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22 pages, 4103 KiB  
Article
Maximal Genetic Code Symmetry Is a Physicochemical Purine–Pyrimidine Symmetry Language for Transcription and Translation in the Flow of Genetic Information from DNA to Proteins
by Marija Rosandić and Vladimir Paar
Int. J. Mol. Sci. 2024, 25(17), 9543; https://doi.org/10.3390/ijms25179543 - 2 Sep 2024
Viewed by 338
Abstract
Until now, research has not taken into consideration the physicochemical purine–pyrimidine symmetries of the genetic code in the transcription and translation processes of proteinogenesis. Our Supersymmetry Genetic Code table, developed in 2022, is common and unique for all RNA and DNA living species. [...] Read more.
Until now, research has not taken into consideration the physicochemical purine–pyrimidine symmetries of the genetic code in the transcription and translation processes of proteinogenesis. Our Supersymmetry Genetic Code table, developed in 2022, is common and unique for all RNA and DNA living species. Its basic structure is a purine–pyrimidine symmetry net with double mirror symmetry. Accordingly, the symmetry of the genetic code directly shows its organisation based on the principle of nucleotide Watson–Crick and codon–anticodon pairing. The maximal purine–pyrimidine symmetries of codons show that each codon has a strictly defined and unchangeable position within the genetic code. We discovered that the physicochemical symmetries of the genetic code play a fundamental role in recognising and differentiating codons from mRNA and the anticodon tRNA and aminoacyl-tRNA synthetases in the transcription and translation processes. These symmetries also support the wobble hypothesis with non-Watson–Crick pairing interactions between the translation process from mRNA to tRNA. The Supersymmetry Genetic Code table shows a specific arrangement of the second base of codons, according to which it is possible that an anticodon from tRNA recognises whether a codon from mRNA belongs to an amino acid with two or four codons, which is very important in the purposeful use of the wobble pairing process. Therefore, we show that canonical and wobble pairings essentially do not lead to misreading and errors during translation, and we point out the role of physicochemical purine–pyrimidine symmetries in decreasing disorder according to error minimisation and preserving the integrity of biological processes during proteinogenesis. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
Show Figures

Figure 1

Figure 1
<p>A direct transformation of the SSyGC table into the DNA molecule with the codons from direct boxes for one DNA strand and the codons from complement boxes for the opposite DNA strand. A+T-rich codons (red) from the first column of code and C+G-rich codons (black) from the second column are in a purine–purine and pyrimidine–pyrimidine relationship between bases (A↔G, U↔C). There is also a purine–pyrimidine double mirror symmetry net between both the horizontal and vertical halves of the DNA molecule. In each column, there is a position of codons with an identical configuration, e.g., AAA, UUU, GGG, CCC or GUG, CAC, ACA, UGU.</p>
Full article ">Figure 2
<p>The first two bases (red) determine the position of each codon from split or non-split boxes of amino acids with two or four codons in the genetic code. The characteristics of the first two bases from codons in each box are as follows: (a) strong (strg) CC, GG, CG, GC → non-split boxes because of two strong bases; (b) weak (wk) AA, UU, AU, UA → split boxes because of both two bases; (c) a mix of weak and strong bases AC, UC, GU, CU → non-split boxes because the second base is pyrimidine; (d) a mix of weak and strong bases AG, UG, CA, GA → split boxes because the second base is purine. The sextets serine, arginine and leucine include one non-split box (4/6) and a half of the neighbouring box with two codons (2/4). The purine–pyrimidine characteristics of the first two bases are very important for the differentiation of codons and translation from mRNA to anticodon tRNA. Namely, the first and second bases in mRNA always have canonical pairing in the process of proteinogenesis. Only the third base can have a wobble pairing. One amino acid with two codons from the same box of genetic code has a third base of purines A and G, and the other amino acid pyrimidines U and C. The third base purines A and G have start/stop signals and tryptophan with only one trinucleotide.</p>
Full article ">Figure 3
<p>Specific symmetries of each base from codons of the genetic code. (<b>a</b>) The centre point of mirror symmetry for the first base of codons in the SSyGC table. Equal first bases in the opposite pair of boxes on each symmetry line passing through the centre point. The first bases point to the composing principle of codon boxes in the whole SSyGC table (in each box, all four codons have identical first and second bases): first bases from a pair of boxes in the vertical direction have Watson–Crick pairing (W-Cp); a pair of boxes in the horizontal direction has purine–purine (pu-pu) and pyrimidine–pyrimidine (py-py) pairing. (<b>b</b>) The second base of codons in the SSyGC table. Each pair of bases in the vertical direction is in the form of Watson–Crick base pairing (A↔U, C↔G), and in the horizontal direction, shows purine–purine (G↔A) and pyrimidine–pyrimidine (C-U) pairing. Both halves of the code are identical according to the horizontal symmetry axis. It is very important to observe that the second bases in the whole left column are weak A and U, and in the right column are strong C and G. Due to this separation, the important rule of the codon second base in the differentiation of the amino acids with two or four codons in the flow from mRNA to tRNA is emphasised, which is important for the translation process, especially wobbling pairing in proteinogenesis (see the text). (<b>c</b>) The centre points of cascade mirror symmetry for the third base of codons in the SSyGC table. All connecting lines between the same bases in the left and right columns pass through the centre point of the 1st, 2nd and 3rd examples of mirror symmetry. Each cascade mirror symmetry comprises all third bases of the whole genetic code. Additionally, each pair of bases in the vertical and horizontal directions is in the form of purine–purine (G↔A) and pyrimidine–pyrimidine (C↔U) pairing. The third bases of the vertical pairs of boxes have Watson–Crick pairing (G-A-C-U → C-U-G-A and A-G-U-C → U-C-A-G) and the newly discovered purine–pyrimidine symmetries of the SSyGC table. Based on these characteristics, it was possible to mutually distinguish all amino acids and start/stop signals as well as all three sextets (See also <a href="#ijms-25-09543-f002" class="html-fig">Figure 2</a> and <a href="#ijms-25-09543-f004" class="html-fig">Figure 4</a>).The Standard Genetic Code table ignores the third base of codons because all 16 boxes had an identical U-C-A-G alignment of the third base, and so it cannot show Watson–Crick (codon–anticodon) symmetries between bases and codons (see <a href="#sec4-ijms-25-09543" class="html-sec">Section 4</a>).</p>
Full article ">Figure 3 Cont.
