News and Events

Wed, Mar 11, 4:00 PM (C215 ESC, and online)
From static images to functional models: Using cryo-EM to reveal dynamic protein machines

Recent advances in structural biology such as cryo-electron microscopy (cryo-EM) and artificial intelligence have radically advanced our ability to visualize molecular protein structures. In this colloquium, I will first highlight how fundamental physical and mathematical principles in imaging, signal processing, and thermodynamics have enabled this biological triumph. I will then turn to the emerging frontier: linking the thermodynamic sampling of protein ensembles to biological function. Proteins are not static objects, but dynamic systems that explore complex energy landscapes through conformational changes and protein–protein interactions. I will outline how cryo-EM is addressing these frontiers through two stories from my research. The first involves a viral polymerase that leverages viral and host proteins to guide itself into a functional protein complex. The second demonstrates how an ion channel transduces chemical signals into electrical signals by sampling various conformational states. A common theme is how physics and biology intertwine in generating the relevant experimental data and interpreting the final results.

Earlier this week, Earth’s shadow swept across the full Moon in the year’s only total lunar eclipse. This stunning sequence combines images showing the Moon’s path across the night sky. Each lunar image captures our planet’s shadow gradually engulfing the Moon, culminating in its red glow. Sunlight scatters and refracts as it passes through Earth’s atmosphere toward the Moon. Shorter wavelength light (blue and green) scatters more efficiently, leaving red, orange, and yellow hues to paint the lunar surface. Tsé Bit'a'í (”rock with wings”, also known as Shiprock), located in Navajo Nation, provides a powerful volcanic foreground central to this photo and to stories of Navajo origin, adventure, and heroism. As the first full moon of the lunar new year, this eclipse held significance across cultures. Visible from East Asia to North America, this eclipse united observers across great distances, a cosmic reminder that we share the same sky.
Temp:  34 °FN2 Boiling:75.9 K
Humidity: 83%H2O Boiling:   368.4 K
Pressure:85 kPaSunrise:6:53 AM
Wind:2 m/s   Sunset:6:23 PM
Precip:2 mm   Sunlight:0 W/m²  
Dr. Michael Ware hopes to help students develop the skills to navigate discussion of science and religion
The university's new electron microscopy facility opened in fall of 2025, offering atomic-level imaging and student-led research.
Brian Anderson and his students celebrated BYU's 150th birthday by blowing out candles using high-intensity focused sound waves.

Selected Publications

Brandon J. Titensor, Lauren W. Miner, Joshua J. Vawdrey, Stuart B. Shaklan, and David D. Allred

Starshade technology represents a promising approach for direct exoplanet imaging, offering stellar light suppression up to a factor of 1010. Particulate contamination that clings to the edge of the starshade causes solar glint which could compromise Earth-like exoplanet detection. In previous research, when testing at atmospheric pressure, McKeithen et al. 2023 observed that the sharp edge have fewer particles larger than 14 microns, and more particles smaller than 14 microns, than expected from the surface distribution. To determine if this observation was reproducible in different environments, we contaminated Starshade edge coupons in low vacuum conditions. We characterized the surface and edge cleanliness level using optical microscopy, a custom ImageJ macro and R program that calculated the counts and area of particles in each image. We then compared our results with McKeithen et al. confirming their result, but the crossover occurred at particle diameters of about 3 microns rather than 14 microns. In our work, we propose different mechanisms which could affect any differences between the vacuum environment tests and the tests performed in air previously.

Joshua J. Vawdrey, Lauren W. Miner, and David D. Allred (et al.)

Xenon difluoride passivated aluminum with a lithium fluoride overcoat (Al+XeLiF) mirror coatings are promising candidates for future space telescope missions due to their high reflectance down to 100nm. The XeLiF mirror coating blocks aluminum oxidation. Aluminum oxide is undesirable since it significantly reduces the far UV (100-to-190nm) reflectance. Cleaning techniques for this ideal coating require the balance of traditional surface cleaning with careful handling of the hygroscopic LiF. Photonic Cleaning Technologies’ First Contact Polymers (FCP) are proven to clean and protect optical surfaces effectively. A specialized FCP formulation may be required for Al+XeLiF. We monitored Al+XeLiF changes under repeated application of four FCP formulations using variable angle spectroscopic ellipsometry (VASE), reflectance, and Atomic Force Microscopy (AFM). We also applied multiple FCP formulations to both Al+XeLiF and Al+LiF samples and stored them in different humidity environments to monitor potential protective qualities of each formulation. We observed that two FCP formulations can effectively protect Al+XeLiF in 40% RH without Al loss over half a year.

Joshua J. Vawdrey, Lauren W. Miner, Brandon J. Titensor, Richard R. Vanfleet, and David D. Allred (et al.)

