Satyavani Vemparala

Soft glassy materials often consist of deformable objects.

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.

Using molecular dynamics simulations, we investigate the aggregation behavior of neutral stiff (rod-like) and flexible polymer chains mediated by attractive crowders.

In this study, we explore cationic amphiphilic methacrylate copolymers incorporating both positively charged AEMA and negatively charged PAMA functional groups, focusing on their interactions with bacterial membranes. Aggregation studies reveal that electrostatic interactions drive the formation of stable polymer aggregates, with block copolymers forming micelle-like structures and random copolymers exhibiting a more uniform distribution. These ternary polymers preferentially interact with deep lipid-packing defects in bacterial membranes, stabilizing and expanding these defects, while shallow defects remain largely unaffected due to the unfavorable interaction of anionic groups with lipid headgroups. The role of interfacial water is also critical, as hydration layers surrounding anionic groups shield them from electrostatic repulsion, enabling deeper penetration into the membrane. Comparative analyses highlight the advantages of anionic-containing polymers over previously studied polar-containing systems, which predominantly engage shallow defects and exhibit limited structural adaptability near membranes. These findings underscore the role of anionic residues in enabling adaptable AMP conformations, enhanced membrane engagement, and effective disruption mechanisms, providing valuable insights for the design of biomimetic antimicrobial polymers incorporating different functional groups.

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.

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 loses 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.

In this study, we explore cationic amphiphilic methacrylate copolymers incorporating both positively charged AEMA and negatively charged PAMA functional groups, focusing on their interactions with bacterial membranes. Aggregation studies reveal that electrostatic interactions drive the formation of stable polymer aggregates, with block copolymers forming micelle-like structures and random copolymers exhibiting a more uniform distribution. These ternary polymers preferentially interact with deep lipid packing defects in bacterial membranes, stabilizing and expanding these defects, while shallow defects remain largely unaffected due to the unfavorable interaction of anionic groups with lipid headgroups. The role of interfacial water is also critical, as hydration layers surrounding anionic groups shield them from electrostatic repulsion, enabling deeper penetration into the membrane. Comparative analyses highlight the advantages of anionic-containing polymers over previously studied polar-containing systems, which predominantly engage shallow defects and exhibit limited structural adaptability near membranes. These findings underscore the role of anionic residues in enabling adaptable AMP conformations, enhanced membrane engagement, and effective disruption mechanisms, providing valuable insights for the design of biomimetic antimicrobial polymers incorporating different functional groups.

We study the influence of tyrosine phosphorylation on PTP-PEST, a cytosolic protein tyrosine phosphatase. Utilizing a combination of experimental data and computational modeling, specific tyrosine sites, notably, Y64 and Y88, are identified for potential phosphorylation. Phosphorylation at these sites affects loop dynamics near the catalytic site, altering interactions among key residues and modifying the size of the binding pocket. This, in turn, impacts substrate binding, as indicated by changes in the binding energy. Our findings provide insights into the structural and functional consequences of tyrosine phosphorylation on PTP-PEST, enhancing our understanding of its effects on substrate binding and catalytic conformation.

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.