About

Monica T. Allen is a Principal Investigator at the Allen Lab, specializing in Quantum Devices and Imaging. She holds a Ph.D. in Physics from Harvard University and is based at UC San Diego, with her office located in Mayer Hall Addition 3611. Her research group focuses on building a diverse and creative team of scientists with expertise spanning physics, engineering, and materials science. The lab seeks individuals with experience in scanning probe microscopy, microwave electronics, 2D materials, or device fabrication, indicating these areas are central to their research activities. Professor Allen actively recruits postdoctoral researchers, PhD candidates, and undergraduates, encouraging prospective students to apply to the UC San Diego Physics PhD program and to contact her directly to discuss research opportunities. The lab has a history of mentoring students who have gone on to pursue PhD studies at prestigious institutions such as UC Berkeley, Princeton University, Columbia University, and the University of California, Irvine.

Research topics

• Chemistry
• Materials science
• Cell biology
• Chemical engineering
• Nanotechnology
• Genetics
• Biology
• Organic chemistry

Selected publications

• Author Correction: In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning

  Nature Communications · 2022-07-26

  erratumOpen access
  PublisherOA PDFDOI

• Inkjet prints structural colours from a single transparent ink

  Physics World · 2021-12-01

  article1st authorCorresponding

  Scientists in China have developed a technique for printing structural colours using a commercial inkjet printer.

  PublisherDOI

• <i>In situ</i> differentiation of iridophore crystallotypes underlies zebrafish stripe patterning

  bioRxiv (Cold Spring Harbor Laboratory) · 2020-03-25 · 1 citations

  preprintOpen access

  Skin color patterns are ubiquitous in nature, evolve rapidly, and impact social behavior 1 , predator avoidance 2 , and protection from ultraviolet irradiation 3 . A leading model system for vertebrate skin patterning is the zebrafish 4-7 ; its alternating blue stripes and yellow interstripes depend on guanine crystal-containing cells called iridophores that reflect light. It was suggested that the zebrafish’s alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes 7-9 . When we tracked iridophores, however, we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro-environment. RNA seq analysis further revealed stripe and interstripe iridophores had different transcriptomic states, while cryogenic scanning electron microscopy and micro-X-ray diffraction showed they had different guanine crystal organizations and responsiveness to norepinephrine, all indicating that stripe and interstripe iridophores are different cell types. Based on these results, we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized, physiologically responsive, subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model, pattern phenotype depends not only on interactions among pigment cells that affect their arrangements, but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles.

  PublisherOA PDFDOI

• Structurally Colored Inks from Synthetic Melanin-Based Crosslinked Supraparticles

  ACS Materials Letters · 2020 · 25 citations

  • Materials science
  • Nanotechnology
  • Chemical engineering

  Structurally colored supraparticles, formed from dispersed nanoparticle building blocks through self-assembly, have tremendous potential for applications in displays, coatings, paints, inks, and cosmetics. Mechanical stability and solvent compatibility of supraparticles is critical in these applications. Here, we describe the scalable synthesis of supraparticles via the assembly of nanoparticles composed of synthetic melanin cores with silica shells (SM@SiO2 NPs) using a vortex-assisted reverse emulsion method. We use a hydrogen-bond driven crosslinking strategy employing polyethylene glycol to lock the SM@SiO2 NP building blocks together. This approach yields multicolor photonic supraparticles stable both in organic and aqueous solvents and in the dry state. Supraparticles crosslinked via 4-arm PEG2k withstand at least a 10-fold increase in compressive force when compared to noncrosslinked versions. Capitalizing on the enhanced stability of crosslinked supraparticles, we directly blend them with painting media and apply them as inks.

  PublisherDOI

• In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning

  Nature Communications · 2020 · 80 citations

  • Biology
  • Cell biology
  • Chemistry

  Skin color patterns are ubiquitous in nature, impact social behavior, predator avoidance, and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on light-reflecting cells called iridophores. It was suggested that the zebrafish's color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. However, here we find that iridophores do not migrate between stripes and interstripes but instead differentiate and proliferate in-place, based on their micro-environment. RNA-sequencing analysis further reveals that stripe and interstripe iridophores have different transcriptomic states, while cryogenic-scanning-electron-microscopy and micro-X-ray diffraction identify different crystal-arrays architectures, indicating that stripe and interstripe iridophores are different cell types. Based on these results, we present an alternative model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized, physiologically responsive, organelles arise in stripe and interstripe by in-situ differentiation.

