arXiv subjects

Satyavani Vemparala

Publications and source records attributed to Satyavani Vemparala.

At least 19 recordsLinked to original sources

arXiv2026

Density-driven reentrant polymer transitions via saturable bridging crowders

Reentrant coil-globule-coil transitions, in which a polymer collapses and then reexpands as a single parameter is varied, have been observed across diverse soft matter systems, yet the minimal ingredients required to produce them remain unclear. Using molecular dynamics simulations of coarse-grained polymers interacting with a single species of attractive crowder, we show that crowder volume fraction $ϕ_c$ alone is sufficient to drive a complete reentrant transition. At low $ϕ_c$, crowders bridge distant monomers and drive cooperative collapse; at high $ϕ_c$, saturation of monomer binding sites suppresses bridging connectivity and produces reentrant expansion. This density-driven transition is absent with purely repulsive crowders, which produce only monotonic compaction while preserving self-avoiding walk (SAW) chain statistics. In contrast, bridging breaks SAW universality: the rescaled size distributions no longer collapse onto a universal curve, and the conformational distributions trace the full coil-globule-coil trajectory as $ϕ_c$ is varied. For charged polymers with explicit counterions, electrostatics amplifies rather than suppresses reentrance: bridging crowders displace counterions from the chain, and upon saturation the unscreened backbone charges drive expansion well beyond the original chain size. Saturable geometric bridging thus emerges as a minimal mechanism linking reentrant phenomena across neutral and charged polymers in crowded environments.

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arXiv2026

Self-organization and memory formation in two-dimensional jammed deformable matter under cyclic compression

We study the athermal mechanical response of deformable ring assemblies to quasistatic compression. Beyond jamming, further densification induces buckling of rings, resulting in macroscopic mechanical softening. Under cyclic compression, monodisperse systems anneal toward a nearly reversible path passing through an ordered state, whereas polydisperse systems converge to stable, hysteretic limit cycles. These limit cycles encode a robust memory of the training history that is retained even under subsequent overdriving. We show that macroscopic hysteresis in the disordered packings originates from directionally asymmetric non-affine deformations at the microscale while keeping contact network largely intact. Our findings demonstrate how particle deformability governs collective self-organization and memory formation in jammed soft matter.

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arXiv2025

Glassy dynamics in two-dimensional ring polymers: size versus stiffness polydispersity

Soft glassy materials often consist of deformable objects. Here, we use a two-dimensional assembly of semi-flexible ring polymers as a model system to investigate how polydispersity in particle stiffness or size influences the onset of glassy dynamics. In simulations at fixed polydispersity 30%, we find that stiffness dispersity drives most rings into elongated conformations at high densities, leading to orientationally ordered structures that cause dynamical slowing down. In contrast, size dispersity generates a bimodal population: small rings remain circular and act as rigid inclusions, while large rings elongate, producing frustration that delays arrest. Real-space maps of bond relaxation reveal strikingly different pathways of dynamical heterogeneity, with long-lived domains persisting under stiffness dispersity but rapidly percolating relaxation under size dispersity. Moreover, local correlations between ring shape, orientational order, and mobility show that stiffness dispersity produces dynamics that are strongly structure-sensitive, whereas size dispersity activates motion from both circular and elongated populations. By linking microscopic deformability to emergent glassy dynamics, this study identifies how the nature of polydispersity controls the relaxation pathways of soft glasses.

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arXiv2025

Accelerated Collapse Kinetics of Charged Polymers in Good Solvent: Role of Counterion Condensation

We investigate the collapse kinetics of charged polymers (polyelectrolytes) induced by counterion condensation using coarse-grained molecular dynamics simulations. Under good solvent conditions, polyelectrolytes above the critical charge density ($A > A_c$) exhibit significantly faster collapse dynamics compared to neutral polymers, with dynamic scaling exponents ($ν_c \approx 0.76-0.84$) distinctly smaller than those observed for neutral polymers ($ν_c \approx 1.44$) . This accelerated collapse is driven primarily by three mechanisms: (1) local charge neutralization due to counterion condensation, which facilitates immediate local compaction, (2) screening of long-range electrostatic repulsions, reducing the conformational search space, and (3) bridging interactions mediated by multivalent counterions, enhancing efficient formation of intra-chain contacts. We systematically explore the effects of polymer length, charge density, and counterion valency (monovalent, divalent, and trivalent) on collapse dynamics, demonstrating that increased counterion valency significantly lowers the critical charge density required for collapse and accelerates the collapse process. Our findings highlight the limitations of modeling charged biopolymers using purely neutral coarse-grained models, underscoring the importance of electrostatic interactions and counterion dynamics in determining their kinetic pathways. These insights may aid in better understanding the folding, organization, and dynamics of inherently charged biomolecules, such as proteins and nucleic acids.

