the proceedings contain 5 papers. the topics discussed include: geometric enumeration of localized dna strand displacement reaction networks;domain-based nucleic-acid minimum free energy: algorithmic hardness and para...
ISBN:
(纸本)9783959773447
the proceedings contain 5 papers. the topics discussed include: geometric enumeration of localized dna strand displacement reaction networks;domain-based nucleic-acid minimum free energy: algorithmic hardness and parameterized bounds;simulation of the abstract tile assembly model using crisscross slats;designing 3D RNA Origami nanostructures with a minimum number of kissing loops;and learning and inference in a lattice model of multicomponent condensates.
Localized molecular devices are a powerful tool for engineering complex information-processing circuits and molecular robots. their practical advantages include speed and scalability of interactions between components...
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We present strand and codeword design schemes for a dna database capable of approximate similarity search over a multidimensional dataset of content-rich media. Our strand designs address crosstalk in associative dna ...
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ISBN:
(数字)9783030000301
ISBN:
(纸本)9783030000301;9783030000295
We present strand and codeword design schemes for a dna database capable of approximate similarity search over a multidimensional dataset of content-rich media. Our strand designs address crosstalk in associative dna databases, and we demonstrate a novel method for learning dna sequence encodings from data, applying it to a dataset of tens of thousands of images. We test our design in the wetlab using one hundred target images and ten query images, and show that our database is capable of performing similarity-based enrichment: on average, visually similar images account for 30% of the sequencing reads for each query, despite making up only 10% of the database.
molecular programmers and nanostructure engineers use domain-level design to abstract away messy dna/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design princip...
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A dna stack nano-device is a bio-computing system that can read and write molecular signals based on dna-dna hybridisation and strand displacement. In vitro implementation of the dna stack faces a number of challenges...
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In molecular biology, sequence alignment is a way of arranging dna, RNA or protein sequences to identify regions of similarity between the sequences. However, this is a challenging problem since the dna sequences are ...
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In molecular biology, sequence alignment is a way of arranging dna, RNA or protein sequences to identify regions of similarity between the sequences. However, this is a challenging problem since the dna sequences are huge in size and the databases are growing at an exponential rate. It requires tremendous amount of memory and large computational power. For example, the human genome in raw format ranges from 2 to 30 Tera-bytes. the inherent property of dna is that it contains many repeats which makes it highly compressible. this paper presents a new approach of aligning the sequences after compressing them. the alignment consists of both ungapped and gapped alignment. Multi-cores and GPUs can be used to align these huge sequences quickly on the compressed sequences. the focus mainly is on aligning the huge sequences accurately. the ungapped alignment achieves a speedup of upto 56 on K20 Kepler GPUs and the gapped alignment achieves a speedup of upto 15 on multi-cores.
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