International Journal of Geometric Methods in Modern Physics
Motivated by the recent interest in Lie algebraic and geometric structures arising from tensor pr... more Motivated by the recent interest in Lie algebraic and geometric structures arising from tensor products of division algebras and their relevance to high energy theoretical physics, we analyze generalized bioctonionic projective and hyperbolic planes. After giving a Veronese representation of the complexification of the Cayley plane [Formula: see text], we present a novel, explicit construction of the bioctonionic Cayley–Rosenfeld plane [Formula: see text], again by exploiting Veronese coordinates. We discuss the isometry groups of all generalized bioctonionic planes, recovering all complex and real forms of the exceptional groups [Formula: see text] and [Formula: see text], and characterizing such planes as symmetric and Hermitian symmetric spaces. We conclude by discussing some possible physical applications.
Every protein consists of a linear sequence over an alphabet of 20 letters/amino acids. The seque... more 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...
Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode... more 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 structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to 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 s...
Starting from first principles and the mathematics of model sets we propose a framework where eme... more Starting from first principles and the mathematics of model sets we propose a framework where emergence of spacetime and matter can be addressed.
A popular account of the mixing patterns for the three generations of quarks and leptons is throu... more A popular account of the mixing patterns for the three generations of quarks and leptons is through the characters κ of a finite group G. Here, we introduce a d-dimensional Hilbert space with d = c c ( G ) , the number of conjugacy classes of G. Groups under consideration should follow two rules, (a) the character table contains both two- and three-dimensional representations with at least one of them faithful and (b) there are minimal informationally complete measurements under the action of a d-dimensional Pauli group over the characters of these representations. Groups with small d that satisfy these rules coincide in a large part with viable ones derived so far for reproducing simultaneously the CKM (quark) and PNMS (lepton) mixing matrices.
We explore the structural similarities in three different languages, first in the protein languag... more We explore the structural similarities in three different languages, first in the protein language whose primary letters are the amino acids, second in the musical language whose primary letters are the notes, and third in the poetry language whose primary letters are the alphabet. For proteins, the non local (secondary) letters are the types of foldings in space (α-helices, β-sheets, etc.); for music, one is dealing with clear-cut repetition units called musical forms and for poems the structure consists of grammatical forms (names, verbs, etc.). We show in this paper that the mathematics of such secondary structures relies on finitely presented groups fp on r letters, where r counts the number of types of such secondary non local segments. The number of conjugacy classes of a given index (also the number of graph coverings over a base graph) of a group fp is found to be close to the number of conjugacy classes of the same index in the free group Fr−1 on r−1 generators. In a concre...
The Kummer surface was constructed in 1864. It corresponds to the desingularisation of the quotie... more 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.
We find that the degeneracies and many peculiarities of the DNA genetic code may be described tha... more We find that the degeneracies and many peculiarities of the DNA genetic code may be described thanks to two closely related (fivefold symmetric) finite groups. The first group has signature $G=\mathbb{Z}_5 \rtimes H$ where $H=\mathbb{Z}_2 . S_4\cong 2O$ is isomorphic to the binary octahedral group $2O$ and $S_4$ is the symmetric group on four letters/bases. The second group has signature $G=\mathbb{Z}_5 \rtimes GL(2,3)$ and points out a threefold symmetry of base pairings. For those groups, the representations for the $22$ conjugacy classes of $G$ are in one-to-one correspondence with the multiplets encoding the proteinogenic amino acids. Additionally, most of the $22$ characters of $G$ attached to those representations are informationally complete. The biological meaning of these coincidences is discussed.
