Biological & Bioinspired Materials

Organisms have had eons to refine their materials.

A sea urchin embryo grows two single crystals that curve, branch, and mirror one another. A single-celled acantharean in the open ocean sifts strontium out of seawater where calcium outnumbers it a hundred to one. Ameloblasts build enamel and then die, leaving a tissue that can last a lifetime with no living cell to maintain it.

We work out the mechanisms: how these tissues are built, how function emerges from them, how they record their environment, and what happens when things go awry. Once we understand the principles evolution landed on, the applications follow, whether that is predicting the course of tooth decay or pulling radioactive strontium-90 out of nuclear waste.

Derk Joester, Professor of Materials Science and Engineering
McCormick School of Engineering, Northwestern University
Evanston, Illinois, USA

Sea urchin pluteus larva at 71 hours, polarized light micrograph showing the two birefringent skeletal rods
Two acanthareans in light micrograph, showing their radiating strontium sulfate spicules
Beaver skull seen from the front: four iron-pigmented incisors, orange against white bone
Research

Hierarchy and history in biological materials

Five projects, spanning marine organisms, human tissue, and synthetic model systems. Each has its own page.

Hierarchical architecture

Dental enamel

Dental enamel is the hardest, most wear-resistant tissue our bodies make. Yet once it is damaged or lost, our options for restoring it remain surprisingly limited. To change this, we study its structure, composition, and degradation from single atoms on up.

Read more →
Selective sequestration

Strontium in acanthareans

To build their skeletons, single-celled acanthareans pick strontium out of seawater in which calcium is a hundred times more abundant. We are working out how, so that one day we can pull radioactive strontium-90 out of nuclear waste and the environment.

Read more →
Branching morphogenesis

Bioengineering single crystal growth

Crystal growth is a fundamentally enabling technology in materials science. We study the sea urchin embryo to learn how it controls the elongation and branching of single crystals along specific crystallographic directions.

Read more →
Far from equilibrium

The sea urchin tooth

Sea urchins tunnel into rock far harder than their own teeth. We want to know how they control the magnesium content of the calcite lattice, driving it far past the equilibrium solubility limit in some parts of the tooth and not others.

Read more →
Size matters

Nucleation in confinement

Phase transformations in biology are often controlled at cellular length scales. We use liposomes and microfluidic droplet reactors to measure how confinement and additives change the kinetics of nucleation and crystal growth.

Page in preparation
Conferences

Coming up soon

Meet us at BioMineralia

Chęciny, Poland

17 to 20 September 2026. Derk will talk about dental enamel, and what its structure, composition and transport processes look like from single atoms up to the whole tissue.

We are recruiting

Postdocs · PhD and MS students · Undergraduates

How to join →
Recent news

News archive

2 Aug 2026

Microscopy and Microanalysis

Milwaukee, Wisconsin

Katsuaki presented the group’s cryogenic atom probe work, which sets out to image mineralized collagen while it is still frozen and hydrated.

26 Jul 2026

Gordon Research Conference on Biomineralization

Il Ciocco, Lucca, Italy

Michaela gave a short talk and a poster on the acantharean project, on what these single-celled organisms carry in their transcriptomes that lets them sift strontium out of seawater. Derk presented on dental enamel.

8 May 2026

MICRO Summit

Northwestern University, Evanston

Michael Angelo presented work on the enamel project, teaching neural networks to find enamel in micro-CT scans of mouse molars.

Feb 2026

Society of Women Engineers 50th Anniversary

Northwestern University, Evanston

Olivia presented on the sea urchin tooth, on how the plumula mineralizes and takes shape.

21 Nov 2025

Midwest Microscopy and Microanalysis Fall Meeting

Deerfield, Illinois

Katsuaki presented the cryogenic atom probe work, which looks at the interface between mineral and matrix without letting the water go.

13 Oct 2025

Enamel 11

Paris, France

Ethan presented on the enamel project, on measuring mouse teeth in bulk from their three-dimensional reconstructions. Derk presented on how ions move through enamel.

4 Apr 2025

MICRO Summit

Northwestern University, Evanston

Melanie presented on the enamel project, on the order in which enamel densifies as it matures.

1 Dec 2024

Materials Research Society Fall Meeting

Boston, Massachusetts

Derk presented on nucleation in confinement, and on how fast amorphous carbonates crystallize when there is very little room.

22 Nov 2024

Midwest Microscopy and Microanalysis Fall Meeting

Deerfield, Illinois

Derk presented on dental enamel, from single atoms up to the whole tissue.

1 Nov 2024

Biotechnology Training Program research meeting

Northwestern University, Evanston

Michaela presented on bioengineering single crystal growth, and on what cryogenic electron tomography shows of a sea urchin spicule as it grows.

Research

Hierarchy and history in biological materials

Organisms control phase transformations with a precision that laboratory synthesis cannot yet reach, building anatomy that ranges from single-crystalline skeletal elements that curve and branch to hierarchically structured teeth that survive a lifetime of chewing.

Time matters as much as space. These materials are built over days or years, serve for decades, and can still be read tens of millions of years later — development, aging, disease, environment and fossilization each leave something behind.

Three questions run through our work:

  • How that control is exerted during development.
  • How function emerges from the resulting gradients in structure and composition — the design principles.
  • How mineralized tissues are affected by, and keep a record of, environmental and pathophysiological conditions.

Depending on the question we work with preserved tissue, animal models, cell culture, or entirely in vitro, combining materials characterization and synthesis with biochemistry, cell biology, and computational modeling.

Hierarchical architecture

Dental enamel

Dental enamel is the hardest, most wear-resistant tissue our bodies make. Yet once it is damaged or lost, our options for restoring it remain surprisingly limited. To change this, we study its structure, composition, and degradation from single atoms on up.

Read more →
Virtual sections of murine hemimandibles: wild type (top) and a mutant with enamel hypomineralization (bottom). Color maps the density of incisor enamel.
Synchrotron µCT
Selective sequestration

Strontium in acanthareans

To build their skeletons, single-celled acanthareans pick strontium out of seawater in which calcium is a hundred times more abundant. We are working out how, so that one day we can pull radioactive strontium-90 out of nuclear waste and the environment.

Read more →
Spicules of three acantharean species differ in shape, evidence that crystal growth is under genetic control. Cross sections shown schematically at right.
Scanning electron micrographs
Branching morphogenesis

Bioengineering single crystal growth

Crystal growth is a fundamentally enabling technology in materials science. We study the sea urchin embryo to learn how it controls the elongation and branching of single crystals along specific crystallographic directions.

Read more →
A spicule deposited by cultured primary mesenchyme cells, labeled with a pulse of calcein red, a brief chase, then a pulse of calcein green.
False-colored fluorescence on DIC
Far from equilibrium

The sea urchin tooth

Sea urchins tunnel into rock far harder than their own teeth. We want to know how they control the magnesium content of the calcite lattice, driving it far past the equilibrium solubility limit in some parts of the tooth and not others.

