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Extensive molecular dynamics simulations were conducted to explore the conformational phase diagram of a neutral polymer in the presence of attractive crowders of varying sizes. For weakly self-attractive polymers, larger crowders induce a transition from an extended state to a bridging-crowder-induced collapse (CB phase) at lower polymer-crowder interaction strengths. Similarly, for strongly self-attractive polymers, a transition from a crowder-excluded collapse (CI phase) to the CB phase occurs with larger crowders and stronger polymer-crowder attraction. The simulations reveal that the collapsed states in both weakly and strongly self-attractive polymers are identical when small bridging crowders are involved. Near the transition threshold for weakly self-attractive polymers, increasing crowder size leads to complex transitions, including collapse, extension, and re-collapse. Additionally, a confined collapse (CC phase) is observed, where the polymer is confined to interstitial spaces among large crowders. Strongly self-attractive polymers show similar transitions, but only with smaller crowders, as larger crowders suppress these changes. These findings underscore the crucial influence of crowder size on the conformational behavior of neutral polymers, especially under varying degrees of polymer-crowder interaction., Comment: 10 pages and an ancillary file

Cononsolvency occurs when two miscible, competing good solvents for a polymer are mixed, resulting in a loss of solubility. In this study, we demonstrate through simulations, supported by theory, that cononsolvency can be driven solely by solvent-cosolvent attraction ($\epsilon_{sc}$). The primary mechanism underlying this behavior is the emergent depletion effect, which is amplified by solvent-cosolvent interactions. The polymer reaches a compact state when the solvent and cosolvent fractions are equal ($x_s = x_c = 0.5$), a finding that aligns with predictions from Flory-Huggins theory and the random phase approximation. We show that this cononsolvency behavior is observed for different cosolvent sizes, provided the cosolvent density remains below the depletion threshold and the sizes of solvent and cosolvent particles are not smaller than the monomer size. Additionally, we investigate the role of temperature and find that cononsolvency weakens as temperature increases, due to a reduction in the depletion effect. Finally, we show that when preferential cosolvent attraction is introduced in this simple model, it leads to cononsolvency driven by bridging interactions, occurring at lower cosolvent fractions ($x_c < 0.5$)., Comment: 10 pages and an ancillary file

The yielding response to an imposed oscillatory shear is investigated for a model two-dimensional dense glass composed of bidisperse, deformable polymer rings, with the ring stiffness being the control parameter. In the quiescent glassy state, the more flexible rings exhibit a broader spectrum of shape fluctuations, which becomes increasingly constrained with increasing ring stiffness. Under shear, the highly packed rings yield, i.e. the thermal assembly looses rigidity, with the threshold yield strain increasing significantly with decreasing ring stiffness. Further, the rings display significant deviations in their shape compared to their unsheared counterparts. This study provides insights into the interplay between shape changes and translational rearrangements under shear, thus contributing to the understanding of yielding transition in densely packed, deformable polymer systems., Comment: 9 pages, 8 figures, SI in anc folder

Using extensive molecular dynamics simulations, we obtain the conformational phase diagram of a charged polymer in the presence of oppositely charged counterions and neutral attractive crowders for monovalent, divalent and trivalent counterion valencies. We demonstrate that the charged polymer can exist in three phases: (1) an extended phase for low charge densities and weak polymer-crowder attractive interactions ($CE$), (2) a collapsed phase for high charge densities and weak polymer-crowder attractive interactions, primarily driven by counterion condensation ($CCI$), and (3) a collapsed phase for strong polymer-crowder attractive interactions, irrespective of the charge density, driven by crowders acting as bridges or crosslinks ($CCB$). Importantly, the simulations reveal that the interaction with crowders can induce collapse, despite the presence of strong repulsive electrostatic interactions, and can replace condensed counterions to facilitate a direct transition from the $CCI$ and $CE$ phases to the $CCB$ phase., Comment: 12 pages, 10 figures

