Research in our group focuses on emerging technologies of storage, computing, and communications such as DNA computing, quantum computing, chemical computing, quantum machine learning, cloud computing, security and cryptography and classical computing. The general theme of our research group focuses on two aspects of information processing viz. deciphering the information processing principles in life (systems biology) and engineering a system using biomolecules. The key expertise is in error-correcting codes. We also work in classical and quantum information processing principles with expertise in coding theory and its wide variety of applications in Information and Communication Technology (ICT).
Natural Information processing is an exciting interdisciplinary new area that deals with the question: How is the nature doing information processing? Research in this field involves all aspects of information and communication technology (ICT). We want to learn how natural computation is done. How nature stores data? What are the principles of biological information processing? Answers to these questions would help us in understanding the basics of molecular health and diseases, deciphering new methods for drug discovery and in building computers using biomolecules.
The main areas of expertise are in mathematics and computer science. We focus on error correcting codes which is at the heart of classical information and communication technologies ranging from sending data from here to there (communication) and sending data from now to then (storage). When we look at natural information processing, we look at from our standpoint where core expertise of error correction has well developed roots in many areas of research of ICT. Currently our ongoing interdisciplinary projects are in RNA secondary structure, HIV-1, systems biology of non-coding RNAs, DNA self-assembly, computational biology, cryptography and information security, network coding, quantum error correction, coding theory. We have also developed 14 software products. In future, we would like to focus on topics such as DNA machine learning, quantum machine learning, quantum algorithms for linear algebra and differential equations. More description and achievements for some of our projects is given below.
Digital DNA Data Storage
Digital data storage posing many challenges such as huge space requirements and their cost. However, in 2012, George Church invented a new technology of DNA based storage systems. One gram of DNA can store 455EB of data. Soon after this Goldman suggested an error correction-based DNA storage system. This system had limitations in encoding only up to 500 MB file. We improved the work of Goldman, and this resulted in the software DNAcloud, and we published our work. We went one step further and stored data on bacteria and retrieved it successfully by doing experiment at NCBS Bangalore. Our project was selected as one of the top 5 innovation for the prime minister demo for India and Israel. We also won DST-DAAD (Indo-German) grant with my collaborator Dr. David Smith of Fraunhofer for doing further work in this direction. We also collaborated with Dr. Vaneet Aggarwal of Purdue University on this project and published papers. We are actively working in this area and hope to work further in the area.
Self-assembly is a process by which supra-molecular species forms spontaneously from its components. This process is ubiquitous throughout life chemistry and is central to biological information processing. It has been suggested that self-assembly will ultimately become a useful tool for bio-molecular computation, crystallography, nanotechnology, and medicine. However, robustness (error correction) is a key challenge in realizing the potential of self-assembly. In this area we have developed several interesting compact error correction schemes for DNA self-assembly, in close analogy with coding theory, where we use redundancy to correct errors.
Computational and Systems Biology
Systems biology of human and pathogens is quite interesting and challenging. Our research here focuses on the viral pathogen HIV-1, the number one killer in Africa that has already killed 25 million people worldwide. We have modeled the HIV-1 infection in CD4+ T cells and the induced NFk-B activation using a recent technique of stochastic pi-calculus. In a more recent work, we have shown how to impede the HIV-1 virus using RNA-i. The goal of our research is to pride a complete molecular picture of this interaction in future.
RNA is an important molecule and Thomas R. Cech discovered its double role. We are interested in RNA regulatory systems, RNA secondary structures, discovery of non-coding RNAs, classification and RNA-i. We have given a new representation of RNA secondary structure that includes pseudo knots. This will help us in classifying RNA secondary structures.
Quantum Computing Technology
Quantum information processing principles are very important to study. After the discovery of Shor's algorithm and subsequently the first quantum error correction scheme in 1995 a lot of work has been done to ensure the reliability of quantum computers. Our work here focuses on constructing optimal quantum codes. These include binary (additive and non-additive) and non-binary quantum codes and their various links to combinatorial structures such as finite geometry. We started work on quantum machine learning and quantum algorithms.
Coding Theory (classical, space-time, network)
Our research here focuses on codes over finite rings, finite fields, unitary space-time codes (wireless communications) and network codes. We have found many new and optimal codes. Some of the key problems that we study in coding theory include the following:
Constructions of error-correcting codes
Bounds (limitations) on the performance of the error-correcting codes
Algorithms for error-corrections (Encoding and Decoding)