Analysis of folding strains on composite bladder structures. Volume 2 - Programming manual. Folding strains analysis program
Computer program for analysis of folding strains on composite bladder structures
Taylor, J. R.↗
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Incidence and Progression of Chorioretinal Folds During Long-Duration Spaceflight
Importance: The primary contributing factor for development of chorioretinal folds during spaceflight is unknown. Characterizing fold types that develop and tracking their progression may provide insight into the pathophysiology of spaceflight-associated neuro-ocular syndrome and elucidate the risk of fold progression for future exploration-class missions exceeding 12 months in duration. Objective: To determine the incidence and presentation of chorioretinal folds in long-duration International Space Station crew members and objectively quantify the progression of choroidal folds during spaceflight. Design, Setting, and Participants: In this retrospective cohort study, optical coherence tomography scans of the optic nerve head and macula of crew members completing long-duration spaceflight missions were obtained on Earth prior to spaceflight and during flight. A panel of experts examined the scans for the qualitative presence of chorioretinal folds. Peripapillary total retinal thickness was calculated to identify eyes with optic disc edema, and choroidal folds were quantified based on surface roughness within macular and peripapillary regions of interest. Interventions or Exposures: Spaceflight missions ranging 6 to 12 months. Main Outcomes and Measures: Incidence of peripapillary wrinkles, retinal folds, and choroidal folds; peripapillary total retinal thickness; and Bruch membrane surface roughness. Results: A total of 36 crew members were analyzed (mean [SD] age, 46 [6] years; 7 [19%] female). Chorioretinal folds were observed in 12 of 72 eyes (17%; 6 crew members). In eyes with early signs of disc edema, 10 of 42 (24%) had choroidal folds, 4 of 42 (10%) had inner retinal folds, and 2 of 42 (5%) had peripapillary wrinkles. Choroidal folds were observed in all eyes with retinal folds and peripapillary wrinkles. Macular choroidal folds developed in 7 of 12 eyes (4 of 6 crew members) with folds and progressed with mission duration; these folds extended into the fovea in 6 eyes. Circumpapillary choroidal folds developed predominantly superior, nasal, and inferior to the optic nerve head and increased in prevalence and severity with mission duration. Conclusions and Relevance: Choroidal folds were the most common fold type to develop during spaceflight; this differs from reports in idiopathic intracranial hypertension, suggesting differences in the mechanisms underlying fold formation. Quantitative measures demonstrate the development and progression of choroidal folds during weightlessness, and these metrics may help to assess the efficacy of spaceflight-associated neuro-ocular syndrome countermeasures.
Connor R. Ferguson↗
Improved Method of Design for Folding Inflatable Shells
An improved method of designing complexly shaped inflatable shells to be assembled from gores was conceived for original application to the inflatable outer shell of a developmental habitable spacecraft module having a cylindrical mid-length section with toroidal end caps. The method is also applicable to inflatable shells of various shapes for terrestrial use. The method addresses problems associated with the assembly, folding, transport, and deployment of inflatable shells that may comprise multiple layers and have complex shapes that can include such doubly curved surfaces as toroids and spheres. One particularly difficult problem is that of mathematically defining fold lines on a gore pattern in a double- curvature region. Moreover, because the fold lines in a double-curvature region tend to be curved, there is a practical problem of how to implement the folds. Another problem is that of modifying the basic gore shapes and sizes for the various layers so that when they are folded as part of the integral structure, they do not mechanically interfere with each other at the fold lines. Heretofore, it has been a common practice to design an inflatable shell to be assembled in the deployed configuration, without regard for the need to fold it into compact form. Typically, the result has been that folding has been a difficult, time-consuming process resulting in a An improved method of designing complexly shaped inflatable shells to be assembled from gores was conceived for original application to the inflatable outer shell of a developmental habitable spacecraft module having a cylindrical mid-length section with toroidal end caps. The method is also applicable to inflatable shells of various shapes for terrestrial use. The method addresses problems associated with the assembly, folding, transport, and deployment of inflatable shells that may comprise multiple layers and have complex shapes that can include such doubly curved surfaces as toroids and spheres. One particularly difficult problem is that of mathematically defining fold lines on a gore pattern in a double- curvature region. Moreover, because the fold lines in a double-curvature region tend to be curved, there is a practical problem of how to implement the folds. Another problem is that of modifying the basic gore shapes and sizes for the various layers so that when they are folded as part of the integral structure, they do not mechanically interfere with each other at the fold lines. Heretofore, it has been a common practice to design an inflatable shell to be assembled in the deployed configuration, without regard for the need to fold it into compact form. Typically, the result has been that folding has been a difficult, time-consuming process resulting in a
