Mutagenic distinction between the receptor-binding and fusion subunits of the SARS-CoV-2 spike glycoprotein
Robert PENNER - 2021-11-11 (M/21/13)
We observe that a residue R of the spike glycoprotein of SARS-CoV-2 which has mutated in one or more of the current Variants of Concern or Interest and under Monitoring rarely participates in a backbone hydrogen bond if R lies in the S1 subunit and usually participates in one if R lies in the S2 subunit. A possible explanation for this based upon free energy is explored as a potentially general principle in the mutagenesis of viral glycoproteins. This observation could help target future vaccine cargos for the evolving coronavirus as well as more generally.
Music of moduli spaces
Robert PENNER - 2021-09-21 (M/21/12)
A musical instrument, the plastic hormonica, is defined here as a birthday present for Dennis Sullivan, who pioneered and helped popularize the hyperbolic geometry underlying its construction. This plastic hormonica is based upon the Farey tesselation of the Poincaré disk decorated by its standard osculating horocycles centered at the rationals. In effect, one taps or holds points of another tesselation tau with the same decorating horocycles to produce sounds depending on the fact that the lambda length of an edge e in tau with this decoration is always an integer. Explicitly, tapping a decorated edge e in tau with lambda length lambda produces a tone of frequency 440 xi^{lambda-12N}, where xi^{12}=2 and N is some fixed positive integer shift of octave. Another type of tap on edges of tau is employed to apply flips, which may be equivariant for a Fuchsian group preserving tau. Sounding the frequency for the edge after an equivariant flip, one can thereby audibly experience paths in Riemann moduli spaces and listen to mapping classes. The resulting chords, which arise from an ideal triangle complementary to tau by sounding the frequencies of its frontier edges, correspond to a generalization of the classical Markoff triples, which are precisely the chords that arise from the once-punctured torus. In the other direction, one can query the genera of specified musical pieces.
Relative topos theory via stacks
Olivia CARAMELLO, Riccardo ZANFA - 2021-07-20 (M/21/11)
We introduce new foundations for relative topos theory based on stacks. One of the central results in our theory is an adjunction between the category of toposes over the topos of sheaves on a given site (C, J) and that of C-indexed categories. This represents a wide generalization of the classical adjunction between presheaves on a topological space and bundles over it, and allows one to interpret several constructions on sheaves and stacks in a geometrical way; in particular, it leads to fibrational descriptions of direct and inverse images of sheaves and stacks, as well as to a geometric understanding of the sheafification process. It also naturally allows one to regard any Grothendieck topos as a 'petit' topos associated with a 'gros' topos, thereby providing an answer to a problem posed by Grothendieck in the seventies. Another key ingredient in our theory is a notion of relative site, which allows one to represent arbitrary geometric morphisms towards a fixed base topos of sheaves on a site as structure morphisms induced by relative sites over that site.
The information loss of a stochastic map
James FULLWOOD, Arthur PARZYGNAT - 2021-07-05 (M/21/10)
We provide a stochastic extension of the Baez--Fritz--Leinster characterization of the Shannon information loss associated with a measure-preserving function. This recovers the conditional entropy and a closely related information-theoretic measure that we call `conditional information loss.' Although not functorial, these information measures are semi-functorial, a concept we introduce that is definable in any Markov category. We also introduce the notion of an `entropic Bayes' rule' for information measures, and we provide a characterization of conditional entropy in terms of this rule.
Noncommutative Differential K-theory
Byungdo PARK, Arthur PARZYGNAT, Corbett REDDEN, Augusto STOFFEL - 2021-06-23 (M/21/09)
We introduce a differential extension of algebraic K-theory of an algebra using Karoubi's Chern character. In doing so, we develop a necessary theory of secondary transgression forms as well as a differential refinement of the smooth Serre-Swan correspondence. Our construction subsumes the differential K-theory of a smooth manifold when the algebra is complex-valued smooth functions. Furthermore, our construction fits into a noncommutative differential cohomology hexagon diagram.
Tropical Fock-Goncharov coordinates for SL3-webs on surfaces I: construction
Daniel C. DOUGLAS, Zhe SUN - 2021-06-07 (M/21/08)
For a finite-type surface S, we study a preferred basis for the commutative algebra of regular functions on the SL3(C)-character variety, introduced by Sikora-Westbury. These basis elements come from the trace functions associated to certain tri-valent graphs embedded in the surface S. We show that this basis can be naturally indexed by positive integer coordinates, defined by Knutson-Tao rhombus inequalities and modulo 3 congruence conditions. These coordinates are related, by the geometric theory of Fock-Goncharov, to the tropical points at infinity of the dual version of the character variety.
