| 1. |
- Chen, Hai-Lin, et al.
(författare)
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Database development and Calphad calculations for high entropy alloys : Challenges, strategies, and tips
- 2018
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Ingår i: Materials Chemistry and Physics. - : Elsevier. - 0254-0584 .- 1879-3312. ; 210, s. 279-290
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Tidskriftsartikel (refereegranskat)abstract
- The development of a reliable multicomponent thermodynamic database for high entropy alloys (HEAs) is a daunting task and it faces new challenges comparing to the development of databases for conventional single principal element alloys, such as the assessment of a large number of ternary systems, the proper estimation of phase stability within metastable compositional and temperature ranges, and the reasonable extrapolation into higher order systems. We have recently established a thermodynamic database (TCHEA1) especially for HEAs within a 15-element framework. This work highlights the usage of high throughput density functional theory (OFT) calculations for validating and refining the binary and ternary parameters of the solid solution phases, and having a more reliable extrapolation into metastable regions and higher order systems. TCHEA1 consists of 105 binaries and 200 ternaries and contains nearly all the stable solution phases and intermetallic compounds in each of the assessed systems. Together with Thermo-Calc, this database enables us to predict the stability of the desired multicomponent solid solution relative to intermetallic compounds and other solid solutions. Calculation examples are presented not only for case studies but also for bridging the knowledge gap between Calphadian and people who do not have a background of the Calphad approach.
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| 2. |
- Hassan, Sameer, et al.
(författare)
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Evolution and identification of DREB transcription factors in the wheat genome: modeling, docking and simulation of DREB proteins associated with salt stress
- 2022
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Ingår i: Journal of Biomolecular Structure & Dynamics. - : Informa UK Limited. - 0739-1102 .- 1538-0254. ; 40:16, s. 7191-7204
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Tidskriftsartikel (refereegranskat)abstract
- Soil salinity and the resulting salt stress it imposes on crop plants is a major problem for modern agriculture. Understanding how salt tolerance mechanisms in plants are regulated is therefore important. One regulatory mechanism is the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor family, including dehydration responsive element binding (DREB) transcription factors. By binding to DNA, specifically upstream of genes that play roles in salt tolerance pathways, DREB proteins upregulate expression of these genes. DREB in Triticum aestivum (wheat) cluster in sub-groups and in this study by scanning the recently extended predicted proteome of wheat for DREB, we increased the number of members of this sub-family. Using the wheat genome, we identified 576 genes coding for the AP2 domain of which 508 were identified to have one AP2 domain, a characteristic of the DREB/ERF subfamily. We confirmed the existing four sub-groups by sequence-based phylogenetic analyses but also identified 32 new DREB subfamily members, not belonging to any known sub-group. Transcription factor profile inference analysis identified two genes, TraesCS2B02G002700 and TraesCS2D02G015200, being homologous to DREB1A of Arabidopsis thaliana. Based on molecular simulation (25 ns) analysis, TraesCS2B02G002700 with a CCGAC motif was observed to interact very stably with DNA. In silico mutational analysis at the 19(th) position in the DREB domain of TraesCS2B02G002700-DNA complex indicated this as a stable part for recognizing and forming interaction with DNA. Moreover, six target genes were predicted having an upstream CCGAC motif regulated by TraesCS2B02G002700. Our study provides an overall framework for exploring the transcription factors in plants and identifying e.g. potential salt stress target genes. Communicated by Ramaswamy H. Sarma
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| 3. |
- Tuite, E., et al.
(författare)
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Probing DNA conductivity with photoinduced electron transfer and scanning tunneling microscopy
- 2000
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Ingår i: Journal of Biomolecular Structure and Dynamics. - : Informa UK Limited. - 0739-1102 .- 1538-0254. ; , s. 277-283
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Tidskriftsartikel (refereegranskat)abstract
- The possibility that the stacked DNA bases can mediate vectorial electron transfer has been examined using two different approaches. Experiments on photoinduced electron transfer with intercalated donors and accepters (either randomly bound or linked dyads of ruthenium complex and viologen) indicate that while DNA may be a better medium than acetonitrile for electron transfer over short distances (2-3-base pair, equivalent to 10-14 Angstrom centre-to-centre separation), it is a poor medium for transport over larger separations. Attempts to measure conductivity of individual DNA molecules using scanning tunneling microscopy to image mixed monolayers of mercaptohexanol (MCH) and 30-mer or 10-mer DNAs with alkanethiol linkers also indicate that DNA in its native state is a poor conductor. AFM images of the DNA/MCH mixed monolayers show that the DNA molecules extend vertically upward from the surface in such surface architectures.
