Search

Future distributed quantum systems and networks are likely to rely, at least in part, on the existing fiber infrastructure for entanglement distribution; hence, a precise understanding of the adverse effects of imperfections in optical fibers on entanglement is essential to their operation. Here, we consider maximally entangled polarization qubits and study the decay of the entanglement caused by spatial fluctuations in the refractive index of optical fibers. We study this entanglement dynamics using the spin-boson model and numerically solve our system of equations using the hierarchical equations of motion (HEOM) formalism. We show that within the range of practically relevant system parameters, our developed model exhibits both Markovian and non-Markovian entanglement decay behavior. Further, to counter the observed entanglement decay, we propose the implementation of dynamical decoupling in optical fibers using spaced half waveplates. In particular, we numerically model the time-dependent Hamiltonians of the Carr-Purcell-Meiboom-Gill and Uhrig dynamical decoupling schemes and show a reduced rate of entanglement decay even with sparsely spaced half waveplates along the length of optical fiber. Finally, we evaluate the performance of these two schemes in multiple system configurations., Comment: 10 pages, 8 figures

The VT and Helberg codes, both in binary and non-binary forms, stand as elegant solutions for rectifying insertion and deletion errors. In this paper we consider the quaternary versions of these codes. It is well known that many optimal binary non-linear codes like Kerdock and Prepreta can be depicted as Gray images (isometry) of codes defined over $\mathbb{Z}_4$. Thus a natural question arises: Can we find similar maps between quaternary and binary spaces which gives interesting properties when applied to the VT and Helberg codes. We found several such maps called Naisargik (natural) maps and we study the images of quaternary VT and Helberg codes under these maps. Naisargik and inverse Naisargik images gives interesting error-correcting properties for VT and Helberg codes. If two Naisargik images of VT code generates an intersecting one deletion sphere, then the images holds the same weights. A quaternary Helberg code designed to correct $s$ deletions can effectively rectify $s+1$ deletion errors when considering its Naisargik image, and $s$-deletion correcting binary Helberg code can corrects $\lfloor\frac{s}{2}\rfloor$ errors with inverse Naisargik image., Comment: 20 pages, 18 Tables, draft, data is at https://github.com/guptalab/GrayVT

In the current world due to the huge demand for storage, DNA-based storage solution sounds quite promising because of their longevity, low power consumption, and high capacity. However in real life storing data in the form of DNA is quite expensive, and challenging. Therefore researchers and developers develop such kind of software that helps simulate real-life DNA storage without worrying about the cost. This paper aims to review some of the software that performs DNA storage simulations in different domains. The paper also explains the core concepts such as synthesis, sequencing, clustering, reconstruction, GC window, K-mer window, etc and some overview on existing algorithms. Further, we present 3 different softwares on the basis of domain, implementation techniques, and customer/commercial usability., Comment: 19 pages, 19 figures, draft, review

The development of secure cryptographic protocols and the subsequent attack mechanisms have been placed in the literature with the utmost curiosity. While sophisticated quantum attacks bring a concern to the classical cryptographic protocols present in the applications used in everyday life, the necessity of developing post-quantum protocols is felt primarily. In post-quantum cryptography, elliptic curve-base protocols are exciting to the researchers. While the comprehensive study of elliptic curves over finite fields is well known, the extended study over finite rings is still missing. In this work, we generalize the study of Weierstrass elliptic curves over finite ring $\mathbb{Z}_n$ through classification. Several expressions to compute critical factors in studying elliptic curves are conferred. An all-around computational classification on the Weierstrass elliptic curves over $\mathbb{Z}_n$ for rigorous understanding is also attached to this work., Comment: 12 pages, 2 figures, draft

This paper introduces an isometry between the modular rings $\Z_{2^s}$ and $\Z_{2^{s-1}}$ with respect to the homogeneous weights. Certain product of these maps gives Carlet's generalised Gray map and also Vega's Gray map. For $s=2$ this reduces to popular Gray map. Several interesting properties of these maps are studied. Towards the end we list several interesting problems to work on., Comment: 12 pages, note, presented at the Special Session on Algebraic Coding Theory, Central Section Meeting \#995, American Mathematical Society, Athens,OH, 26-27 March 2004

