Langevin dynamics simulation of polymer-assisted virus-like assembly

Starting from a coarse grained representation of the building units of the minute virus of mice and a flexible polyelectrolyte molecule, we have explored the mechanism of assembly into icosahedral structures with the help of Langevin dynamics simulations and the parallel tempering technique. Regular icosahedra with appropriate symmetry form only in a narrow range of temperature and polymer length. Within this region of parameters where successful assembly would proceed, we have systematically investigated the growth kinetics. The assembly of icosahedra is found to follow the classical nucleation and growth mechanism in the absence of the polymer, with the three regimes of nucleation, linear growth, and slowing down in the later stage. The calculated average nucleation time obeys the laws expected from the classical nucleation theory. The linear growth rate is found to obey the laws of secondary nucleation as in the case of lamellar growth in polymer crystallization. The same mechanism is seen in the simulations of the assembly of icosahedra in the presence of the polymer as well. The polymer reduces the nucleation barrier significantly by enhancing the local concentration of subunits via adsorbing them on their backbone. The details of growth in the presence of the polymer are also found to be consistent with the classical nucleation theory, despite the smallness of the assembled structures.     

Theory of volume transition in polyelectrolyte gels with charge regularization

We present a theory for polyelectrolyte gels that allow the effective charge of the polymer backbone to self-regulate. Using a variational approach, we obtain an expression for the free energy of gels that accounts for the gel elasticity, free energy of mixing, counterion adsorption, local dielectric constant, electrostatic interaction among polymer segments, electrolyte ion correlations, and self-consistent charge regularization on the polymer strands. This free energy is then minimized to predict the behavior of the system as characterized by the gel volume fraction as a function of external variables such as temperature and salt concentration. We present results for the volume transition of polyelectrolyte gels in salt-free solvents, solvents with monovalent salts, and solvents with divalent salts. The results of our theoretical analysis capture the essential features of existing experimental results and also provide predictions for further experimentation. Our analysis highlights the importance of the self-regularization of the effective charge for the volume transition of gels in particular, and for charged polymer systems in general. Our analysis also enables us to identify the dominant free energy contributions for charged polymer networks and provides a framework for further investigation of specific experimental systems.     

Translocation of a heterogeneous polymer

We present results on the sequence dependence of translocation kinetics for a partially charged heteropolymer moving through a very thin pore using theoretical tools and Langevin dynamics simulational techniques. The chain is composed of two types of monomers of differing frictional interaction with the pore and charge. We present exact analytical expressions for passage probability, mean first passage time, and mean successful passage times for both reflecting/absorbing and absorbing/absorbing boundary conditions, showing rich and unexpected dependence of translocation behavior on charge fraction, distribution along the chain, and electric field configuration. We find excellent qualitative and good quantitative agreement between theoretical and simulation results. Surprisingly, there emerges a threshold charge fraction of a diblock copolymer beyond which the success rate of translocation is independent of charge fraction. Also, the mean successful translocation time of a diblock copolymer displays non-monotonic behavior with increasing length of the charged block; there is an optimum length of the charged block where the mean translocation rate is the slowest; and there can be a substantial range of higher charge fractions which make the translocation slower than even a minimally charged chain. Additionally, we find for a fixed total charge on the chain, finer distribution along the backbone significantly decreases mean translocation time.     

Ruthenium(II) chalconate complexes: Synthesis, characterization, catalytic, and biological studies

A series of new hexa-coordinated ruthenium(II) carbonyl complexes of the type [RuCl(CO)(EPh₃)(B)(L)] (E = P or As; B = PPh₃, AsPh₃ or Py; L = 2′-hydroxychalcones) have been prepared by reacting [RuHCl(CO)(EPh₃)₂(B)] (E = P or As; B = PPh₃, AsPh₃ or Py) with 2′-hydroxychalcones in benzene under reflux. The new complexes have been characterized by analytical and spectral (IR, electronic, ¹H, ³¹P and ¹³C NMR) data. Based on the above data, an octahedral structure has been assigned for all the complexes. The new complexes exhibit catalytic activity for the oxidation of primary and secondary alcohols into their corresponding aldehydes and ketones in the presence of N-methylmorpholine-N-oxide (NMO) as co-oxidant and also found efficient catalyst in the transfer hydrogenation of ketones. The antifungal properties of the complexes have also been examined and compared with standard Bavistin.     

