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Can Polymer Chains Cross Each Other and Still Be Entangled?
Chang, Rakwoo,Yethiraj, Arun American Chemical Society 2019 Macromolecules Vol.52 No.5
<P>The effect of chain crossing on polymer entanglement behavior is studied using molecular dynamics simulations of linear hard-sphere chains. The degree of chain crossing is controlled by changing the amplitude of bond vibrations while keeping the average bond length fixed. When the vibration amplitude is small, chain crossing is strictly prohibited, but for larger amplitudes the chains can cross. When chain crossing is strictly prohibited, the apparent scaling of the self-diffusion coefficient, <I>D</I>, and rotational relaxation time, τ<SUB>R</SUB>, with degree of polymerization, <I>N</I>, is consistent with entangled behavior, and when chains cross freely Rouse dynamics is recovered. There is an intermediate regime, however, when chains are allowed to cross, but crossing events are rare. Under these conditions entanglement behavior is recovered. We therefore conclude that polymer chains can cross and still be entangled for finite length chains. There is no discernible change in the intermolecular static structure factor between the unentangled and entangled systems.</P> [FIG OMISSION]</BR>
Computer Simulations of Protein Diffusion in Compartmentalized Cell Membranes
Sung, B.J.,Yethiraj, A. Biophysical Society ; Published for the Biophysica 2009 Biophysical journal Vol.97 No.2
The diffusion of proteins in the cell membrane is investigated using computer simulations of a two-dimensional model. The membrane is assumed to be divided into compartments, with adjacent compartments separated by a barrier of stationary obstacles. Each compartment contains traps represented by stationary attractive disks. Depending on their size, these traps are intended to model either smaller compartments or binding sites. The simulations are intended to model the double-compartment model, which has been used to interpret single molecule experiments in normal rat kidney cells, where five regimes of transport are observed. The simulations show, however, that five regimes are observed only when there is a large separation between the sizes of the traps and large compartments, casting doubt on the double compartment model for the membrane. The diffusive behavior is sensitive to the concentration and size of traps and the strength of the barrier between compartments suggesting that the diffusion of proteins can be effectively used to characterize the structure of the membrane.
Dynamics in Crowded Environments: Is Non-Gaussian Brownian Diffusion Normal?
Kwon, Gyemin,Sung, Bong June,Yethiraj, Arun American Chemical Society 2014 The Journal of physical chemistry B Vol.118 No.28
<P>The dynamics of colloids and proteins in dense suspensions is of fundamental importance, from a standpoint of understanding the biophysics of proteins in the cytoplasm and for the many interesting physical phenomena in colloidal dispersions. Recent experiments and simulations have raised questions about our understanding of the dynamics of these systems. Experiments on vesicles in nematic fluids and colloids in an actin network have shown that the dynamics of particles can be “non-Gaussian”; that is, the self-part of the van Hove correlation function, <I>G</I><SUB>s</SUB>(<I>r</I>,<I>t</I>), is an exponential rather than Gaussian function of <I>r</I>, in regimes where the mean-square displacement is linear in <I>t</I>. It is usually assumed that a linear mean-square displacement implies a Gaussian <I>G</I><SUB>s</SUB>(<I>r</I>,<I>t</I>). In a different result, simulations of a mixture of proteins, aimed at mimicking the cytoplasm of <I>Escherichia coli</I>, have shown that hydrodynamic interactions (HI) play a key role in slowing down the dynamics of proteins in concentrated (relative to dilute) solutions. In this work, we study a simple system, a dilute tracer colloidal particle immersed in a concentrated solution of larger spheres, using simulations with and without HI. The simulations reproduce the non-Gaussian Brownian diffusion of the tracer, implying that this behavior is a general feature of colloidal dynamics and is a consequence of local heterogeneities on intermediate time scales. Although HI results in a lower diffusion constant, <I>G</I><SUB>s</SUB>(<I>r</I>,<I>t</I>) is very similar to and without HI, provided they are compared at the same value of the mean-square displacement.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2014/jpcbfk.2014.118.issue-28/jp5011617/production/images/medium/jp-2014-011617_0010.gif'></P>