In the last 60 years coding theory has been studied a lot over finite fields $\mathbb{F}_q$ or commutative rings $\mathcal{R}$ with unity. Although in $1993$, a study on the classification of the rings (not necessarily commutative or ring with unity) of order $p^2$ had been presented, the construction of codes over non-commutative rings or non-commutative non-unital rings surfaced merely two years ago. In this letter, we extend the diverse research on exploring the codes over the non-commutative and non-unital ring $E= \langle 2a=2b=0, a^2=a, b^2=b, ab=a, ba=b \rangle$ by presenting the classification of optimal and nice codes of length $n\leq7$ over $E$, along-with respective weight enumerators and complete weight enumerators., Comment: 5 pages, draft, data available at https://guptalab.org/codesnur4/

In this paper, we discuss DNA codes that are cyclic or quasi-cyclic over $\Z_{4}+\omega \Z_{4}$, where $\omega^{2}=2+2\omega$ along with methods to construct these with combinatorial constraints. We also generalize results obtained for the ring $\Z_{4}+\omega \Z_{4}$, where $\omega^{2}=2+2\omega$, and some other rings to the sixteen rings $R_{\theta}=\Z_{4}+\omega \Z_{4}$, where $\omega^{2}=\theta\in \Z_{4}+\omega \Z_{4}$, using the generalized Gau map and Gau distance in \cite{3}. We determine a relationship between the Gau distance and Hamming distance for linear codes over the sixteen rings $R_{\theta}$ which enables us to attain an upper boundary for the Gau distance of free codes that are self-dual over the rings $R_{\theta}$., Comment: draft, 16 pages

In this present work, we generalize the study of construction of DNA codes over the rings $\mathcal{R}_\theta=\mathbb{Z}_4+w\mathbb{Z}_4$, $w^2 = \theta $ for $\theta \in \mathbb{Z}_4+w\mathbb{Z}_4$. Rigorous study along with characterization of the ring structures is presented. We extend the Gau map and Gau distance, defined in \cite{DKBG}, over all the $16$ rings $\mathcal{R}_\theta$. Furthermore, an isometry between the codes over the rings $\mathcal{R}_\theta$ and the analogous DNA codes is established in general. Brief study of dual and self dual codes over the rings is given including the construction of special class of self dual codes that satisfy reverse and reverse-complement constraints. The technical contributions of this paper are twofold. Considering the Generalized Gau distance, Sphere Packing-like bound, GV-like bound, Singleton like bound and Plotkin-like bound are established over the rings $\mathcal{R}_\theta$. In addition to this, optimal class of codes are provided with respect to Singleton-like bound and Plotkin-like bound. Moreover, the construction of family of DNA codes is proposed that satisfies reverse and reverse-complement constraints using the Reed-Muller type codes over the rings $\mathcal{R}_\theta$., Comment: 32 pages

Two quantum measurements sequentially acting one after the other, if they are mutually unbiased, will lead to a complete removal of information encoded in the input quantum state. We find that if the order of the two sequential measurements can be superposed, with a quantum switch, then the information encoded in the input can still be retained in the output state., Comment: 8 Pages, 1 figure

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., Comment: 8 pages, 13 figures, poster abstract DNA Computing and Molecular Programming, DNA24 conference, Jinan, China, Oct 2018

DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a special constraint. Each codeword of the DNA code has a specific property that any two consecutive sub-strings of the DNA codeword will not be the same (a generalization of homo-polymers constraint). This is in addition to the usual constraints such as Hamming, reverse, reverse-complement and $GC$-content. We believe that the new constraint will help further in reducing the errors during reading and writing data into the synthetic DNA strings. We also present a construction (based on a variant of stochastic local search algorithm) to calculate the size of the DNA codes with all the above constraints, which improves the lower bounds from the existing literature, for some specific cases. Moreover, a recursive isometric map between binary vectors and DNA strings is proposed. Using the map and the well known binary codes we obtain few classes of DNA codes with all the constraints including the property that the constructed DNA codewords are free from the hairpin-like secondary structures., Comment: 12 pages, Draft (Table VI and Table VII are updated)

