temperature behavior of an overall free volume and a free volume separated into individual cavities is shown. The origin of large free volume cavities is explained. A complex view on the cavity number is provided, while a complicated behavior previously observed is now explained. The number of large cavities remained almost constant with the temperature. Oppositely, the number of small cavities related to the atomic packing changes with temperature in a distinct way for glassy and supercooled regions. The cavity number maxima determine a percolation threshold according to percolation theory. The change in polymer properties with temperature can be related to a percolation of the free volume according to the free volume theory, when proper probe radii ∼0.8 Å are used for its observation. A construction of probabilistic distribution of free volume sizes is suggested. The free volume distributions reported here are bimodal. The bimodal character is explained by two different packings--atomic and segmental--forming a prepeak and a main peak on the distribution. Further attention is dedicated to comparisons of the computed free volume sizes and the ortho-positronium (o-Ps) lifetimes. The prepeak of the free volume distribution is probably unseen by o-Ps because of a cavity threshold limit. The effect of the shape factor on the computed o-Ps lifetimes is tested. The quasicavities obtained by redistributing the free volume maintain the ratio of the main dimensions with temperature. Finally, novel data on the cavity environment are provided, while it is suggested how these can be useful with the recent developments in the positron annihilation methods. The coordination number of large cavities with the polymer segments is around 1, as predicted in the free volume theory. Similarly to the percolation and the cavity number, the coordination number exhibits a change when explored by a suitable probe radius ∼0.8 Å. The insightful visualizations showed properties of interest investigated within the actual work.

Positron annihilation lifetime spectroscopy and atomistic modeling – effective tools for the disordered condensed systems characterization

The complex structure-property relationships in the disordered systems under normal and exogenic conditions can be understood after characterizing the spatial arrangement of constituents. Here, an integral approach including the relevant experimental technique, phenomenological, and theoretical analyses as well as atomistic modeling is presented. Application of such a combined approach is demonstrated for the cases of glycerol and propylene glycol.

In situ electron microscopy of Braille microsystems: photo-actuation of ethylene vinyl acetate/carbon nanotube composites

The development of new types of tactile displays based on the actuation of composite materials can aid the visually impaired. Micro/nano systems based on ethylene vinyl acetate (EVA) polymeric matrices enriched with multiwalled carbon nanotubes (MWCNT) can produce ensembles capable of light-induced actuation. In this report, we investigate two types of commercial EVA copolymers matrices containing 28 and 50 wt% vinyl-acetate (VA). Non-covalent modification of carbon nanotubes was achieved through a compatibilization technique that appends the pyrenenyl and cholesteryl groups on the carbon nanotubes (CNTs) surface. EVA/MWCNT nanocomposites were prepared by casting from a solution. These composites were shaped into Braille elements using molds. The deformation of the Braille element (BE) under light-emitting diode (LED) illumination was observed for the first time by in situ scanning electron microscopy (SEM). The superior actuation performance promoted by the EVA/MWCNT nanocomposites indicates that these materials will be useful in the future as light-driven micro/nano system actuators.

On the Relationship of the Relative Intensity I3 and a Cavity Number as Obtained from Computer Simulations

In this contribution a generalized picture of the cavity number behavior is obtained by means of molecular dynamics simulations and consequent free volume analysis. The cavity number obtained for free volume cavities defined by different probe radii shows a complex behavior with the temperature. The number of cavities determined by small probes drops with the temperature. The number of cavities determined by large probes increases. This complex behavior of the cavity number can be discussed with the distinct behavior of the relative intensity, as observed in the experiment, and a support for the most basic of assumptions, that the cavity number relates to the relative intensity, is given.

The Free Volume Dynamics

In the present contribution the dynamics of the intermolecular free volume is investigated. For this purpose a new computational algorithm has been proposed and programmed. The free volume is analyzed along the atomistic trajectory obtained by molecular dynamics simulations and a picture on time averaged free volume structure is obtained. The picture showed two distinct regimes of the free volume dynamics at pico-second and nano-second time-scale in liquid. The analysis has shown that at the time scale of the ortho-positronium lifetime and in the liquid phase the free volume microstructure ceases to exist in rigid cavities. This picture is consistent with the common considerations on the o-Ps existence, which suppose the o-Ps atom digging its own holes/cavities in liquids around the temperature of the o-Ps lifetime saturates.

Chromatin Loop Extrusion and Chromatin Unknotting

It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium. The topological equilibrium in highly crowded interphase chromosomes forming chromosome territories would result in formation of highly knotted chromatin fibres. However, Chromosome Conformation Capture (3C) methods revealed that the decay of contact probabilities with the genomic distance in interphase chromosomes is practically the same as in the crumpled globule state that is formed when long polymers condense without formation of any knots. To remove knots from highly crowded chromatin, one would need an active process that should not only provide the energy to move the system from the state of topological equilibrium but also guide topoisomerase-mediated passages in such a way that knots would be efficiently unknotted instead of making the knots even more complex. We perform coarse-grained molecular dynamics simulations of the process of chromatin loop extrusion involving knotted and catenated chromatin fibres to check whether chromatin loop extrusion may be involved in active unknotting of chromatin fibres. Our simulations show that the process of chromatin loop extrusion is ideally suited to actively unknot, decatenate and demix chromatin fibres in interphase chromosomes.

A Computational Model for Nano Scale Cavities in the Atomic Structure of Polymer Melt and Comparisons to PALS

In the Present Contribution the Atomistic Structure of the Polymer Melt at 300 K Is Simulated by Means of Molecular Dynamics. the Agreement with an Experimental Density Is Obtained with a Deviation Lower than 1%. the Free Volume Is Analyzed in 1,000 Structures and 6.5 X 108 Cubic Å of Molecular Space. a Model for the Free Volume Cavities Is Proposed. in the Model the Size and Number of the Cavities Can Be Scaled by Three Parameters: Probe Radius, Cavity Depth and Cavity Threshold Volume. the Experimental Values of the Nano-Sized Cavity Volumes as Well as Ortho-Positronium Lifetimes Are Obtained, as Compared to Models with Cylindrical and Spherical Geometry. a Typical Value of the Number Density of Free Volume Cavities at 0.001 Å-3 Is Obtained. the Cavities Have Typically Elongated Shape with a Side-to-Length Ratio 1:2.