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Nanoscale biosystems are widely used in numerous medical applications. The approaches for structure and function of the nanomachines that are available in the cell (natural nanomachines) are discussed. Molecular simulation studies have been…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
The design of structural & functional materials for specialized applications is being fueled by rapid advancements in materials synthesis, characterization, manufacturing, with sophisticated computational materials modeling frameworks that…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
In contrast to designing nanophotonic devices by tuning a handful of device parameters, we have developed a computational method which utilizes the full parameter space to design linear nanophotonic devices. We show that our method may…
We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and…
Recent advances in generative deep learning have transformed small molecule design, but most methods lack biological systems context, focusing narrowly on specific protein pockets. We introduce a non-differentiable diffusion guidance method…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
In this work, we demonstrate three ultra-compact integrated-photonics devices, which are designed via a machine-learning algorithm coupled with finite-difference time-domain (FDTD) modeling. Through digitizing the design domain into "binary…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
Novel assembly processes for nanocircuits could present compelling alternatives to the detailed design and placement currently used for computers. The resulting architectures however may not be programmable by standard means. In this paper,…
In the last two decades, DNA self-assembly has grown into a major area of research attracting people from diverse background. It has numerous potential applications such as targeted drug delivery, artificial photosynthesis etc. In the last…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
Engineering shape and interactions of nanoscopic building blocks allows for the assembly of rationally designed macroscopic three-dimensional (3D) materials with spatial accuracy inaccessible to top-down fabrication methods. Owing to its…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
We report our design, development, installation and troubleshooting of an open source Gnome X Scanning Microscopy (GXSM) software package for controlling and processing of modern Scanning Probe Microscopy (SPM) system as a development tool…
Table of Content 1. Introduction 2. DNA fundamentals 3. Attachment of DNA to surface 4. Fabrication of nanostructures using DNA 4.1 Nanostructures of pure DNA 4.2 DNA-based assembly of metal nanoparticles 4.3 Construction of semiconductor…
Unlocking the full potential of nanocrystals in electronic devices requires scalable and deterministic manufacturing techniques. A platform offering promising alternative paths to scalable production is microtomy, the technique of cutting…
The recent decades have seen various attempts at accelerating the process of developing materials targeted towards specific applications. The performance required for a particular application leads to the choice of a particular material…