Read more →
Aristotle's lantern with five teeth (top and middle left); one tooth in T-shaped cross section (bottom left); microstructure of the middle part of the flange (right).
Synchrotron µCT and scanning electron micrograph
Size matters

Nucleation in confinement

Phase transformations in biology are often controlled at cellular length scales. We use liposomes and microfluidic droplet reactors to measure how confinement and additives change the kinetics of nucleation and crystal growth.

Page in preparation
Water droplets in fluorous oil are microreactors in which amorphous calcium carbonate forms (A, B). In one, a crystal nucleates after about 14 hours (D) and grows at the expense of the ACC (E to H).
Polarized light
Research · Dental enamel

Dental enamel is the hardest, most wear-resistant tissue our bodies make. Repairing it is another matter.

Once enamel is deposited on the surface of our teeth, the cells that built it die. After eruption it can survive a century or more of the conditions inside the mouth: hundreds of millions of chewing cycles, acidic and abrasive foods, repeated swings in temperature. It is considered the most durable of biological materials, and in fossils it preserves usable information for more than 40 million years.

Things can go awry during development, as in the rare inherited disorder amelogenesis imperfecta, or the far more common molar hypomineralization — "chalky teeth". They can also go wrong after eruption, when enamel is the first tissue damaged by erosive wear and by tooth decay. These conditions are rarely life-threatening, but their burden on patients and on society is enormous. Dental expenditure in the United States is approaching $200 billion a year, and around three billion people worldwide have untreated caries.

What makes enamel both fascinating and hard to understand is that its properties arise from a hierarchical architecture spanning many length scales. It is built from highly elongated crystallites only tens of nanometers across, each like a strand of uncooked spaghetti. Tens of thousands of these are bundled into rods, and the rods are woven together to form the enamel layer. As we and others have learned over the past decade, the hierarchy continues below the crystallite itself. Crystallites are joined by a vanishingly thin amorphous inorganic glue; their composition differs between core and shell; and even neighboring structural domains such as rod and interrod enamel are chemically and crystallographically distinct. These differences amount to only a few atomic percent, yet they strongly influence how enamel dissolves, wears, and resists damage.

A tooth, and a slice through it, at 1 cm. A human premolar, and a section through its crown. The pale outer layer is enamel; the yellow interior is dentin. Everything that follows happens inside that outer couple of millimetres.Enamel is woven, not solid, at 5 µm. Enamel is built from rods — bundles a few micrometres across that weave past one another. The traced line follows the edge of a single rod.Inside a rod, at 250 nm. Within each rod are the crystallites themselves — long, thin ribbons of mineral packed almost parallel.And the gaps between them, at 100 nm. Cut across, the crystallites are flattened hexagons. The dark spaces between them turn out to matter as much as the crystals do.Each crystallite has a core, at 50 nm. A crystallite is not chemically uniform. It has a core with a different composition from its shell — a gradient inside an object 50 nanometres wide.Down to the planes of atoms, at 10 nm. At this magnification the regular planes of atoms show up as fine stripes running through the crystal.Individual columns of atoms, at 1 nm. Each bright spot is a column of atoms seen end-on, in the hexagonal arrangement of the mineral hydroxylapatite.The repeating unit, at 1 nm. And finally the unit that repeats to build all of it — drawn over the image of the real thing, nine orders of magnitude below where we started.

A tooth, and a slice through it

A human premolar, and a section through its crown. The pale outer layer is enamel; the yellow interior is dentin. Everything that follows happens inside that outer couple of millimetres.

What you're looking at

Light micrographs. DEJ marks the dentin–enamel junction, EES the enamel exterior surface. Scale bars 1 cm and 1 mm.

Step 1 of 8 · 1 cm

Enamel is woven, not solid

Enamel is built from rods — bundles a few micrometres across that weave past one another. The traced line follows the edge of a single rod.

What you're looking at

Scanning electron micrograph of a polished and etched surface. Each rod bundles thousands of crystallites of shared orientation; the weave is what resists cracks.

Step 2 of 8 · 5 µm

Inside a rod

Within each rod are the crystallites themselves — long, thin ribbons of mineral packed almost parallel.

What you're looking at

SEM of a fractured surface showing crystallite ends and long axes.

Step 3 of 8 · 250 nm

And the gaps between them

Cut across, the crystallites are flattened hexagons. The dark spaces between them turn out to matter as much as the crystals do.

What you're looking at

SEM of crystallite cross-sections; the dashed outline marks one crystallite. The intergranular space hosts a chemically distinct phase.

Step 4 of 8 · 100 nm

Each crystallite has a core

A crystallite is not chemically uniform. It has a core with a different composition from its shell — a gradient inside an object 50 nanometres wide.

What you're looking at

STEM image; arrows mark core, shell and intergranular phase. Reported in DeRocher et al., Nature 583, 66 (2020).
Chemical gradients in human enamel crystallites · Nature 2020

Step 5 of 8 · 50 nm

Down to the planes of atoms

At this magnification the regular planes of atoms show up as fine stripes running through the crystal.

What you're looking at

High-resolution TEM. Crystallographic directions [001], ⟨010⟩ and ⟨100⟩ are indicated.

Step 6 of 8 · 10 nm

Individual columns of atoms

Each bright spot is a column of atoms seen end-on, in the hexagonal arrangement of the mineral hydroxylapatite.

What you're looking at

HRTEM with FFT inset; (002) and (100) reflections indexed. Inset scale 5 nm⁻¹.

Step 7 of 8 · 1 nm

The repeating unit

And finally the unit that repeats to build all of it — drawn over the image of the real thing, nine orders of magnitude below where we started.

What you're looking at

Hydroxylapatite unit cell model overlaid on the lattice image.

Step 8 of 8 · 1 nm

We use imaging, microanalytical, and spectroscopic techniques to map the structure and composition of enamel across nine orders of magnitude in length scale and throughout its development, from an entire tooth down to individual atoms, and from the first deposition of the enamel matrix to fully mature enamel. We are now folding these measurements into computational models that aim to predict how enamel forms, matures, and dissolves under physiological conditions. This work frequently involves collaborators across the United States and around the world and contributes to a shared enamel atlas rather than remaining in a single laboratory’s drawer. Ultimately, we hope that understanding how enamel is built and deteriorates across scales will help us learn how to better protect, repair, and perhaps one day replace it.

In depth

Why this matters

Human enamel is remarkable: once it is formed, the cells that built it disappear, yet it can survive decades of mechanical and chemical challenges. At the same time, enamel cannot meaningfully regenerate after eruption. Our long-term goal is to understand how enamel acquires its extraordinary durability, how its structure and composition change during disease and aging, and how those changes influence dissolution and failure. Ultimately, we hope these insights will guide improved prevention, diagnostics, and future approaches to enamel repair or replacement.

What we are doing now

Predicting how enamel dissolves

One of our major current efforts is the development of predictive models of enamel dissolution across length scales. With Peter Voorhees, James Rondinelli, and Stuart Stock (Northwestern), Lara Estroff (Cornell), and Michel Koo (Penn), we are combining atomistic approaches — DFT, molecular dynamics, and AI-assisted simulation — with continuum phase-field models to understand how enamel responds to clinically relevant chemical challenges. On the experimental side this is supported by systematic mapping of enamel structure and composition across individuals, developmental stages, and disease states.