We propose a novel approach to qubit thermometry using a quantum switch, that introduces an indefinite causal order in the probe-bath interaction, to significantly enhance the thermometric precision. The resulting qubit probe shows improved precision in both low and high temperature regimes when compared to optimal qubit probes studied previously. It even performs better than a Harmonic oscillator probe, in spite of having only two energy levels rather than an infinite number of energy levels as that in a harmonic oscillator. We thereby show unambiguously that quantum resources such as the quantum switch can significantly improve equilibrium thermometry. We also derive a new form of thermodynamic uncertainty relation that is tighter and depends on the energy gap of the probe. The present work may pave the way for using indefinite causal order as a metrological resource., Comment: 4 pages, 5 figures, comments are welcome

We propose a magnetometer for the precise measurement of AC magnetic fields that uses a Terbium-doped optical fiber with half-waveplates built into it at specified distances. Our scheme uses an open-loop quantum control technique called dynamical decoupling to reduce the noise floor and thus increase the sensitivity. We show that dynamical decoupling is extremely effective in preserving the photon state evolution due to the external AC magnetic field from random birefringence in the fiber, even when accounting for errors in pulse timing. Hence we achieve high sensitivity. For a given inter-waveplate distance, the minimum detectable field is inversely proportional to fiber length, as is the bandwidth of detectable frequencies., Comment: 6 pages and 6 figures

For a Distributed Storage System (DSS), the \textit{Fractional Repetition} (FR) code is a class in which replicas of encoded data packets are stored on distributed chunk servers, where the encoding is done using the Maximum Distance Separable (MDS) code. The FR codes allow for exact uncoded repair with minimum repair bandwidth. In this paper, FR codes are constructed using finite binary sequences. The condition for universally good FR codes is calculated on such sequences. For some sequences, the universally good FR codes are explored., Comment: 18 pages, 2 Figures, submitted to SETA 2018

In \textit{Distributed Storage Systems} (DSSs), usually, data is stored using replicated packets on different chunk servers. Recently a new paradigm of \textit{Fractional Repetition} (FR) codes have been introduced, in which, data is replicated in a smart way on distributed servers using a \textit{Maximum Distance Separable} (MDS) code. In this work, for a non-uniform FR code, bounds on the FR code rate and DSS code rate are studied. Using matrix representation of an FR code, some universally good FR codes have been obtained., Comment: 11 pages, 0 figures

In the \textit{Distributed Storage Systems} (DSSs), an encoded fraction of information is stored in the distributed fashion on different chunk servers. Recently a new paradigm of \textit{Fractional Repetition} (FR) codes have been introduced, in which, encoded data information is stored on distributed servers, where encoding is done using a \textit{Maximum Distance Separable} (MDS) code and a smart replication of packets. In this work, we have shown that an FR code is equivalent to a hypergraph. Using the correspondence, the properties and the bounds of a hypergraph are directly mapped to the associated FR code. In general, the necessary and sufficient conditions for the existence of an FR code is obtained by using the correspondence. Some of the bounds are new and FR codes meeting these bounds are unknown. It is also shown that any FR code associated with a linear hypergraph is universally good., Comment: 8 pages, 2 figures

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., Comment: Revised version with new results and corrections. Submitted to ISIT 2018