The authors previously found a model of universal quantum computation by making use of the coset ... more The authors previously found a model of universal quantum computation by making use of the coset structure of subgroups of a free group G with relations. A valid subgroup H of index d in G leads to a ‘magic’ state ψ in d-dimensional Hilbert space that encodes a minimal informationally complete quantum measurement (or MIC), possibly carrying a finite ‘contextual’ geometry. In the present work, we choose G as the fundamental group π 1 ( V ) of an exotic 4-manifold V, more precisely a ‘small exotic’ (space-time) R 4 (that is homeomorphic and isometric, but not diffeomorphic to the Euclidean R 4 ). Our selected example, due to S. Akbulut and R. E. Gompf, has two remarkable properties: (a) it shows the occurrence of standard contextual geometries such as the Fano plane (at index 7), Mermin’s pentagram (at index 10), the two-qubit commutation picture G Q ( 2 , 2 ) (at index 15), and the combinatorial Grassmannian Gr ( 2 , 8 ) (at index 28); and (b) it allows the interpretation of MICs mea...
In this paper, a new fractal signature possessing the cardioid shape in the Mandelbrot set is pre... more In this paper, a new fractal signature possessing the cardioid shape in the Mandelbrot set is presented in the Fourier space of a Fibonacci chain with two lengths, L and S, where L / S = ϕ . The corresponding pointwise dimension is 1.7. Various modifications, such as truncation from the head or tail, scrambling the orders of the sequence and changing the ratio of the L and S, are done on the Fibonacci chain. The resulting patterns in the Fourier space show that that the fractal signature is very sensitive to changes in the Fibonacci order but not to the L / S ratio.
Let H be a nontrivial subgroup of index d of a free group G and N be the normal closure of H in G... more Let H be a nontrivial subgroup of index d of a free group G and N be the normal closure of H in G. The coset organization in a subgroup H of G provides a group P of permutation gates whose common eigenstates are either stabilizer states of the Pauli group or magic states for universal quantum computing. A subset of magic states consists of states associated to minimal informationally complete measurements, called MIC states. It is shown that, in most cases, the existence of a MIC state entails the two conditions (i) N = G and (ii) no geometry (a triple of cosets cannot produce equal pairwise stabilizer subgroups) or that these conditions are both not satisfied. Our claim is verified by defining the low dimensional MIC states from subgroups of the fundamental group G = π 1 ( M ) of some manifolds encountered in our recent papers, e.g., the 3-manifolds attached to the trefoil knot and the figure-eight knot, and the 4-manifolds defined by 0-surgery of them. Exceptions to the aforementi...
The fundamental group π 1 ( L ) of a knot or link L may be used to generate magic states appropri... more The fundamental group π 1 ( L ) of a knot or link L may be used to generate magic states appropriate for performing universal quantum computation and simultaneously for retrieving complete information about the processed quantum states. In this paper, one defines braids whose closure is the L of such a quantum computer model and computes their braid-induced Seifert surfaces and the corresponding Alexander polynomial. In particular, some d-fold coverings of the trefoil knot, with d = 3 , 4, 6, or 12, define appropriate links L, and the latter two cases connect to the Dynkin diagrams of E 6 and D 4 , respectively. In this new context, one finds that this correspondence continues with Kodaira’s classification of elliptic singular fibers. The Seifert fibered toroidal manifold Σ ′ , at the boundary of the singular fiber E 8 ˜ , allows possible models of quantum computing.
It has been shown that the concept of a magic state (in universal quantum computing: uqc) and tha... more It has been shown that the concept of a magic state (in universal quantum computing: uqc) and that of a minimal informationally complete positive operator valued measure: MIC-POVMs (in quantum measurements) are in good agreement when such a magic state is selected in the set of non-stabilizer eigenstates of permutation gates with the Pauli group acting on it [1]. Further work observed that most found low-dimensional MICs may be built from subgroups of the modular group PS L(2, Z) [2] and that this can be understood from the picture of the trefoil knot and related 3-manifolds [3]. Here one concentrates on Bianchi groups PS L(2, O10) (with O10 the integer ring over the imaginary quadratic field) whose torsion-free subgroups define the appropriate knots and links leading to MICs and the related uqc. One finds a chain of Bianchi congruence n-cusped links playing a significant role [4].
