arXiv subjects
Publications and source records attributed to Dixita Limbachiya.
Recently, DNA data storage systems have attracted many researchers worldwide. Motivated by the success stories of such systems, in this work we propose a software called BacSoft to clone the data in a bacterial plasmid by using the concept of genetic engineering. We consider the encoding schemes such that it satisfies constraints significant for bacterial data storage.
In this work, we study the DNA codes from the ring R = Z4 + wZ4, where w^2 = 2+2w with 16 elements. We establish a one to one correspondence between the elements of the ring R and all the DNA codewords of length 2 by defining a distance-preserving Gau map phi. Using this map, we give several new classes of the DNA codes which satisfies reverse and reverse complement constraints. Some of the constructed DNA codes are optimal.
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 decade, another area received wide attention known as DNA origami, where using M13 virus and carefully designed staple strands one can fold the DNA into desired 2-D and 3-D shapes. In 2016, a group of researchers at MIT have developed an automated DNA nanostructures strategy and an open source software 'daedalus' based on MATLAB for developing the nanostructures. In this work, we present a truly open source software '3dnaprinter' based on Java (without MATLAB) that can do the same work.
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to understand the DNA self-assembly process, many mathematical models have been proposed in the literature. In particular, abstract Tile Assembly Model (aTAM) received much attention. In this work, we investigate pixel pattern generation using aTAM. For a given image, a tile assembly system is given which can generate the image by self-assembly process. We also consider image blocks with specific cyclic pixel patterns (uniform shift and non uniform shift) self assembly. A software, DNA Image Pro, for generating pixel patterns using DNA tile assembly is also given.
The idea of computing with DNA was given by Tom Head in 1987, however in 1994 in a seminal paper, the actual successful experiment for DNA computing was performed by Adleman. The heart of the DNA computing is the DNA hybridization, however, it is also the source of errors. Thus the success of the DNA computing depends on the error control techniques. The classical coding theory techniques have provided foundation for the current information and communication technology (ICT). Thus it is natural to expect that coding theory will be the foundational subject for the DNA computing paradigm. For the successful experiments with DNA computing usually we design DNA strings which are sufficiently dissimilar. This leads to the construction of a large set of DNA strings which satisfy certain combinatorial and thermodynamic constraints. Over the last 16 years, many approaches such as combinatorial, algebraic, computational have been used to construct such DNA strings. In this work, we survey this interesting area of DNA coding theory by providing key ideas of the area and current known results.
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by using non-linear families of ternary codes. In particular, we proposes an algorithm to encode data into DNA with high information storage density and better error correction using a sub code of Golay code. Theoretically, 115 exabytes (EB) data can be stored in one gram of DNA by our method.
Digital data explosion drives a demand for robust and reliable data storage medium. Development of better digital storage device to accumulate Zetta bytes (1 ZB = $10^{21}$ bytes ) of data that will be generated in near future is a big challenge. Looking at limitations of present day digital storage devices, it will soon be a big challenge for data scientists to provide reliable. affordable and dense storage medium. As an alternative, researcher used natural medium of storage like DNA, bacteria and protein as information storage systems. This article discuss DNA based information storage system in detail along with an overview about bacterial and protein data storage systems.
The term Big Data is usually used to describe huge amount of data that is generated by humans from digital media such as cameras, internet, phones, sensors etc. By building advanced analytics on the top of big data, one can predict many things about the user such as behavior, interest etc. However before one can use the data, one has to address many issues for big data storage. Two main issues are the need of large storage devices and the cost associated with it. Synthetic DNA storage seems to be an appropriate solution to address these issues of the big data. Recently in 2013, Goldman and his collegues from European Bioinformatics Institute demonstrated the use of the DNA as storage medium with capacity of storing 2.2 peta bytes of information on one gram of DNA and retrived the data successfully with low error rate. This significant step shows a promise for synthetic DNA storage as a useful technology for the future data storage. Motivated by this, we have developed a software called DNACloud which makes it easy to store the data on the DNA. In this work, we present detailed description of the software.
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures. One such technique involves the implementation of DNA Bricks proposed by Ke et al., 2012 to create complex three-dimensional (3D) structures. Modeling these DNA nano structures can prove to be a cumbersome and tedious task. Exploiting the programmability of base-pairing to produce self-assembling custom shapes, we present a software suite 3DNA, which can be used for modeling, editing and visualizing such complex structures. 3DNA is an open source software which works on the simple and modular self assembly of DNA Bricks, offering a more intuitive better approach for constructing 3D shapes. Apart from modeling and envisaging shapes through a simple graphical user interface, 3DNA also supports an integrated random sequence generator that generates DNA sequences corresponding to the designed model. The software is available at www.guptalab.org/3dna
DNA origami is an interdisciplinary area where DNA can be used as a building block for making useful stuff at nanoscale. This work presents an open source software DNA pen (based on the recent work of Peng Yin and his group) which can be used (using free hand and digital molecular canvas) to draw an object at nanoscale. Software generates error free DNA sequences which can be used in the wet lab to create the object at the nanoscale. Using DNA pen we have drawn several objects including the map of India and sanskrit letter "Om" from free hand molecular canvas and digital letter DNA using digitized molecular canvas.
Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies, and interactions for the design of robust synthetic systems. To the best of our knowledge,there are no literature reports for the synthetic circuit construction for protozoan parasites. This paper describes the construction of genetic circuit for the targeted enzyme inositol phosphorylceramide synthase belonging to the protozoan parasite Leishmania. To explore the dynamic nature of the circuit designed, simulation was done followed by circuit validation by qualitative and quantitative approaches. The genetic circuit designed for inositol phosphorylceramide synthase shows responsiveness, oscillatory and bistable behavior, together with intrinsic robustness.