Quantum mechanics ensures that the information stored in a quantum state is secure and the ability to send private information through a quantum channel is at least as great as the coherent information. We derive trade-off relations between quantum privacy, information gain by Eve and the disturbance caused by Eve to the quantum state that is being sent through a noisy channel. For tripartite quantum states, we show that monogamy of privacy exists in the case of a single sender and multiple receivers. When Alice prepares a tripartite entangled state and shares it with Bob and Charlie through two different noisy quantum channels, we prove that if the minimally guaranteed quantum privacy between Alice and Bob is positive, then the privacy of information between Alice and Charlie has to be negative. Thus, quantum privacy for more than two parties respects mutual exclusiveness. Then, we prove a monogamy relation for the minimally guaranteed quantum privacy for tripartite systems. We also prove a trade-off relation between the entanglement of formation across one partition and the quantum privacy along another partition. Our results show that quantum privacy cannot be freely shared among multiple parties and can have implication in future quantum networks., Comment: 7 pages, 2 figures

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., Comment: 5 pages, 9 figures, 3DNAprinter software available at http://www.guptalab.org/3dnaprinter

Data storage in Distributed Storage Systems (DSSs) is a multidimensional optimization problem. Using network coding, one wants to provide reliability, scalability, security, reduced storage overhead, reduced bandwidth for repair and minimal disk I/O etc. in such systems. Regenerating codes have been used to optimize some of these parameters, where a file can be reconstructed by contacting any k nodes in the system and in case of node failure it can be repaired by using any d nodes in the system. This was further generalized to Fractional repetition (FR) codes (a smart replication of encoded packets) on n nodes which also provides optimized disk I/O and where a node failure can be repaired by contacting some specific set of nodes in the system. Several constructions of FR codes using graphs and combinatorial designs are known. In particular, some constructions of codes for heterogeneous DSSs are given using partial regular graph (where number of packets on each node is different) and ring construction. In this work, we show that the codes constructed using the partial regular graph are universally good code. Further, we found several universally good codes using ring construction and t-construction., Comment: 8 pages, draft

Heterogeneous Distributed Storage Systems (DSSs) are close to the real world applications for data storage. Each node of the considered DSS, may store different number of packets and each having different repair bandwidth with uniform repair traffic. For such heterogeneous DSS, a failed node can be repaired with the help of some specific nodes. In this work, a family of codes based on graph theory, is constructed which achieves the fundamental bound on file size for the particular heterogeneous DSS., Comment: 7 pages, 2 figures, draft

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., Comment: 14 pages, draft

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., Comment: 19 pages, 4 figures, draft review on DNA codes

Traditionally, spectroscopy is performed by examining the position of absorption lines. However, at frequencies near the transition frequency, additional information can be obtained from the phase shift. In this work we consider the information about the transition frequency obtained from both the absorption and the phase shift, as quantified by the Fisher information in an interferometric measurement. We examine the use of multiple single-photon states, NOON states, and numerically optimized states that are entangled and have multiple photons. We find the optimized states that improve over the standard quantum limit set by independent single photons for some atom number densities., Comment: 6 pages, 8 figures, comments are welcome

We analytically derive a decoherence model for orbital angular momentum states of a photon in a multimode optical fiber and show that rate of decoherence scales exponentially with $l^2$, where $l$ is the azimuthal mode order.~We also show numerically that for large values of $l$ the orbital angular momentum photon state completely dephases.~However for lower values of $l$ the decoherence can be minimized by using dynamical decoupling to allow for qudit high-bandwidth quantum communication and similar applications. \end{abstract}, Comment: 11 pages, 5 figures, ICOAM 2015, DAMOP 2015

Generation of optimal codes is a well known problem in coding theory. Many computational approaches exist in the literature for finding record breaking codes. However generating codes with long lengths $n$ using serial algorithms is computationally very expensive, for example the worst case time complexity of a Greedy algorithm is $\mathcal{O}(n\; 4^n)$. In order to improve the efficiency of generating codes with long lengths, we propose and investigate some parallel algorithms using General Purpose Graphic Processing Units (GPGPU). This paper considers the implementation of parallel Greedy algorithm using GPGPU-CUDA (Computed Unified Device Architecture) framework and discusses various optimization techniques to accelerate the GPU code. The performance achieved for optimized parallel implementations is more than two to three orders of magnitude faster than that of serial implementation and shows a great potential of GPGPU in the field of coding theory applications., Comment: 8 pages, draft