Johnson, Christopher J.↗
Deep crustal deformation by sheath folding in the Adirondack Mountains, USA
As described by McLelland and Isachsen, the southern half of the Adirondacks are underlain by major isoclinal (F sub 1) and open-upright (F sub 2) folds whose axes are parallel, trend approximately E-W, and plunge gently about the horizontal. These large structures are themselves folded by open upright folds trending NNE (F sub 3). It is pointed out that elongation lineations in these rocks are parallel to X of the finite strain ellipsoid developed during progressive rotational strain. The parallelism between F sub 1 and F sub 2 fold axes and elongation lineations led to the hypothesis that progressive rotational strain, with a west-directed tectonic transport, rotated earlier F sub 1-folds into parallelism with the evolving elongation lineation. Rotation is accomplished by ductile, passive flow of F sub 1-axes into extremely arcuate, E-W hinges. In order to test these hypotheses a number of large folds were mapped in the eastern Adirondacks. Other evidence supporting the existence of sheath folds in the Adirondacks is the presence, on a map scale, of synforms whose limbs pass through the vertical and into antiforms. This type of outcrop pattern is best explained by intersecting a horizontal plane with the double curvature of sheath folds. It is proposed that sheath folding is a common response of hot, ductile rocks to rotational strain at deep crustal levels. The recognition of sheath folds in the Adirondacks reconciles the E-W orientation of fold axes with an E-W elongation lineation.
Mclelland, J. M.↗
Exploring the Evolutionary Accident Hypothesis: Are Extant Protein Folds the Fittest or the Luckiest?
Considering the range of functions proteins perform, it is surprising they fold into a relatively small set of structures or "folds" that facilitate such function. One explanation is that only a minority were fit enough to emerge from Darwinian selection during the early evolution of life. Alternatively, perhaps only a fraction of all possible folds were trialed. Understanding proto-catalyst selection will aid understanding of the origins and early evolution of life. To investigate which explanation is correct, we study a protein evolved in vitro to bind ATP by Jack Szostak (Fig. 1). This protein adopts a fold which is absent from nature. We are testing whether this fold would have possessed the capability to evolve that would have been essential to survive natural selection on early Earth. Folds that couldn't improve their fitness and evolve to perform new functions would have been replaced by rivals that could. To determine whether the fold is evolvable, we are attempting to change the function of the protein by rationally redesigning to bind GTP. Two design strategies in the region of the nucleobase have been implemented to provide hydrogen bonding partners for the ligand i) an insertion ii) a MET to ASN mutation. Redesigns are being studied computationally at Ames Research Center including free energy of binding calculations. Binding affinities of promising redesigns are to be validated by experimental collaborators at ForteBio using Super Streptavidin Biosensors. If the fold is found to be non-evolvable, this may suggest that many structures were trialed, but the majority were pruned on the basis of their evolvability. Alternatively, if the fold is demonstrated to be evolvable, it would be difficult to explain its absence from nature without considering the possibility that the fold simply wasn't sampled on early Earth. This would not only further our understanding of the origins of life on Earth but also suggest a common phe-nomenon of proto-catalyst evolution.
Shannon, G.↗
Evolution and folding of repeat proteins
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. These proteins constitute excellent model systems to investigate how evolution relates to structure, folding, and function. Here, we propose a scheme to map evolutionary information at the sequence level to a coarse-grained model for repeat-protein folding and use it to investigate the folding of thousands of repeat proteins. We model the energetics by a combination of an inverse Potts-model scheme with an explicit mechanistic model of duplications and deletions of repeats to calculate the evolutionary parameters of the system at the single-residue level. These parameters are used to inform an Ising-like model that allows for the generation of folding curves, apparent domain emergence, and occupation of intermediate states that are highly compatible with experimental data in specific case studies. We analyzed the folding of thousands of natural Ankyrin repeat proteins and found that a multiplicity of folding mechanisms are possible. Fully cooperative all-or-none transitions are obtained for arrays with enough sequence-similar elements and strong interactions between them, while noncooperative element-by-element intermittent folding arose if the elements are dissimilar and the interactions between them are energetically weak. Additionally, we characterized nucleation-propagation and multidomain folding mechanisms. We show that the global stability and cooperativity of the repeating arrays can be predicted from simple sequence scores.
