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Students

Acta Biomaterialia Paper on Silk Microrheology

Posted on September 12, 2025

in Partnership, Publications, Students

by Holland Lab

Excited to share our latest work with Prof. Rae M. Robertson-Anderson (USD) just accepted in Acta Biomaterialia:“Local viscoelasticity of denaturing spider silk dope is governed by dynamic hierarchical intermolecular interactions”Special shout-out to the lead experimentalists:Karthik Peddireddy (Rae’s postdoc), who spearheaded the optical tweezers microrheology,Hannah Johnson (my recently graduated PhD student), who carried out the spider dissection and dope prep experiments.Together, they uncovered:A universal relaxation timescale (~0.5 s) tied to transient crosslinking,The crucial role of hierarchical assemblies in tuning local viscoelasticity,How concentration and aging reshape mechanical responses through entanglement, crosslinking, and phase separation.These results provide fresh insight into how spiders store aggregation-prone disordered proteins in their glands without premature assembly — and highlight the power of microrheology to probe hierarchical protein assemblies.Huge thanks to my collaborators and mentees for their amazing contributions!Grateful for support from the Air Force Office of Scientific Research (AFOSR) that made this work possible. https://www.sciencedirect.com/science/article/pii/S1742706125006737 ...

Soft Matter Conference at USD

Posted on September 12, 2025

in Presentations, Students

by Holland Lab

Our lab had a great time yesterday at the Frontiers in Soft Matter and Macromolecular Networks conference at the University of San Diego! PhD students presented their research on silk protein structure, function, and assembly: Alexia de Loera – Structural Insights into the GGX Domain of Spider Silk MaSp1 Using Solution NMR and Molecular ModelingAli Kiaaefar – Conformational Structure, Dynamics, and Assembly of Native Silkworm Silk Protein by Solution NMR and ModelingDavit Alimbarashvili – Structural Biology of Aciniform Spider Silk Guides Biomimetics for a New Class of BiomaterialsMS student John Malki also presented:Use of Differential Scanning Calorimetry and Solid-State NMR to Determine Beta-Sheet Crystallization of Native B. mori Silkworm Fibroin Films Assembled on Various SurfacesSpecial thanks to Prof. Rae M. Robertson-Anderson for chairing the conference. Beautiful campus, lots of engagement with SoCal colleagues, and great discussions with researchers from across the country! ...

Building Collaborations: Lorenz Lab Visits SDSU

Posted on September 12, 2025

in Awards, Partnership, Students, Travel

by Holland Lab

Kicked off the new semester at SDSU by hosting Prof. Chris Lorenz (King’s College London) and his postdoc Dr. Fran Thomas for a week of collaboration on our AFOSR project, “Elucidating the Intrinsically Disordered State, Supramolecular Assembly and Protein Condensates in Natural Materials Formation.”Even in the hectic first week of classes, Chris and Fran made a big impact:Chris delivered a fantastic seminar, “Peptide and Protein Interactions Across Scales: Molecular Dynamics Perspectives from Antimicrobial Assemblies to Neuroimmune Signaling and Biomaterials.”They worked closely with my postdocs and PhD students — going beyond the basics to tackle the advanced aspects of molecular dynamics simulations and analysis that are critical for our research.We had in-depth group and one-on-one discussions on ongoing and future directions, building on our strong history of co-authored papers and manuscripts under review.A great way to launch the semester — grateful for the chance to strengthen our SDSU–King’s College London collaboration and excited about the discoveries ahead! ...

Summer 2025 ARO–AEOP Internships in the Lab

Posted on September 12, 2025

in Students

by Holland Lab

This August and September we wrapped up another successful summer hosting Army Educational Outreach Program (AEOP) interns through our DOD–ARO funded project: "Structural Biology of Aciniform Spider Silk Guides Biomimetics for a New Class of Biomaterials". We were fortunate to work with a talented group of students:• Undergraduate participants: Fatimah Ali and Alexa Flores• High school participants: Jamie Carter and Jaden Ma Throughout the summer, students gained authentic hands-on experience in biochemistry and structural biology of spider silk. Their work included:• Caring for Argiope spiders and collecting prey-wrapping silk under isotope-labeled diets.• Preparing samples for solid-state NMR (SSNMR) to investigate secondary structure in fibers.• Using solution NMR to characterize the soluble protein dope prior to fiber formation.• Exploring computational tools such as AlphaFold structure prediction and molecular dynamics simulations to interpret their data . The program was supported by close mentorship:• Dr. Kevin Chalek (Postdoctoral Researcher) guided both undergraduate and high school students in isotope labeling, SSNMR sample preparation, and structural modeling.• Dr. David Onofrei (Research Scientist) worked with the undergraduates on solution NMR and complementary biophysical studies. Our interns also developed skills in scientific communication, preparing lab reports, presenting in weekly group meetings, and engaging with the broader SDSU research community. We are grateful to Fatimah, Alexa, Jamie, and Jaden for their enthusiasm and dedication this summer, and to the AEOP program for supporting this opportunity. We look forward to seeing where their paths in science lead next! ...