A single qubit may be represented on the Bloch sphere or similarly on the $3$-sphere $S^3$. Our g... more A single qubit may be represented on the Bloch sphere or similarly on the $3$-sphere $S^3$. Our goal is to dress this correspondence by converting the language of universal quantum computing (uqc) to that of $3$-manifolds. A magic state and the Pauli group acting on it define a model of uqc as a POVM that one recognizes to be a $3$-manifold $M^3$. E. g., the $d$-dimensional POVMs defined from subgroups of finite index of the modular group $PSL(2,\mathbb{Z})$ correspond to $d$-fold $M^3$- coverings over the trefoil knot. In this paper, one also investigates quantum information on a few \lq universal' knots and links such as the figure-of-eight knot, the Whitehead link and Borromean rings, making use of the catalog of platonic manifolds available on SnapPy. Further connections between POVMs based uqc and $M^3$'s obtained from Dehn fillings are explored.
We present the emergence of a root system in six dimensions from the tetrahedra of an icosahedral... more We present the emergence of a root system in six dimensions from the tetrahedra of an icosahedral core known as the 20-group (20G) within the framework of Clifford’s geometric algebra. Consequently, we establish a connection between a three-dimensional icosahedral seed, a six-dimensional (6D) Dirichlet quantized host and a higher dimensional lattice structure. The 20G, owing to its icosahedral symmetry, bears the signature of a 6D lattice that manifests in the Dirichlet integer representation. We present an interpretation whereby the three-dimensional 20G can be regarded as the core substratum from which the higher dimensional lattices emerge. This emergent geometry is based on an induction principle supported by the Clifford multi-vector formalism of three-dimensional (3D) Euclidean space. This lays a geometric framework for understanding several physics theories related to S U ( 5 ) , E 6 , E 8 Lie algebras and their composition with the algebra associated with the even unimodular...
International Journal of Geometric Methods in Modern Physics
Motivated by the recent interest in Lie algebraic and geometric structures arising from tensor pr... more Motivated by the recent interest in Lie algebraic and geometric structures arising from tensor products of division algebras and their relevance to high energy theoretical physics, we analyze generalized bioctonionic projective and hyperbolic planes. After giving a Veronese representation of the complexification of the Cayley plane [Formula: see text], we present a novel, explicit construction of the bioctonionic Cayley–Rosenfeld plane [Formula: see text], again by exploiting Veronese coordinates. We discuss the isometry groups of all generalized bioctonionic planes, recovering all complex and real forms of the exceptional groups [Formula: see text] and [Formula: see text], and characterizing such planes as symmetric and Hermitian symmetric spaces. We conclude by discussing some possible physical applications.
Every protein consists of a linear sequence over an alphabet of 20 letters/amino acids. The seque... more 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...
Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode... more 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 structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to 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 s...
Starting from first principles and the mathematics of model sets we propose a framework where eme... more Starting from first principles and the mathematics of model sets we propose a framework where emergence of spacetime and matter can be addressed.
A popular account of the mixing patterns for the three generations of quarks and leptons is throu... more A popular account of the mixing patterns for the three generations of quarks and leptons is through the characters κ of a finite group G. Here, we introduce a d-dimensional Hilbert space with d = c c ( G ) , the number of conjugacy classes of G. Groups under consideration should follow two rules, (a) the character table contains both two- and three-dimensional representations with at least one of them faithful and (b) there are minimal informationally complete measurements under the action of a d-dimensional Pauli group over the characters of these representations. Groups with small d that satisfy these rules coincide in a large part with viable ones derived so far for reproducing simultaneously the CKM (quark) and PNMS (lepton) mixing matrices.