Mapping the Enamel Atlas

Using high-throughput imaging, spectroscopy, and machine learning, we are building the Biophysical Enamel Atlas: a framework for comparing enamel across developmental stages, genetic backgrounds, and disease models. The effort relies on genetically engineered mouse models from Ophir Klein (Cedars-Sinai/UCSF), Tom Diekwisch (Rochester), Michael Paine and Janet Moradian-Oldak (USC), and Jan Hu and Jim Simmer (Michigan), and on automated pipelines for segmenting the large three-dimensional datasets that SMCT, laboratory microCT, and FIB/SEM tomography produce.

Testing models of enamel architecture

With Tilman Grünewald (Aix-Marseille Université, CNRS, Institut Fresnel) and Manfred Burghammer (ESRF, Grenoble), we are using texture tomography (TexTom) to determine how enamel crystallites are oriented in space — letting us test long-standing models of enamel architecture rigorously, and follow how orientation changes during development, across species, and in disease.

Understanding ion transport and therapeutic interventions

Using APT, ToF-SIMS, XPS, and STEM we study how ions move through and are retained within enamel and dentin. How does fluoride become incorporated into dental tissues, and what limits its effectiveness? How do treatments such as silver fluoride and nanozyme-based therapies alter tissue chemistry? How do environmental and physiological exposures accumulate over a lifetime? With Michel Koo (Penn), and Mikako Hayashi and Katsuaki Naito (Osaka University).

Key discoveries
2015

Amorphous intergranular phases in enamel

Using atom probe tomography, we found that rodent enamel crystallites are joined by an ultrathin amorphous inorganic interphase rather than fused directly to one another. This previously unknown component helps control the mechanical behavior of enamel and changed how the field thinks about its structure.

Gordon et al., Science, 2015
Atom probe tomography reconstruction showing the amorphous intergranular phase between enamel crystallites
2020

Core-shell architecture of human enamel crystallites

We showed that human enamel crystallites are chemically heterogeneous: each contains a core and a shell of slightly different composition. The difference amounts to only a few atomic percent, yet it strongly influences solubility and mechanical behavior.

DeRocher et al., Nature, 2020
Atom probe reconstruction showing the compositional core and shell of a human enamel crystallite
2022

Mesoscale gradients in rod and interrod enamel

We demonstrated that enamel architecture varies systematically between rod and interrod enamel. These structural and compositional gradients give a new framework for understanding how enamel balances strength, toughness, and controlled dissolution.

Free et al., PNAS, 2022
Map of rod and interrod enamel showing systematic differences in orientation and composition
How we study enamel

Electron and ion beam methods

structure and chemistry from the micrometer to the atomic scale

SEM · FIB/SEM tomography · STEM · Atom probe tomography (APT) · ToF-SIMS

X-ray imaging

three-dimensional structure and elemental distributions

Synchrotron micro-computed tomography (SMCT) · X-ray fluorescence microscopy (XFM)

Diffraction and scattering

crystallography and local order

Micro-XRD · Texture tomography (TexTom) · Total scattering

Spectroscopy

local atomic environments

X-ray photoelectron spectroscopy (XPS) · X-ray absorption spectroscopy (XANES, EXAFS)

Computational and data science

interpreting measurements, building predictive models

DFT · Molecular dynamics · AI/ML-assisted simulation · Phase-field modeling · ML image segmentation

Collaborations and support

Representative collaborative projects

  • Aging and long-term stability of dentin — Ana Bedran-Russo (UIC)
  • Developmental defects of enamel, including fluorosis and molar hypomineralization — Sophia Houari-Mejri (Centre de Recherche des Cordeliers, Paris)
  • Biomineralization in organoids — Han-Sung Jung (Yonsei University)
  • Developmental and environmental stress during amelogenesis — Sylvie Babajko (INSERM)
  • Novel ameloblast reporter mouse models — Ophir Klein and collaborators
  • The ameloblastin amphipathic helix motif in amelogenesis — Janet Moradian-Oldak (USC)

Supported by

NIH-NIDCR · National Science Foundation · Nakano Foundation · Nakao Foundation · Graduate research fellowships and training grants

People

The group

We come from materials science, chemistry, biology, physics and engineering. What unites us is curiosity about the natural world.

Derk Joester

Derk Joester

Professor of Materials Science and Engineering
Keith Alvares

Keith Alvares

Research Associate Professor
On leave
Katsuaki Naito

Katsuaki Naito

Postdoctoral fellow
Michaela Hennebury

Michaela Hennebury

Graduate student
Ethan Suwandi

Ethan Suwandi

Graduate student
Mauricio Ceballos

Mauricio Ceballos

Graduate student
Julia Dreher-Threlkeld

Julia Dreher-Threlkeld

Graduate student
On leave
Eugene Jung

Eugene Jung

Undergraduate researcher
Olivia Lee

Olivia Lee

Undergraduate researcher
Since 2007

Our alumni

We have been fortunate to work with a remarkably diverse group of people over the years. They are listed here, most recent departures first. We try to keep tabs on everyone, but each entry records only the last position we knew of — if yours is out of date, drop us a line and we will fix it.