  PublisherOA PDFDOI

• Fate plasticity and reprogramming in genetically distinct populations of <i>Danio</i> leucophores

  Proceedings of the National Academy of Sciences · 2019-05-28 · 81 citations

  articleOpen access

  Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including the zebrafish Danio rerio , we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another of which develops from a yellow–orange xanthophore or xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical, and ultrastructural analyses of zebrafish leucophores revealed cell-type–specific chemical compositions, organelle configurations, and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching, and we showed that leucophore complement influences behavior. Together, our studies reveal independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.

  PublisherOA PDFDOI

• Fate plasticity and reprogramming in genetically distinct populations of <i>Danio</i> leucophores

  bioRxiv (Cold Spring Harbor Laboratory) · 2019-01-22 · 1 citations

  preprintOpen accessCorresponding

  Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including zebrafish Danio rerio , we identified two populations of white pigment cells--leucophores--one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical and ultrastructural analyses of zebrafish leucophores revealed cell-type specific chemical compositions, organelle configurations and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together, our studies revealed new, independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish, and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.

  PublisherOA PDFDOI

• New printer can use honey or liquid metal as ink

  Physics World · 2018-10-01

  article1st authorCorresponding

  A new technique for printing highly viscous fluids, such as honey, has been developed by researchers in the US and Switzerland.

  PublisherDOI

• Rainbow peacock spiders inspire miniature super-iridescent optics

  Nature Communications · 2017-12-18 · 87 citations

  articleOpen access

  Abstract Colour produced by wavelength-dependent light scattering is a key component of visual communication in nature and acts particularly strongly in visual signalling by structurally-coloured animals during courtship. Two miniature peacock spiders ( Maratus robinsoni and M. chrysomelas ) court females using tiny structured scales (~ 40 × 10 μm 2 ) that reflect the full visual spectrum. Using TEM and optical modelling, we show that the spiders’ scales have 2D nanogratings on microscale 3D convex surfaces with at least twice the resolving power of a conventional 2D diffraction grating of the same period. Whereas the long optical path lengths required for light-dispersive components to resolve individual wavelengths constrain current spectrometers to bulky sizes, our nano-3D printed prototypes demonstrate that the design principle of the peacock spiders’ scales could inspire novel, miniature light-dispersive components.

  PublisherOA PDFDOI

• Hyperspectral imaging of snow algae and green algae from aeroterrestrial habitats

  Journal of Photochemistry and Photobiology B Biology · 2016-07-04 · 32 citations

  articleOpen access

  Snow algae and green algae living in aeroterrestrial habitats are ideal objects to study adaptation to high light irradiation. Here, we used a detailed description of the spectral properties as a proxy for photo-acclimation/protection in snow algae (Chlamydomonas nivalis, Chlainomonas sp. and Chloromonas sp.) and charophyte green algae (Zygnema sp., Zygogonium ericetorum and Klebsormidium crenulatum). The hyperspectral microscopic mapping and imaging technique allowed us to acquire total absorption spectra of these microalgae in the waveband of 400-900nm. Particularly in Chlamydomonas nivalis and Chlainomonas sp., a high absorbance between 400-550nm was observed, due to naturally occurring secondary carotenoids; in Chloromonas sp. and in the charopyhte algae this high absorbance was missing, the latter being close relatives to land plants. To investigate if cellular water loss has an influence on the spectral properties, the cells were plasmolysed in sorbitol or desiccated at ambient air. While in snow algae, these treatments did hardly change the spectral properties, in the charopyhte algae the condensation of the cytoplasm and plastids increased the absorbance in the lower waveband of 400-500nm. These changes might be ecologically relevant and photoprotective, as aeroterrestrial algae are naturally exposed to occasional water limitation, leading to desiccation, which are conditions usually occurring together with higher irradiation.

  PublisherDOI

Frequent coauthors

• Dimitri D. Deheyn

  University of California, San Diego

  49 shared

• Roy Bullingham

  Royal Free London NHS Foundation Trust

  34 shared

• Dene Baldwin

  Abingdon Health (United Kingdom)

  23 shared

• Andrew Moore

  19 shared

• Henry McQuay

  19 shared

• Peter J. Teddy

  The Royal Melbourne Hospital

  16 shared

• Dvir Gur

  Weizmann Institute of Science

  16 shared

• J. G. WATSON

  University of Oxford

  16 shared

Labs

• Allen LabPI

  Quantum Devices and Imaging

Education

• B.A.

  Harvard University

• Ph.D.

  Harvard University

Awards & honors

• Gareth Thomas Materials Excellence Award