Silk Gordon Research Conference (GRC)

Posted on August 13, 2025

in Presentations, Students, Travel

by Holland Lab

In July the lab attended the 2nd Gordon Research Conference (GRC) on Silk at Bryant University in Smithfield, RI! Our lab was out in full force — research scientist David Onofrei, postdoc Kevin Chalek, graduate student Alexia de Loera, and even the PI all presented posters. Alexia also gave a short talk on her poster at the GRS, and David delivered a short poster talk as well.We covered a wide range of silk science: Pre-assembled silk spinning states Recombinant protein solution NMR (in collaboration with Thomas Scheibel’s group, U. Bayreuth) DNP-MAS NMR of spun fibers to probe sidechain packing And a PI poster on prey wrap spider silk biomimetics informed by native structure and assembly.Huge thanks to Keiji Numata and Chris Holland for organizing such a dynamic and inspiring conference. Great science, great people, and exciting directions ahead in silk materials research! Look forward to the next one! ...

ACS Spring 2025 Meeting

Posted on June 4, 2025

in Presentations, Students

by Holland Lab

Recently wrapped up an exciting and inspiring week at the ACS Spring 2025 Conference right here in San Diego!Our lab had a fantastic presence, with postdocs Yuan Li and Kevin Chalek delivering great talks on:Solid-State NMR of morphologically distinct hydroxyapatite nanoparticles (Yuan)Spider silk fibers and their structural insights via SSNMR (Kevin)We also had a strong poster showing from our grad students:Alexia de Loera, Lado Shapakidze, Davit Alimbarashvili, and John Malki — presenting exciting work on the Bio-Nano Interface and Spider Silk projects.Special shoutout to undergrads Alexa Aishia Flores and Brianna Duarte, who presented a joint poster on validating AlphaFold-predicted spider silk structures using SSNMR data—a critical step toward bridging computational predictions with experimental structural biology. They're mentored by Kevin Chalek and did a fantastic job!Proud of the whole team for representing the lab so well—excellent science, thoughtful discussions, and strong community engagement all around. ...

New Publication in Ultramicroscopy

Posted on June 4, 2025

in Publications, Students

by Holland Lab

The lab has new paper out in Ultramicroscopy! Led by recent PhD graduate student Hannah Johnson, the paper lays out a protocol for NS-TEM of native spider silk protein micelle-like assemblies extracted directly from the spinning dope of spiders. Spider silk proteins prior to spinning are very sensitive to aggregation and preserving the native structure under EM staining conditions is challenging. Commonly used stains such uranyl acetate induce fibril formation because the stain is acidic and acidic pH is known to trigger fiber formation. By utilizing ammonium molybdate stain at pH 7, we were able to show that native silk superstructures could be preserved that closely matched our previously published cryoEM tomography data. Silk protein micelle pre-assembly is critical for fiber formation and we anticipate that this protocol will be useful for the characterization of other spider and silkworm silk dopes and those attempting to recapitulate this pre-assembly in recombinant silk systems. The published manuscript can be found here: https://www.sciencedirect.com/science/article/pii/S0304399125000233 ...

Summer Research Opportunities UG and HS Students

Posted on January 15, 2025

in Students

by Holland Lab

The lab has two openings this coming summer for high school (HS) students and two openings for undergraduate (UG) researchers. These research internships will occur in June, July and August and require ~300 hr of total committed time. These positions are funded by the Army Educational Outreach Program (AEOP) and interns will work on spider silk research projects. For more information and to apply, see links below. Please feel free to reach out to me directly if you have any additional questions or know any outstanding candidates. *UG: https://apps.ideal-logic.com/aeop?key=JKR5-G7ZD1_K9KH-5PTF_7174578e615f (students will need to create a login) *High School: https://apps.ideal-logic.com/aeop?key=JKR5-G7ZD1_K9KH-5PTF_7174578e615f (students will need to create a login and have parental consent) ...

New Langmuir Manuscript

Posted on October 30, 2024

in Graduates, Publications, Students

by Holland Lab

Holland Lab has a new manuscript out in Langmuir titled: "Aspartic Acid Binding on Hydroxyapatite Nanoparticles with Varying Morphologies Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulation". The paper illustrates the significant impact nanoscale morphology has on biomolecule surface binding and organization. The study was led by recent lab PhD graduate and now lab post-doc, Yuan Li. Yuan used a bevy of SSNMR methods to structurally characterize aspartic acid adsorbed to HAP surfaces which was combined with MD simulations conducted by collaborator, Prof. Chris Lorenz @ King's College London. Excellent agreement was found between experimental SSNMR distance measurements and MD models providing atomistic-level structural insights of the bio-nano interface. This work is support by the National Science Foundation (NSF), Division of Chemistry (CHE). The paper can be found here: https://pubs.acs.org/doi/10.1021/acs.langmuir.4c02880 Yuan created some cool cover art that was published with the article: ...

