scholarly journals Simulations of higher-order protein assemblies using a fuzzy framework

2018 ◽  
Author(s):  
B. Tüű-Szabó ◽  
L. Kóczy ◽  
M. Fuxreiter
Keyword(s):  
Driving Forces ◽  
Critical Role ◽  
Simulation Method ◽  
Low Complexity ◽  
Mathematical Framework ◽  
Binding Model ◽  
Spatiotemporal Regulation ◽  
Alternative Scenarios ◽  
The One ◽  
Fuzzy Framework

AbstractSpatiotemporal regulation of the biochemical information is often linked to supramolecular organizations proteins and nucleic acids, which generate membraneless cellular organelles. Owing to difficulties in high-resolution structural studies, the driving forces of assembling these low-complexity polymers have yet to be elucidated. Polymer physics approaches captured the experimentally demonstrated critical role of binding element multivalency and highlighted the importance of linker solvation. Here we present a simulation method based on a fuzzy mathematical framework. This approach is suitable to handle the heterogeneity of interactions pattern generated by redundant binding motifs and the resulted multiplicity of conformational states. Using a hypothetical polymer, fuzzy simulations recapitulate the experimental observations on valency-dependence and are more efficient than the one-to-one binding model. Systematic studies on binding element affinity and linker dynamics demonstrate that these two factors present alternative scenarios to promote polymerization: stronger binding result in more ordered states, whereas increasing dynamics contributes to heterogeneity and a more favorable entropy of the assembly. We propose that the fuzzy framework could be employed to characterize/predict mutations leading to pathological aggregates.

scholarly journals Simulations of Higher-Order Protein Organizations Using a Fuzzy Framework

Complexity ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
B. Tüű-Szabó ◽  
L. T. Kóczy ◽  
M. Fuxreiter
Keyword(s):  
Driving Forces ◽  
Critical Role ◽  
Critical Factor ◽  
Higher Order ◽  
Mathematical Framework ◽  
Protein Assemblies ◽  
Binding Motifs ◽  
Spatiotemporal Regulation ◽  
The Impact

Spatiotemporal regulation of the biochemical information is often linked to supramolecular organizations proteins and nucleic acids, the driving forces of which have yet to be elucidated. Although the critical role of multivalency in phase transition has been recognized, the organization principles of higher-order structures need to be understood. Here, we present a fuzzy mathematical framework to handle the heterogeneity of interactions patterns and the resultant multiplicity of conformational states in protein assemblies. In this model, redundant binding motifs can establish simultaneous and partial interactions with multiple targets. We demonstrate that these multivalent, weak contacts facilitate polymer formation, while recapitulating the observed valency-dependence. In addition, the impact of linker dynamics and motif binding affinity, as well as the interplay between the two effects was studied. Our results support that fuzziness is a critical factor in driving higher-order protein organizations, and this could be used as a general framework to simulate different kinds of supramolecular assemblies.

scholarly journals Comparative Study of the Field Performances of Pressure-Grouted Micropiles Using Gravity and Packers

2021 ◽  
Vol 11 (15) ◽  
pp. 6736
Author(s):  
Ong Heo ◽  
Yeowon Yoon ◽  
Jinung Do
Keyword(s):  
Urban Areas ◽  
High Performance ◽  
Driving Forces ◽  
Field Performance ◽  
Underground Space ◽  
Creep Tests ◽  
Deep Foundation ◽  
Installation Depth ◽  
Pressure Grouting ◽  
The One

When underground space requires excavation in areas below the water table, the foundation system suffers from buoyancy, which leads to the uplifting of the superstructure. A deep foundation system can be used; however, in cases where a hard layer is encountered, high driving forces and corresponding noises cause civil complaints in urban areas. Micropiles can be an effective alternative option, due to their high performance despite a short installation depth. Pressurized grouting is used with a packer to induce higher interfacial properties between micropile and soil. In this study, the field performance of micropiles installed using gravitational grouting or pressure-grouted using either a geotextile packer or rubber packer was comparatively evaluated by tension and creep tests. Micropiles were installed using pressure grouting in weak and fractured zones. As results, the pressure-grouted micropiles showed more stable and stronger behaviors than ones installed using the gravitational grouting. Moreover, the pressure-grouted micropile installed using the rubber packer showed better performance than the one using the geotextile packer.

