John D. Treado
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View article: Localized growth and remodelling drives spongy mesophyll morphogenesis
Localized growth and remodelling drives spongy mesophyll morphogenesis Open
The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other biological tissues, which remain confluent throughout development, the spongy mesophyll…
View article: Localized growth drives spongy mesophyll morphogenesis
Localized growth drives spongy mesophyll morphogenesis Open
The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other biological tissues, which remain confluent throughout development, the spongy mesophyll…
View article: Erratum: Bridging particle deformability and collective response in soft solids [Phys. Rev. Materials <b>5</b>, 055605 (2021)]
Erratum: Bridging particle deformability and collective response in soft solids [Phys. Rev. Materials <b>5</b>, 055605 (2021)] Open
Received 25 March 2022DOI:https://doi.org/10.1103/PhysRevMaterials.6.059901©2022 American Physical SocietyPhysics Subject Headings (PhySH)Research AreasCollective behaviorJammingPhysical SystemsEmulsionsFoamsTissuesTechniquesMolecular dyna…
View article: Correction: The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions
Correction: The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions Open
Correction for ‘The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions’ by Dong Wang et al. , Soft Matter , 2021, 17 , 9901–9915, DOI: 10.1039/D1SM01228B.
View article: The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions
The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions Open
We investigate the structural, vibrational, and mechanical properties of jammed packings of deformable particles with shape degrees of freedom in three dimensions (3D). Each 3D deformable particle is modeled as a surface-triangulated polyh…
View article: The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions
The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions Open
We investigate the structural, vibrational, and mechanical properties of jammed packings of deformable particles with shape degrees of freedom in three dimensions (3D).
View article: Current MD forcefields fail to capture key features of protein structure and fluctuations: A case study of cyclophilin A and T4 lysozyme
Current MD forcefields fail to capture key features of protein structure and fluctuations: A case study of cyclophilin A and T4 lysozyme Open
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways w…
View article: Cover Image, Volume 88, Issue 9
Cover Image, Volume 88, Issue 9 Open
Obverse Cover: The cover image is based on the Original Article Analyses of protein cores reveal fundamental differences between solution and crystal structures by Corey O'Hern et al., https://doi.org/10.1002/prot.25884
View article: Using physical features of protein core packing to distinguish real proteins from decoys
Using physical features of protein core packing to distinguish real proteins from decoys Open
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical fe…
View article: Analyses of protein cores reveal fundamental differences between solution and crystal structures
Analyses of protein cores reveal fundamental differences between solution and crystal structures Open
There have been several studies suggesting that protein structures solved by NMR spectroscopy and X‐ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high‐quality pr…
View article: Analyses of protein cores reveal fundamental differences between solution and crystal structures
Analyses of protein cores reveal fundamental differences between solution and crystal structures Open
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality pr…
View article: Void distributions reveal structural link between jammed packings and protein cores
Void distributions reveal structural link between jammed packings and protein cores Open
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped…
View article: A threonine zipper that mediates protein–protein interactions: Structure and prediction
A threonine zipper that mediates protein–protein interactions: Structure and prediction Open
We present the structure of an engineered protein–protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr) residues. This Thr zipper structure suggests that the protein interface is stab…