<p>Specific symmetries of each base from codons of the genetic code. (<b>a</b>) The centre point of mirror symmetry for the first base of codons in the SSyGC table. Equal first bases in the opposite pair of boxes on each symmetry line passing through the centre point. The first bases point to the composing principle of codon boxes in the whole SSyGC table (in each box, all four codons have identical first and second bases): first bases from a pair of boxes in the vertical direction have Watson–Crick pairing (W-Cp); a pair of boxes in the horizontal direction has purine–purine (pu-pu) and pyrimidine–pyrimidine (py-py) pairing. (<b>b</b>) The second base of codons in the SSyGC table. Each pair of bases in the vertical direction is in the form of Watson–Crick base pairing (A↔U, C↔G), and in the horizontal direction, shows purine–purine (G↔A) and pyrimidine–pyrimidine (C-U) pairing. Both halves of the code are identical according to the horizontal symmetry axis. It is very important to observe that the second bases in the whole left column are weak A and U, and in the right column are strong C and G. Due to this separation, the important rule of the codon second base in the differentiation of the amino acids with two or four codons in the flow from mRNA to tRNA is emphasised, which is important for the translation process, especially wobbling pairing in proteinogenesis (see the text). (<b>c</b>) The centre points of cascade mirror symmetry for the third base of codons in the SSyGC table. All connecting lines between the same bases in the left and right columns pass through the centre point of the 1st, 2nd and 3rd examples of mirror symmetry. Each cascade mirror symmetry comprises all third bases of the whole genetic code. Additionally, each pair of bases in the vertical and horizontal directions is in the form of purine–purine (G↔A) and pyrimidine–pyrimidine (C↔U) pairing. The third bases of the vertical pairs of boxes have Watson–Crick pairing (G-A-C-U → C-U-G-A and A-G-U-C → U-C-A-G) and the newly discovered purine–pyrimidine symmetries of the SSyGC table. Based on these characteristics, it was possible to mutually distinguish all amino acids and start/stop signals as well as all three sextets (See also <a href="#ijms-25-09543-f002" class="html-fig">Figure 2</a> and <a href="#ijms-25-09543-f004" class="html-fig">Figure 4</a>).The Standard Genetic Code table ignores the third base of codons because all 16 boxes had an identical U-C-A-G alignment of the third base, and so it cannot show Watson–Crick (codon–anticodon) symmetries between bases and codons (see <a href="#sec4-ijms-25-09543" class="html-sec">Section 4</a>).</p>
Full article ">Figure 4
<p>According to symmetries, all three sextets in the SSyGC table have an alignment of codons in continuity: one after another, such as arginine (Arg)–serine (Ser), and one after another, such as serine–leucine (Leu). Only serine has a Watson–Crick relationship of codons between two boxes in the whole genetic code: AGU and AGC are direct—UCA and UCG are their complement (red). Through Watson–Crick pairing, we deciphered the symmetries of the whole genetic code.</p>
Full article ">Figure 5
<p>Algorithm of proteinogenesis. All stages from coding DNA over mRNA to tRNA are based on Watson–Crick pairing. The critical point is the process of translation because the number of mRNA codons is larger than the number of tRNA anticodons. As a result, canonical base pairing must be supplemented with wobble non-canonical hydrogen bonding 5′G→3′U or 5′U→3′G for an amino acid with two codons, and inosine A, inosine U or inosine C for amino acids with four codons. In this case, the SSyGC table plays an important role as it reveals the core purine–pyrimidine symmetry net in which each codon has a strictly defined position with respect to other codons. At the same time, each codon with its purine–pyrimidine structure of first and second bases reveals whether it is from an amino acid with two or four codons. The sextets leucine (Leu), serine (Ser) and arginine (Arg) have a combination of both types of wobble pairing.</p>
Full article ">Figure 6
<p>The mitochondrial trematode (liver-fluke) code incorporated in the Supersymmetry Genetic Code table. Methionine (Met) expands to the neighbouring isoleucine (Ile) codon AUA; tryptophan (Trp) expands to the neighbouring stop UGA codon; arginine (Arg) neighbouring AGA and AGG codons become the 7th and 8th codons for serine (Ser); asparagine (Asn) expands to the neighbouring AAA codon from lysine (Lys). In alternative genetic codes, individual amino acids usually capture a codon from a neighbouring amino acid in the SSyGC table. But the purine–pyrimidine symmetry net always remains unchangeable. All (more than thirty) nuclear or mitochondrial genetic codes different from the Standard Genetic Code have also been incorporated into the SSyGC table without interrupting the symmetries. Blue: purine–pyrimidine (pu-py) symmetry net. The leading group, due to the position of serine, led to the discovery of symmetries in the whole SSyGC table (<a href="#ijms-25-09543-f004" class="html-fig">Figure 4</a>).</p>
Full article ">Figure 7
