About

Vinothan N. Manoharan is the Wagner Family Professor of Chemical Engineering and a Professor of Physics at Harvard University. He is a faculty member in both the School of Engineering and Applied Sciences (SEAS) and the Physics department at Harvard. Vinny earned his PhD in Chemical Engineering from the University of California, Santa Barbara, where he conducted research under the guidance of Professor David J. Pine. Following his doctoral studies, he pursued postdoctoral research with Professor John Crocker. His research interests lie at the intersection of soft matter, biophysics, and optics, as indicated by his leadership of the Manoharan Lab, which focuses on these areas.

Research topics

• Computer Science
• Materials science
• Optics
• Physics
• Mathematics
• Artificial Intelligence
• Statistical physics
• Optoelectronics
• Molecular physics
• Computational physics
• Engineering
• Computer vision
• Nanotechnology
• Chemistry
• Statistics
• Chemical engineering

Selected publications

• Movie 1

  Figshare · 2026-03-04

  otherSenior author

  Confocal microscopy imaging of direct seeding

  DOI

• Supplementary Material

  AIP Publishing · 2026-03-04

  otherOpen accessSenior author

  All experimental and analytical methods, along with additional data.

  PublisherDOI

• Supplementary Material

  Figshare · 2026-03-04

  otherSenior author

  All experimental and analytical methods, along with additional data.

  DOI

• Seeding and controlling colloidal self-assembly through focused ion beam deposition

  AIP Publishing · 2026-03-04

  otherOpen access1st authorCorresponding

  To obtain high yields of a desired structure from self-assembly, one often needs a seed: a template that favors formation of the structure. The physical mechanisms of seeding have been studied in detail in micrometer-scale colloidal systems, but much of this prior work has focused on quasi-planar substrates. Our overarching aim is to seed colloidal self-assembly on curved surfaces, for which the orientation of a two-dimensional (2D) crystal nucleus---typically unimportant for assembly on a flat surface---determines whether defects form. Because existing methods lack the spatial control to seed colloidal crystals on curved surfaces, we develop a new method that can be applied to both flat and curved surfaces. Our method leverages the spatial precision of focused ion beam (FIB) deposition. We deposit perhaps the simplest nanostructures that can seed the growth of 2D crystals: triangular configurations of three wells. We then use confocal microscopy to monitor the dynamics of depletion-mediated colloidal self-assembly in the presence and absence of the FIB nanostructures. On flat surfaces we find that nucleation can be either directly or indirectly controlled by the seeding nanostructure, depending on the supersaturation and the interaction strength, and we observe growth occurring by both particle attachment and oriented attachment. Based on these results, we extend our seeding method to control the crystal orientation on a highly-curved \SI{5}{\micro\meter} glass fiber. Our FIB-deposition approach to seeding might be useful not only for controlling assembly on geometrically frustrated systems, but also for modifying functional devices such as optical fibers and neural probes.

  PublisherDOI

• Seeding and controlling colloidal self-assembly through focused ion beam deposition

  AIP Publishing · 2026-03-04

  otherOpen access1st authorCorresponding

  To obtain high yields of a desired structure from self-assembly, one often needs a seed: a template that favors formation of the structure. The physical mechanisms of seeding have been studied in detail in micrometer-scale colloidal systems, but much of this prior work has focused on quasi-planar substrates. Our overarching aim is to seed colloidal self-assembly on curved surfaces, for which the orientation of a two-dimensional (2D) crystal nucleus---typically unimportant for assembly on a flat surface---determines whether defects form. Because existing methods lack the spatial control to seed colloidal crystals on curved surfaces, we develop a new method that can be applied to both flat and curved surfaces. Our method leverages the spatial precision of focused ion beam (FIB) deposition. We deposit perhaps the simplest nanostructures that can seed the growth of 2D crystals: triangular configurations of three wells. We then use confocal microscopy to monitor the dynamics of depletion-mediated colloidal self-assembly in the presence and absence of the FIB nanostructures. On flat surfaces we find that nucleation can be either directly or indirectly controlled by the seeding nanostructure, depending on the supersaturation and the interaction strength, and we observe growth occurring by both particle attachment and oriented attachment. Based on these results, we extend our seeding method to control the crystal orientation on a highly-curved \SI{5}{\micro\meter} glass fiber. Our FIB-deposition approach to seeding might be useful not only for controlling assembly on geometrically frustrated systems, but also for modifying functional devices such as optical fibers and neural probes.

