A guide to the visual analysis and communication of biomolecular structural data

Johnson, Graham; Hertig, Samuel

doi:10.1038/nrm3874

Cited by 50 publications

(46 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…To measure the distance of atomic‐scale spacing, the label‐analysis has been performed on the distances between particles in the 3D‐structure, based on a finite element model. The method for image processing in this work has been also reported previously …”

Section: Experimental and Theoretical Sectionmentioning

confidence: 99%

Atomic‐Scale Spacing between Copper Facets for the Electrochemical Reduction of Carbon Dioxide

Jeong

Kwon

Won

et al. 2020

Advanced Energy Materials

View full text Add to dashboard Cite

Copper (Cu) offers a means for producing value‐added fuels through the electrochemical reduction of carbon dioxide (CO2), i.e., the CO2 reduction reaction (CO2RR), but designing Cu catalysts with significant Faradaic efficiency to C2+ products remains as a great challenge. This work demonstrates that the high activity and selectivity of Cu to C2+ products can be achieved by atomic‐scale spacings between two facets of Cu particles. These spacings are created by lithiating CuOx particles, removing lithium oxides formed, and electrochemically reducing CuOx to metallic Cu. Also, the range of spacing (ds) is confirmed via the 3D tomographs using the Cs‐corrected scanning transmission electron microscopy (3D tomo‐STEM), and the operando X‐ray absorption spectra show that oxidized Cu reduces to the metallic state during the CO2RR. Moreover, control of ds to 5–6 Å allows a current density exceeding that of unmodified CuOx nanoparticles by about 12 folds and a Faradaic efficiency of ≈80% to C2+. Density functional theory calculations support that ds of 5–6 Å maximizes the binding energies of CO2 reduction intermediates and promotes C–C coupling reactions. Consequently, this study suggests that control of ds can be used to realize the high activity and C2+ product selectivity for the CO2RR.

show abstract

Section: Experimental and Theoretical Sectionmentioning

confidence: 99%

Atomic‐Scale Spacing between Copper Facets for the Electrochemical Reduction of Carbon Dioxide

Jeong

Kwon

Won

et al. 2020

Advanced Energy Materials

View full text Add to dashboard Cite

show abstract

“…Many more specialized packages have also been developed, such as MorphographX [53], which was designed for the analysis of 3D plant images. Professional illustration and animation software may also become increasingly useful for cell biologists and were recently described in a review of visual analysis for the structural biology community [54]. An emerging alternative to the direct visualization of 3D images is the construction of 3D cell models based on experimental parameters and mathematical rules of cell organizational principles [55].…”

Section: Visualizing 3d Cell Migrationmentioning

confidence: 99%

Quantifying Modes of 3D Cell Migration

Driscoll

Danuser

2015

Trends in Cell Biology

View full text Add to dashboard Cite

Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to the analyses performed today on cells crawling on flat substrates.

show abstract

“…Several resources for such dynamic data exist and provide for instance short movies describing molecular functions based on their structure (e.g. [Ber07, Iwa08, JH14]). These educational solutions mainly focus on the artistic appearance and use pre‐rendered, non‐interactive visualizations.…”

Section: Visualization Of Molecular Dynamicsmentioning

confidence: 99%