FAST SPRINGBACK SIMULATION OF BENDING FORMING BASED ON ONE-STEP INVERSE ANALYSIS

2008 ◽  
Vol 22 (31n32) ◽  
pp. 6057-6063
Author(s):  
YI-DONG BAO ◽  
WEN-LIANG CHEN ◽  
HONG WU
Keyword(s):  
Sheet Metal Forming ◽  
Metal Forming ◽  
Inverse Analysis ◽  
Simulation Method ◽  
Spring Back ◽  
Deformation Path ◽  
Bending Process ◽  
One Step ◽  
Implicit Solver ◽  
The One

A simplified one-step inverse analysis of sheet metal forming is a suitable tool to simulate the bending forming since the deformation path of bending forming is an approximately proportion one. A fast spring-back simulation method based on one-step analysis is proposed. First, the one-step inverse analysis is applied to obtain the stress distribution at the final stage of bending. Then, the unloading to get a spring back is simulated by LS-DYNA implicit solver. These processes are applied to the unconstrained cylindrical bending and the truck member rail. The spring-back and member rail widths at the several key sections are compared with experimental ones. It is well demonstrated that the proposed method is an effective way to predict the spring-back by unloading after bending process.

Eternal Guests, Mimics, and Dönme: The Place of German and Turkish Jews in Modern Turkey

2007 ◽  
Vol 37 ◽  
pp. 5-30 ◽  
Author(s):  
Kader Konuk
Keyword(s):  
Critical Role ◽  
The Other ◽  
Turkish Republic ◽  
German Jews ◽  
Other Hand ◽  
Turkish Culture ◽  
The Status ◽  
Modern Turkey ◽  
The One ◽  
European Civilization

AbstractThe place of Jews was highly ambiguous in the newly founded Turkish Republic: In 1928 an assimilationist campaign was launched against Turkish Jews, while only a few years later, in 1933, German scholars—many of them Jewish—were taken in so as to help Europeanize the nation. Turkish authorities regarded the emigrants as representatives of European civilization and appointed scholars like Erich Auerbach to prestigious academic positions that were vital for redefining the humanities in Turkey. This article explores the country's twofold assimilationist policies. On the one hand, Turkey required of its citizens—regardless of ethnic or religious origins—that they conform to a unified Turkish culture; on the other hand, an equally assimilationist modernization project was designed to achieve cultural recognition from the heart of Europe. By linking historical and contemporary discourses, this article shows how tropes of Jewishness have played—and continue to play—a critical role in the conception of Turkish nationhood. The status of Erich Auerbach, Chair of the Faculty for Western Languages and Literatures at İstanbul University from 1936 to 1947, is central to this investigation into the place of Turkish and German Jews in modern Turkey.

scholarly journals ARMC Subfamily: Structures, Functions, Evolutions, Interactions, and Diseases

2021 ◽  
Vol 8 ◽  
Author(s):  
Yutao Huang ◽  
Zijian Jiang ◽  
Xiangyu Gao ◽  
Peng Luo ◽  
Xiaofan Jiang
Keyword(s):  
Signal Transduction ◽  
Amino Acids ◽  
Cell Adhesion ◽  
Tandem Repeats ◽  
Critical Role ◽  
The Other ◽  
Biological Functions ◽  
Armadillo Repeat ◽  
The One ◽  
Similar Domain

