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Evans, James E.

Publications and source records attributed to Evans, James E..

7 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Graph Identification of Proteins in Tomograms (GRIP-Tomo) 2.0: Topologically aware classification for proteins

Cryo-electron tomography (cryo-ET) enables structural characterization of biomolecules under near-native conditions. Existing approaches for interpreting the resulting three-dimensional volumes are computationally expensive and have difficulty interpreting density associated with small proteins/complexes. To explore alternate approaches for identifying proteins in cryo-ET data we pursued a Graph Network and topologically invariant approach. Here, we report on a fast algorithm that classifies particles by searching for nuances of evolutionarily conversed motifs and the geometrical characteristics of protein structure. GRIP-Tomo 2.0 is a machine-learning pipeline that extracts interpretable topological features of protein structures within noisy experimental backgrounds. Compared to version 1.0, the new pipeline includes three upgrades that significantly improve performance including synthetic tomogram generation simulating realistic noise, graph-based persistent feature extraction as protein fingerprints, and high-performance computing acceleration. GRIP-Tomo 2.0 achieves over 90% accuracy in classifying between proteins and noise using both real and synthetic datasets which represents a foundational step toward advancing cryo-ET workflows and empowering automated visual proteomics.

Li, Chengxuan↗
DOE OSTI2026

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET derived 3D segmented volumes as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the “dark complex,” modulate metabolic flux at a conserved regulatory node of the Calvin–Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.

Johnson, Connah G.↗
DOE OSTI2026

Beyond Component Optimization: Systems Level Biodesign for Lanthanide Recovery

Global demand for lanthanides (Ln) is projected to rise sharply over the next decade, while geographically concentrated supply chains and the low concentrations and matrix complexity of secondary feedstocks limit the reach of conventional hydro- and pyrometallurgical separation. Engineered biological systems offer a selective, low-energy alternative, and component-level advances in Ln-binding proteins, AI-designed selective scaffolds, and cell-surface display platforms now rival synthetic chelators in affinity and selectivity. These components, however, remain functionally isolated. Currently, there are no engineered chassis coupling recognition, intracellular trafficking, accumulation, and controlled release into an end-to-end pipeline. Here, we outline how new biodesign strategies and chassis selection must move beyond bioleaching to encompass the full recovery pathway. Achieving this requires integrating AI/ML-guided design, genome-scale build tools, high-throughput phenotyping, and biophysical transport modeling within a Design–Build–Test–Learn cycle tuned to recognition, trafficking, accumulation, and release.

Biodesign↗
DOE OSTI2024

APOA2 increases cholesterol efflux capacity to plasma HDL by displacing the C-terminus of resident APOA1

The ability of high-density lipoprotein (HDL) to promote cellular cholesterol efflux is a more robust predictor of cardiovascular disease protection than HDL-cholesterol levels in plasma. Previously, we found that lipidated HDL containing both apolipoprotein A-I (APOA1) and A-II (APOA2) promotes cholesterol efflux via the ATP-binding cassette transporter (ABCA1). In the current study, we directly added purified, lipid-free APOA2 to human plasma and found a dose-dependent increase in whole plasma cholesterol efflux capacity. APOA2 likewise increased the cholesterol efflux capacity of isolated HDL with the maximum effect occurring when equal masses of APOA1 and APOA2 coexisted on the particles. Follow-up experiments with reconstituted HDL corroborated that the presence of both APOA1 and APOA2 were necessary for the increased efflux. Using limited proteolysis and chemical cross-linking mass spectrometry, we found that APOA2 induced a conformational change in the N- and C-terminal helices of APOA1. Using reconstituted HDL with APOA1 deletion mutants, we further showed that APOA2 lost its ability to stimulate ABCA1 efflux to HDL if the C-terminal domain of APOA1 was absent, but retained this ability when the N-terminal domain was absent. Based on these findings, we propose a model in which APOA2 displaces the C-terminal helix of APOA1 from the HDL surface which can then interact with ABCA1—much like it does in lipid-poor APOA1. These findings suggest APOA2 may be a novel therapeutic target given this ability to open a large, high-capacity pool of HDL particles to enhance ABCA1-mediated cholesterol efflux.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1994

Ground-based wake vortex monitoring, prediction, and ATC interface

This talk will discuss three elements of a proposed Wake Vortex Advisory Service: monitoring, prediction and ATC interface. The monitoring element is needed to ensure safety by warning controllers of hazardous wake vortex conditions. Such conditions exist when wake vortices persist in the approach/departure flight paths due to advection or to atmospheric conditions which prevent their decay. The prediction element is needed to provide ATC supervisors with advance warning that wake vortex separation conditions are about to change (i.e., require increased or decreased wake vortex separation). The ATC interface element is needed to provide controllers with adaptive wake vortex separations. The use of these adaptive wake vortex separations would lead to increased airport capacity under most conditions, while maintaining safety under conditions of wake vortex hazard.

Campbell, Steven D.↗
NASA NTRS1988

The Federal Aviation Administration/Massachusetts Institute of Technology (FAA/MIT) Lincoln Laboratory Doppler weather radar program

The program focuses on providing real-time information on hazardous aviation weather to end users such as air traffic control and pilots. Existing systems will soon be replaced by a Next Generation Weather Radar (NEXRAD), which will be concerned with detecting such hazards as heavy rain and hail, turbulence, low-altitude wind shear, and mesocyclones and tornadoes. Other systems in process are the Central Weather Processor (CWP), and the terminal Doppler weather radar (TDWR). Weather measurements near Memphis are central to ongoing work, especially in the area of microbursts and wind shear.

Evans, James E.↗