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| 4. |
- Allen, Matthew S., et al.
(författare)
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Experimental substructuring
- 2020
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Ingår i: CISM International Centre for Mechanical Sciences, Courses and Lectures. - Cham : Springer International Publishing. - 2309-3706 .- 0254-1971. ; 594, s. 75-181
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- In this chapter, we outline techniques to use measured dynamic characteristics of components to build an assembled model. Although the basic theory is pretty straightforward, the difficulty in experimental substructuring lies in the limitations in what can be measured and the special techniques needed to alleviate errors in the measured signals.—(Chapter Authors: Daniel Rixen, Maarten van der Seijs, Randall Mayes, Matt Allen & Thomas Abrahamsson).
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| 5. |
- Allen, Matthew S., et al.
(författare)
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Industrial applications & related concepts
- 2020
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Ingår i: CISM International Centre for Mechanical Sciences, Courses and Lectures. - Cham : Springer International Publishing. - 2309-3706 .- 0254-1971. ; 594, s. 183-231
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This section highlights some specialized substructuring methods, such as methods for estimating the fixed-interface modes of a substructure from measurements of the free–free structure with a fixture attached at the interface, and also highlights some industrial examples. Transfer path analysis is reviewed, elaborating some of the similarities in the theoretical foundations. Most information about TPA has been obtained from van der Seijs et al. (2016), please refer to the original paper for a more elaborate discussion.
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| 6. |
- Allen, Matthew S., et al.
(författare)
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Introduction and Motivation
- 2020
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Ingår i: CISM International Centre for Mechanical Sciences, Courses and Lectures. - Cham : Springer International Publishing. - 2309-3706 .- 0254-1971. ; 594, s. 1-4
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- “Divide and Conquer” is a paradigm that helped Julius Cesar to dominate on the wide Roman Empire. The power of dividing systems, then analyze them as parts before combining them in an assembly, is also an approach often followed in science and engineering. In this introductory chapter, we shortly discuss the main idea behind domain decomposition and substructuring applied to mechanical systems.
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| 7. |
- Allen, Matthew S., et al.
(författare)
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Model reduction concepts and substructuring approaches for linear systems
- 2020
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Ingår i: CISM International Centre for Mechanical Sciences, Courses and Lectures. - Cham : Springer International Publishing. - 2309-3706 .- 0254-1971. ; 594, s. 25-73
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- In this chapter, we give an overview of some of the most common reduction techniques based on substructuring. Although all techniques follow a similar approach, the main difference between the methods lies into the basis vectors used in the approximation subspace to represent the dynamics of each substructure and the manner in which the substructures are a couple.
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| 8. |
- Allen, Matthew S., et al.
(författare)
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Model reduction concepts and substructuring approaches for nonlinear systems
- 2020
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Ingår i: CISM International Centre for Mechanical Sciences, Courses and Lectures. - Cham : Springer International Publishing. - 2309-3706 .- 0254-1971. ; 594, s. 233-267
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This chapter reviews common nonlinearities that are encountered in engineering structures, with a particular emphasis on geometric nonlinearity. Popular ways to construct reduced order models for geometrically nonlinear problems are discussed. The concept of nonlinear normal modes is presented to help understand the dynamics of these structures, and some recently presented substructuring methods are reviewed.
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| 9. |
- Allen, Matthew S., et al.
(författare)
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Preface
- 2020
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Ingår i: CISM International Centre for Mechanical Sciences, Courses and Lectures. - 2309-3706 .- 0254-1971. ; 594, s. v-vi
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 10. |
- Allen, Matthew S., et al.
(författare)
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Preliminaries: Primal and dual assembly of dynamic models
- 2020
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Ingår i: CISM International Centre for Mechanical Sciences, Courses and Lectures. - Cham : Springer International Publishing. - 2309-3706 .- 0254-1971. ; 594, s. 5-24
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- There are several ways to formulate the dynamics of a substructure. The different domains in which the dynamics can be described will be reviewed since the manner in which substructures are characterized will later determine the substructuring methodology that can be applied. In addition to how the substructures are formulated, the way in which the coupling/decoupling problem is expressed will allow us in the subsequent chapters to develop different numerical and experimental techniques. Two conditions must be satisfied on the interface between substructures: a condition on the displacement field (compatibility) and on the interface stresses (force equilibrium). Those conditions can be accounted for following several different formulations, all mathematically equivalent, but each leading to different numerical methods, experimental approaches, and approximation techniques, as will be explained in the following chapters. In this chapter, we outline the basic concepts of the so-called three-field formulation, dual and primal assembly
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