NameRoleDegree or majorWhere they are now
Litzy GorostietaUndergraduate → Post-baccalaureate researcher2025–2026Biologyunknown
Maddox ClarkeUndergraduate2026BiologyDental Intern, Domino Dental, Brooklyn, NY
Ana CollitonUndergraduate2025–2026PhD Student, Northwestern University
Michael Angelo San JuanUndergraduate2025–2026unknown
Xingchen ZhaoPostdoctoral fellow2022–2025UPenn
Sarah BoyerPhD studentPhD (MSE) 2025Argonne National Laboratory
Mel Andrade-MuñozUndergraduate2024–2025Neuroscience/Computer Scienceunknown
Siya BrownUndergraduate2024–2025Biol Sci/pre-dentalDental Assistant, Evanston Dental Center
Erin MeyerPostdoctoral fellow2022–2024University of North Caroline Wilmington
Lauren JinglesUndergraduate2024Biologyunknown
Danielle DugginsPhD student → Postdoctoral fellow2022–2023PhD (MSE) 2022Data Analysis Manager, University of Manchester (Harwell Science Campus, UK)
Victoria CooleyPhD studentPhD (MSE) 2023Northwestern University, then ANL/APS
Yvette CalvilloMS studentMS (MBP) 2023UIC (Dental School)
Xiangyu GuMS studentMS (MBP) 2023Biogen Inc, Boston, MA
Nilofar KhanbhaiMS studentMS (MBP) 2023Chicago Venture Fellow
Guanying LiMS studentMS (MSE) 2023PhD student in Mechanical Engineering, Northwestern University
Youssef AboukouraUndergraduate2022–2023Biologyunknown
Ava ConyerUndergraduate2023Chemical EngineeringMS student in Industrial Engineering, New York University
Jacob CoxUndergraduate2023CBEunknown
Layla JohnsonUndergraduate2023Chemistryunknown
Genesis KangUndergraduate2022–2023MSEunknown
Bradley MorenoPhD studentPhD (MSE) 2022Intel Corporation, Portland, OR
Jaron MaMS studentMS (MSE) 2022Celadyne Technologies
Wenle XuMS studentMS (MSE) 2022Texas A&M University, College Station, TX.
Yiheng DuUndergraduate2022MSEunknown
Maya KompellaUndergraduate2019–2022BMEStudent Success Coach at City Year Chicago
Dylan McAfeeUndergraduate2021–2022Physicsunknown
Allessandra DicoratoPhD studentPhD (MSE) 2021Broad Institute, Boston, MA.
Bisma AjazMS studentMS (MBP) 2021Solid Bioscience, Cambridge, MA.
Maxine FaasMS studentMS (MBP) 2021Exicure, Chicago, IL.
Samiha SyedUndergraduate2021Chemistrystudent at Benedictine University
Tarek ZakiUndergraduate2019–2021MSEGateway to Graduate School Postbaccalaureate Research Internship & Mentoring (PRISM) Program, Novartis Institutes for Biomedical Research (NIBR).
Jessica WalkerPostdoctoral fellow2018–2020Diamond Light Source, UK
Karen DeRocherPhD studentPhD (MSE) 2020NIST Gaithersburg, MD.
Robert FreePhD studentPhD (MSE) 2020unknown
Sho HarisawaMS studentMS (MSE) 2020Intel Corporation, Hillsboro, OR.
Yanfang SongMS studentMS (MBP) 2020Catalent Pharma Solutions, Bloomington, IN.
Dante MontotoUndergraduate2019–2020MSEMattiq, Skokie, IL.
Noah MetokiPostdoctoral fellow2017–2019Sibel Health
Paul SmeetsPostdoctoral fellow2016–2019Northwestern University (NUANCE)
Linus StegbauerPostdoctoral fellow2016–2019University Stuttgart, Germany
Ning HanMS studentMS (MBP) 2019WuXi Biologics, Cambridge, MA.
Utthara RameshbabuMS studentMS (MSE) 2019Impossible Foods, Redwood City, CA.
Vivian MerkPostdoctoral fellow2017–2018Florida Atlantic University
Alp AlptekinUndergraduate2017–2018MSEunknown
Brian LeeUndergraduate2018Biologyunknown
Michael WhittakerPhD studentPhD (MSE) 2017LBNL/UC Berkeley.
Emilie CampbellMS studentMS (MSE) 2017Razorfish Health, Chicago, IL.
Irene Yin-Ting ChangPostdoctoral fellow2012–2016Merck & Co.
Robert (Jack) CavanaughMS student2013–2016BS/MS 2016Ginkgo Bioworks, Inc., Boston, MA.
David CadenaUndergraduate2016PhysicsAccenture Federal Services, San Antonio, TX.
Jonathan HuangUndergraduate2015–2016MSEApple, San Francisco, CA.
Kayla MoellerUndergraduate2016BiologyColumbia University School of Dental Medicine
Victoria NelsonUndergraduate2016MSEunknown
Barghava MarisaUndergraduate2015MSEunknown
Regina KnappPostdoctoral fellow2010–2014PerkinElmer, Munich, Germany
Lyle GordonPhD studentPhD (MSE) 2014Nano Precision Medical, CA.
Michael CohenMS studentMS (MSE) 2014CVS/Aetna, New York, NY.
Huey-Ming MakMS studentMS (MBP) 2014Ginkgo Bioworks, Inc., Boston, MA.
Darcie PattersonMS studentMS (MBP) 2014Alexion Pharmaceuticals, Inc., Glenview, IL.
Leanne FriedrichUndergraduate2013–2014MSENIST Gaithersburg, MD.
Alexandra RindoneUndergraduate2014BMEPhD student, Johns Hopkins University
Keara SaudUndergraduate2014MSEPhD student, U. Michigan Ann Arbor
Chantel TesterPhD studentPhD (MSE) 2013Johnson & Johnson, NJ.
Ching-Hsuan WuPhD studentPhD (MSE) 2013unknown
David GoetschUndergraduate2013MSEUSC, Pasadena, CA.
Huang VickieUndergraduate2013MSEunknown
Minna Pace (née Krejci)PhD studentPhD (MSE) 2012Astellas Pharma, Northbrook, IL.
Fei Yin LukMS student2010–2012MS 2012US Department of Justice
Kimberly BlakeUndergraduate2011–2012African American StudiesDeputy Counsel - ICC International Court of Arbitration, New York, NY
Wisaruth MaethasithUndergraduate2010–2012MSEunknown
Kellen MobiliaUndergraduate2010–2012ChBEBerkeley Lights, Inc., San Francisco, CA.
Yuchen YangUndergraduate2011–2012BiologyNorthwestern University
Elina ZaoneginaUndergraduate2011–2012BiologyNICE Ltd, Chicago, IL.
Evan ZarubaUndergraduate2012BMEunknown
Christopher CarhartUndergraduate2011MEBoeing, Seattle, WA.
Laura MuellerUndergraduate2009–2011BMEPhilips Healthcare
Alexander ParkUndergraduate2008–2011MSEGoogle, Chicago, IL.
Lawrence TranUndergraduate2010–2011MSEFacebook, San Francisco, CA
Kathryn West (Halpern)Intern → Undergraduate2010BiologyECHO-Chicago, University of Chicago, IL.
Rose GruenhagenUndergraduate2009–2010BMEMedtronic, Minneapolis-St Paul, MN.
Janesh LakhooUndergraduate2007–2010BMEVanderbilt U. Medical Center, Nashville, TN.
Piotr ManiakUndergraduate2007–2010BMEBaxter Healthcare, Evanston, IL.
Fangzheng QianUndergraduate2009–2010MSEunknown
Jonathan BrickeyUndergraduate2008–2009MSEColorado Department of Public Health and Environment, Englewood, CO.
Jan BruecknerUndergraduate2009ChemistryTesla, Grünheide, Brandenburg, Germany.
Pongkarn ChakthranontUndergraduate2009ChBENational Nanotechnology Center of Thailand, Bangkok City, Thailand.
Boping LuUndergraduate2009MSEunknown
Brian WassermanUndergraduate2008–2009MSEMD student, University of Miami
Ryan BrockUndergraduate2008MSEExponent, Menlo Park, CA.
Steve FitzgeraldUndergraduate2007–2008MSEunknown
Mackenzie MarshallUndergraduateunknown
Xinjie (Jack) WuUndergraduateunknown
Rhiannon Flanagan-RosarioInternBarge Design Solutions, Inc., Atlanta, GA.
Laura McGinnInternunknown
Haley SproullInternCreative Artists Agency, Los Angeles, CA.
Research · Bioengineering single crystal growth

Sea urchin embryos grow single crystals from the bottom up.

Mineralized tissues are organic–inorganic composites that provide mechanical strength to an organism, helping it feed, move, defend itself, and even sense its environment. Their hierarchical architectures tolerate damage, resist fatigue, and can regenerate, remodel, or repair themselves. And they are made in water, near ambient temperature and pressure, from abundant ingredients, a route inherently more sustainable than the high-temperature processing we use to make ceramics.