<p>The difference between the symmetry structures of the Supersymmetry Genetic Code (SSyGC) table and the Standard Genetic Code table. (<b>a</b>) The SSyGC table incorporates 2 × 8 boxes with four codons in each box and starts with an AUG initiation start signal. Only the SSyGC table has in continuity the codons of three amino acids with six codons each: serine, arginine and leucine. The SSyGC table has the same distribution of the purine/pyrimidine profile in both columns, and simultaneously the same profile distribution pairs of codon rows within each box. With horizontal and vertical central mirror symmetry axes, it creates the purine–pyrimidine symmetry net as “the golden rule” for all RNA and DNA living species. Between both columns in the same row, there are alternate transformations of A+U-rich and C+G-rich codons. There is a symmetrical position between the split and non-split codon boxes. The symmetries of the genetic code mean that each codon has a powerful, specific symmetrical position in the SSyGC table. This can be observed, for example, in the symmetrical position of the symmetrical codons (in italics). 0 pu, purine; 1 py, pyrimidine; dark yellow, two pairs of split boxes with direct–complement symmetry between codons; dark blue, two pairs of non-split boxes with direct–complement symmetry between codons; light yellow, two pairs of split boxes with purine ↔ purine, pyrimidine ↔ pyrimidine transformation between codons; light blue, two pairs of non-split boxes with purine ↔ purine, pyrimidine ↔ pyrimidine transformation between codons. (<b>b</b>) The Standard Genetic Code incorporates 4x4 boxes, also with four codons in each box. Codons are positioned alphabetically in a horizontal and vertical array of U-C-A-G bases. The role of the third base of codons was ignored in the search for the Standard Genetic Code symmetries because the U-C-A-G arrays were the same in all boxes. The second base of codons divides the standard code into two halves, with pyrimidine (U, C) symmetries and purine (G, A) symmetries. However, these base halves do not communicate with each other on the principle of physicochemical symmetries as in the SSyGC table. The colour is identical in boxes with the same codons as in the SSyGC table in (<b>a</b>), but neither boxes nor codons have an identical position to in the SSyGC table.</p>
Full article ">Figure 7 Cont.
<p>The difference between the symmetry structures of the Supersymmetry Genetic Code (SSyGC) table and the Standard Genetic Code table. (<b>a</b>) The SSyGC table incorporates 2 × 8 boxes with four codons in each box and starts with an AUG initiation start signal. Only the SSyGC table has in continuity the codons of three amino acids with six codons each: serine, arginine and leucine. The SSyGC table has the same distribution of the purine/pyrimidine profile in both columns, and simultaneously the same profile distribution pairs of codon rows within each box. With horizontal and vertical central mirror symmetry axes, it creates the purine–pyrimidine symmetry net as “the golden rule” for all RNA and DNA living species. Between both columns in the same row, there are alternate transformations of A+U-rich and C+G-rich codons. There is a symmetrical position between the split and non-split codon boxes. The symmetries of the genetic code mean that each codon has a powerful, specific symmetrical position in the SSyGC table. This can be observed, for example, in the symmetrical position of the symmetrical codons (in italics). 0 pu, purine; 1 py, pyrimidine; dark yellow, two pairs of split boxes with direct–complement symmetry between codons; dark blue, two pairs of non-split boxes with direct–complement symmetry between codons; light yellow, two pairs of split boxes with purine ↔ purine, pyrimidine ↔ pyrimidine transformation between codons; light blue, two pairs of non-split boxes with purine ↔ purine, pyrimidine ↔ pyrimidine transformation between codons. (<b>b</b>) The Standard Genetic Code incorporates 4x4 boxes, also with four codons in each box. Codons are positioned alphabetically in a horizontal and vertical array of U-C-A-G bases. The role of the third base of codons was ignored in the search for the Standard Genetic Code symmetries because the U-C-A-G arrays were the same in all boxes. The second base of codons divides the standard code into two halves, with pyrimidine (U, C) symmetries and purine (G, A) symmetries. However, these base halves do not communicate with each other on the principle of physicochemical symmetries as in the SSyGC table. The colour is identical in boxes with the same codons as in the SSyGC table in (<b>a</b>), but neither boxes nor codons have an identical position to in the SSyGC table.</p>
Full article ">
26 pages, 5396 KiB  
Article
Double-Step Shape Invariance of Radial Jacobi-Reference Potential and Breakdown of Conventional Rules of Supersymmetric Quantum Mechanics
by Gregory Natanson
Axioms 2024, 13(4), 273; https://doi.org/10.3390/axioms13040273 - 19 Apr 2024
Viewed by 770
Abstract
The paper reveals some remarkable form-invariance features of the ‘Jacobi-reference’ canonical Sturm–Liouville equation (CSLE) in the particular case of the density function with the simple pole at the origin. It is proven that the CSLE under consideration preserves its form under the two [...] Read more.
