About

Saksham Agarwal is an Assistant Professor at The Grainger College of Engineering, University of Illinois Urbana-Champaign. His research areas include communications, computer architecture, networking and distributed computing, operating systems, and systems and networking. He has received several honors, including the Google Research Scholar Award in June 2025, the ACM SIGCOMM Dissertation Award in 2025, the IRTF Applied Networking Research Prize in January 2025, and the SIGCOMM Best Student Paper Award in August 2024. He teaches courses such as Communication Networks, Introduction to Computing, and Modern Cloud Infrastructure. His work has been recognized within the academic community, and he is actively involved in advancing research in networking and systems.

Research topics

• Statistical physics
• Physics
• Mathematics
• Classical mechanics
• Geometry
• Aerospace engineering
• Mathematical analysis
• Quantum mechanics
• Optics
• Engineering
• Mechanics

Selected publications

• BPS2026 – Beyond diffusion: How influenza A navigates complex glycan landscapes

  Biophysical Journal · 2026-02-01

  article1st authorCorresponding
  PublisherDOI

• SurFlex microscopy: Measuring flexibility of surface-tethered biomolecules

  Proceedings of the National Academy of Sciences · 2025-11-25

  articleOpen access

  The flexibility of tethered molecules, such as those bound to biological membranes, is an important property that can influence molecular height, mobility, and accessibility. However, quantifying the flexibility of surface-tethered biomolecules in aqueous environments has been difficult due to a lack of experimental tools. Here, we introduce SurFlex microscopy, a method based on fluorescence anisotropy that exploits the relationship between the conformational dynamics of a tethered molecule and the rotational diffusion of an attached fluorophore to extract information about molecular flexibility. By analyzing the polarization state of photons emitted after polarized excitation, we quantify apparent molecular flexibilities that include effects of tethering, self-interactions, and buffer conditions. We first demonstrate the capabilities of SurFlex microscopy by measuring the flexibility of bilayer-tethered single-stranded DNA (ssDNA) of different lengths and nucleotide sequences. We find that sequence significantly impacts ssDNA flexibility, consistent with theoretical estimates, with weak intramolecular interactions in random sequences leading to higher apparent stiffness. Interestingly, we show that a pathological DNA sequence linked to Huntington's disease exhibits unusual flexibility despite intramolecular interactions. We next extend SurFlex microscopy to live cells by measuring surface glycoprotein flexibility on red blood cells using fluorescent lectins. We show that trypsinization decreases glycan fluctuations, demonstrating that modifications to the cell surface can alter the flexibility of remaining surface molecules. SurFlex microscopy provides a tool for quantifying molecular flexibility that can be used to study the role of tethered surface molecules in fundamental biological processes.

  PublisherOA PDFDOI

• SurFlex Microscopy: Measuring Flexibility of Surface-Tethered Biomolecules

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-17 · 1 citations

  preprint

  Abstract The flexibility of tethered molecules, such as those bound to biological membranes, is an important property that can influence molecular height, mobility, and accessibility. However, quantifying the flexibility of surface-tethered biomolecules in aqueous environments has been difficult due to a lack of experimental tools. Here we introduce SurFlex microscopy, a method based on fluorescence anisotropy that exploits the relationship between the conformational dynamics of a tethered molecule and the rotational diffusion of an attached fluorophore to extract information about molecular flexibility. By analyzing the polarization state of photons emitted after polarized excitation, we quantify apparent molecular flexibilities that include effects of tethering, self-interactions and buffer conditions. We first demonstrate the capabilities of SurFlex microscopy by measuring the flexibility of bilayer-tethered single-stranded DNA (ssDNA) of different lengths and nucleotide sequences. We find that sequence significantly impacts ssDNA flexibility, consistent with theoretical estimates, with weak intramolecular interactions in random sequences leading to higher apparent stiffness. Interestingly, we show that a pathological DNA sequence linked to Huntington’s disease exhibits unusual flexibility despite intramolecular interactions. We next extend SurFlex microscopy to live cells by measuring surface glycoprotein flexibility on red blood cells using fluorescent lectins. We show that trypsinization decreases glycan fluctuations, demonstrating that modifications to the cell surface can alter the flexibility of remaining surface molecules. SurFlex microscopy provides a new tool for quantifying molecular flexibility that can be used to study the role of tethered surface molecules in fundamental biological processes. Significance statement Biomolecules immobilized on one end play crucial roles in diverse cellular processes, from cell-cell signaling through surface receptors to the formation of DNA secondary structures. However, measuring biomolecular flexibility on surfaces has remained challenging. Here we present SurFlex microscopy, a technique that uses fluorescence anisotropy to quantify the flexibility of surface-anchored molecules. By analyzing the rotational dynamics of fluorophores attached to the ends of fluctuating biomolecules, SurFlex microscopy can be used to quantify persistence length. We demonstrate its capabilities by measuring sequence-dependent flexibility of DNA and crowding-dependent changes in glycan flexibility on native cell surfaces. This method opens new avenues for understanding how biomolecular flexibility influences key biological processes, such as those at cell surfaces during cell-cell contact formation and subsequent signaling.