The sea urchin embryo is an excellent model system for studying how an organism controls phase transformations. Its skeleton is two mirror-symmetric spicules of calcite (CaCO3, as in limestone or chalk). Each spicule is a single crystal that curves and branches at closely controlled times and in precise crystallographic directions. Spicules from different species have distinct shapes, which suggests their growth is under genetic control. Each one is deposited by a small number of primary mesenchyme cells (PMCs) working so closely together that they fuse into a syncytium, sharing a single plasma membrane. The ability to shape the crystal may depend on the calcium carbonate arriving as a transient amorphous phase rather than crystallizing directly from solution.

Micromeres arise in the 4th cleavage.

In the embryo, primary mesenchyme cells (PMCs) build two spicules that serve as a skeleton. The PMCs are descendants of the micromeres that form in the 4th cleavage of the sea urchin embryo, about 6.5 hours after the egg is fertilized (hpf = hours post fertilization).

Schematic drawing, lateral view. The animal pole of the embryo is on top, the vegetal pole on the bottom. Micromeres are colored red.

Panel 1 of 12

Micromeres further divide.

Subsequent divisions give rise to 32 (or 64, depending on the species) descendants at the vegetal pole of the early blastula.

Schematic cutaway drawing, lateral view. The blastocoel is the fluid-filled cavity surrounded by a monolayer of cells. The descendants of the micromeres are rendered in dark red.

Panel 2 of 12

The descendants of the micromeres ingress and become PMCs.

This marks an epithelial-to-mesenchymal transition, where tightly bound cells become loosely organized, migratory cells. This stage is also called the mesenchyme blastula. At this point, the endoderm (green) starts to differentiate from the ectoderm (yellow) and begins to invaginate.

Schematic cutaway drawing, lateral view. The blastocoel is the fluid-filled cavity surrounded by a monolayer of cells. The descendants of the micromeres are rendered in dark red.

Panel 3 of 12

PMCs migrate, cluster, and fuse.

As the endoderm continues to invaginate, PMCs migrate to form two ventrolateral clusters (VLC), a ring around the endoderm, and two strands towards the animal pole. Fusion of PMCs results in two syncytial masses. Each syncytium contains 16 (or 32) nuclei and is surrounded by a shared plasma membrane.

Schematic cutaway drawing, lateral view. PMCs (red), ectoderm (yellow), endoderm (green).

Panel 4 of 12

Within the VLCs, mineral is deposited.

Biomineralization commences with the formation of a single crystalline calcite granule within each of the VLCs. The granule grows into the three-fold symmetric triradiate rudiment.

Schematic cutaway drawing, showing the vegetal half of the embryo seen along the animal–vegetal axis. PMCs (red), ectoderm (yellow), endoderm (green), granule and triradiate rudiment (black).

Panel 5 of 12

Within the VLCs, mineral is deposited.

Biomineralization commences with the formation of a single crystalline calcite granule within each of the VLCs. The granule grows into the three-fold symmetric triradiate rudiment.

Brightfield image of a S. purpuratus embryo at 31 hpf. Both a granule (asterisk, and inset on bottom right) and an early triradiate rudiment (tr, inset on top right) are present.

Panel 6 of 12

Within the VLCs, mineral is deposited.

Biomineralization commences with the formation of a single crystalline calcite granule within each of the VLCs. The granule grows into the three-fold symmetric triradiate rudiment.

Brightfield image of a S. purpuratus embryo at 35 hpf. Two triradiate rudiments (red arrowheads) are present.

Panel 7 of 12

The triradiate grows along the a-axes.

The three arms of the triradiate rudiment grow in the crystallographic a-directions of the hexagonal calcite structure.

Schematic drawing of the triradiate rudiment (black) and the basal plane (001) of the calcite lattice (yellow). The crystallographic a- and c-directions are indicated.

Panel 8 of 12

The growth direction of one of the three radii changes.

On the way between the late gastrula and the prism stage of embryo development, one of the three radii changes growth direction by 90 degrees and turns into the body rod. The antero-lateral rod branches off the body rod. A little later, the second radius also changes growth direction by 90 degrees and turns into the post-oral rod.

Polarized light image of a S. purpuratus embryo at 51 hpf. br: body rod; al: antero-lateral rod; po: post-oral rod.

Panel 9 of 12

The growth direction of one of the three radii changes.

On the way between the late gastrula and the prism stage of embryo development, one of the three radii changes growth direction by 90 degrees and turns into the body rod. The antero-lateral rod branches off the body rod. A little later, the second radius also changes growth direction by 90 degrees and turns into the post-oral rod.

Schematic drawing of one prism-stage spicule (black and gray) and the basal plane (001) of the calcite lattice (yellow). The crystallographic a- and c-directions are indicated.

Panel 10 of 12

Rods elongate and thicken.

From the prism to the pluteus stage, the second radius completes its change of direction and, as the post-oral rod, elongates along the c-axis direction. The antero-lateral and body rods also elongate, the latter thickens at the distal end. Note that the two spicules are mirror images.

Polarized light image of a S. purpuratus pluteus at 71 hpf. br: body rod; al: antero-lateral rod; po: post-oral rod; mv: mid-ventral rod.

Panel 11 of 12

Rods elongate and thicken.

From the prism to the pluteus stage, the second radius completes its change of direction and, as the post-oral rod, elongates along the c-axis direction. The antero-lateral and body rods also elongate, the latter thickens at the distal end. Note that the two spicules are mirror images.

Schematic drawing of a pluteus stage embryo with two mirror-symmetric spicules (gray). The location of the original triradiate is indicated for one of the spicules (black).

Panel 12 of 12

What sets this system apart is that the PMCs keep working outside the embryo. That is rare enough among mineralizing cells to be worth a project in its own right. It means we can manipulate the process by genetic engineering or by providing molecular cues to the cells, and observe both cellular behavior and crystal growth in real time. This is what makes the long-term goal plausible: putting PMCs, or the molecules they depend on, to work making materials.

We use a broad range of techniques to get there. Cryo-electron tomography, STEM, and FIB/SEM tomography show us the cellular structures and the crystals themselves. Transcriptomics, proteomics, and recombinant antibodies tell us which molecules are present and where. Cell culture and in vitro experiments let us test what those molecules actually do. What we want to know is how specific proteins are assembled and patterned in the spicule matrix, and how that patterning sets nucleation kinetics and the direction the crystal grows. That is the first step towards porting the key players into a system that can be engineered and scaled using the tools of synthetic biology.

In depth

Why this matters

Sea urchins make masterful use of calcite throughout their lives. The embryo’s skeleton is only two single crystals; the adult’s test, spines, and teeth are orders of magnitude larger in volume and more complex in microstructure, composition, and function. We expect the design principles and the molecular toolkit to be shared. The embryo is where they are simplest to study, and what we learn there should show how skeletal elements arise from cellular processes across length scales, and how those processes shape crystal growth. That is a first step towards connecting developmental biology to the materials genome. The knowledge could reach areas as far apart as the programmed synthesis of bone grafts and the large-scale sequestration of carbon dioxide.