The paper reveals some remarkable form-invariance features of the ‘Jacobi-reference’ canonical Sturm–Liouville equation (CSLE) in the particular case of the density function with the simple pole at the origin. It is proven that the CSLE under consideration preserves its form under the two second-order Darboux–Crum transformations (DCTs) with the seed functions represented by specially chosen pairs of ‘basic’ quasi-rational solutions (q-RSs), i.e., such that their analytical continuations do not have zeros in the complex plane. It is proven that both transformations generally either increase or decrease by 2 the exponent difference (ExpDiff) for the mentioned pole while keeping two other parameters unchanged. The change is more complicated in the latter case if the ExpDiff for the pole of the original CSLE at the origin is smaller than 2. It was observed that the DCTs in question do not preserve bound energy levels according to the conventional supersymmetry (SUSY) rules. To understand this anomaly, we split the DCT in question into the two sequential Darboux deformations of the Liouville potentials associated with the CSLEs of our interest. We found that the first Darboux transformation turns the initial CSLE into the Heun equation written in the canonical form while the second transformation brings us back to the canonical form of the hypergeometric equation. It is shown that the first of these transformations necessarily places the mentioned ExpDiff into the limit-circle (LC) range and then the second transformation keeps the pole within the LC region, violating the conventional prescriptions of SUSY quantum mechanics. Full article
(This article belongs to the Special Issue Advances in Differential Geometry and Mathematical Physics)
13 pages, 767 KiB  
Article
Revisiting a Realistic Intersecting D6-Brane with Modified Soft SUSY Terms
by Imtiaz Khan, Waqas Ahmed, Tianjun Li and Shabbar Raza
Universe 2024, 10(4), 176; https://doi.org/10.3390/universe10040176 - 11 Apr 2024
Viewed by 846
Abstract
Because there are a few typos in the supersymmetry-breaking sfermion masses and trilinear soft term, regarding the current Large Hadron Collider (LHC) and dark matter searches, we revisit a three-family Pati–Salam model based on intersecting D6-branes in Type IIA string theory on a [...] Read more.
Because there are a few typos in the supersymmetry-breaking sfermion masses and trilinear soft term, regarding the current Large Hadron Collider (LHC) and dark matter searches, we revisit a three-family Pati–Salam model based on intersecting D6-branes in Type IIA string theory on a T6/(Z2×Z2) orientifold with a realistic phenomenology. We study the viable parameter space and discuss the spectrum consistent with the current LHC Supersymmetry searches and the dark matter relic density bounds from the Planck 2018 data. For the gluinos and first two generations of sfermions, we observe that the gluino mass is in the range [2, 14] TeV, the squarks mass range is [2, 13] TeV and the sleptons mass is in the range [1, 5] TeV. We achieve the cold dark matter relic density consistent with 5σ Planck 2018 bounds via A-funnel and coannihilation channels such as stop–neutralino, stau–neutralino, and chargino–neutralino. Except for a few chargino–neutralino coannihilation solutions, these solutions satisfy current nucleon-neutralino spin-independent and spin-dependent scattering cross-sections and may be probed by future dark matter searches. Full article
Show Figures

Figure 1

Figure 1
<p>Grey points satisfy the REWSB and yield LSP neutralinos. The blue points are the subset of gray points that satisfy the LEP bound, Higgs mass bound, B-physics, and LHC sparticle mass bounds. Red points are a subset of blue points that satisfy 5<math display="inline"><semantics> <mi>σ</mi> </semantics></math> Planck relic density bounds.</p>
Full article ">Figure 2
<p>Plots of results in <math display="inline"><semantics> <msub> <mi>M</mi> <mn>1</mn> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mi>M</mi> <mn>2</mn> </msub> </semantics></math>, <math display="inline"><semantics> <msub> <mi>M</mi> <mn>1</mn> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mi>M</mi> <mn>3</mn> </msub> </semantics></math>, and <math display="inline"><semantics> <msub> <mi>M</mi> <mn>3</mn> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mi>M</mi> <mn>2</mn> </msub> </semantics></math> planes. The color coding and the panel description are the same as in <a href="#universe-10-00176-f001" class="html-fig">Figure 1</a>.</p>
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<p>Plots in <math display="inline"><semantics> <mrow> <mo form="prefix">tan</mo> <mi>β</mi> </mrow> </semantics></math>–<math display="inline"><semantics> <msub> <mover accent="true"> <mi>m</mi> <mo stretchy="false">˜</mo> </mover> <msub> <mi>H</mi> <mrow> <mi>u</mi> <mo>,</mo> <mi>d</mi> </mrow> </msub> </msub> </semantics></math>, <math display="inline"><semantics> <mrow> <msub> <mi>A</mi> <mn>0</mn> </msub> <mo>−</mo> <msub> <mi>m</mi> <mrow> <mn>3</mn> <mo>/</mo> <mn>2</mn> </mrow> </msub> </mrow> </semantics></math>, and <math display="inline"><semantics> <msub> <mover accent="true"> <mi>m</mi> <mo stretchy="false">˜</mo> </mover> <mi>L</mi> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mover accent="true"> <mi>m</mi> <mo stretchy="false">˜</mo> </mover> <mi>R</mi> </msub> </semantics></math> planes. The color coding and the panel description are the same as in <a href="#universe-10-00176-f001" class="html-fig">Figure 1</a>.</p>