Armadillo repeat-containing proteins (ARMCs) are widely distributed in eukaryotes and have important influences on cell adhesion, signal transduction, mitochondrial function regulation, tumorigenesis, and other processes. These proteins share a similar domain consisting of tandem repeats approximately 42 amino acids in length, and this domain constitutes a substantial platform for the binding between ARMCs and other proteins. An ARMC subfamily, including ARMC1∼10, ARMC12, and ARMCX1∼6, has received increasing attention. These proteins may have many terminal regions and play a critical role in various diseases. On the one hand, based on their similar central domain of tandem repeats, this ARMC subfamily may function similarly to other ARMCs. On the other hand, the unique domains on their terminals may cause these proteins to have different functions. Here, we focus on the ARMC subfamily (ARMC1∼10, ARMC12, and ARMCX1∼6), which is relatively conserved in vertebrates and highly conserved in mammals, particularly primates. We review the structures, biological functions, evolutions, interactions, and related diseases of the ARMC subfamily, which involve more than 30 diseases and 40 bypasses, including interactions and relationships between more than 100 proteins and signaling molecules. We look forward to obtaining a clearer understanding of the ARMC subfamily to facilitate further in-depth research and treatment of related diseases.

scholarly journals Revisiting the guidelines for ending isolation for COVID-19 patients

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Yong Dam Jeong ◽  
Keisuke Ejima ◽  
Kwang Su Kim ◽  
Shoya Iwanami ◽  
Ana I Bento ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Fixed Time ◽  
Fixed Number ◽  
Mathematical Framework ◽  
Viral Dynamics ◽  
Repeated Testing ◽  
Personalized Approach ◽  
The One ◽  
Scientific Rationale

Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0–6.6%). However, this policy entails lengthy unnecessary isolations (4.8–8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.

Asia’s Mediterranean

2017 ◽  
Author(s):  
Jude Woodward
Keyword(s):  
South China Sea ◽  
South China ◽  
Critical Role ◽  
The South China Sea ◽  
The South ◽  
American Power ◽  
China Sea ◽  
The Us ◽  
Dramatic Shift ◽  
The One

This chapter (and the next) look at the US’s recent intervention in the South China Sea and China’s responses. It considers the varying domestic and strategic concerns of these primarily island countries. It analyses the drivers of their responses to the sovereignty disputes in the Sea and to the key US initiative of the TPP. This chapter and the next are linked to the one that follows on Vietnam, which also plays a critical role in the shifting relation of forces in the South China Sea disputes. This is the region where the US has invested most hopes in a dramatic shift in regional alignments against China. These chapters assess the US’s progress, and conclude that – despite its lack of a local ally with anything like the weight of Japan or South Korea and the immense geographic extension of American power involved in maintaining its presence in the region – in some respects the US ’rebalance’ strategies have made more progress here to China’s south than to its east.

The Duel and the Daïs: Iliadic Warfare as Spectacle

2019 ◽  
pp. 65-108
Author(s):  
Tobias Myers
Keyword(s):  
Critical Role ◽  
The Other ◽  
Mise En Abyme ◽  
Other Hand ◽  
The One ◽  
The Relationship

Chapter 2 explores how the Olympians and the Iliad’s audience are positioned as viewers for the warfare in Books 1–4, and their roles defined. The first section focuses on the gods. Homer initially defines the gods’ role as viewers by drawing on two specific paradigms of live event: entertainment at a daïs (banquet), and the formal duel. Each of these paradigms carries its own suggestions as to the nature of the event, its stakes, and the relationship between viewer and action. As entertainment accompanying a daïs, the warfare may generate pleasure (terpein) for viewers whose critical role is to praise or blame the dramatic figure pulling the strings. As a spectacle modelled on the formal duel, the warfare is observed by implicated, partisan viewers, who are themselves a part of the conflict, and can become actors by entering the central space. Rich tension is generated by the combination of these paradigms. The chapter’s second section reads the opening of Book 4, in which the gods watch a duel from their daïs, as a mise en abyme of the spectacle experience offered by the Iliad to its listeners. On the one hand, the combination of duel and daïs shapes audience understanding of the kind of spectacle that they, too, are witnessing, and their own relationship to the action. On the other hand, the gods’ particular responses—both to the events on the ground and to their staging and direction—dramatize possible responses on the part of Homer’s audience.

Sign in / Sign up

Export Citation Format

Share Document