Fractional Repetition (FR) codes are well known class of Distributed Replication-based Simple Storage (Dress) codes for the Distributed Storage Systems (DSSs). In such systems, the replicas of data packets encoded by Maximum Distance Separable (MDS) code, are stored on distributed nodes. Most of the available constructions for the FR codes are based on combinatorial designs and Graph theory. In this work, we propose an elegant sequence based approach for the construction of the FR code. In particular, we propose a beautiful class of codes known as Flower codes and study its basic properties., Comment: 7 pages, updated draft, submitted to conference

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., Comment: draft

In this paper, we consider heterogeneous distributed storage systems (DSSs) having flexible reconstruction degree, where each node in the system has dynamic repair bandwidth and dynamic storage capacity. In particular, a data collector can reconstruct the file at time $t$ using some arbitrary nodes in the system and for a node failure the system can be repaired by some set of arbitrary nodes. Using $min$-$cut$ bound, we investigate the fundamental tradeoff between storage and repair cost for our model of heterogeneous DSS. In particular, the problem is formulated as bi-objective optimization linear programing problem. For an arbitrary DSS, it is shown that the calculated $min$-$cut$ bound is tight., Comment: 10 pages, 5 figures, draft

DNA Self-Assembly has emerged as an interdisciplinary field with many intriguing applications such DNA bio-sensor, DNA circuits, DNA storage, drug delivery etc. Tile assembly model of DNA has been studied for various computational primitives such as addition, subtraction, multiplication, and division. Xuncai et. al. gave computational DNA tiles to perform division of a number but the output had integer quotient. In this work, we simply modify their method of division to improve its compatibility with further computation and this modification has found its application in computing rational numbers, both recurring and terminating, with computational tile complexity of $\mathcal{O} (1)$ and $\mathcal{O} (h)$ respectively. Additionally, we also propose a method to compute square-root of a number with computational tile complexity of $\mathcal{O} (n)$ for an n bit number. Finally, after combining tiles of division and square-root, we propose a simple way to compute the ubiquitously used irrational number, $\pi$, using its infinite series., Comment: 21 pages, draft

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., Comment: Supplementary file and the software DNA Cloud 2.0 is available at http://www.guptalab.org/dnacloud This is the preliminary version of the paper that appeared in Proceedings of IWSDA 2015, pp. 143--147

The implementation of polarization-based quantum communication is limited by signal loss and decoherence caused by the birefringence of a single-mode fiber. We investigate the Knill dynamical decoupling scheme, implemented using half-wave plates, to minimize decoherence and show that a fidelity greater than $99\%$ can be achieved in absence of rotation error and fidelity greater than $96\%$ can be achieved in presence of rotation error. Such a scheme can be used to preserve any quantum state with high fidelity and has potential application for constructing all optical quantum delay line, quantum memory, and quantum repeater., Comment: 8 pages, 6 figures

This paper introduces new reduction and torsion codes for an octonary code and determines their basic properties. These could be useful for the classification of self-orthogonal and self dual codes over $\mathbb{Z}_8$. We also focus our attention on covering radius problem of octonary codes. In particular, we determine lower and upper bounds of the covering radius of several classes of Repetition codes, Simplex codes of Type $\alpha$ and Type $\beta$ and their duals, MacDonald codes, and Reed-Muller codes over $\mathbb{Z}_8$., Comment: 16 pages, some errors fixed

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, Comment: 5 pages, 11 figures, appeared as a poster paper in FNANO 2014 conference, Software available at http://www.guptalab.org/3dna

RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a single class or type. Many different types of techniques exist to classify RNA secondary structure data but none of them have ever used permutation based approach which is very simple and yet powerful. We have written a small JAVA program to generate permutation, apply our algorithm on those permutations and analyze the data and create different logical clusters. We believe that these clusters can be utilized to untangle the mystery of RNA secondary structure and analyze the development patterns of unknown RNA., Comment: 9 pages, 5 figures, 3 tables