We explore the structural similarities in three different languages, first in the protein languag... more We explore the structural similarities in three different languages, first in the protein language whose primary letters are the amino acids, second in the musical language whose primary letters are the notes, and third in the poetry language whose primary letters are the alphabet. For proteins, the non local (secondary) letters are the types of foldings in space (α-helices, β-sheets, etc.); for music, one is dealing with clear-cut repetition units called musical forms and for poems the structure consists of grammatical forms (names, verbs, etc.). We show in this paper that the mathematics of such secondary structures relies on finitely presented groups fp on r letters, where r counts the number of types of such secondary non local segments. The number of conjugacy classes of a given index (also the number of graph coverings over a base graph) of a group fp is found to be close to the number of conjugacy classes of the same index in the free group Fr−1 on r−1 generators. In a concre...
The Kummer surface was constructed in 1864. It corresponds to the desingularisation of the quotie... more 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.
We find that the degeneracies and many peculiarities of the DNA genetic code may be described tha... more We find that the degeneracies and many peculiarities of the DNA genetic code may be described thanks to two closely related (fivefold symmetric) finite groups. The first group has signature $G=\mathbb{Z}_5 \rtimes H$ where $H=\mathbb{Z}_2 . S_4\cong 2O$ is isomorphic to the binary octahedral group $2O$ and $S_4$ is the symmetric group on four letters/bases. The second group has signature $G=\mathbb{Z}_5 \rtimes GL(2,3)$ and points out a threefold symmetry of base pairings. For those groups, the representations for the $22$ conjugacy classes of $G$ are in one-to-one correspondence with the multiplets encoding the proteinogenic amino acids. Additionally, most of the $22$ characters of $G$ attached to those representations are informationally complete. The biological meaning of these coincidences is discussed.
The authors previously found a model of universal quantum computation by making use of the coset ... more The authors previously found a model of universal quantum computation by making use of the coset structure of subgroups of a free group G with relations. A valid subgroup H of index d in G leads to a ‘magic’ state ψ in d-dimensional Hilbert space that encodes a minimal informationally complete quantum measurement (or MIC), possibly carrying a finite ‘contextual’ geometry. In the present work, we choose G as the fundamental group π 1 ( V ) of an exotic 4-manifold V, more precisely a ‘small exotic’ (space-time) R 4 (that is homeomorphic and isometric, but not diffeomorphic to the Euclidean R 4 ). Our selected example, due to S. Akbulut and R. E. Gompf, has two remarkable properties: (a) it shows the occurrence of standard contextual geometries such as the Fano plane (at index 7), Mermin’s pentagram (at index 10), the two-qubit commutation picture G Q ( 2 , 2 ) (at index 15), and the combinatorial Grassmannian Gr ( 2 , 8 ) (at index 28); and (b) it allows the interpretation of MICs mea...
In this paper, a new fractal signature possessing the cardioid shape in the Mandelbrot set is pre... more In this paper, a new fractal signature possessing the cardioid shape in the Mandelbrot set is presented in the Fourier space of a Fibonacci chain with two lengths, L and S, where L / S = ϕ . The corresponding pointwise dimension is 1.7. Various modifications, such as truncation from the head or tail, scrambling the orders of the sequence and changing the ratio of the L and S, are done on the Fibonacci chain. The resulting patterns in the Fourier space show that that the fractal signature is very sensitive to changes in the Fibonacci order but not to the L / S ratio.
Let H be a nontrivial subgroup of index d of a free group G and N be the normal closure of H in G... more Let H be a nontrivial subgroup of index d of a free group G and N be the normal closure of H in G. The coset organization in a subgroup H of G provides a group P of permutation gates whose common eigenstates are either stabilizer states of the Pauli group or magic states for universal quantum computing. A subset of magic states consists of states associated to minimal informationally complete measurements, called MIC states. It is shown that, in most cases, the existence of a MIC state entails the two conditions (i) N = G and (ii) no geometry (a triple of cosets cannot produce equal pairwise stabilizer subgroups) or that these conditions are both not satisfied. Our claim is verified by defining the low dimensional MIC states from subgroups of the fundamental group G = π 1 ( M ) of some manifolds encountered in our recent papers, e.g., the 3-manifolds attached to the trefoil knot and the figure-eight knot, and the 4-manifolds defined by 0-surgery of them. Exceptions to the aforementi...
