Search

The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain both individual oligo (fragment) symbol errors as well as missing DNA oligo errors, with rates that exceed those of modern storage systems by orders of magnitude. These errors can be corrected either through the use of a large number of redundant oligos or through cycles of writing, reading, and rewriting of information that eliminate the errors. Both approaches add to the overall storage cost and are hence undesirable. Here we propose the first method for storing quantized images in DNA that uses signal processing and machine learning techniques to deal with error and cost issues without resorting to the use of redundant oligos or rewriting. Our methods rely on decoupling the RGB channels of images, performing specialized quantization and compression on the individual color channels, and using new discoloration detection and image inpainting techniques. We demonstrate the performance of our approach experimentally on a collection of movie posters stored in DNA., Comment: 5 pages, revision of ICASSP version

Strange metal behavior is ubiquitous to correlated materials ranging from cuprate superconductors to bilayer graphene. There is increasing recognition that it arises from physics beyond the quantum fluctuations of a Landau order parameter which, in quantum critical heavy fermion antiferromagnets, may be realized as critical Kondo entanglement of spin and charge. The dynamics of the associated electronic delocalization transition could be ideally probed by optical conductivity, but experiments in the corresponding frequency and temperature ranges have remained elusive. We present terahertz time-domain transmission spectroscopy on molecular beam epitaxy-grown thin films of YbRh$_2$Si$_2$, a model strange metal compound. We observe frequency over temperature scaling of the optical conductivity as a hallmark of beyond-Landau quantum criticality. Our discovery implicates critical charge fluctuations as playing a central role in the strange metal behavior, thereby elucidating one of the longstanding mysteries of correlated quantum matter., Comment: preprint with 15 pages, 4 figures

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and for synchronization of communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized and cyclic codes., Comment: 14 pages, 3 figures, 1 Table. arXiv admin note: text overlap with arXiv:1601.08176

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based storage systems and synchronization protocols. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. In addition, WMU sequences used in DNA-based storage systems are required to have balanced compositions of symbols and to be at large mutual Hamming distance from each other. We present a number of constructions for balanced, error-correcting WMU codes using Dyck paths, Knuth's balancing principle, prefix synchronized and cyclic codes., Comment: 1 table

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 access DNA storage channels. The mathematical basis of our work is the construction and design of sequences over discrete alphabets that avoid pre-specified address patterns, have balanced base content, and exhibit other relevant substring constraints. These schemes adapt the stored signals to the DNA medium and thereby reduce the inherent error-rate of the system.

We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications., Comment: 26 pages, 12 figures

We demonstrate that images of flux vortices in a superconductor taken with a transmission electron microscope can be used to measure the penetration depth and coherence length in all directions at the same temperature and magnetic field. This is particularly useful for MgB$_2$, where these quantities vary with the applied magnetic field and values are difficult to obtain at low field or in the $c$-direction. We obtained images of flux vortices from an MgB$_2$ single crystal cut in the $ac$ plane by focussed ion beam milling and tilted to $45^\circ$ with respect to the electron beam about its $a$ axis. A new method was developed to simulate these images which accounted for vortices with a non-zero core in a thin, anisotropic superconductor and a simplex algorithm was used to make a quantitative comparison between the images and simulations to measure the penetration depths and coherence lengths. This gave penetration depths $\Lambda_{ab}=100\pm 35$ nm and $\Lambda_c=120\pm 15$ nm at 10.8 K in a field of 4.8 mT. The large error in $\Lambda_{ab}$ is a consequence of tilting the sample about $a$ and had it been tilted about $c$, the errors would be reversed. Thus, obtaining the most precise values requires taking images of the flux lattice with the sample tilted in more than one direction. In a previous paper, we obtained a more precise value using a sample cut in the $ab$ plane. Using this value gives $\Lambda_{ab}=107\pm 8$ nm, $\Lambda_c=120\pm 15$ nm, $\xi_{ab}=39\pm 11$ nm and $\xi_c=35\pm 10$ nm which agree well with measurements made using other techniques. The experiment required two days to conduct and does not require large-scale facilities. It was performed on a very small sample: $30\times 15$ microns and 200 nm thick so this method could prove useful for characterising new superconductors where only small single crystals are available., Comment: 12 pages, 6 figures. Typos corrected and titles added to references. Accepted for publication in Physical Review B