  PublisherDOI

• Measuring molecular flexibility with polarization microscopy

  Biophysical Journal · 2024-02-01

  article
  PublisherDOI

• Superdiffusive motion of influenza A on surfaces

  Biophysical Journal · 2024-02-01

  article1st authorCorresponding
  PublisherDOI

• Density-contrast induced inertial forces on particles in oscillatory flows

  Journal of Fluid Mechanics · 2024-04-23 · 3 citations

  articleOpen access1st author

  Oscillatory flows have become an indispensable tool in microfluidics, inducing inertial effects for displacing and manipulating fluid-borne objects in a reliable, controllable and label-free fashion. However, the quantitative description of such effects has been confined to limit cases and specialized scenarios. Here we develop an analytical formalism yielding the equation of motion of density-mismatched spherical particles in oscillatory background flows, generalizing previous work. Inertial force terms are systematically derived from the geometry of the flow field together with analytically known Stokes number dependences. Supported by independent, first-principles direct numerical simulations, we find that these forces are important even for nearly density-matched objects such as cells or bacteria, enabling their fast displacement and separation. Our formalism thus consistently incorporates particle inertia into the Maxey–Riley equation, and in doing so provides a generalization of Auton's modification to added mass, as well as recovering the description of acoustic radiation forces on particles as a limiting case.

  PublisherOA PDFDOI

• Kinetics and Optimality of Influenza A Virus Locomotion

  Physical Review Letters · 2024-12-11 · 3 citations

  article1st authorCorresponding

  Influenza A viruses (IAVs) must navigate through a dense extracellular mucus to infect airway epithelial cells. The mucous layer, composed of glycosylated biopolymers (mucins), presents sialic acid that binds to ligands on the viral envelope and can be irreversibly cleaved by viral enzymes. It was recently discovered that filamentous IAVs exhibit directed persistent motion along their long axis on sialic acid-coated surfaces. This Letter demonstrates through stochastic simulations and mean-field theory, how IAVs harness a "burnt-bridge" Brownian ratchet mechanism for directed persistent translational motion. Importantly, our analysis reveals that equilibrium features of the system primarily control the dynamics, even out of equilibrium, and that asymmetric distribution of ligands on the virus allows for more robust directed transport. We show viruses occupy the optimal parameter range ("Goldilocks zone") for efficient mucous transport, possibly due to the evolutionary adaptation of enzyme kinetics. Our findings suggest novel therapeutic targets and provide insight into possible mechanisms of zoonotic transmission.

  PublisherDOI

• Kinetics and optimality of influenza A virus locomotion

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-05-09 · 1 citations

  preprintOpen access1st authorCorresponding

  Influenza A viruses (IAVs) must navigate through a dense extracellular mucus to infect airway epithelial cells. The mucous layer, composed of glycosylated biopolymers (mucins), presents sialic acid that binds to ligands on the viral envelope and can be irreversibly cleaved by viral enzymes. It was recently discovered that filamentous IAVs exhibit directed persistent motion along their long axis on sialic acid-coated surfaces. This study demonstrates through stochastic simulations and mean-field theory, how IAVs harness a ‘burnt-bridge’ Brownian ratchet mechanism for directed persistent translational motion. Importantly, our analysis reveals that equilibrium features of the system primarily control the dynamics, even out-of-equilibrium, and that ligand asymmetry allows for more robust directed transport. We show viruses occupy the optimal parameter range (‘Goldilocks zone’) for efficient mucous transport, possibly due to the evolutionary adaptation of enzyme kinetics. Our findings suggest novel therapeutic targets and provide insight into possible mechanisms of zoonotic transmission.

  PublisherOA PDFDOI

• Density-contrast induced inertial forces on particles in oscillatory flows

  arXiv (Cornell University) · 2023-08-08

  preprintOpen access1st authorCorresponding

  Oscillatory flows have become an indispensable tool in microfluidics, inducing inertial effects for displacing and manipulating fluid-borne objects in a reliable, controllable, and label-free fashion. However, the quantitative description of such effects has been confined to limit cases and specialized scenarios. Here we develop an analytical formalism yielding the equation of motion of density-mismatched spherical particles in arbitrary background flows, generalizing previous work. Inertial force terms are systematically derived from the geometry of the flow field together with analytically known Stokes number dependences. Supported by independent, first-principles direct numerical simulations, we find that these forces are important even for nearly density-matched objects such as cells or bacteria, enabling their fast displacement and separation. Our formalism thus generalizes the Maxey--Riley equation, encompassing not only particle inertia, but consistently recovering, in the limit of large Stokes numbers, the Auton modification to added mass as well as the far-field acoustofluidic secondary radiation force.

  PublisherOA PDFDOI

• Characteristics of transition to disclination disorder on curved crystalline surfaces

  Bulletin of the American Physical Society · 2021-03-18

  article1st authorCorresponding
  Publisher

Frequent coauthors

• Sascha Hilgenfeldt

  University of Illinois Urbana-Champaign

  24 shared

• Daniel A. Fletcher

  Berkeley College

  10 shared

• Bhargav Rallabandi

  University of California, Riverside

  9 shared

• Boris Veytsman

  Chan Zuckerberg Initiative (United States)

  7 shared

• Mattia Gazzola

  National Center for Supercomputing Applications

  7 shared

• David Raju

  6 shared

• Greg Huber

  Chan Zuckerberg Initiative (United States)

  5 shared

• Fan Kiat Chan

  4 shared

Awards & honors

• Google Research Scholar Award (June 2025)
• ACM SIGCOMM Dissertation Award 2025 (June 2025)
• IRTF Applied Networking Research Prize 2025 (Jan 2025)
• SIGCOMM Best Student Paper Award 2024 (Aug 2024)