The fundamental group π 1 ( L ) of a knot or link L may be used to generate magic states appropri... more The fundamental group π 1 ( L ) of a knot or link L may be used to generate magic states appropriate for performing universal quantum computation and simultaneously for retrieving complete information about the processed quantum states. In this paper, one defines braids whose closure is the L of such a quantum computer model and computes their braid-induced Seifert surfaces and the corresponding Alexander polynomial. In particular, some d-fold coverings of the trefoil knot, with d = 3 , 4, 6, or 12, define appropriate links L, and the latter two cases connect to the Dynkin diagrams of E 6 and D 4 , respectively. In this new context, one finds that this correspondence continues with Kodaira’s classification of elliptic singular fibers. The Seifert fibered toroidal manifold Σ ′ , at the boundary of the singular fiber E 8 ˜ , allows possible models of quantum computing.
It has been shown that the concept of a magic state (in universal quantum computing: uqc) and tha... more It has been shown that the concept of a magic state (in universal quantum computing: uqc) and that of a minimal informationally complete positive operator valued measure: MIC-POVMs (in quantum measurements) are in good agreement when such a magic state is selected in the set of non-stabilizer eigenstates of permutation gates with the Pauli group acting on it [1]. Further work observed that most found low-dimensional MICs may be built from subgroups of the modular group PS L(2, Z) [2] and that this can be understood from the picture of the trefoil knot and related 3-manifolds [3]. Here one concentrates on Bianchi groups PS L(2, O10) (with O10 the integer ring over the imaginary quadratic field) whose torsion-free subgroups define the appropriate knots and links leading to MICs and the related uqc. One finds a chain of Bianchi congruence n-cusped links playing a significant role [4].
A single qubit may be represented on the Bloch sphere or similarly on the $3$-sphere $S^3$. Our g... more A single qubit may be represented on the Bloch sphere or similarly on the $3$-sphere $S^3$. Our goal is to dress this correspondence by converting the language of universal quantum computing (uqc) to that of $3$-manifolds. A magic state and the Pauli group acting on it define a model of uqc as a POVM that one recognizes to be a $3$-manifold $M^3$. E. g., the $d$-dimensional POVMs defined from subgroups of finite index of the modular group $PSL(2,\mathbb{Z})$ correspond to $d$-fold $M^3$- coverings over the trefoil knot. In this paper, one also investigates quantum information on a few \lq universal' knots and links such as the figure-of-eight knot, the Whitehead link and Borromean rings, making use of the catalog of platonic manifolds available on SnapPy. Further connections between POVMs based uqc and $M^3$'s obtained from Dehn fillings are explored.
We present the emergence of a root system in six dimensions from the tetrahedra of an icosahedral... more We present the emergence of a root system in six dimensions from the tetrahedra of an icosahedral core known as the 20-group (20G) within the framework of Clifford’s geometric algebra. Consequently, we establish a connection between a three-dimensional icosahedral seed, a six-dimensional (6D) Dirichlet quantized host and a higher dimensional lattice structure. The 20G, owing to its icosahedral symmetry, bears the signature of a 6D lattice that manifests in the Dirichlet integer representation. We present an interpretation whereby the three-dimensional 20G can be regarded as the core substratum from which the higher dimensional lattices emerge. This emergent geometry is based on an induction principle supported by the Clifford multi-vector formalism of three-dimensional (3D) Euclidean space. This lays a geometric framework for understanding several physics theories related to S U ( 5 ) , E 6 , E 8 Lie algebras and their composition with the algebra associated with the even unimodular...
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Papers by Raymond ASCHHEIM