The effect of ring stiffness and pressure on the glassy dynamics of a thermal assembly of two-dimensional ring polymers is investigated using extensive coarse-grained molecular dynamics simulations. In all cases, dynamical slowing down is observed with increasing pressure and thereby a phase space for equilibrium dynamics is identified in the plane of obtained monomer density and ring stiffness. When the rings are highly flexible, i.e. low ring stiffness, glassiness sets in via crowding of crumpled polymers which take a globular form. In contrast, at large ring stiffness, when the rings tend to have large asphericity under compaction, we observe the emergence of local domains having orientational ordering, at high pressures. Thus, our simulations highlight how varying the deformability of rings leads to contrasting mechanisms in driving the system towards the glassy regime., Comment: Supplementary Information added as ancillary document

Via large-scale molecular dynamics simulations, we observe the melting of a topological glass of stiff ring polymers by incorporating flexible ring polymers, along an isobaric path. As more flexible ring polymers are introduced, cluster glass-like structures emerge in the stiffer ring polymers with reduced orthogonal threading. This eventually evolves to a stacked columnar structure at an increased fraction of flexible ring polymers. Depletion interactions between the stiff and flexible rings drive the stacking, contingent on the disparity in flexibility in the ring polymer mixture., Comment: 6 pages, 3 figures. Please contact authors for movies related to SI

Conformations of a crowded neutral semiflexible polymer under confinement near an attractive wall are studied via coarse-grained simulations. We study the effects of the interplay of the length of the polymer, bending rigidity, and the repulsive crowder density on such equilibrium semiflexible polymer conformations. The length of the polymer dictates the number of distinct conformations of the adsorbed semiflexible polymer, suggesting that previous studies of short polymers are limited. The crowder density is shown to effectively reduce the bending rigidity of the polymers and at the highest crowder density considered, a crumpled wall-adsorbed polymer conformation is seen regardless of the semiflexibility. In addition, we study the role of the topology of the semiflexible polymer by comparing the results of linear semiflexible polymers with those of ring polymers. The conformational landscape of crowded ring polymers shows less diversity than that of a linear polymer and crowders are seen to affect the ring polymers differently than their linear counterparts.

Extensive coarse grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowded densities, the polymer predominantly shows three phases as a function of both intra polymer and polymer-crowder interactions: (1) weak intra polymer and weak polymer-crowder attractive interactions induce extended or coil polymer conformations (phase E) (2) strong intra polymer and relatively weak polymer-crowder attractive interactions induce collapsed or globular conformations (phase CI) and (3) strong polymer-crowder attractive interactions, regardless of intra polymer interactions, induce a second collapsed or globular conformation that encloses bridging crowders (phase CB). The detailed phase diagram is obtained by determining the phase boundaries delineating the different phases based on an analysis of the radius of gyration as well as bridging crowders. The dependence of the phase diagram on strength of crowder-crowder attractive interactions and crowder density is clarified. We also show that when the crowder density is increased, a third collapsed phase of the polymer emerges for weak intra polymer attractive interactions. This crowder density induced compaction is shown to be enhanced by stronger crowder-crowder attraction and is different from the depletion induced collapse mechanism which is primarily driven by repulsive interactions. We also provide a unified explanation of the observed reentrant swollen/extended conformations of earlier simulations of weak and strongly self interacting polymers in terms of crowder-crowder attractive interactions.

