A Method to Decipher "Genome" from Interatomic Cohesion in the Exploration for a "Central Dogma" Replacement in Material Science Article Swipe
X. -J. Zhang
,
Hui Jia
,
Fangzhen Tian
,
Yandi Liu
,
Ullrich Carsten
,
Yulong Wu
,
Changlong Liu
,
Xiaodong Zhang
,
Yonghui Li
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2305.07942
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2305.07942
In the ball-stick model, interatomic cohesions are considered "sticks". But enormous details and features of the "sticks" are usually oversimplified as indexed quantities or equivocated as geometry characteristics. These indexed quantities or geometry characteristics not only limit the explanatory capability to a few chemical/physical aspects but also eliminate generativity for expected resemblance. And these limitations can be related to the information loss during the conversion. Herein, inspired by the central dogma, a framework is introduced to compact interatomic cohesions into a detailed residue-by-residue "genome" with matched encoding/decoding tools. The framework fuses the quantum mechanical aspects, auto feature extraction, nanostructures and/or simulations, and generative models. As a proof of concept, the realization introduced in this work adopted bosonic/fermionic features, an autoencoder with image recognition processes, Density Functional Theory simulations, and a thiolate-protected gold nanocluster dataset. After repetitive modeling, validating, and analysis based on 26,528 simulated interatomic images, the interatomic cohesion can be almost losslessly encoded into an 8-value-genome, and the genome encoder-decoder pair is also obtained. The model is then automatically extended into a generative model which converts any arbitrary 8-value-genome to a bond image.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- http://arxiv.org/abs/2305.07942
- https://arxiv.org/pdf/2305.07942
- OA Status
- green
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4376652710
All OpenAlex metadata
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- OpenAlex ID
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https://openalex.org/W4376652710Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.48550/arxiv.2305.07942Digital Object Identifier
- Title
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A Method to Decipher "Genome" from Interatomic Cohesion in the Exploration for a "Central Dogma" Replacement in Material ScienceWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-05-13Full publication date if available
- Authors
-
X. -J. Zhang, Hui Jia, Fangzhen Tian, Yandi Liu, Ullrich Carsten, Yulong Wu, Changlong Liu, Xiaodong Zhang, Yonghui LiList of authors in order
- Landing page
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https://arxiv.org/abs/2305.07942Publisher landing page
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https://arxiv.org/pdf/2305.07942Direct link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://arxiv.org/pdf/2305.07942Direct OA link when available
- Concepts
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Nanoclusters, Bond, Computer science, Artificial intelligence, Function (biology), Bond length, Materials science, Nanotechnology, Physics, Molecule, Quantum mechanics, Finance, Biology, Evolutionary biology, EconomicsTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.analysis | 139 |
| abstract_inverted_index.aspects, | 94 |
| abstract_inverted_index.cohesion | 148 |
| abstract_inverted_index.concept, | 108 |
| abstract_inverted_index.converts | 176 |
| abstract_inverted_index.dataset. | 133 |
| abstract_inverted_index.detailed | 81 |
| abstract_inverted_index.enormous | 10 |
| abstract_inverted_index.expected | 50 |
| abstract_inverted_index.extended | 170 |
| abstract_inverted_index.features | 13 |
| abstract_inverted_index.geometry | 26, 32 |
| abstract_inverted_index.inspired | 66 |
| abstract_inverted_index."sticks". | 8 |
| abstract_inverted_index.arbitrary | 178 |
| abstract_inverted_index.cohesions | 5, 78 |
| abstract_inverted_index.eliminate | 47 |
| abstract_inverted_index.features, | 117 |
| abstract_inverted_index.framework | 72, 89 |
| abstract_inverted_index.modeling, | 136 |
| abstract_inverted_index.obtained. | 164 |
| abstract_inverted_index.simulated | 143 |
| abstract_inverted_index.Functional | 125 |
| abstract_inverted_index.ball-stick | 2 |
| abstract_inverted_index.capability | 39 |
| abstract_inverted_index.considered | 7 |
| abstract_inverted_index.generative | 102, 173 |
| abstract_inverted_index.introduced | 74, 111 |
| abstract_inverted_index.losslessly | 152 |
| abstract_inverted_index.mechanical | 93 |
| abstract_inverted_index.processes, | 123 |
| abstract_inverted_index.quantities | 22, 30 |
| abstract_inverted_index.repetitive | 135 |
| abstract_inverted_index.autoencoder | 119 |
| abstract_inverted_index.conversion. | 64 |
| abstract_inverted_index.equivocated | 24 |
| abstract_inverted_index.explanatory | 38 |
| abstract_inverted_index.extraction, | 97 |
| abstract_inverted_index.information | 60 |
| abstract_inverted_index.interatomic | 4, 77, 144, 147 |
| abstract_inverted_index.limitations | 54 |
| abstract_inverted_index.nanocluster | 132 |
| abstract_inverted_index.realization | 110 |
| abstract_inverted_index.recognition | 122 |
| abstract_inverted_index.validating, | 137 |
| abstract_inverted_index.generativity | 48 |
| abstract_inverted_index.resemblance. | 51 |
| abstract_inverted_index.simulations, | 100, 127 |
| abstract_inverted_index.automatically | 169 |
| abstract_inverted_index.8-value-genome | 179 |
| abstract_inverted_index.nanostructures | 98 |
| abstract_inverted_index.oversimplified | 19 |
| abstract_inverted_index.8-value-genome, | 156 |
| abstract_inverted_index.characteristics | 33 |
| abstract_inverted_index.encoder-decoder | 160 |
| abstract_inverted_index.characteristics. | 27 |
| abstract_inverted_index.bosonic/fermionic | 116 |
| abstract_inverted_index.chemical/physical | 43 |
| abstract_inverted_index.encoding/decoding | 86 |
| abstract_inverted_index.residue-by-residue | 82 |
| abstract_inverted_index.thiolate-protected | 130 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 9 |
| citation_normalized_percentile.value | 0.05193843 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |