Satyavani Vemparala

Cell-Membrane Active Polymers

Antimicrobial peptides (AMPs) are a key component of the innate immune system, but their therapeutic use is limited by cost and stability. We study synthetic biomimetic polymers — particularly methacrylate-based copolymers — that mimic AMP activity. Using all-atom and coarse-grained molecular dynamics, we investigate how these polymers selectively interact with bacterial membranes, induce lipid packing defects, and disrupt membrane integrity while sparing mammalian cells.

Our long-standing work with the Kuroda group (U. Michigan) combines computational design feedback with experimental synthesis to optimize charge distribution, hydrophobicity, and globular conformation in these antimicrobial agents.

Polyelectrolytes

Polyelectrolytes — charged polymers in solution with neutralising counterions — exhibit rich phase behaviour including counterintuitive collapse and aggregation driven by multivalent counterion condensation. Using coarse-grained molecular dynamics, we have mapped the conformational phase diagram of flexible and semiflexible polyelectrolytes, identified distinct collapse regimes in poor solvents, and characterised the kinetics of these transitions.

Our work revealed that strongly charged polymers above a critical charge density collapse significantly faster than their neutral counterparts, with dynamic scaling exponents that differ from classical predictions.

Polymers in Crowded Environments

Inside cells, macromolecules function in highly crowded environments where volume exclusion and specific interactions with surrounding crowders can dramatically alter polymer conformations. We study how attractive crowder particles induce polymer collapse through two distinct mechanisms: bridging (small crowders adsorbing onto multiple monomers simultaneously) and confinement (large crowders forcing the polymer into interstitial spaces).

Our recent work maps how crowder size and attraction strength control the conformational phase diagram, revealing non-monotonic collapse–extension–recollapse sequences that arise from competition between monomer cohesion and crowder adsorption.

Glassy Dynamics in Ring Polymers

Ring polymers under dense packing exhibit topological constraints — particularly threading interactions — that drive glass formation without the conventional entanglement mechanisms of linear chains. Through large-scale MD simulations, I, along with my collaborator Prof. Pinaki Chaudhuri (IMSc) study how ring stiffness, size polydispersity, and ambient pressure control the onset of glassy dynamics, aging behaviour after thermal quench, and yielding under oscillatory shear.

We discovered that introducing flexible rings into a stiff ring glass can melt the topological glass via depletion-driven stacking, offering a new route to tune glassy behaviour in polymeric systems.

Water & Solvent Structure

Despite its apparent simplicity, liquid water exhibits long-range dipolar correlations and a complex hydrogen bond network whose disruption by solutes remains poorly understood at the atomic level. We use MD simulations to probe how simple ions and small molecules perturb these correlations, induce reorientationally slow water molecules beyond the first hydration shell, and modify the effective interactions between solvated species.

Globular & Membrane Proteins

We investigate how post-translational modifications — particularly phosphorylation — modulate protein–protein binding affinities and alter loop dynamics near catalytic sites. Our work on the Rap-Raf signalling complex showed that phosphorylation at interfacial sites promotes binding through allosteric modulation of switch loop dynamics. We also study viral peptide–membrane interactions, including the role of cholesterol and disulfide bonds in partitioning of Hepatitis A virus peptides into lipid bilayers.