Topology and Dynamics of Transcriptome (Dys)Regulation.

RNA transcripts play a crucial role as witnesses of gene expression health. Identifying disruptive short sequences in RNA transcription and regulation is essential for potentially treating diseases. Let us delve into the mathematical intricacies of these sequences. We have previously devised a mathematical approach for defining a "healthy" sequence. This sequence is characterized by having at most four distinct nucleotides (denoted as nt≤4). It serves as the generator of a group denoted as fp. The desired properties of this sequence are as follows: fp should be close to a free group of rank nt-1, it must be aperiodic, and fp should not have isolated singularities within its SL2(C) character variety (specifically within the corresponding Groebner basis). Now, let us explore the concept of singularities. There are cubic surfaces associated with the character variety of a four-punctured sphere denoted as S24. When we encounter these singularities, we find ourselves dealing with some algebraic solutions of a dynamical second-order differential (and transcendental) equation known as the Painlevé VI Equation. In certain cases, S24 degenerates, in the sense that two punctures collapse, resulting in a "wild" dynamics governed by the Painlevé equations of an index lower than VI. In our paper, we provide examples of these fascinating mathematical structures within the context of miRNAs. Specifically, we find a clear relationship between decorated character varieties of Painlevé equations and the character variety calculated from the seed of oncomirs. These findings should find many applications including cancer research and the investigation of neurodegenative diseases.

DNA Sequence and Structure under the Prism of Group Theory and Algebraic Surfaces.

Taking a DNA sequence, a word with letters/bases A, T, G and C, as the relation between the generators of an infinite group π, one can discriminate between two important families: (i) the cardinality structure for conjugacy classes of subgroups of π is that of a free group on one to four bases, and the DNA word, viewed as a substitution sequence, is aperiodic; (ii) the cardinality structure for conjugacy classes of subgroups of π is not that of a free group, the sequence is generally not aperiodic and topological properties of π have to be determined differently. The two cases rely on DNA conformations such as A-DNA, B-DNA, Z-DNA, G-quadruplexes, etc. We found a few salient results: Z-DNA, when involved in transcription, replication and regulation in a healthy situation, implies (i). The sequence of telomeric repeats comprising three distinct bases most of the time satisfies (i). For two-base sequences in the free case (i) or non-free case (ii), the topology of π may be found in terms of the SL(2,C) character variety of π and the attached algebraic surfaces. The linking of two unknotted curves-the Hopf link-may occur in the topology of π in cases of biological importance, in telomeres, G-quadruplexes, hairpins and junctions, a feature that we already found in the context of models of topological quantum computing. For three- and four-base sequences, other knotting configurations are noticed and a building block of the topology is the four-punctured sphere. Our methods have the potential to discriminate between potential diseases associated to the sequences.

Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding.

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA 'word' in the binding domain-the motif-may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structures close to free groups of rank three or less, a property that we call 'syntactical freedom'. Such a property is associated with the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs, such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such DNA syntactical rules and their functional roles. This includes the TATA box in the promoter region of some genes, the single-nucleotide markers (SNP) and the motifs of some genes of ubiquitous roles in transcription and regulation.

Magic informationally complete POVMs with permutations.

Eigenstates of permutation gates are either stabilizer states (for gates in the Pauli group) or magic states, thus allowing universal quantum computation (Planat, Rukhsan-Ul-Haq 2017 Adv. Math. Phys. 2017, 5287862 (doi:10.1155/2017/5287862)). We show in this paper that a subset of such magic states, when acting on the generalized Pauli group, define (asymmetric) informationally complete POVMs. Such informationally complete POVMs, investigated in dimensions 2-12, exhibit simple finite geometries in their projector products and, for dimensions 4 and 8 and 9, relate to two-qubit, three-qubit and two-qutrit contextuality.

The Poincaré Half-Plane for Informationally-Complete POVMs.

It has been shown in previous papers that classes of (minimal asymmetric) informationally-complete positive operator valued measures (IC-POVMs) in dimension d can be built using the multiparticle Pauli group acting on appropriate fiducial states. The latter states may also be derived starting from the Poincaré upper half-plane model H . To do this, one translates the congruence (or non-congruence) subgroups of index d of the modular group into groups of permutation gates, some of the eigenstates of which are the sought fiducials. The structure of some IC-POVMs is found to be intimately related to the Kochen-Specker theorem.

Ramanujan sums for signal processing of low-frequency noise.

An aperiodic (low-frequency) spectrum may originate from the error term in the mean value of an arithmetical function such as Möbius function or Mangoldt function, which are coding sequences for prime numbers. In the discrete Fourier transform the analyzing wave is periodic and not well suited to represent the low-frequency regime. In place we introduce a different signal processing tool based on the Ramanujan sums c(q)(n), well adapted to the analysis of arithmetical sequences with many resonances p/q. The sums are quasiperiodic versus the time n and aperiodic versus the order q of the resonance. Different results arise from the use of this Ramanujan-Fourier transform in the context of arithmetical and experimental signals.