Magnesium fluoride on xenon difluoride passivated aluminum (Al+XeMgF2) mirrors have high reflectance encompassing the H Lyman-α at 121.6 nm. Al+XeMgF2 is a key candidate for space telescopes and satellites that demand far-UV (FUV) measurements coupled with high reflectance at longer wavelengths. Contamination can significantly reduce FUV reflectance, so Al+XeMgF2 mirrors must be as clean as possible. Protecting the surfaces while in storage is also desirable. We investigated the suitability of four different formulations of Photonic Cleaning Technologies' First Contact Polymer for cleaning and protecting Al+XeMgF2 coatings by repeatedly cleaning test samples. These were cleaved from a silicon wafer coated with 300 nm of chemical vapor deposited (CVD) silicon nitride (Si3N4). All the formulations could clean samples at least once. Using Variable-Angle, Spectroscopic Ellipsometry (VASE), we determined that two (S2 and S3) of the four tested formulations were able to clean and protect the Al+XeMgF2 surfaces multiple times (>20) over 5 months without detectable alumina growth on the Al in a low humidity environment. There were also no changes to the thickness of 'apparent' MgF2. Apparent MgF2 includes the deposited MgF2, the 2–3 nm AlF3 layer produced by the XeF2 passivation step, and contributions from surface roughening. There was also no detectable alumina growth for the controls. The fact that the samples were stored between tests in a desiccator with their First Contact overcoat provides evidence that Al+XeMgF2 samples can successfully be protected and stored under some First Contact formulations for at least five months in a dry environment. Far-ultraviolet reflectance is not reported here.

Brian E. Anderson, Spencer T. Neu, Joshua F. Gregg, Sarah M. Young, and Timothy W. Leishman

Passive radiators are notoriously difficult to characterize because one cannot effectively assess their mechanical parameters with loudspeaker electrical impedance techniques and no motors. This paper discusses the details of passive radiator and dynamic loudspeaker driver parameter measurements through practical experiments conducted with a plane wave tube, the two-microphone transfer function technique, and the two-load method to remove the need for an ideal anechoic termination. A previous theoretical paper demonstrated how normal-incidence transmission losses through these devices in an anechoically terminated tube could yield their mechanical and electrical parameters [Leishman and Anderson, J. Acoust. Soc. Am. 134(1), 223–236 (2013)]. The mechanical parameters follow from an open-circuit transmission loss condition, whereas a driver's electrical parameters follow from an additional closed-circuit condition. This paper presents several experimental results and compares extracted parameters to those derived from electrical impedance measurements and destructive methods. In addition to other parameters, the masses of diaphragm assemblies show favorable agreement. The presented techniques effectively assess passive radiator parameters without employing active driver configurations and then removing their motors, which changes the measured properties. PACS numbers: 43.38.Ja, 43.20.Ye, 43.20.Mv, 43.55.Rg

Volume 3 of the FCC Feasibility Report presents studies related to civil engineering, the development of a project implementation scenario, and environmental and sustainability aspects. The report details the iterative improvements made to the civil engineering concepts since 2018, taking into account subsurface conditions, accelerator and experiment requirements, and territorial considerations. It outlines a technically feasible and economically viable civil engineering configuration that serves as the baseline for detailed subsurface investigations, construction design, cost estimation, and project implementation planning. Additionally, the report highlights ongoing subsurface investigations in key areas to support the development of an improved 3D subsurface model of the region. The report describes the development of the project scenario based on the ‘avoid-reduce-compensate’ iterative optimisation approach. The reference scenario balances optimal physics performance with territorial compatibility, implementation risks, and costs. Environmental field investigations covering almost 600 hectares of terrain—including numerous urban, economic, social, and technical aspects—confirmed the project’s technical feasibility and contributed to the preparation of essential input documents for the formal project authorisation phase. The summary also highlights the initiation of public dialogue as part of the authorisation process. The results of a comprehensive socio-economic impact assessment, which included significant environmental effects, are presented. Even under the most conservative and stringent conditions, a positive benefit-cost ratio for the FCC-ee is obtained. Finally, the report provides a summary of the studies conducted to document the current state of the environment.

Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer S. Gardiner, Bradley C. Bundy, and Dennis Della Corte

Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD (r = 0.53 to 0.84). Principal component analysis reveals that AF3 predictions capture the same collective motion patterns observed in molecular dynamics trajectories, with eigenvector similarities significantly exceeding random distributions. ChronoSort trajectories exhibit structural evolution profiles comparable to MD. These findings suggest that modern AI-based structure prediction tools encode conformational flexibility information that can be systematically extracted without expensive MD. We provide ChronoSort as open-source software to enable broad community adoption. This work offers a novel approach to extracting functional insights from structure prediction tools in minutes, with significant implications for synthetic biology, protein engineering, drug discovery, and structure–function studies.