Full article ">Figure 4
<p>Plots of results in <math display="inline"><semantics> <mrow> <msub> <mover accent="true"> <mi>t</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> </msub> <mo>−</mo> <msub> <mi>m</mi> <mover accent="true"> <mi>g</mi> <mo>^</mo> </mover> </msub> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <msub> <mi>m</mi> <mi>h</mi> </msub> <mo>−</mo> <mi>μ</mi> </mrow> </semantics></math> planes. The color coding and the panel description are the same as in <a href="#universe-10-00176-f001" class="html-fig">Figure 1</a>.</p>
Full article ">Figure 5
<p>Plots in <math display="inline"><semantics> <msub> <mi>m</mi> <msubsup> <mover accent="true"> <mi>χ</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> <mn>0</mn> </msubsup> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mi>m</mi> <mi>A</mi> </msub> </semantics></math>, <math display="inline"><semantics> <msub> <mi>m</mi> <msubsup> <mover accent="true"> <mi>χ</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> <mn>0</mn> </msubsup> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mi>m</mi> <msubsup> <mover accent="true"> <mi>χ</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> <mo>±</mo> </msubsup> </msub> </semantics></math>, <math display="inline"><semantics> <msub> <mi>m</mi> <msubsup> <mover accent="true"> <mi>χ</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> <mn>0</mn> </msubsup> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mi>m</mi> <msub> <mover accent="true"> <mi>τ</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> </msub> </msub> </semantics></math> and <math display="inline"><semantics> <msub> <mi>m</mi> <msubsup> <mover accent="true"> <mi>χ</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> <mn>0</mn> </msubsup> </msub> </semantics></math>–<math display="inline"><semantics> <msub> <mi>m</mi> <msub> <mover accent="true"> <mi>t</mi> <mo stretchy="false">˜</mo> </mover> <mn>1</mn> </msub> </msub> </semantics></math> planes. Color coding and panel description are the same as in <a href="#universe-10-00176-f001" class="html-fig">Figure 1</a>.</p>
Full article ">Figure 6
<p>The spin-independent (<b>left</b>) and spin-dependent (<b>right</b>) neutralino–proton scattering cross-section vs. the neutralino mass. In the left panel, the solid black and orange lines depict the current LUX [<a href="#B66-universe-10-00176" class="html-bibr">66</a>] and XENON1T [<a href="#B67-universe-10-00176" class="html-bibr">67</a>,<a href="#B68-universe-10-00176" class="html-bibr">68</a>] bounds, and the solid green and red lines show the projection of future limits [<a href="#B69-universe-10-00176" class="html-bibr">69</a>] of XENON1T with 2 <math display="inline"><semantics> <mrow> <mi>t</mi> <mo>·</mo> <mi>y</mi> </mrow> </semantics></math> exposure and XENONnT with 20 <math display="inline"><semantics> <mrow> <mi>t</mi> <mo>·</mo> <mi>y</mi> </mrow> </semantics></math> exposure, respectively. In the right panel, the black solid line is the current LUX bound [<a href="#B70-universe-10-00176" class="html-bibr">70</a>], the blue solid line represents the IceCube DeepCore [<a href="#B72-universe-10-00176" class="html-bibr">72</a>], and the orange line shows the future LZ bound [<a href="#B71-universe-10-00176" class="html-bibr">71</a>]. The color code in the description is the same as in the <a href="#universe-10-00176-f001" class="html-fig">Figure 1</a>.</p>
Full article ">
12 pages, 794 KiB  
Article
Weak Scale Supersymmetry Emergent from the String Landscape
by Howard Baer, Vernon Barger, Dakotah Martinez and Shadman Salam
Entropy 2024, 26(3), 275; https://doi.org/10.3390/e26030275 - 21 Mar 2024
Cited by 2 | Viewed by 954
Abstract
Superstring flux compactifications can stabilize all moduli while leading to an enormous number of vacua solutions, each leading to different 4d laws of physics. While the string landscape provides at present the only plausible explanation for the size of the cosmological [...] Read more.
Superstring flux compactifications can stabilize all moduli while leading to an enormous number of vacua solutions, each leading to different 4d laws of physics. While the string landscape provides at present the only plausible explanation for the size of the cosmological constant, it may also predict the form of weak scale supersymmetry which is expected to emerge. Rather general arguments suggest a power-law draw to large soft terms, but these are subject to an anthropic selection of a not-too-large value for the weak scale. The combined selection allows one to compute relative probabilities for the emergence of supersymmetric models from the landscape. Models with weak scale naturalness appear most likely to emerge since they have the largest parameter space on the landscape. For finetuned models such as high-scale SUSY or split SUSY, the required weak scale finetuning shrinks their parameter space to tiny volumes, making them much less likely to appear compared to natural models. Probability distributions for sparticle and Higgs masses from natural models show a preference for Higgs mass mh125 GeV, with sparticles typically beyond the present LHC limits, in accord with data. From these considerations, we briefly describe how natural SUSY is expected to be revealed at future LHC upgrades. This article is a contribution to the Special Edition of the journal Entropy, honoring Paul Frampton on his 80th birthday. Full article