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arXiv2025

Aging of ring polymeric topological glass formers via thermal quench

We investigate the dynamical response of glass-forming systems composed of topologically constrained ring polymers subjected to an instantaneous thermal quench, employing large-scale molecular dynamics simulations. We demonstrate that the onset of glassiness depends on polymer stiffness, with increased rigidity enhancing configurational constraints and delaying structural relaxation. In the glassy regime, the system exhibits hallmark aging characteristics, as evidenced by two-time correlation functions, namely the mean square displacement and self-intermediate scattering function, which display a clear dependence on the waiting time following the thermal quench. The extracted relaxation timescale ($τ_α$) follows an approximate simple aging scenario with waiting time ($t_w$), described by $τ_α\sim t_w^b$, where $0.8 < b < 0.93$. Finally, we analyze the threading of rings during the thermal quench, demonstrating that both increased and persistent threading correlate with the emergence of glassiness. Moreover, the threading persistence timescale exhibits a strong correlation with the structural relaxation timescale. Our study thus provides a comprehensive view of structural relaxation and aging in dense ring polymer systems, highlighting the critical roles of topological constraints and polymer stiffness in governing non-equilibrium glassy dynamics.

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arXiv2025

Bridging-induced Aggregation in Neutral Polymers: Dynamics and Morphologies

Using molecular dynamics simulations, we investigate the aggregation behavior of neutral stiff (rod-like) and flexible polymer chains mediated by attractive crowders. Attractive crowders serve as bridging agents, inducing aggregation through effective intra-polymer attractions. The critical monomer-crowder attraction strength ($ε_{mc}^*$) required for aggregation differs notably between rigid rods and flexible polymers. Interestingly, this aggregation threshold closely matches the critical attraction required for the extended-to-collapsed (coil-globule) transition of a single flexible polymer chain, suggesting a fundamental connection between single-chain collapse and multi-chain aggregation. Furthermore, we demonstrate that $ε_{mc}^*$ decreases with increasing system density and larger crowder sizes, highlighting the synergistic roles of crowding effects and crowder dimensions. Aggregate morphologies exhibit strong dependence on polymer flexibility: rigid rods predominantly form elongated cylindrical bundles, whereas flexible polymers aggregate into compact spherical clusters. These findings provide comprehensive insights into how bridging interactions driven by attractive crowders regulate polymer aggregation dynamics and morphologies, emphasizing the importance of polymer rigidity, crowder size, and system density.

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arXiv2024

Neutral polymer conformations with attractive bridging crowder interactions: role of crowder size

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.

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arXiv2024

Solvent-cosolvent attraction is sufficient to induce polymer collapse in good solvent mixtures

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 ($ε_{sc}$). 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 ($x_c < 0.5$).

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arXiv2024

Two-dimensional squishy glass: yielding under oscillatory shear

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.

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arXiv2023

The conformational phase diagram of charged polymers in the presence of attractive bridging crowders

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.

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arXiv2023

Onset of glassiness in two-dimensional ring polymers: interplay of stiffness and crowding

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.

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arXiv2023

Bidisperse ring polymers: topological glass to stacking

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.

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arXiv2023

Conformational landscape of long semiflexible linear and ring polymers near attractive surfaces

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.

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arXiv2022

The conformational phase diagram of neutral polymers in the presence of attractive crowders

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.

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arXiv2022

Effect of ring stiffness and ambient pressure on the dynamical slowdown in ring polymers

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.

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arXiv2020

Aggregation dynamics of methacrylate binary and ternary biomimetic polymers in solution

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.

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arXiv2019

Confined crowded polymers near attractive surfaces

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.

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arXiv2017

Aggregation of flexible polyelectrolytes: Phase diagram and dynamics

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.

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