Ezequiel A. Galpern↗
Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A molecular dynamics study
The undecamer of poly-L-leucine at the water-hexane interface is studied by molecular dynamics simulations. This represents a simple model relevant to folding and insertion of hydrophobic peptides into membranes. The peptide, initially placed in a random coil conformation on the aqueous side of the system, rapidly translocates toward the hexane phase and undergoes interfacial folding into an alpha-helix in the subsequent 36 ns. Folding is nonsequential and highly dynamic. The initially formed helical segment at the N-terminus of the undecamer becomes transiently broken and, subsequently, reforms before the remainder of the peptide folds from the C-terminus. The formation of intramolecular hydrogen bonds during the folding of the peptide is preceded by a dehydration of the participating polar groups, as they become immersed in hexane. Folding proceeds through a short-lived intermediate, a 3(10)-helix, which rapidly interconverts to an alpha-helix. Both helices contribute to the equilibrium ensemble of folded structures. The helical peptide is largely buried in hexane, yet remains adsorbed at the interface. Its preferred orientation is parallel to the interface, although the perpendicular arrangement with the N-terminus immersed in hexane is only slightly less favorable. In contrast, the reversed orientation is highly unfavorable, because it would require dehydration of C-terminus carbonyl groups that do not participate in intramolecular hydrogen bonding. For the same reason, the transfer of the undecamer from the interface to the bulk hexane is also unfavorable. The results suggest that hydrophobic peptides fold in the interfacial region and, simultaneously, translocate into the nonpolar side of the interface. It is further implied that peptide insertion into the membrane is accomplished by rotating from the parallel to the perpendicular orientation, most likely in such a way that the N-terminus penetrates the bilayer.
NASA Discipline Exobiology↗
Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC
AbstractThe folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.
Zhao, Yanyan (ORCID:0000000323021763)↗
Origami-Inspired Folding of Thick, Rigid Panels
To achieve power of 250 kW or greater, a large compression ratio of stowed-to-deployed area is needed. Origami folding patterns were used to inspire the folding of a solar array to achieve synchronous deployment; however, origami models are generally created for near-zero-thickness material. Panel thickness is one of the main challenges of origami-inspired design. Three origami-inspired folding techniques (flasher, square twist, and map fold) were created with rigid panels and hinges. Hinge components are added to the model to enable folding of thick, rigid materials. Origami models are created assuming zero (or near zero) thickness. When a material with finite thickness is used, the panels are required to bend around an increasingly thick fold as they move away from the center of the model. The two approaches for dealing with material thickness are to use membrane hinges to connect the panels, or to add panel hinges, or hinges of the same thickness, at an appropriate width to enable folding.
Trease, Brian P.↗
SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations
ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.
Cell Biology↗
Life prediction of expulsion bladders through fatigue test and fold strain analysis.
Consideration of the problem of reducing the probability of mechanical failure of bladder systems used for the expulsion of propellants into liquid rocket engines. It is shown that individual local folds in collapsing bladders can be classified into single and double folds, specifiable by nondimensional geometrical parameters which directly define the maximum strains at these folds. From these maximum strains the number of collapse/inflation cycles to failure can be obtained from low-cycle fatigue data experimentally determined for the bladder material of interest. Cycle life data are presented in terms of true maximum strain for four metals, two plastics, and two elastomers. It is found that double folds give rise to much more severe folding strains than do simple folds.
Chu, H. N.↗
Observations of Convective and Dynamical Instabilities in Tropopause Folds and their Contribution to Stratosphere-Troposphere Exchange
With aircraft-mounted in-situ and remote sensing instruments for dynamical, thermal. and chemical measurements, we studied two cases of tropopause folding. In both folds we found Kelvin-Helmholtz billows with horizontal wavelength of about 900 m and thickness of about 120 m. In one case the instability was effectively mixing the bottomside of the fold, leading to the transfer of stratospheric air into the troposphere. Also we discovered in both cases small-scale secondary ozone maxima shortly after the aircraft ascended past the topside of the fold that corresponded to regions of convective instability. We interpreted this phenomenon as convectively breaking gravity waves. Therefore, we posit that convectively breaking gravity waves acting on tropopause folds must be added to the list of important irreversible mixing mechanisms leading to stratosphere-troposphere exchange.