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Figure 1

Figure 1
<p>The ABDS-allowed window within the range of <math display="inline"><semantics> <msubsup> <mi>m</mi> <mi>Z</mi> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msubsup> </semantics></math> values.</p>
Full article ">Figure 2
<p>The <math display="inline"><semantics> <msup> <mi>μ</mi> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msup> </semantics></math> vs. <math display="inline"><semantics> <msqrt> <mrow> <mo>−</mo> <msubsup> <mi>m</mi> <mrow> <msub> <mi>H</mi> <mi>u</mi> </msub> </mrow> <mn>2</mn> </msubsup> <mrow> <mo>(</mo> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> <mo>)</mo> </mrow> </mrow> </msqrt> </semantics></math> parameter space in a toy model ignoring radiative corrections to the Higgs potential. The region between the red and green curves leads to <math display="inline"><semantics> <mrow> <msubsup> <mi>m</mi> <mrow> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> </mrow> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msubsup> <mo>&lt;</mo> <mn>4</mn> <msubsup> <mi>m</mi> <mrow> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> </mrow> <mrow> <mi>O</mi> <mi>U</mi> </mrow> </msubsup> </mrow> </semantics></math> so that the atomic principle is satisfied.</p>
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<p>The value of <math display="inline"><semantics> <mrow> <msub> <mi>m</mi> <msub> <mi>H</mi> <mi>u</mi> </msub> </msub> <mrow> <mo>(</mo> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> <mo>)</mo> </mrow> </mrow> </semantics></math> vs. <math display="inline"><semantics> <msup> <mi>μ</mi> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msup> </semantics></math> The green points denote vacua with appropriate EWSB and with <math display="inline"><semantics> <mrow> <msubsup> <mi>m</mi> <mrow> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> </mrow> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msubsup> <mo>&lt;</mo> <mn>4</mn> <msubsup> <mi>m</mi> <mrow> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> </mrow> <mrow> <mi>O</mi> <mi>U</mi> </mrow> </msubsup> </mrow> </semantics></math> so that the atomic principle is satisfied. Blue points have <math display="inline"><semantics> <mrow> <msubsup> <mi>m</mi> <mrow> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> </mrow> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msubsup> <mo>&gt;</mo> <mn>4</mn> <msubsup> <mi>m</mi> <mrow> <mi>w</mi> <mi>e</mi> <mi>a</mi> <mi>k</mi> </mrow> <mrow> <mi>O</mi> <mi>U</mi> </mrow> </msubsup> </mrow> </semantics></math>.</p>
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<p>Values of <math display="inline"><semantics> <msubsup> <mi>m</mi> <mi>Z</mi> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msubsup> </semantics></math> vs. <math display="inline"><semantics> <msub> <mi>μ</mi> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msub> </semantics></math> or <math display="inline"><semantics> <msub> <mi>μ</mi> <mrow> <mi>S</mi> <mi>M</mi> </mrow> </msub> </semantics></math> for various natural (RNS) and unnatural SUSY models and the SM. The ABDS window extends here from <math display="inline"><semantics> <mrow> <msubsup> <mi>m</mi> <mi>Z</mi> <mrow> <mi>P</mi> <mi>U</mi> </mrow> </msubsup> <mo>∼</mo> <mn>50</mn> </mrow> </semantics></math> to 500 GeV.</p>
Full article ">Figure 5
<p>Probability distributions for the light Higgs scalar mass <math display="inline"><semantics> <msub> <mi>m</mi> <mi>h</mi> </msub> </semantics></math> from the <math display="inline"><semantics> <mrow> <msub> <mi>f</mi> <mrow> <mi>S</mi> <mi>U</mi> <mi>S</mi> <mi>Y</mi> </mrow> </msub> <mo>=</mo> <msubsup> <mi>m</mi> <mrow> <mi>s</mi> <mi>o</mi> <mi>f</mi> <mi>t</mi> </mrow> <mrow> <mo>±</mo> <mn>1</mn> </mrow> </msubsup> </mrow> </semantics></math> distributions of soft terms in the string landscape with <math display="inline"><semantics> <mrow> <mi>μ</mi> <mo>=</mo> <mn>150</mn> </mrow> </semantics></math> GeV.</p>
Full article ">Figure 6
<p>Probability distribution for <math display="inline"><semantics> <msub> <mi>m</mi> <mover accent="true"> <mi>g</mi> <mo>˜</mo> </mover> </msub> </semantics></math> from the <math display="inline"><semantics> <mrow> <msub> <mi>f</mi> <mrow> <mi>S</mi> <mi>U</mi> <mi>S</mi> <mi>Y</mi> </mrow> </msub> <mo>=</mo> <msubsup> <mi>m</mi> <mrow> <mi>s</mi> <mi>o</mi> <mi>f</mi> <mi>t</mi> </mrow> <mrow> <mo>±</mo> <mn>1</mn> </mrow> </msubsup> </mrow> </semantics></math> distributions of soft terms in the string landscape with <math display="inline"><semantics> <mrow> <mi>μ</mi> <mo>=</mo> <mn>150</mn> </mrow> </semantics></math> GeV.</p>
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22 pages, 574 KiB  
Article
Fibonacci-like Sequences Reveal the Genetic Code Symmetries, Also When the Amino Acids Are in a Physiological Environment
by Tidjani Négadi
Symmetry 2024, 16(3), 293; https://doi.org/10.3390/sym16030293 - 2 Mar 2024
Viewed by 2162
Abstract
In this study, we once again use a set of Fibonacci-like sequences to examine the symmetries within the genetic code. This time, our focus is on the physiological state of the amino acids, considering them as charged, in contrast to our previous work [...] Read more.