What we are doing now

Identifying the molecular players

We are re-assessing the spicule proteome using modern proteomics and transcriptomics, with the goal of extending the analysis of functional roles beyond the known set of occluded proteins, SM50 and SM30. We are also mapping how spicule matrix proteins are distributed within the spicule.

Dissecting functional roles

Using in vitro experiments in microfluidic droplets and in vivo knock-down experiments, we are analyzing how native and recombinant spicule matrix proteins affect nucleation, polymorph selection, and crystal growth.

Examining the spicule–cell interface

Imaging and tomography let us study interfacial processes at the spicule growth front. We are also working to elucidate the ultrastructure of the spicule elongation apparatus: the machinery that we hypothesize allows the PMCs to elongate the spicule in specific crystallographic directions.

Key discoveries
2011

Patterning PMCs in vitro

Building on prior work by Okazaki, Wilt, and others, we used micro-contact printing in an in vitro culture system of sea urchin embryo primary mesenchyme cells (PMCs) to control the deposition of endoskeletal spicules made from single-crystalline calcite (CaCO3).

Wu, Park & Joester, Journal of the American Chemical Society, 2011
Micro-contact printed pattern with spicules deposited by cultured primary mesenchyme cells
2012

VEGF activates a molecular switch that controls crystal growth direction

Again using an in vitro culture system, we discovered that recombinant vascular endothelial growth factor (rVEGF) can be used to control the shape and crystallographic growth direction of spicules.

Knapp, Wu, Mobilia & Joester, Journal of the American Chemical Society, 2012
Spicules grown in culture with recombinant VEGF, showing altered shape and growth direction
2019

Protocols for isolating and culturing PMCs

We published our optimized PMC isolation and culture protocols as part of a two-volume series of invited contributions on echinoderm biology.

Moreno et al., Methods in Cell Biology, 2019
Stages of the primary mesenchyme cell isolation and culture protocol

More recently, transcriptional profiling using RNAseq has given us deep insight into the molecular players that may be involved. Together with the culture system, that gives us an unusual opportunity: to investigate the mechanism behind this example of biological control over crystal growth in a well-characterized in vitro system.

How we study crystal growth in PMCs

Light and fluorescence microscopy

cell behavior, crystal growth, the role of the cytoskeleton, seawater uptake, vesicular transport, small-molecule inhibitors

Polarized light · Fluorescence · DIC · Live-cell microscopy · Confocal microscopy · µ-Raman

Electron and ion beam methods

crystal habit and lattice orientation, composition, defects, interfacial processes, cellular ultrastructure

SEM · VolumeScope · TEM · STEM · Cryo-SEM · Cryo-ET · (Cryo-)FIB/SEM tomography

Spectroscopy

local atomic environments, the amorphous-to-crystalline transition

X-ray absorption spectroscopy (XANES, EXAFS)

X-ray imaging

three-dimensional structure and elemental distributions

X-ray fluorescence microscopy (XFM)

Diffraction and scattering

crystallography and local order, strain mapping

Nano-XRD

Omics

which genes and proteins are involved, and when they appear

Transcriptomics (RNAseq) · Proteomics

Collaborations and support

Representative collaborative projects

  • Characterization of the shell of the slipper snail (Deirdre Lyons, Scripps Institution of Oceanography)
  • Analysis of echinoderm stereom polymorphs (Yael Politi and Luca Bertinetti, TU Dresden)
  • From the discovery of new biominerals in the chiton tooth to bioinspired inks for 3D printing (Mark Hersam, Northwestern University)
  • Polymorph selectivity and the formation of metastable ferrihydrite in the chiton tooth (Jon Wilker, Purdue University)

Supported by

National Science Foundation · Graduate research fellowships and training grants

Research · Strontium in acanthareans

Acanthareans sequester strontium from seawater.

Acanthareans are marine, single-celled organisms that build an endoskeleton of celestine (SrSO4). Three things about them are worth the attention. They grow their spicules as single crystals with shapes that are very different from those observed in lab-grown crystals, and those shapes are specific to the species. They remodel the skeleton, and even dissolve it, at defined points in the life cycle. And they select Sr2+ out of seawater in which Ca2+ is a hundred times more abundant.

Each individual has either ten diametral or twenty radial spicules. Shape, connectivity, and the architecture of the central junction that joins them differ markedly among the roughly 150 known species. Spicules are faceted in some, smoothly curving in others, and can carry barbs, wings, or branches that anastomose into regular lattices and porous plates. Aspect ratios reach twenty, where synthetic celestine grows as faceted tablets. In the few species examined so far, the long axis of the spicule runs parallel to the crystallographic a-axis. Form this consistent, and this specific to a species, is strong evidence that the process is under genetic control.

Image viewer — to buildA stepper or gallery of acantharean spicules: whole cells, the central junction, and the range of spicule form across species. Rows go in figures.csv under a new set_id.
→ content/figures.csv + images/projects/acantharea/

The form is not fixed within a single life either. Spicules grow more elaborate as an individual matures, and in some clades the endoskeleton is remodelled into a mineralized cyst before hundreds or thousands of flagellated swarmer cells are released. So the organism can reshape its crystals at different points in its development and dissolve them in a controlled way, which suggests genetic regulation here too, perhaps through overlapping or life-stage-specific sets of genes.

Seawater holds 88 µM Sr2+ against 10.5 mM Ca2+, and it is undersaturated with respect to celestine. Sulfate, at 28.9 mM, is not limiting. Because their ionic radii are similar, Ca2+ and Sr2+ are usually transported more or less indiscriminately by calcium channels and pumps, so most biominerals take up strontium at close to the ambient ratio. Acanthareans do not. How they manage it is unknown: the answer could lie in selective channels or pumps, or in holding the local sulfate concentration in the narrow range that precipitates celestine but none of the calcium sulfates.

In depth

Why this matters

The organic and inorganic biochemistry and physiology of acanthareans is largely unexplored. Our long-term goals are to identify the design principles used by acanthareans and apply them in bio-inspired materials and bio-enabled routes to capture Sr2+ in the presence of chemically similar ions. That ability matters directly for the efficient removal of 90Sr, a highly active radioisotope present in nuclear fallout, in spent fuel rods, and in the high-level nuclear waste held at federal facilities. 90Sr is dangerous precisely because nothing distinguishes it from calcium: a similar ionic radius and similar chemistry mean transport proteins take it up indiscriminately, so it accumulates in bone and teeth, where its beta decay, with a half-life of about 29 years, goes on delivering a dose for decades.

What we are doing now

Identifying the molecular players

We are profiling acantharean transcriptomes to find the genes expressed during skeleton formation and the proteins they encode.

Mapping the transport routes

We are identifying the Sr2+ and SO42− transporters and characterizing what they do, to work out how the ions reach the site of mineralization. In parallel, we use elemental mapping to determine uptake routes and the incorporation of elements into the biomineral.