New Advanced Functional Materials Paper

Posted on July 23, 2024

in Publications, Students

by Holland Lab

The lab has a new paper out in Advanced Functional Materials titled: "Unraveling the Molecular Origin of Prey-wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR". Prey wrap spider silk exhibits high extensibility and superior toughness compared to other types of spider silk and is a promising target for biomaterials design. In this paper, the lab combines mechanical testing, solution NMR on native glands, SSNMR on spun fibers and AlphaFold structure prediction to elucidate the silk's unique liquid-to-solid transition and further correlate the silk fibers conformational structure with the silk's fantastic mechanics. These results and models are providing the fundamental basis for the design of biomimetic materials inspired by the prey wrap spider silk system. The study was led by lab post-doc, Kevin Chalek, with major contributions from David Onofrei, Julian Aldana, Hannah Johnson, and NREL scientist, Bennett Addison. For anyone interested, you can check out the paper here: Unraveling the Molecular Origin of Prey‐Wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR onlinelibrary.wiley.com ...

SDSU Graduation – Hannah Johnson & Yuan Li PhDs

Posted on May 13, 2024

in Graduates, Students

by Holland Lab

SDSU Graduation was this past weekend. Proud of the two most recent PhD students from the Holland Lab, Yuan Li and Hannah Johnson!!! Yuan's thesis is on: "Elucidating Bio-Nano Interface Atomic Structure in Hydroxyapatite Nanoparticles with SSNMR". Hannah's thesis is on: "The Role of Liquid-Liquid Phase Separation in Spider Silk Formation". A busy summer ahead getting all of their awesome manuscripts out!!! ...

Julian Aldana and Yuan Li Receive Research Awards

Posted on May 8, 2024

in Awards, Students

by Holland Lab

Julian and Yuan were awarded Outstanding Research Awards by the SDSU Department of Chemistry and Biochemistry. Julian was awarded his for Outstanding Undergraduate Research and Yuan for Outstanding Research at the PhD level. Julian's research work is focused on molecular dynamics (MD) simulation of spider silk proteins. Yuan is working on Bio-Nano interface atomic structure in hydroxyapatite nanoparticles with SSNMR. Congratulations Julian and Yuan!!! ...

Holland Lab Attends ENC Conference

Posted on April 14, 2024

in Awards, Presentations, Students, Travel

by Holland Lab

The Holland Lab attended the Experimental NMR Conference (ENC) at Asilomar Conference Center in Pacific Grove, CA https://www.enc-conference.org/Conference-2024. This is the premier conference in experimental magnetic resonance including solution and solid-state NMR and magnetic resonance imaging (MRI). The lab gave two talks and presented three posters. Lab post-doc, Dr. Kevin Chalek's talk was on Sunday (4/7) in the Young Scientist Symposium titled "Studying Sidechain Interactions in Dragline Spider Silk Fibers Using MAS Solid-state NMR and DNP". Kevin also presented a poster on the same topic Tues/Thurs. Research scientist and SDSU NMR Facility Manager, Dr. David Onofrei gave a talk in the Biomolecular Solution NMR Session on Tuesday (4/9) titled "Using CS-ROSETTA to Probe Assembly of Intrinsically Disordered Spider Silk Proteins in Solution". PhD grad student, Hannah Johnson presented a poster on Tues/Thurs titled "Solution NMR of Liquid-Liquid Phase Separation in Native Major Ampullate Spider Silk Proteins Indicates Arg and Tyr Influence Pre-Assembly". PhD grad student, Yuan Li presented a poster on Mon/Wed titled "The Calcium Sites of Hydroxyapatite with Different Morphologies and Crystal Phases Investigated by 43Ca MAS Solid-state NMR". Yuan was also awarded an ENC graduate student travel award to support her attendance. Congrats Yuan!!! Below is a picture from the Lab Dinner at the Fish Hopper in Monterey where we caught up with Lab alumni, Dr. Haley Swanson, who is now Bruker NMR West Coast Sales Rep. We had fantastic discussions regarding our upcoming 600 MHz Ascend NMR magnet install and some plans for new cutting edge probes in Diffusion and Solid-state NMR for the future. Check out the picture from dinner below: ...

Congratulations to our graduate students!

Posted on July 19, 2022

in Graduates, Students

by Sarah White

Haley Swanson graduated with her PhD and Rich Thai graduated with his master's of science degree in May 2022. PhD student Hannah Johnson also successfully passed her 3rd year qualifying exam! ...

Francisco Botello Featured on SDSU NewsCenter

Posted on July 19, 2022

in Students

by Sarah White

Undergraduate mechanical engineering major Francisco was interviewed about his love of Spider-Man and how it connects to his research in our lab. Check out the full story on SDSU NewsCenter! ...