About

Niels Volkmann is a Professor of Bioengineering at UC Santa Barbara, with a focus on the development and application of innovative computational, artificial intelligence, and data science tools to bridge information between the atomic and cellular scales. His work covers more than six orders of magnitude from Ångstroms to tens of microns, emphasizing the integration of data science with biological and engineering principles. His research aims to create new methodologies for understanding complex biological systems through advanced computational approaches.

Research topics

• Cell biology
• Biochemistry
• Biology
• Chemistry
• Biophysics
• Medicine
• Physics

Selected publications

• Structure And Dynamic States of Actin Filaments

  Preprints.org · 2026-04-29

  preprintOpen accessSenior author

  Actin, a highly conserved and ubiquitous eukaryotic protein, underlies essential cellular processes including motility, shape maintenance and muscle contraction. Its dynamic transition between monomeric and filamentous states is powered by ATP hydrolysis, which undergoes structural rearrangements that accelerate turnover in filaments and serve as a measure of filament aging. A wide range of actin binding proteins (ABPs) regulate polymerization, depolymerization, and network organization. Recent high resolution cryo-EM and cryo-ET studies have revealed detailed structures of actin, its isoforms, and ABP complexes, including their organization in cells, deepening our understanding of actin function in health and disease.

  PublisherDOI

• Interpretation of cellular tomograms

  Elsevier eBooks · 2025-01-01

  book-chapter1st authorCorresponding
  PublisherDOI

• BPS2025 - Molecular mechanism of actin filament stiffening by cations

  Biophysical Journal · 2025-02-01

  article
  PublisherDOI

• BPS2025 - Molecular mechanism of actin filament stiffening by cations

  Biophysical Journal · 2025-02-01

  article
  PublisherDOI

• Contributors

  Elsevier eBooks · 2025-01-01

  book-chapter
  PublisherDOI

• Correlative cryogenic light and electron tomography of eukaryotic cells

  Nature Reviews Methods Primers · 2025-12-11

  article
  PublisherDOI

• Optimizing Transmembrane Protein Assemblies in Nanodiscs for Structural Studies: A Comprehensive Manual

  BIO-PROTOCOL · 2024-01-01 · 3 citations

  articleOpen access

  Membrane protein structures offer a more accurate basis for understanding their functional correlates when derived from full-length proteins in their native lipid environment. Producing such samples has been a primary challenge in the field. Here, we present robust, step-by-step biochemical and biophysical protocols for generating monodisperse assemblies of full-length transmembrane proteins within lipidic environments. These protocols are particularly tailored for cases where the size and molecular weight of the proteins align closely with those of the lipid islands (nanodiscs). While designed for single-span bitopic membrane proteins, these protocols can be easily extended to proteins with multiple transmembrane domains. The insights presented have broad implications across diverse fields, including biophysics, structural biology, and cryogenic electron microscopy (cryo-EM) studies. Key features • Overview of the sample preparation steps from protein expression and purification and reconstitution of membrane proteins in nanodiscs, as well as biobeads and lipids preparation. • Focus on single-span bitopic transmembrane proteins. • Includes protocols for validation procedures via characterization using biochemical, biophysical, and computational techniques. • Guide for cryogenic electron microscopy data acquisition from vitrification to image processing.

  PublisherDOI

• Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

  PubMed · 2024-01-23 · 2 citations

  preprintOpen access

  . This White Paper details a comprehensive set of requirements for integrated image data and metadata management - from acquisition through dissemination - ensuring the contextual information necessary for assessing quality, interpreting scientific validity, and enabling meaningful reuse remains intrinsically linked to the data throughout its lifecycle. Critically, it recognizes that generating harmonized, well-annotated publicly available corpora of FAIR bioimage data requires these datasets to be "FAIR-from-the-start" - an objective that can only be achieved by enabling experimental scientists to manage, organize, and analyze their data according to community standards from the very first experiment. Building on recent progress made by the bioimaging field towards establishing shared practices for bioimaging Quality Control (QC) and metadata capture, we present actionable recommendations to advance these efforts through embedding researcher-friendly integrated software infrastructure directly into pre-publication workflows, thus transforming disorganized data capture into structured, shareable resources ready for aggregation and reuse. Our ultimate goal is to expand the use of streamlined tools and practices thus transforming how researchers capture, annotate, analyze and eventually publish bioimaging data thus laying the foundation for a new era of data-driven discovery.

  PublisherOA PDFDOI

• Functional Studies of the Actin Cytoskeleton by Cryogenic Electron Tomography

  2024-08-28

  book-chapterSenior author

  Cryogenic electron tomography is transforming our understanding of the actin cytoskeleton within intact cells. When combined with techniques such as subtomogram averaging and vectorized actin trace analysis, it offers high-resolution insights into in situ actin structures in their unperturbed cellular context. Yet these approaches are often resource-intensive and generally rely on a small number of tomograms. This chapter addresses the emergence of high-throughput methods for analyzing larger datasets, facilitating robust cell biology conclusions through statistical tools. Incorporation of environmental control via micropatterning, variations in stiffness and dimensionality, adjustments in extracellular matrix composition, and temporal analysis enable investigations in more complex, biologically relevant scenarios. Correlative live-cell imaging and functional probes introduce dynamic aspects, facilitating a direct correlation between functional states governed by signaling events or forces and changes in the nanoarchitecture of the actin cytoskeleton.

  PublisherDOI

• CryoEM Workflow Acceleration with Feret Signatures

  International Journal of Molecular Sciences · 2024-07-11 · 1 citations

  articleOpen accessSenior authorCorresponding

  Common challenges in cryogenic electron microscopy, such as orientation bias, conformational diversity, and 3D misclassification, complicate single particle analysis and lead to significant resource expenditure. We previously introduced an in silico method using the maximum Feret diameter distribution, the Feret signature, to characterize sample heterogeneity of disc-shaped samples. Here, we expanded the Feret signature methodology to identify preferred orientations of samples containing arbitrary shapes with only about 1000 particles required. This method enables real-time adjustments of data acquisition parameters for optimizing data collection strategies or aiding in decisions to discontinue ineffective imaging sessions. Beyond detecting preferred orientations, the Feret signature approach can serve as an early-warning system for inconsistencies in classification during initial image processing steps, a capability that allows for strategic adjustments in data processing. These features establish the Feret signature as a valuable auxiliary tool in the context of single particle analysis, significantly accelerating the structure determination process.

  PublisherOA PDFDOI

Recent grants

• Structure and function of the Plasmodium myosin XIV-actin glideosome.

  NIH · $6.3M · 2017–2027

• Project-004

  NIH · $3.8M · 2023

• alpha-Catenin/F-actin Structure at Cell-Cell Junctions

  NIH · $1.9M · 2017–2021

• Structural basis of allostery and mechanical properties of F-actin

  NIH · $2.3M · 2016–2020

• NIH Grant R01GM064473

  NIH · $1.6M · 2008

Frequent coauthors

• Dorit Hanein

  239 shared

• Mark F. Swift

  Scintillon Institute

  79 shared

• Armel Bezault

  Université Paris Cité

  48 shared

• Cécile Sauvanet

  Commissariat à l'Énergie Atomique et aux Énergies Alternatives

  40 shared

• Borja Rodríguez de Francisco

  Centro Nacional de Biotecnología

  37 shared

• Karen Anderson

  35 shared

• Xiaoping Xu

  Second People’s Hospital of Yibin

  34 shared

• Fernando Vilela

  Université Paris Cité

  24 shared

Education

• Ph.D.

  Max Planck Institute

• B.S.

  University of Hamburg