Langevin dynamics of semiflexible polyelectrolytes: rod-toroid-globule-coil structures and counterion distribution

We have investigated the nature of counterion condensation on uniformly charged semiflexible polyelectrolyte chains and the concomitant configurations by monitoring the role of chain stiffness, chain length, counterion valency, and the strength of electrostatic interaction. The counterion condensation is seen to follow the adsorption process and the effective polymer charge increases with chain stiffness. Size and shape, as calculated through the radius of gyration, effective persistence length, and hydrodynamic radius, are studied. Stable coil-like, globular, folded-chain, toroidal, and rodlike configurations are possible at suitable combinations of values of chain stiffness, chain length, electrostatic interaction strength, and the valency of counterion. For high strengths of electrostatic interactions, sufficiently stiff polyelectrolytes form toroids in the presence of multivalent counterions, whereas flexible polyelectrolytes form disordered globules. The kinetic features of the nucleation and growth of toroids are monitored. Several metastable structures are found to frustrate the formation of toroids. The generic pathway involves the nucleation of one primary loop somewhere along the chain contour, followed by a growth process where the rest of the chain is folded continuously on top of the primary loop. The dependence of the average radii of toroids on the chain length is found to be roughly linear, in disagreement with existing scaling arguments.     

Synchronization of memristor‐based delayed BAM neural networks with fractional‐order derivatives

This article deals with the problem of synchronization of fractional‐order memristor‐based BAM neural networks (FMBNNs) with time‐delay. We investigate the sufficient conditions for adaptive synchronization of FMBNNs with fractional‐order 0 < α < 1. The analysis is based on suitable Lyapunov functional, differential inclusions theory, and master‐slave synchronization setup. We extend the analysis to provide some useful criteria to ensure the finite‐time synchronization of FMBNNs with fractional‐order 1 < α < 2, using Mittag‐Leffler functions, Laplace transform, and linear feedback control techniques. Numerical simulations with two numerical examples are given to validate our theoretical results. Presence of time‐delay and fractional‐order in the model shows interesting dynamics. © 2016 Wiley Periodicals, Inc. Complexity 21: 412–426, 2016     

Electrostatic correlations in polyelectrolyte solutions

The major attribute of polyelectrolyte solutions is that all chains are strongly correlated both electrostatically and topologically. Even in very dilute solutions such that the chains are not interpenetrating, the chains are still strongly correlated. These correlations are manifest in the measured scattering intensity when such solutions are subjected to light, X-ray, and neutron radiation. The behavior of scattering intensity from polyelectrolyte solutions is qualitatively different from that of solutions of uncharged polymers. Using the technique introduced by Sir Sam Edwards, and extending the earlier work by the author on the thermodynamics of polyelectrolyte solutions, extrapolation formulas are derived for the scattering intensity from polyelectrolyte solutions. The emergence of the polyelectrolyte peak and its concentration dependence are derived. The derived theory shows that there are five regimes. Published experimental data from many laboratories are also collected into a master figure and a comparison between the present theory and experiments is presented.     

Synthesis and spectral characterization of 2'-hydroxy chalconate complexes of ruthenium(II) and their catalytic and biological applications

The reactions of [RuHCl(CO)(B)(EPh(3))(2)] (B=EPh(3) or pyridine; E=P or As) and 2'-hydroxychalcones in 1:2 ratio led to the formation of [Ru(CO)(B)(L)(2)] (B=PPh(3), AsPh(3) or Py; L=2'-hydroxychalcones). The new complexes have been characterized by analytical and spectral (IR, electronic and (1)H NMR) data. They have been assigned an octahedral structure. The new complexes were found to catalyze the oxidation of alcohols to aldehydes using N-methylmorpholine-N-oxide as co-oxidant. All the new complexes were found to be active against bacteria such as E. coli, Salmonella typhi and fungi Aspergillus niger. The activity was compared with standard Streptomycin or Bavistin.     

Proton motion of poly(γ-benzyl L-glutamate) in benzyl alcohol during gelation as measured by quasielastic neutron scattering

Quasielastic neutron scattering has been used to study the motion of protons in two solutions of poly(γ-benzyl L -glutamate) (PBLG) and deuterated benzyl alcohol (DBA) as they are brought from the high temperature (cholesteric and isotropic) phase towards the gel. Quasielastic neutron scattering results demonstrate that, in both the isotropic and cholesteric phases, the local rotational dynamics of the polymer are continuous in the high temperature phases, but become more constrained as the system approaches and enters the gel phase. The results also show that the energetics of the rotational motion of the protons below the gelation threshold are independent of the initial phase and the protons are not rendered immobile in the gel phase. © 1996 John Wiley & Sons, Inc.