In this study, we once again use a set of Fibonacci-like sequences to examine the symmetries within the genetic code. This time, our focus is on the physiological state of the amino acids, considering them as charged, in contrast to our previous work where they were seen as neutral. In a pH environment around 7.4, there are four charged amino acids. We utilize the properties of our sequences to accurately describe the symmetries in the genetic code table. These include Rumer’s symmetry, the third-base symmetry and the “ideal” symmetry, along with the “supersymmetry” classification schemes. We also explore the special chemical structure of the amino acid proline, presenting two perspectives—shCherbak’s view and the Downes–Richardson view—which are included in the description of the above-mentioned symmetries. Our investigation also employs elementary modular arithmetic to precisely describe the chemical structure of proline, connecting the two views seamlessly. Finally, our Fibonacci-like sequences prove instrumental in quickly establishing the multiplet structure of non-standard versions of the genetic code. We illustrate this with an example, showcasing the efficiency of our method in unraveling the complex relationships within the genetic code. Full article
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<p>Proline (the molecule). The side chain is boxed in red color and the arrow is the possible transfer of one hydrogen atom (or one nucleon) from the side chain to the backbone (see text).</p>
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9 pages, 273 KiB  
Perspective
Particle Physics and Cosmology Intertwined
by Pran Nath
Entropy 2024, 26(2), 110; https://doi.org/10.3390/e26020110 - 25 Jan 2024
Viewed by 894
Abstract
While the standard model accurately describes data at the electroweak scale without the inclusion of gravity, beyond the standard model, physics is increasingly intertwined with gravitational phenomena and cosmology. Thus, the gravity-mediated breaking of supersymmetry in supergravity models leads to sparticle masses, which [...] Read more.
While the standard model accurately describes data at the electroweak scale without the inclusion of gravity, beyond the standard model, physics is increasingly intertwined with gravitational phenomena and cosmology. Thus, the gravity-mediated breaking of supersymmetry in supergravity models leads to sparticle masses, which are gravitational in origin, observable at TeV scales and testable at the LHC, and supergravity also provides a candidate for dark matter, a possible framework for inflationary models and for models of dark energy. Further, extended supergravity models and string and D-brane models contain hidden sectors, some of which may be feebly coupled to the visible sector, resulting in heat exchange between the visible and hidden sectors. Because of the couplings between the sectors, both particle physics and cosmology are affected. The above implies that particle physics and cosmology are intrinsically intertwined in the resolution of essentially all of the cosmological phenomena, such as dark matter and dark energy, and in the resolution of cosmological puzzles, such as the Hubble tension and the EDGES anomaly. Here, we give a brief overview of the intertwining and its implications for the discovery of sparticles, as well as the resolution of cosmological anomalies and the identification of dark matter and dark energy as major challenges for the coming decades. Full article
16 pages, 381 KiB  
Article
Quantum-Spacetime Symmetries: A Principle of Minimum Group Representation
by Diego J. Cirilo-Lombardo and Norma G. Sanchez
Universe 2024, 10(1), 22; https://doi.org/10.3390/universe10010022 - 4 Jan 2024
Cited by 3 | Viewed by 1355
Abstract
We show that, as in the case of the principle of minimum action in classical and quantum mechanics, there exists an even more general principle in the very fundamental structure of quantum spacetime: this is the principle of minimal group representation, [...] Read more.
We show that, as in the case of the principle of minimum action in classical and quantum mechanics, there exists an even more general principle in the very fundamental structure of quantum spacetime: this is the principle of minimal group representation, which allows us to consistently and simultaneously obtain a natural description of spacetime’s dynamics and the physical states admissible in it. The theoretical construction is based on the physical states that are average values of the generators of the metaplectic group Mp(n), the double covering of SL(2C) in a vector representation, with respect to the coherent states carrying the spin weight. Our main results here are: (i) There exists a connection between the dynamics given by the metaplectic-group symmetry generators and the physical states (the mappings of the generators through bilinear combinations of the basic states). (ii) The ground states are coherent states of the Perelomov–Klauder type defined by the action of the metaplectic group that divides the Hilbert space into even and odd states that are mutually orthogonal. They carry spin weight of 1/4 and 3/4, respectively, from which two other basic states can be formed. (iii) The physical states, mapped bilinearly with the basic 1/4- and 3/4-spin-weight states, plus their symmetric and antisymmetric combinations, have spin contents s=0,1/2,1,3/2 and 2. (iv) The generators realized with the bosonic variables of the harmonic oscillator introduce a natural supersymmetry and a superspace whose line element is the geometrical Lagrangian of our model. (v) From the line element as operator level, a coherent physical state of spin 2 can be obtained and naturally related to the metric tensor. (vi) The metric tensor is naturally discretized by taking the discrete series given by the basic states (coherent states) in the n number representation, reaching the classical (continuous) spacetime for n. (vii) There emerges a relation between the eigenvalue α of our coherent-state metric solution and the black-hole area (entropy) as Abh/4lp2=α, relating the phase space of the metric found, gab, and the black hole area, Abh, through the Planck length lp2 and the eigenvalue α of the coherent states. As a consequence of the lowest level of the quantum-discrete-spacetime spectrum—e.g., the ground state associated to n=0 and its characteristic length—there exists a minimum entropy related to the black-hole history. Full article
(This article belongs to the Special Issue Quantum Physics including Gravity: Highlights and Novelties)
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<p>Quantum gravity regime and that of a dynamical quantum microscopic picture (the complete process of black hole emission in all its stages being a clear example).</p>
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46 pages, 3799 KiB  
Review
Torsion at Different Scales: From Materials to the Universe
by Nick E. Mavromatos, Pablo Pais and Alfredo Iorio
Universe 2023, 9(12), 516; https://doi.org/10.3390/universe9120516 - 14 Dec 2023
Cited by 6 | Viewed by 1522
Abstract
The concept of torsion in geometry, although known for a long time, has not gained considerable attention from the physics community until relatively recently, due to its diverse and potentially important applications to a plethora of contexts of physical interest. These range from [...] Read more.
