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Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the…
Microstructure plays a critical role in determining the macroscopic properties of materials, with applications spanning alloy design, MEMS devices, and tissue engineering, among many others. Computational frameworks have been developed to…
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…
Engineering nanostructures from the bottom up enables the creation of carefully engineered complex structures that are not accessible via top down fabrication techniques, in particular, complex periodic structures for applications in…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
Dynamically tunable nanoengineered structures for coloration show promising applications in sensing, displays, and communication. However, their potential challenge remains in having a scalable manufacturing process over large scales in…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
One of the main goals of DNA nanotechnology is to provide a viable solution to the limitations of top-down approaches in microfabrication schemes. Although a completely practical bottom-up approach is yet to be realized, there has been…
The development of novel strategies for self-assembly in the field of nanotechnology has witnessed remarkable progress in recent years. Here, we present a DNA-driven programmable self-assembly to fabricate the targeted nanophotonic…
Stimulus-responsive DNA-hydrogels with swelling capabilities are a promising class of materials for biomedical applications such as drug delivery and biosensing. However, translation of these systems to microscale applications requires…
The design of the nanostructures that are used in the field of nano-photonics has remained complex, very often relying on the intuition and expertise of the designer, ultimately limiting the reach and penetration of this groundbreaking…
A construction method for duplex cage structures with icosahedral sym- metry made out of single-stranded DNA molecules is presented and applied to an icosidodecahedral cage. It is shown via a mixture of analytic and computer techniques that…
The quest for realizing and manipulating ever smaller man-made movable structures and dynamical machines has spurred tremendous endeavors, led to important discoveries, and inspired researchers to venture to new grounds. Scientific feats…
DNA has the potential to realize a controllable liquid-liquid phase separation (LLPS) system, because the design of its base sequences results in programmable interactions. Here, we have developed a novel DNA-based LLPS system which enables…
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…
Targeting RNA with small molecules offers significant therapeutic potential. Machine learning could substantially accelerate preclinical drug discovery, from hit identification to lead optimization. Yet a fundamental limitation emerges:…
Integrative modeling enables structure determination for large macromolecular assemblies by combining data from multiple sources of experiment data with theoretical and computational predictions. Recent advancements in AI-based structure…
Computational experiments are exploited in finding a well-designed processing path to optimize material structures for desired properties. This requires understanding the interplay between the processing-(micro)structure-property linkages…