Quantum Information in the Protein Codes, 3-Manifolds and the Kummer Surface

Every protein consists of a linear sequence over an alphabet of 20 letters/amino acids. The sequence unfolds in the 3-dimensional space through secondary (local foldings), tertiary (bonds) and quaternary (disjoint multiple) structures. The mere existence of the genetic code for the 20 letters of the linear chain could be predicted with the (informationally complete) irreducible characters of the finite group Gn:=Zn⋊2O (with n=5 or 7 and 2O the binary octahedral group) in our previous two papers. It turns out that some quaternary structures of protein complexes display n-fold symmetries. We propose an approach of secondary structures based on free group theory. Our results are compared to other approaches of predicting secondary structures of proteins in terms of α helices, β sheets and coils, or more refined techniques. It is shown that the secondary structure of proteins shows similarities to the structure of some hyperbolic 3-manifolds. The hyperbolic 3-manifold of smallest volume—Gieseking manifold—some other 3 manifolds and the oriented hypercartographic group are singled out as tentative models of such secondary structures. For the quaternary structure, there are links to the Kummer surface.

Quantum Information in the Protein Codes, $3$-manifolds and the Kummer Surface

Every protein consists of a linear sequence over an alphabet of $20$ letters/amino acids. The sequence unfolds in the $3$-dimensional space through secondary (local foldings), tertiary (bonds) and quaternary (disjoint multiple) structures. The mere existence of the genetic code for the $20$ letters of the linear chain could be predicted with the (informationally complete) irreducible characters of the finite group $G_n:=\mathbb{Z}_n \rtimes 2O$ (with $n=5$ or $7$ and $2O$ the binary octahedral group) in our previous two papers. It turns out that some quaternary structures of protein complexes display $n$-fold symmetries. We propose an approach of secondary structures based on free group theory. Our results are compared to other approaches of predicting secondary structures of proteins in terms of $\alpha$ helices, $\beta$ sheets and coils, or more refined techniques. It is shown that the secondary structure of proteins shows similarities to the structure of some hyperbolic $3$-manifolds. The hyperbolic $3$-manifold of smallest volume --Gieseking manifold--, some other $3$ manifolds and Grothendieck's cartographic group are singled out as tentative models of such secondary structures. For the quaternary structure, there are links to the Kummer surface.

Finite Groups for the Kummer Surface: The Genetic Code and a Quantum Gravity Analogy

The Kummer surface was constructed in 1864. It corresponds to the desingularization of the quotient of a 4-torus by 16 complex double points. Kummer surface is known to play a role in some models of quantum gravity. Following our recent model of the DNA genetic code based on the irreducible characters of the finite group G5:=(240,105)≅Z5⋊2O (with 2O the binary octahedral group), we now find that groups G6:=(288,69)≅Z6⋊2O and G7:=(336,118)≅Z7⋊2O can be used as models of the symmetries in hexamer and heptamer proteins playing a vital role for some biological functions. Groups G6 and G7 are found to involve the Kummer surface in the structure of their character table. An analogy between quantum gravity and DNA/RNA packings is suggested.

Finite Groups for the Kummer Surface: the Genetic Code and a Quantum Gravity Analogy

The Kummer surface was constructed in 1864. It corresponds to the desingularisation of the quotient of a 4-torus by 16 complex double points. Kummer surface is kwown to play a role in some models of quantum gravity. Following our recent model of the DNA genetic code based on the irreducible characters of the finite group G5:=(240,105)≅Z5⋊2O (with 2O the binary octahedral group), we now find that groups G6:=(288,69)≅Z6⋊2O and G7:=(336,118)≅Z7⋊2O can be used as models of the symmetries in hexamer and heptamer proteins playing a vital role for some biological functions. Groups G6 and G7 are found to involve the Kummer surface in the structure of their character table. An analogy between quantum gravity and DNA/RNA packings is suggested.

Birational Geometry of Blow-ups of Projective Spaces Along Points and Lines

Consider the blow-up $X$ of ${\mathbb{P}}^3$ at $6$ points in very general position and the $15$ lines through the $6$ points. We construct an infinite-order pseudo-automorphism $\phi _X$ on $X$. The effective cone of $X$ has infinitely many extremal rays and, hence, $X$ is not a Mori Dream Space. The threefold $X$ has a unique anticanonical section, which is a Jacobian K3 Kummer surface $S$ of Picard number 17. The restriction of $\phi _X$ on $S$ realizes one of Keum’s 192 infinite-order automorphisms. We show the blow-up of ${\mathbb{P}}^n$ ($n\geq 3$) at $(n+3)$ very general points and certain $9$ lines through them is not a Mori Dream Space. As an application, for $n\geq 7$, the blow-up of $\overline{M}_{0,n}$ at a very general point has infinitely many extremal effective divisors.

Degeneration of Kummer surfaces

We prove that a Kummer surface defined over a complete strictly Henselian discretely valued field K of residue characteristic different from 2 admits a strict Kulikov model after finite base change. The Kulikov models we construct will be schemes, so our results imply that the semistable reduction conjecture is true for Kummer surfaces in this setup, even in the category of schemes. Our construction of Kulikov models is closely related to an earlier construction of Künnemann, which produces semistable models of Abelian varieties. It is well known that the special fibre of a strict Kulikov model belongs to one of three types, and we shall prove that the type of the special fibre of a strict Kulikov model of a Kummer surface and the toric rank of a corresponding Abelian surface are determined by each other. We also study the relationship between this invariant and the Galois representation on the second ℓ-adic cohomology of the Kummer surface. Finally, we apply our results, together with earlier work of Halle–Nicaise, to give a proof of the monodromy conjecture for Kummer surfaces in equal characteristic zero.

Classification of double octic Calabi–Yau threefolds with h1,2 ≤ 1 defined by an arrangement of eight planes

In this paper, we propose a combinatorial approach to study Calabi–Yau threefolds constructed as a resolution of singularities of a double covering of [Formula: see text] branched along an arrangement of eight planes. We use this description to give a complete classification of arrangements of eight planes in [Formula: see text] defining Calabi–Yau threefolds modulo projective transformation with [Formula: see text] and to derive their geometric properties (Kummer surface fibrations, automorphisms, special elements in families).

Fast FPGA Implementations of Diffie-Hellman on the Kummer Surface of a Genus-2 Curve

We present the first hardware implementations of Diffie-Hellman key exchange based on the Kummer surface of Gaudry and Schost’s genus-2 curve targeting a 128-bit security level. We describe a single-core architecture for lowlatency applications and a multi-core architecture for high-throughput applications. Synthesized on a Xilinx Zynq-7020 FPGA, our architectures perform a key exchange with lower latency and higher throughput than any other reported implementation using prime-field elliptic curves at the same security level. Our single-core architecture performs a scalar multiplication with a latency of 82 microseconds while our multicore architecture achieves a throughput of 91,226 scalar multiplications per second. When compared to similar implementations of Microsoft’s Fourℚ on the same FPGA, this translates to an improvement of 48% in latency and 40% in throughput for the single-core and multi-core architecture, respectively. Both our designs exhibit constant-time execution to thwart timing attacks, use the Montgomery ladder for improved resistance against SPA, and support a countermeasure against fault attacks.