Optimal staged self-assembly of linear assemblies

We analyze the complexity of building linear assemblies, sets of linear assemblies, and O(1)-scale general shapes in the staged tile assembly model. For systems with at most b bins and t tile types, we prove that the minimum number of stages to uniquely assemble a 1 n line is (logt n + logb n t + 1). Generalizing to O(1) n lines, we prove the minimum number of stages is O( log n tb t log t b2 + log log b log t ) and ( log n tb t log t b2 ). Next, we consider assembling sets of lines and general shapes using t = O(1) tile types. We prove that the minimum number of stages needed to assemble a set of k lines of size at most O(1) n is O( k log n b2 + k p log n b + log log n) and ( k log n b2 ). In the case that b = O( p k), the minimum number of stages is (log n). The upper bound in this special case is then used to assemble \hefty shapes of at least logarithmic edge-length-to- edge-count ratio at O(1)-scale using O( p k) bins and optimal O(log n) stages

A General Polynomial Selection Method and New Asymptotic Complexities for the Tower Number Field Sieve Algorithm

In a recent work, Kim and Barbulescu had extended the tower number field sieve algorithm to obtain improved asymptotic complexities in the medium prime case for the discrete logarithm problem on $\mathbb{F}_{p^n}$ where $n$ is not a prime power. Their method does not work when $n$ is a composite prime power. For this case, we obtain new asymptotic complexities, e.g., $L_{p^n}(1/3,(64/9)^{1/3})$ (resp. $L_{p^n}(1/3,1.88)$ for the multiple number field variation) when $n$ is composite and a power of 2; the previously best known complexity for this case is $L_{p^n}(1/3,(96/9)^{1/3})$ (resp. $L_{p^n}(1/3,2.12)$). These complexities may have consequences to the selection of key sizes for pairing based cryptography. The new complexities are achieved through a general polynomial selection method. This method, which we call Algorithm-$\mathcal{C}$, extends a previous polynomial selection method proposed at Eurocrypt 2016 to the tower number field case. As special cases, it is possible to obtain the generalised Joux-Lercier and the Conjugation method of polynomial selection proposed at Eurocrypt 2015 and the extension of these methods to the tower number field scenario by Kim and Barbulescu. A thorough analysis of the new algorithm is carried out in both concrete and asymptotic terms

New Complexity Trade-Offs for the (Multiple) Number Field Sieve Algorithm in Non-Prime Fields

The selection of polynomials to represent number fields crucially determines the efficiency of the Number Field Sieve (NFS) algorithm for solving the discrete logarithm in a finite field. An important recent work due to Barbulescu et al. builds upon existing works to propose two new methods for polynomial selection when the target field is a non-prime field. These methods are called the generalised Joux-Lercier (GJL) and the Conjugation methods. In this work, we propose a new method (which we denote as $\mathcal{A}$) for polynomial selection for the NFS algorithm in fields $\mathbb{F}_{Q}$, with $Q=p^n$ and $n>1$. The new method both subsumes and generalises the GJL and the Conjugation methods and provides new trade-offs for both $n$ composite and $n$ prime. Let us denote the variant of the (multiple) NFS algorithm using the polynomial selection method ``{X} by (M)NFS-{X}. Asymptotic analysis is performed for both the NFS-$\mathcal{A}$ and the MNFS-$\mathcal{A}$ algorithms. In particular, when $p=L_Q(2/3,c_p)$, for $c_p\in [3.39,20.91]$, the complexity of NFS-$\mathcal{A}$ is better than the complexities of all previous algorithms whether classical or MNFS. The MNFS-$\mathcal{A}$ algorithm provides lower complexity compared to NFS-$\mathcal{A}$ algorithm; for $c_p\in (0, 1.12] \cup [1.45,3.15]$, the complexity of MNFS-$\mathcal{A}$ is the same as that of the MNFS-Conjugation and for $c_p\notin (0, 1.12] \cup [1.45,3.15]$, the complexity of MNFS-$\mathcal{A}$ is lower than that of all previous methods

Solving discrete logarithms on a 170-bit MNT curve by pairing reduction

Pairing based cryptography is in a dangerous position following the breakthroughs on discrete logarithms computations in finite fields of small characteristic. Remaining instances are built over finite fields of large characteristic and their security relies on the fact that the embedding field of the underlying curve is relatively large. How large is debatable. The aim of our work is to sustain the claim that the combination of degree 3 embedding and too small finite fields obviously does not provide enough security. As a computational example, we solve the DLP on a 170-bit MNT curve, by exploiting the pairing embedding to a 508-bit, degree-3 extension of the base field.Comment: to appear in the Lecture Notes in Computer Science (LNCS

Exploring Naccache-Stern Knapsack Encryption

The Naccache–Stern public-key cryptosystem (NS) relies on the conjectured hardness of the modular multiplicative knapsack problem: Given $p,\{v_i\},\prod v_i^{m_i} \bmod p$, find the $\{m_i\}$. Given this scheme\u27s algebraic structure it is interesting to systematically explore its variants and generalizations. In particular it might be useful to enhance NS with features such as semantic security, re-randomizability or an extension to higher-residues. This paper addresses these questions and proposes several such variants

A Survey on Continuous Time Computations

We provide an overview of theories of continuous time computation. These theories allow us to understand both the hardness of questions related to continuous time dynamical systems and the computational power of continuous time analog models. We survey the existing models, summarizing results, and point to relevant references in the literature

Programmable disorder in random DNA tilings

Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network—random loops, mazes and trees—on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures

High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks

Our ability to recreate complex biochemical mechanisms in designed, artificial systems provides a stringent test of our understanding of these mechanisms and opens the door to their exploitation in artificial biotechnologies. Motivated by this philosophy, here we have recapitulated in vitro the “target sequestration” mechanism used by nature to improve the sensitivity (the steepness of the input/output curve) of many regulatory cascades. Specifically, we have employed molecular beacons, a commonly employed optical DNA sensor, to recreate the sequestration mechanism and performed an exhaustive, quantitative study of its key determinants (e.g., the relative concentrations and affinities of probe and depletant). We show that, using sequestration, we can narrow the pseudo-linear range of a traditional molecular beacon from 81-fold (i.e., the transition from 10% to 90% target occupancy spans an 81-fold change in target concentration) to just 1.5-fold. This narrowing of the dynamic range improves the sensitivity of molecular beacons to that equivalent of an oligomeric, allosteric receptor with a Hill coefficient greater than 9. Following this we have adapted the sequestration mechanism to steepen the binding-site occupancy curve of a common transcription factor by an order of magnitude over the sensitivity observed in the absence of sequestration. Given the success with which the sequestration mechanism has been employed by nature, we believe that this strategy could dramatically improve the performance of synthetic biological systems and artificial biosensors