Using extensive molecular dynamics simulations, we investigate the slowing down of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the rings determines the dynamics of the ring polymers, leading to glassiness at lower pressures for stiffer rings. The threading of the ring polymers, a unique feature that emerges only due to the topological nature of such polymers in three dimensions, is shown to be the determinant feature of dynamical slowing down, albeit only in a certain stiffness range. Our results suggest a possible framework of exploring the phase space spanned by ring stiffness and pressure to obtain spontaneously emerging topologically constrained polymer glasses., Comment: 10 pages, 7 figures

Using detailed atomistic simulations,we explore the conformational landscape of aggregates formed by biomimetic antimicrobial(AM) binary methacrylate copolymers,with hydrophobic and charged functional groups and the role of inclusion of polar functional groups on such aggregate morphologies.The effect of sequence of the constituent functional groups on aggregate conformation is also studied by considering random and block sequences along the polymer backbone.Our results suggest that block binary copolymers form large spherical aggregates with effective shielding of hydrophobic groups by charged groups.In contrast, random binary copolymers tend to form more bundle-like structures with exposed hydrophobic groups.The strong aggregation of binary polymers is driven primarily by attractive interactions between hydrophobic groups.However,replacing some of the hydrophobic groups with overall charge neutral polar groups weakens the aggregate considerably, leading to increased conformational fluctuations and formation of loose-packed,open aggregates,particularly in case of random ternary polymers.Interaction energy calculations strongly suggest that the role of inclusion of polar groups is two-fold: (1)to reduce possible strong local concentration of hydrophobic groups and smear the hydrophobicity along the polymer backbone to increase the solubility of the polymers (2)to compensate the loss of attractive hydrophobic interactions by forming attractive electrostatic interactions with charged groups and contribute to aggregation formation,albeit weak.Given that most of the naturally occurring AM peptides have contributions from all the three functional groups,this study elucidates the functionally tuneable role of inclusion of polar groups in the way AM agents interact with each other in solution phase,which can eventually dictate their partitioning behavior into bacterial and mammalian membranes.

We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the density of crowders. The conformations of the polymer under good solvent conditions are largely independent of crowder density, even when the polymer is strongly confined. However, for poor solvents and attractive walls, the polymer shows a transition between an adsorbed extended state to a globular conformation on the surface as a function of crowder particle density. This state differs from both the desorbed globular conformation in the absence of any wall interactions and the adsorbed globular conformation at low values of the attractive wall interactions. We revisit the earlier understanding of the adsorption of confined polymers on curved, attractive surfaces in the light of these results.

Similarly-charged polymers in solution, known as polyelectrolytes, are known to form aggregated structures in the presence of oppositely charged counterions. Understanding the dependence of the equilibrium phases and the dynamics of the process of aggregation on parameters such as backbone flexibility and charge density of such polymers is crucial for insights into various biological processes which involve biological polyelectrolytes such as protein, DNA etc., Here, we use large-scale coarse-grained molecular dynamics simulations to obtain the phase diagram of the aggregated structures of flexible charged polymers and characterize the morphology of the aggregates as well as the aggregation dynamics, in the presence of trivalent counterions. Three different phases are observed depending on the charge density: no aggregation, a finite bundle phase where multiple small aggregates coexist with a large aggregate, and a fully phase separated phase. We show that the flexibility of the polymer backbone causes strong entanglement between charged polymers leading to additional time scales in the aggregation process. Such slowing down of the aggregation dynamics results in the exponent, characterizing the power law decay of the number of aggregates with time, to be dependent on the charge density of the polymers. These results are contrary to those obtained for rigid polyelectrolytes, emphasizing the role of backbone flexibility., Comment: 13 pages, 10 figures

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, $R_g \sim \ell_B^{-\gamma}$, in the dependence of the gyration radius of the chain $R_g$ on $\ell_B$. In contrast to a good solvent, the exponent $\gamma$ 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., Comment: 9 pages, 5 figures

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.

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., Comment: 10 pages, 3 figures

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.

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., Comment: 5 pages, 4 figures

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., Comment: 6 pages, 4 figures

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., Comment: 8 pages, 5 figures

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., Comment: Manuscript with 5 figures, Supplementary Information, 10 Supplementary Figures

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., Comment: 7 pages, 8 figures

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 \AA{} and falls-off exponentially with a correlation length of about 24 \AA{} 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 \AA{}), Comment: 11 pages, 3 figures