Cho, John Y. N.↗
Molecular Dynamics of Peptide Folding at Aqueous Interfaces
Even though most monomeric peptides are disordered in water they can adopt sequence-dependent, ordered structures, such as a-helices, at aqueous interfaces. This property is relevant to cellular signaling, membrane fusion, and the action of toxins and antibiotics. The mechanism of folding nonpolar peptides at the water-hexane interface was studied in the example of an 11-mer, of poly-L-leucine. Initially placed as a random coil on the water side of the interface, the peptide folded into an a-helix in 36 ns. Simultaneously, the peptide translocated into the hexane side of the interface. Folding was not sequential and involved a 3/10-helix as an intermediate. The folded peptide was either parallel to the interface or had its C-terminus exposed to water. An 11-mer, LQQLLQQLLQL, composed of leucine (L) and glutamine (G), was taken as a model amphiphilic peptide. It rapidly adopted an amphiphilic, disordered structure at the interface. Further folding proceeded through a series of amphiphilic intermediates.
Pohorille, Andrew↗
Carbon Storage in Fold‐and‐Thrust Belts: An Overlooked Gigatonne Storage Opportunity
This study presents numerical investigations of the trapping characteristics of fold-and-thrust belt structures, defining three carbon capture and storage (CCS) play types that could be used to store commercial volumes (millions of tonnes) of CO 2 . Specifically, we present simulations of CO 2 storage in three fold-and-thrust belt models comprising a thrust-ramp, duplex, and thrust-fold geometry. To constrain these play types in realistic geology, each model is based on a study site, including a novel investigation of a greenfield saline reservoir in Virginia, USA, being considered for commercial carbon storage and two well-characterized petroleum fields: the Wilburton field in Oklahoma, USA, and the Incahuasi field in Bolivia. Our results provide insight into several key parameters, such as the long-term security of injected CO 2 in these geologies and injection strategies for maximizing storage efficiency while reducing pressure-related risk. These results improve the understanding of CCS in fold-and-thrust belt storage sites globally by describing general storage parameters that may be applied to site-specific projects. We find that thrust-ramp geometries may securely trap CO 2 through solubility and hydrodynamic trapping under suitable reservoir conditions, duplex structures may store some quantities of CO 2 but are pressure-constrained, and that thrust-ramp structures may store large quantities of CO 2 by maximizing fetch volume, which simultaneously lowers geomechanical risk by reducing pressure buildup along zones of weakness.
42 ENGINEERING↗
Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering
Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.
Biochemistry & Molecular Biology↗
Life prediction of expulsion bladders through fatigue test and fold strain analysis
Cycle life data are presented in terms of true maximum strain for four metals, two plastics, and two elastomers. The Coffin-Manson fatigue theory was applied for metals and plastics, and cut-growth fatigue theory for elastomers. The data are based on measurements made at room and elevated temperatures. It was found that double folds give rise to far severer folding strains than do simple folds. It was also found that, except for the elastomers, all the bladder materials develop surface cracks due to double folds after only one cycle. The findings indicate that metals, which are bets for premeation resistance, are worst for fatigue resistance, and vice versa for elastomers. The intermediate plastics were found to be unsatisfactory for both permeation and fatigue resistance for missions of extended duration.
Chu, H. N.↗
The President's Day cyclone of 18-19 February 1979 - Influence of a tropopause fold on rapid cyclogenesis
The surface and satellite imagery data from the cyclone of February 18-19, 1979 are analyzed. Operational radiosonde data are utilized to study the tropopause fold associated with the polar jet streak. Patterns of vertical motion compatible with the tropopause fold are calculated by the diagnostic ageostrophic circulation equation of Sawyer (1956) and Eliassen (1962); the verification of the calculated patterns is described. The relationship between the stratospheric extrusion and the folded tropopause is determined by examining the potential vorticity and ozone concentrations. The influence of the stratospheric extrusion within the folded tropopause on the development of the cyclone is investigated by analyzing the potential vorticity, static stability, and absolute vorticity from the Eulerian and Lagrangian perspective.
Uccellini, L. W.↗
The Arctic tropopause fold
Analyses of research-aircraft observations, satellite total-columnar-ozone retrievals, and synoptic upper-air soundings are used to describe the structure of Arctic jetstreams and their associated frontal zones and tropopause folds. These analyses document the presence of major tropopause folding events within the Arctic that occur at the flanks of large-scale (about 2000 km) polar vortices. One example shows a solar vortex and its associated tropopause fold and Arctic front that migrated from the high Canadian Arctic southward into midlatitudes over central North America. Total columnar ozone measurements from the Total Ozone Mapping Spectrometer are shown to identify the location of polar vortices and the mesoscale (about 200 km) ozone gradients at the flanks of these vortices, which coincide with regions of Arctic tropopause folding and associated stratospheric-tropospheric exchange processes.
Shapiro, M. A.↗