arXiv subjects

Satyavani Vemparala

Publications and source records attributed to Satyavani Vemparala.

29 records · Page 2Linked to original sources

arXiv2016

Regimes of strong electrostatic collapse of a highly charged polyelectrolyte in a poor solvent

We perform extensive molecular dynamics simulations of a highly charged flexible polyelectrolyte (PE) chain in a poor solvent for the case when the chain is in a collapsed state and the electrostatic interactions, characterized by the reduced Bjerrum length $\ell_B$, are strong. We detect the existence of several sub-regimes, $R_g \sim \ell_B^{-γ}$, in the dependence of the gyration radius of the chain $R_g$ on $\ell_B$. In contrast to a good solvent, the exponent $γ$ for a poor solvent crucially depends on the size and valency of counterions. To explain the different sub-regimes we generalize the existing counterion fluctuation theory by a more complete account of the volume interactions in the free energy of the chain. These include interactions between the chain monomers, between monomers and counterions and the counterions themselves. We also demonstrate that the presence of the condensed counterions can modify the effective attraction among the chain monomers and impact the sign of the second virial coefficient.

cond-mat.soft↗

arXiv2016

Mechanism of chain collapse of strongly charged polyelectrolytes

We perform extensive molecular dynamics simulations of a charged polymer in a good solvent in the regime where the chain is collapsed. We analyze the dependence of the gyration radius $R_g $ on the reduced Bjerrum length $\ell_B$ and find two different regimes. In the first one, called as a weak electrostatic regime, $R_g \sim \ell_B^{-1/2}$, which is consistent only with the predictions of the counterion-fluctuation theory. In the second one, called a strong electrostatic regime, we find $R_g \sim \ell_B^{-1/5}$. To explain the novel regime we modify the counterion-fluctuation theory.

cond-mat.soft↗

arXiv2015

Effect of simple solutes on the long range dipolar correlations in liquid water

Intermolecular correlations in liquid water at ambient conditions have generally been characterized through short range density fluctuations described through the atomic pair distribution functions (PDF). Recent numerical and experimental results have suggested that such a description of order or structure in liquid water is incomplete and there exists considerably longer ranged orientational correlations in water that can be studied through dipolar correlations. In this study, using large scale classical, atomistic molecular dynamics (MD) simulations using TIP4P-Ew and TIP3P models of water, we show that salts such as sodium chloride (NaCl), potassium chloride (KCl), caesium chloride (CsCl) and magnesium chloride (MgCl$_2$) have a long range effect on the dipolar correlations, which can not be explained by the notion of structure making and breaking by dissolved ions. The relative effects of cations on dipolar correlations are observed to be consistent with the well-known Hofmeister series. Observed effects are explained through orientational stratification of water molecules around ions, and their long range coupling to the global hydrogen bond network by virtue of the sum rule for water. The observations for single hydrophilic solutes are contrasted with the same for a single methane (CH$_4$) molecule. We observe that even a single small hydrophobe can result in enhancement of long range orientational correlations in liquid water,- contrary to the case of dissolved ions, which have been observed to have a reducing effect. The observations from this study are discussed in the context of hydrophobic effect.

cond-mat.soft↗

arXiv2015

Aggregation Dynamics of Rigid Polyelectrolytes

Similarly-charged polyelectrolytes are known to attract each other and aggregate into bundles when the charge density of the polymers exceeds a critical value that depends on the valency of the counterions. The dynamics of aggregation of such rigid polyelectrolytes are studied using large scale molecular dynamics simulations. We find that the morphology of the aggregates depends on the value of the charge density of the polymers. For values close to the critical value, the shape of the aggregates is cylindrical with height equal to the length of a single polyelectrolyte chain. However, for larger values of charge, the linear extent of the aggregates increases as more and more polymers aggregate.In both the cases, we show that the number of aggregates decrease with time as power laws with exponents that are not numerically distinguishable from each other, and are independent of charge density of the polymers, valency of the counterions, density, and length of the polyelectrolyte chain. We model the aggregation dynamics using the Smoluchowski coagulation equation with kernels determined from the molecular dynamics simulations, and justify the numerically obtained value of the exponent. Our results suggest that, once counterions condense, effective interactions between polyelectrolyte chains short-ranged and the aggregation of polyelectrolytes is diffusion-limited.

cond-mat.soft↗

arXiv2014

Ion Hydration and Associated Defects in Hydrogen Bond Network of Water: Observation of Reorientationally Slow Water Molecules Beyond First Hydration Shell in Aqueous Solutions of MgCl$_2$

Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations reveal that the presence of magnesium chloride (MgCl$_2$) induces perturbations in the hydrogen bond network of water leading to the formation of bulk-like domains with \textquoteleft defect sites\textquoteright~on boundaries of such domains: water molecules at such defect sites have less number of hydrogen bonds than those in bulk water. Reorientational autocorrelation functions for dipole vectors of such defect water molecules are computed at different concentrations of ions and compared with system of pure water. Earlier experimental and simulation studies indicate significant differences in reorientational dynamics for water molecules in the first hydration shell of many dissolved ions. Results of this study suggest that defect water molecules, which are beyond the first hydration shells of ions, also experience significant slowing down of reorientation times as a function of concentration in the case of MgCl$_2$. However, addition of cesium chloride(CsCl) to water does not perturb the hydrogen bond network of water significantly even at higher concentrations. This difference in behavior between MgCl$_2$ and CsCl is consistent with the well-known Hofmeister series.

cond-mat.soft↗

arXiv2014

Force fluctuations in stretching a tethered polymer

The recently proposed fluctuation relation in unfolding forces [Phys. Rev. E ${\bf 84}$, $060101$(R) $(2011)$] is re-examined taking into account the explicit time dependence of the force distribution. The stretching of a tethered Rouse polymer is exactly solved and the ratio of the probabilities of positive to negative forces is shown to be an exponential in force. Extensive steered molecular dynamics simulations of unfolding of deca alanine peptide confirm the form of fluctuation relation proposed earlier, but with explicit correct time dependence of unfolding forces taken into account. From exact calculations and simulations, a linear dependence of the constant in the exponential of the fluctuation relation on average unfolding forces and inverse temperature is proposed.

cond-mat.stat-mech↗

arXiv2012

Aggregation of rod-like polyelectrolyte chains in the presence of monovalent counterions

Using molecular dynamics simulations, it is demonstrated that monovalent counterions can induce aggregation of similarly charged rod-like polyelectrolyte chains. The critical value of the linear charge density for aggregation is shown to be close to the critical value for the extended-collapsed transition of a single flexible polyelectrolyte chain, and decreases with increasing valency of the counterions. The effective interaction potential between two rod-like polyelectrolyte chains is measured, and is related to the angular distribution of the condensed counterions.

cond-mat.soft↗

arXiv2012

Atomistic simulations of a multicomponent asymmetric lipid bilayer

The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid bilayer system comprising of an unsaturated POPC (palmitoyl-oleoyl-phosphatidyl-choline), a saturated SM (sphingomyelin) and cholesterol are investigated. In these simulations, the initial stages of liquid ordered, $l_o$, domain formation are observed and such domains are found to be highly enriched in cholesterol and SM. The current simulations also suggest that the cholesterol molecules may partition into these SM-dominated regions in the ratio of $3:1$ when compared to POPC-dominated regions. SM molecules exhibit a measurable tilt and long range tilt correlations are observed within the $l_o$ domain as a consequence of the asymmetry of the bilayer, with implications to local membrane deformation and budding. Tagged particle diffusion for SM and cholesterol molecules, which reflects spatial variations in the physical environment encountered by the tagged particle, is computed and compared with recent experimental results obtained from high resolution microscopy.

cond-mat.soft↗

arXiv2011

Ensemble Equivalence for Counterion Condensation on a Two Dimensional Charged Disc

We study the counterion condensation on a two dimensional charged disc in the limit of infinite dilution, and compare the energy-temperature relation obtained from the canonical free energy and microcanonical entropy. The microcanonical entropy is piecewise linear in energy, and is shown to be concave for all energies. As a result, even though the interactions are long-ranged, the energy-temperature relation and hence the counterion condensation transition points are identical in both the ensembles.

cond-mat.stat-mech↗

arXiv2011

Phase transitions of a single polyelectrolyte in a poor solvent with explicit counterions

Conformational properties of a single flexible polyelectrolyte chain in a poor solvent are studied using constant temperature molecular dynamics simulation. The effects of counterions are explicitly taken in to account. Structural properties of various phases and the transition between these phases are studied by tracking the values of asphericity, radius of gyration, fraction of condensed counterions, number of non-bonded neighbours and Coulomb interaction energies. From our simulations, we find strong evidence for a first-order phase transition from extended to collapsed phase consistent with earlier theoretical predictions. We also identify a continuous phase transition associated with the condensation of counterions and estimate the critical exponents associated with the transition. Finally, we argue that previous suggestions of existence of an independent intermediate phase between extended and collapsed phases is only a finite size effect.

cond-mat.stat-mech↗

arXiv2009

Long Distance Correlations in Molecular Orientations of Liquid Water and Shape Dependant Hydrophobic Force

Liquid water, at ambient conditions, has short-range density correlations which are well known in literature. Surprisingly, large scale molecular dynamics simulations reveal an unusually long-distance correlation in `longitudinal' part of dipole-dipole orientational correlations. It is non-vanishing even at 75 Å and falls-off exponentially with a correlation length of about 24 Å beyond solvation region. Numerical evidence suggests that the long range nature of dipole-dipole correlation is due to underlying fluctuating network of hydrogen-bonds in the liquid phase. This correlation is shown to give a shape dependant attraction between two hydrophobic surfaces at large distances of separation and the range of this attractive force is in agreement with experiments. In addition it is seen that quadrupolar fluctuations vanish within the first solvation peak (3 Å)

cond-mat.soft↗