Cohomological Descent for Faltings' $p$-adic Hodge Theory and Applications
Tongmu HE - 2021-04-27 (M/21/07)
Faltings' approach in $p$-adic Hodge theory can be schematically divided into two main steps: firstly, a local reduction of the computation of the $p$-adic n and then, the establishment of a link between the latter and differential forms. These relations are organized through Faltings ringed topos whose definition relies on the choice of an integral model of the variety, and whose good properties depend on the (logarithmic) smoothness of this model. Scholze's generalization for rigid analytic varieties has the advantage of depending only on the variety (i.e. the generic fibre). Inspired by Deligne's approach to classical Hodge theory for singular varieties, we establish a cohomological descent result for the structural sheaf of Faltings topos, which makes it possible to extend Faltings' approach to any integral model, i.e. without any smoothness assumption. An essential ingredient of our proof is a descent result of perfectoid algebras in the arc-topology due to Bhatt and Scholze. As an application of our cohomological descent, using a variant of de Jong's alteration theorem for morphisms of schemes, we generalize Faltings' main $p$-adic comparison theorem to any proper and finitely presented morphism of coherent schemes over an absolute integral closure of $\mathbb{Z}_p$ (without any assumption of smoothness) for torsion
The over-topos at a model
Olivia CARAMELLO, Axel OSMOND - 2021-04-15 (M/21/06)
With a model of a geometric theory in an arbitrary topos, we associate a site obtained by endowing a category of generalized elements of the model with a Grothendieck topology, which we call the antecedent topology. Then we show that the associated sheaf topos, which we call the over-topos at the given model, admits a canonical totally connected morphism to the given base topos and satisfies a universal property generalizing that of the colocalization of a topos at a point. We first treat the case of the base topos of sets, where global elements are sufficient to describe our site of definition; in this context, we also introduce a geometric theory classified by the over-topos, whose models can be identified with the model homomorphisms towards the (internalizations of the) model. Then we formulate and prove the general statement over an arbitrary topos, which involves the stack of generalized elements of the model. Lastly, we investigate the geometric and 2-categorical aspects of the over-topos construction, exhibiting it as a bilimit in the bicategory of Grothendieck toposes.
Super Hyperbolic Law of Cosines: same formula with different content
Robert PENNER - 2021-03-12 (M/21/05)
We derive the Laws of Cosines and Sines in the super hyperbolic plane using Minkowski supergeometry and find the identical formulae to the classical case, but remarkably involving different expressions for cosines and sines of angles which include substantial fermionic corrections. In further analogy to the classical case, we apply these results to show that two parallel supergeodesics which are not ultraparallel admit a unique common orthogonal supergeodesic, and we briefly describe aspects of elementary supernumber theory, leading to a prospective analogue of the Gauss product of quadratic forms.
Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS CoV-2
Robert PENNER - 2021-02-25 (M/21/04)
New tools developed by Moderna, BioNTech/Pfizer and Oxford/Astrazeneca provide universal solutions to previously problematic aspects of drug or vaccine delivery, uptake and toxicity, portending new tools across the medical sciences. A novel method is presented based on estimating protein backbone free energy via geometry to predict effective antiviral targets, antigens and vaccine cargoes that are resistant to viral mutation. This method, partly described in earlier work of the author, is reviewed and reformulated here in light of the profusion of recent structural data on the SARS CoV-2 spike glycoprotein and its latest mutations. Scientific and regulatory challenges to nucleic acid therapeutic and vaccine development and deployment are also discussed.
Conditional distributions for quantum systems
Arthur PARZYGNAT - 2021-02-02 (P/21/03)
Conditional distributions, as defined by the Markov category framework, are studied in the setting of matrix algebras (quantum systems). Their construction as linear unital maps are obtained via a categorical Bayesian inversion procedure. Simple criteria establishing when such linear maps are positive are obtained. Several examples are provided, including the standard EPR scenario, where the EPR correlations are reproduced in a purely compositional (categorical) manner. A comparison between the Bayes map and the Petz recovery map is provided, illustrating some key differences.
Superselection of the weak hypercharge and the algebra of the Standard Model
Ivan TODOROV - 2021-01-28 (P/21/02)
Restricting the $\mathbb{Z}_2$-graded tensor product of Clifford algebras $C\ell_4\hat{$C\ell_4^1$. We emphasize the role of the exactly conserved weak hypercharge Y, promoted here to a superselection rule for both observables and gauge transformations. This yields a change of the definition of the particle subspace adopted in recent work with Michel Dubois-Violette \cite{DT20}; here we exclude the zero eigensubspace of Y consisting of the sterile (anti)neutrinos which are allowed to mix. One thus modifies the Lie superalgebra generated by the Higgs field. Equating the normalizations of $\Phi$ in the lepton and the quark subalgebras we obtain a relation between the masses of the W boson and the Higgs that fits the experimental values within one percent accuracy.
Sketch of a Program for Universal Automorphic Functions to Capture Monstrous Moonshine
Igor FRENKEL, Robert PENNER - 2021-01-05 (M/21/01)
We review and reformulate old and prove new results about the triad $ {\rm PPSL}_2({\mathbb Z})\subseteq{\rm PPSL}_2({\mathbb R})\circlearrowright ppsl_2({\mathbb R}) $, which provides a universal generalization of the classical automorphic triad ${\rm PSL}_2({\mathbb Z})\subseteq{\rm PSL}_2({\mathbb R})\circlearrowright psl_2({\mathbb R})$. The leading P or $p$ in the universal setting stands for $piecewise$, and the group ${\rm PPSL}_2({\mathbb Z})$ plays at once the role of universal modular group, universal mapping class group, Thompson group $T$ and Ptolemy group. We produce a new basis of the Lie algebra $ppsl_2({\mathbb R})$, compute its structure constants, define a central extension which is compared with the Weil-Petersson 2-form, and discuss its representation theory. We construct and study new framed holographic coordinates on the universal Teichmrm analogous to the invariant Eisenstein 1-form $E_2(z)dz$, which gives rise to the spin 1 representation of $psl_2({\mathbb R})$ extended by the trivial representation. This suggests the full program for developing the theory of universal automorphic functions conjectured to yield the bosonic CFT$_2$. Relaxing the automorphic condition to the commutant leads to our ultimate conjecture on realizing the Monster CFT$_2$ via the automorphic representation for the universal triad. This conjecture is als