How we study acanthareans

Light and fluorescence microscopy

identification, seawater uptake

Polarized light · Fluorescence · DIC · Live-cell microscopy · Confocal microscopy

Electron and ion beam methods

crystal habit and lattice orientation, composition, defects, cellular ultrastructure

SEM · TEM · STEM · FIB/SEM

X-ray imaging

three-dimensional structure and elemental distributions

X-ray fluorescence microscopy (XFM)

Diffraction and scattering

crystallography and local order, strain mapping

Nano-XRD

Omics

which genes and proteins are involved, and when they appear

Transcriptomics (RNAseq) · Proteomics

Collaborations and support

Collaborators

  • John Burns (Bigelow Laboratory for Ocean Sciences)
  • Leocadio Blanco-Bercial (Bermuda Institute of Ocean Sciences)

Supported by

National Science Foundation · Army Research Office

Who to talk to

Michaela Hennebury · Derk Joester

Research · The sea urchin tooth

The sea urchin tooth uses far-from-equilibrium materials for strength.

Many sea urchins graze on rocky reefs, frequently occupying pits they excavate themselves. They erode not only soft lime- and mudstone (Mohs 2 to 3) but substantially harder substrates, including sandstone and granite (Mohs 6 to 7). Their teeth, however, are composed largely of calcite (Mohs 3), softer than much of the substrate they cut. Sea urchins compensate through a strongly hierarchical, compositionally and functionally graded architecture, and through continuous growth.

Continuous growth means that every stage of tooth development is present in a single tooth at any one time. Odontoblasts arise in the plumula attached to the cervical end and fuse into a syncytium that deposits magnesian calcite (Ca1-xMgxCO3). As the maturing tissue advances towards the incisal end, the syncytium withdraws, connecting the crystalline elements with widening mineral columns and ultimately yielding an acellular tissue. In effect, the bricks go down first and the mortar is filled in afterwards.

The tooth combines fibrous and platy elements that in combination confer wear resistance, toughness, and self-sharpening. These microstructural elements differ markedly in Mg content. Primary and secondary plates, among others, consist of high magnesian calcite (HMC), with up to 13 at% Mg on Ca lattice sites. The columns that connect the plates reach 35 at% Mg, far beyond the nominal solubility limit of Mg in calcite; we refer to this phase as very high magnesian calcite (VHMC).

Sea urchins have five continuously growing teeth.

Many sea urchins graze on rocky reefs, occupying pits they excavate themselves. The five teeth that do the cutting are carried in Aristotle’s lantern.

Volume rendering of Strongylocentrotus purpuratus Aristotle’s lantern, oblique view.

Panel 1 of 15

Sea urchins have five continuously growing teeth.

Each tooth in Aristotle’s lantern is held by an independently controlled jaw apparatus that also advances it as it grows.

Volume rendering of S. purpuratus lantern, oral view.

Panel 2 of 15

Each tooth runs most of the length of the jaw.

Only the self-sharpening tip meets the substrate the sea urchin grazes on. The rest of the tooth is a reserve, still maturing, that will be pushed forward to replace what is worn away.

Cutaway view of S. purpuratus lantern, the section plane slicing the tooth on the left along its center line.

Panel 3 of 15

Each tooth runs most of the length of the jaw.

In this transverse section, the five-fold symmetry of the lantern is on display.

Cutaway view of S. purpuratus lantern, the section plane normal to the lantern’s axis.

Panel 4 of 15

The teeth of regular sea urchins (Euechinoidea) have a characteristic T-shape.

In this mature tooth, the keel (vertical) is well developed and topped by a broad flange.

Cross section of a mature Lytechinus variegatus tooth.

Panel 5 of 15

The teeth of regular sea urchins (Euechinoidea) have a characteristic T-shape.

At increasing magnification, the intricate microstructure of the tooth emerges.

Cross section of a mature L. variegatus tooth.

Panel 6 of 15

The tooth comprises plates and needles.

Primary plates (pp) and secondary plates (sp) are laid down first, then connected by columns.

Cross section of a mature L. variegatus tooth.

Panel 7 of 15

The tooth comprises plates and needles.

As the syncytium of odontoblasts withdraws, the columns grow laterally until they fill space.

Cross section of a mature L. variegatus tooth.

Panel 8 of 15

The stone part of the tooth is a fiber-reinforced composite.

It lies roughly along the center line of the flange and appears darker in BSE images. As the hardest part of the tooth, it forms the cutting edge.

Cross section of a mature L. variegatus tooth.

Panel 9 of 15

The stone part of the tooth is a fiber-reinforced composite.

In this closeup, the continuity of primary and secondary plates in the lateral parts of the flange is apparent.

Cross section of a mature L. variegatus tooth.

Panel 10 of 15

The stone part of the tooth is a fiber-reinforced composite.

In this closeup, the very fine needles that reinforce the composite become apparent.

Cross section of a mature L. variegatus tooth.

Panel 11 of 15

Magnesium is placed, not merely tolerated.

Elemental mapping reveals the high Mg content in the stone.

Mg/(Mg+Ca) ratio map of the previous panel.

Panel 12 of 15

Magnesium is placed, not merely tolerated.

In this closeup, the primary plates, secondary plates, and needles appear brighter; the columns appear darker due to their high Mg content.

Cross section of a mature L. variegatus tooth.

Panel 13 of 15

Magnesium is placed, not merely tolerated.

Primary and secondary plates are high magnesian calcite, with up to 13 at% Mg on Ca lattice sites. The columns that connect them reach 35 at%, far beyond the nominal solubility limit of Mg in calcite.

Mg/(Mg+Ca) ratio map of the previous panel.

Panel 14 of 15

A protein family tracks the magnesium-rich phase.

Immunohistochemical imaging (IHC) using a fluorescently labeled secondary antibody reveals the distribution of a member of a family of proline-alanine-rich phosphoproteins (PARPs).

Tissue section, flange right, stained with anti-PARP.

Panel 15 of 15

Both HMC and VHMC are thermodynamically unstable under ambient conditions, and no ambient synthesis of VHMC is known. The strongly hydrated Mg2+ ion poisons calcite growth, so large single crystals of HMC or VHMC are difficult to obtain under mild solution conditions. Synthetic routes rely on elevated temperature and pressure and yield polycrystalline material with small grain sizes. Given the substantial increase in hardness on Mg substitution, and evidence of precipitation hardening in Mg-substituted calcites, there is considerable interest in how organisms achieve it. For this reason we are working to understand the mechanism by which sea urchins control Mg content far from equilibrium. Candidates are already in hand: comparing the proteome of the sea urchin tooth, which contains VHMC, with those of mineralized tissues that contain only HMC, Keith Alvares and co-workers identified a family of proline-alanine-rich phosphoproteins (PARPs).

In depth

Why this matters

Developmental, cellular, and physicochemical processes are inextricably linked in the biosynthesis of mineralized tissues, and biological control over phase transformations is an integral part of it. Properties and performance depend strongly on microstructure: the arrangement of inorganic and organic components, and the compositional gradients running through them. Understanding how cells pattern and maintain a privileged environment for mineral deposition, how they transport and modulate precursor concentrations, and what cellular machinery they use to control crystal growth across length scales is a prerequisite for intervening when developmental processes go awry, for engineering strategies to regrow and replace damaged tissue, and for designing bio-enabled and bio-inspired materials and processes. No hierarchical, functionally graded tissue of this kind is yet understood at that level. The availability of transgenic adult sea urchins now makes the tooth a tractable system in which to bring developmental and structural biology, biochemistry, and materials science to bear together.