Well-controlled sub-unit-cell layer-by-layer epitaxial growth of spinel alumina is achieved at room temperature on the TiO2-terminated SrTiO3 single crystalline substrate. By tailoring the interface redox reaction, two-dimensional electron gases with mobilities exceeding 3000 cm2V-1s-1 are achieved at this novel oxide interface., Comment: Adv. Mater. published on-line

Symmetric fix-free codes are prefix condition codes in which each codeword is required to be a palindrome. Their study is motivated by the topic of joint source-channel coding. Although they have been considered by a few communities they are not well understood. In earlier work we used a collection of instances of Boolean satisfiability problems as a tool in the generation of all optimal binary symmetric fix-free codes with n codewords and observed that the number of different optimal codelength sequences grows slowly compared with the corresponding number for prefix condition codes. We demonstrate that all optimal symmetric fix-free codes can alternatively be obtained by sequences of codes generated by simple manipulations starting from one particular code. We also discuss simplifications in the process of searching for this set of codes.

In this paper, we consider a synchronization problem between nodes $A$ and $B$ that are connected through a two--way communication channel. {Node $A$} contains a binary file $X$ of length $n$ and {node $B$} contains a binary file $Y$ that is generated by randomly deleting bits from $X$, by a small deletion rate $\beta$. The location of deleted bits is not known to either node $A$ or node $B$. We offer a deterministic synchronization scheme between nodes $A$ and $B$ that needs a total of $O(n\beta\log \frac{1}{\beta})$ transmitted bits and reconstructs $X$ at node $B$ with probability of error that is exponentially low in the size of $X$. Orderwise, the rate of our scheme matches the optimal rate for this channel., Comment: Accepted to the IEEE Transactions on Information Theory

We propose a new way to construct a multicast coding scheme for linear deterministic relay networks. Our construction can be regarded as a generalization of the well-known multicast network coding scheme of Jaggi et al. to linear deterministic relay networks and is based on the notion of flow for a unicast session that was introduced by the authors in earlier work. We present randomized and deterministic polynomial--time versions of our algorithm and show that for a network with $g$ destinations, our deterministic algorithm can achieve the capacity in $\left\lceil \log(g+1)\right\rceil $ uses of the network., Comment: 12 pages, 2 figures, submitted to CISS 2011

The routing capacity region of networks with multiple unicast sessions can be characterized using Farkas' lemma as an infinite set of linear inequalities. In this paper this result is sharpened by exploiting properties of the solution satisfied by each rate-tuple on the boundary of the capacity region, and a finite description of the routing capacity region which depends on network parameters is offered. For the special case of undirected ring networks additional results on the complexity of the description are provided.

In this paper, we investigate optimal coding strategies for a class of linear deterministic relay networks. The network under study is a relay network, with one source, one destination, and two relay nodes. Additionally, there is a disturbing source of signals that causes interference with the information signals received by the relay nodes. Our model captures the effect of the interference of message signals and disturbing signals on a single relay network, or the interference of signals from multiple relay networks with each other in the linear deterministic framework. For several ranges of the network parameters we find upper bounds on the maximum achievable source--destination rate in the presense of the disturbing node and in each case we find an optimal coding scheme that achieves the upper bound., Comment: 5 pages, 1 figure

Given a matrix with partitions of its rows and columns and entries from a field, we give the necessary and sufficient conditions that it has a non--singular submatrix with certain number of rows from each row partition and certain number of columns from each column partition., Comment: 4 pages

In the last few years the so--called "linear deterministic" model of relay channels has gained popularity as a means of studying the flow of information over wireless communication networks, and this approach generalizes the model of wireline networks which is standard in network optimization. There is recent work extending the celebrated max--flow/min--cut theorem to the capacity of a unicast session over a linear deterministic relay network which is modeled by a layered directed graph. This result was first proved by a random coding scheme over large blocks of transmitted signals. We demonstrate the same result with a simple, deterministic, polynomial--time algorithm which takes as input a single transmitted signal instead of a long block of signals. Our capacity-achieving transmission scheme for a two--layer network requires the extension of a one--dimensional Rado--Hall transversal theorem on the independent subsets of rows of a row--partitioned matrix into a two--dimensional variation for block matrices. To generalize our approach to larger networks we use the submodularity of the capacity of a cut for our model and show that our complete transmission scheme can be obtained by solving a linear program over the intersection of two polymatroids. We prove that our transmission scheme can achieve the max-flow/min-cut capacity by applying a theorem of Edmonds about such linear programs. We use standard submodular function minimization techniques as part of our polynomial--time algorithm to construct our capacity-achieving transmission scheme., Comment: 24 pages, 2 figures