  PublisherDOI

• Seeding and controlling colloidal self-assembly through focused ion beam deposition

  The Journal of Chemical Physics · 2026-03-04

  articleSenior author

  To obtain high yields of a desired structure from self-assembly, one often needs a seed: a template that favors formation of the structure. The physical mechanisms of seeding have been studied in detail in micrometer-scale colloidal systems, but much of this prior work has focused on quasi-planar substrates. Our overarching aim is to seed colloidal self-assembly on curved surfaces, for which the orientation of a two-dimensional (2D) crystal nucleus-typically unimportant for assembly on a flat surface-determines whether defects form. Because existing methods lack the spatial control to seed colloidal crystals on curved surfaces, we develop a new method that can be applied to both flat and curved surfaces. Our method leverages the spatial precision of focused ion beam (FIB) deposition. We deposit perhaps the simplest nanostructures that can seed the growth of 2D crystals: triangular configurations of three wells. We then use confocal microscopy to monitor the dynamics of depletion-mediated colloidal self-assembly in the presence and absence of the FIB nanostructures. On flat surfaces, we find that nucleation can be either directly or indirectly controlled by the seeding nanostructure, depending on the supersaturation and the interaction strength, and we observe growth occurring by both particle attachment and oriented attachment. Based on these results, we extend our seeding method to control the crystal orientation on a highly curved 5 μm glass fiber. Our FIB-deposition approach to seeding might be useful not only for controlling assembly on geometrically frustrated systems but also for modifying functional devices such as optical fibers and neural probes.

  PublisherDOI

• Movie 2

  Figshare · 2026-03-04

  otherSenior author

  Confocal microscopy imaging of direct seeding

  DOI

• Movie 2

  AIP Publishing · 2026-03-04

  otherOpen accessSenior author

  Confocal microscopy imaging of direct seeding

  PublisherDOI

• Movie 1

  AIP Publishing · 2026-03-04

  otherOpen accessSenior author

  Confocal microscopy imaging of direct seeding

  PublisherDOI

• Extracellular uncoating of bacteriophage MS2

  Journal of Molecular Biology · 2025-07-03 · 1 citations

  articleOpen accessSenior authorCorresponding

  • Fluorescence microscopy shows bacteriophage MS2 during infection of E. coli • The majority of MS2 phages uncoat at a distance from the cell body • Uncoating can happen anywhere along the F-pilus of the E. coli host cells • MS2 may have multiple uncoating mechanisms • These uncoating mechanisms may balance different risks and benefits for the phage In the early stages of infection of its host, Escherichia coli , bacteriophage MS2 sheds its icosahedral protein capsid, after which the single-stranded genomic RNA (gRNA) and maturation protein enter the cell as a complex. Although the steps preceding uncoating, which include the binding of the Mat protein to the extracellular filament F-pilus, have been studied in detail, the uncoating step is not well understood. To study when and where uncoating happens, we image the infection process using fluorescence microscopy, separately labelling the MS2 capsid, its gRNA, and the cells. We do two types of experiments. In the first, we incubate the phage in a nonspecific intercalating dye, and we count the number of uncoated and intact phages before and after adding the labeled phages to cells. In the second, we examine the time course of infection by fixing unlabeled samples at different times after adding the phage, and then we label the MS2 gRNA using amplified fluorescence in situ hybridization. In both cases, we find that uncoating can occur anywhere on the F-pili, and that MS2 usually uncoats at a distance from the cell rather than at the cell surface. While these results do not rule out a current hypothesis that virus particles uncoat when the F-pilus retracts and brings them into contact with the cell body, they demonstrate an alternative, extracellular uncoating pathway. We discuss the possiblity that MS2 may have multiple uncoating pathways, and that the rate of each pathway could reflect a trade-off between different risk factors.

  PublisherDOI

Recent grants

• CAREER: High-speed 3D Imaging of Colloidal Self-Assembly with Digital Holographic Microscopy

  NSF · $451k · 2008–2013

• Structural transitions, energetics, and folding pathways of colloidal clusters

  NSF · $378k · 2013–2018

Frequent coauthors

• Brian Leahy

  Harvard University

  919 shared

• Ronald Alexander

  Harvard University Press

  774 shared

• Ronald Alexander

  Harvard University Press

  141 shared

• Rees F. Garmann

  San Diego State University

  39 shared

• Ryan McGorty

  University of San Diego

  32 shared

• David J. Pine

  New York University

  30 shared

• Gi‐Ra Yi

  Pohang University of Science and Technology

  29 shared

• David M. Kaz

  Harvard University

  27 shared

Labs

• Manoharan LabPI