What we are doing now

Characterizing what PARPs do

We are testing how PARPs affect Mg incorporation and mechanical properties, both in vivo and in vitro.

Identifying further candidates

We are using transcriptomics and proteomics to identify additional candidate proteins.

How we study the sea urchin tooth

Electron and ion beam methods

mapping of the microstructure and compositional gradients

SEM · SEM-EDS · SEM-EBSD · STEM · FIB/SEM

X-ray imaging

three-dimensional structure and elemental distributions

X-ray fluorescence microscopy (XFM)

Omics

which genes and proteins are involved, and when they appear

Transcriptomics (RNAseq) · Proteomics

Genetic engineering

dissecting the functional roles of PARPs

Loss-of-function and gain-of-function mutants

In vitro assays

the effect of PARPs on nucleation and growth

Magnesian calcite growth assays

Collaborations and support

Collaborators

  • Amro Hamdoun (Scripps Institution of Oceanography, UC San Diego)

Supported by

National Science Foundation

Research products

Selected, peer-reviewed publications

Also

Book chapters and other articles

Beyond papers

Other products

Data and code the group has published for others to use.

EnamelBase

Our enamel data on FaceBase, the NIDCR-funded repository for craniofacial research.

bbimat-group on GitHub

Analysis code and processing pipelines from the group.

Zenodo datasetsDeposited datasets with their own DOIs. A DOI is better than a bare link here — it is what someone would cite.
→ content/products.csv
Join us

What’s open now

Last updated September 2026

Multi-scale modeling of the dynamics of dissolution of murine and human enamel

An NIH- and NSF-funded effort with James Rondinelli and Peter Voorhees. Open to postdocs, PhD students and MS students in three thrusts:

  • Atomistic modeling of bioapatites and amorphous phases, using DFT and molecular dynamics. Primary mentor: James Rondinelli
  • Continuum modeling of enamel dissolution with phase-field methods. Primary mentor: Peter Voorhees
  • Experimental mapping of the compositional and structural heterogeneity of human enamel, and of the variance between individuals, using atom probe tomography and advanced electron-optical and X-ray methods. Primary mentor: Derk Joester

Bioengineering single crystal growth

NSF-funded. Open to PhD and MS students. We ask how the primary mesenchyme cells of the sea urchin embryo control the branching of a single crystal of calcium carbonate in precise crystallographic directions, using a wide range of techniques from materials science and the life sciences. Primary mentor: Derk Joester

Other projects

PhD students who bring their own fellowship support are welcome in any of our active research areas, as are MS students. See the five current projects.

Self-funded postdocs

Welcome in any of our active research areas. Derk is glad to discuss projects for submission to funding agencies or foundations.

Northwestern undergraduates

We prefer that you join a project in Fall or Winter, so that we get to know you and you get to know us before the summer. We look for students who are open to full-time, paid work over the summer.

How to apply is under Routes in, just below.

The lab

What it is like to work here

Our research is transdisciplinary, drawing on materials science and engineering, chemistry, and the life sciences. Whichever of those you trained in, you will pick up skills from the others. The work runs from experiments at the bench, in core facilities at Northwestern and at our Chicagoland partners, and at national user facilities — the Advanced Photon Source, the Advanced Light Source, the Midwest Center for Cryo-Electron Tomography — through demanding data analysis and visualization to computational modeling. No single project needs all of it. Wherever possible, you will learn to run even the most sophisticated instruments yourself rather than hand samples to someone else.

Trainees who do well here

  • are curious about how things really work.
  • appreciate the beauty and complexity of the natural world and of living organisms.
  • are eager to learn new skills, and to get good at them.
  • are ready to take ownership of a project and lead where it goes.
  • are ready to join a team and contribute to other people's projects.
  • are keen to teach and mentor less experienced members, including undergraduates and interns.
  • can see themselves working across disciplines, with collaborators trained very differently from themselves.
Applying

Routes in

Postdocs should write directly with a CV and a letter covering what you have worked on, what you want to work on here, and why.

PhD students apply through the Materials Science and Engineering PhD program at Northwestern. The department receives more than 600 applications each cycle, and every one is vetted by the graduate admissions committee. Individual professors are much easier to reach once the committee has offered you a place in the department. When you do write, Derk generally replies only to inquiries that make clear why our field, and this lab in particular, appeal to you.

MS students also apply through Materials Science and Engineering. Once you are admitted, write to Derk to discuss projects for MSE 499 Independent Study or for the thesis-track MS.

Northwestern and Chicagoland undergraduates from any science or engineering background are welcome to write and ask about research opportunities.

Undergraduates at other US and international institutions should come through one of the Northwestern-run summer programs: the MRSEC REU, the IIN REU, SROP, or MICRO. We cannot host students from outside the US except through these or equivalent programs. Note that the MRSEC and IIN REU programs require US citizenship or permanent residency.

Interns from Chicagoland schools are welcome to write and ask what is currently available.

Where to write. Derk Joester, Northwestern University · d-joester@northwestern.edu

Broadening participation

Recent undergraduate research projects

Research figure by Maddox Clarke

Maddox Clarke

WS/Fellowship · 2026 · Northwestern University

Maddox characterized the microstructure of the continuously growing teeth of the sea urchin Lytechinus pictus. Shown here is a ground and polished cross section using backscattered electron contrast in SEM (left), and a false-colored map of the cation ratio for Mg (right).

Mentor: Julia Dreher-Threlkeld
Figure to comeimages/undergrad-research/olivia-lee.jpg

Olivia Lee

Undergraduate research · 2026 · Northwestern University

Summary to come from the mentor.

Mentor: Michaela Hennebury
Research figure by Eugene Jung

Eugene Jung

Undergraduate research · 2026 · Northwestern University

Eugene analyzed diffraction patterns of ice crystals formed in fruit fly larvae that express a putative antifreeze protein. Shown here are a 2D WAXS pattern (left), 1D diffraction data recorded at different temperatures (top right), and the a lattice parameter in wild-type and CaAFP-expressing larvae at 245 K (bottom right).

Mentor: Mauricio Ceballos
Figure to comeimages/undergrad-research/litzy-gorostieta.jpg

Litzy Gorostieta

I-SURE · 2025 · Northeastern Illinois University

Summary to come from the mentor.

Mentor: Mauricio Ceballos
Figure to comeimages/undergrad-research/ana-colliton.jpg

Ana Colliton

MICRO · 2025 · St Olaf College

Summary to come from the mentor.

Mentor: Julia Dreher-Threlkeld
Research figure by Michael Angelo San Juan

Michael Angelo San Juan

MICRO · 2025 · University of Texas at San Antonio

Michael evaluated how convolutional neural networks (CNNs) of different architectures perform when trained to segment mineralized tissues in synchrotron µCT reconstructions. Shown here are three tomographic slices of a murine hemimandible (left), the architectures compared (middle), and the same three slices after segmentation (right).

Presented at the MICRO Summit.
Mentor: Ethan Suwandi