The concept of torsion in geometry, although known for a long time, has not gained considerable attention from the physics community until relatively recently, due to its diverse and potentially important applications to a plethora of contexts of physical interest. These range from novel materials, such as graphene and graphene-like materials, to advanced theoretical ideas, such as string theory and supersymmetry/supergravity, and applications thereof in terms of understanding the dark sector of our Universe. This work reviews such applications of torsion at different physical scales. Full article
(This article belongs to the Special Issue Quantum Gravity Phenomenology)
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Figure 1
<p>Tangent hyperplane <math display="inline"><semantics> <mrow> <msub> <mi>T</mi> <mi>p</mi> </msub> <mi mathvariant="script">M</mi> </mrow> </semantics></math> at a point <span class="html-italic">p</span> of a curved <math display="inline"><semantics> <mrow> <mo>(</mo> <mi>d</mi> <mo>+</mo> <mn>1</mn> <mo>)</mo> </mrow> </semantics></math>-dimensional manifold <math display="inline"><semantics> <mi mathvariant="script">M</mi> </semantics></math>, used in the first order formalism of GR to define the vielbein <math display="inline"><semantics> <mrow> <mi>e</mi> <msup> <mrow/> <mi>a</mi> </msup> <msub> <mrow/> <mi>μ</mi> </msub> </mrow> </semantics></math> map <math display="inline"><semantics> <mrow> <mi mathvariant="script">M</mi> <mspace width="4pt"/> <mo>→</mo> <mspace width="4pt"/> <msub> <mi>T</mi> <mi>p</mi> </msub> <mi mathvariant="script">M</mi> </mrow> </semantics></math>.</p>
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<p>A geometric interpretation of torsion in Riemann–Cartan spaces. Consider two vector fields, <span class="html-italic">X</span> and <span class="html-italic">Y</span>, at a point <span class="html-italic">P</span>. First, parallel-transport <span class="html-italic">X</span> along <span class="html-italic">Y</span> to the infinitesimally close point <span class="html-italic">R</span>. Then, again from <span class="html-italic">P</span>, parallel-transport <span class="html-italic">Y</span> along <span class="html-italic">X</span> to reach a point <span class="html-italic">Q</span>. The failure of the closure of the parallelogram is the geometrical signal of torsion, and its value is the difference <math display="inline"><semantics> <mrow> <mi>T</mi> <mo>(</mo> <mi>X</mi> <mo>,</mo> <mi>Y</mi> <mo>)</mo> </mrow> </semantics></math> (here in red) between the two resulting vectors. An <span class="html-italic">n</span>-dimensional manifold <span class="html-italic">M</span> with a linear connection preserving local distances, i.e., fulfilling condition (<a href="#FD19-universe-09-00516" class="html-disp-formula">19</a>), is called a <span class="html-italic">Riemann–Cartan space</span>, denoted by <math display="inline"><semantics> <msub> <mi>U</mi> <mi>n</mi> </msub> </semantics></math>. In Riemannian spaces, <math display="inline"><semantics> <msub> <mi>V</mi> <mi>n</mi> </msub> </semantics></math>, this tensor is assumed to be zero. The picture was inspired by [<a href="#B8-universe-09-00516" class="html-bibr">8</a>] but with the notation of [<a href="#B5-universe-09-00516" class="html-bibr">5</a>], and was taken from [<a href="#B9-universe-09-00516" class="html-bibr">9</a>].</p>
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<p>The honeycomb lattice of graphene, and its two triangular sublattices <math display="inline"><semantics> <msub> <mi>L</mi> <mi>A</mi> </msub> </semantics></math> and <math display="inline"><semantics> <msub> <mi>L</mi> <mi>B</mi> </msub> </semantics></math>. The choice of the basis vectors, <math display="inline"><semantics> <mrow> <mo>(</mo> <msub> <mover accent="true"> <mi>a</mi> <mo>→</mo> </mover> <mn>1</mn> </msub> <mo>,</mo> <msub> <mover accent="true"> <mi>a</mi> <mo>→</mo> </mover> <mn>2</mn> </msub> <mo>)</mo> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <mo>(</mo> <msub> <mover accent="true"> <mi>s</mi> <mo>→</mo> </mover> <mn>1</mn> </msub> <mo>,</mo> <msub> <mover accent="true"> <mi>s</mi> <mo>→</mo> </mover> <mn>2</mn> </msub> <mo>,</mo> <msub> <mover accent="true"> <mi>s</mi> <mo>→</mo> </mover> <mn>3</mn> </msub> <mo>)</mo> </mrow> </semantics></math>, is, of course, not unique. Figure taken from [<a href="#B52-universe-09-00516" class="html-bibr">52</a>].</p>
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<p>(<b>a</b>) The dispersion relation <math display="inline"><semantics> <mrow> <mi>E</mi> <mo>(</mo> <mover accent="true"> <mi>k</mi> <mo>→</mo> </mover> <mo>)</mo> </mrow> </semantics></math> for graphene, setting <math display="inline"><semantics> <mrow> <mi>t</mi> <mo>ℓ</mo> <mo>=</mo> <mn>1</mn> </mrow> </semantics></math>. We only take into account the near neighbours contribution in (<a href="#FD69-universe-09-00516" class="html-disp-formula">71</a>). (<b>b</b>) A zoom near the Dirac point <math display="inline"><semantics> <msub> <mi>K</mi> <mrow> <mi>D</mi> <mo>+</mo> </mrow> </msub> </semantics></math> showing the linear approximation works well in the low energies regime.</p>
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<p>Edge dislocation from two disclinations. Two disclinations, a heptagon, and a pentagon add-up to zero total intrinsic curvature, and make a dislocation with Burgers vector <math display="inline"><semantics> <mover accent="true"> <mi>b</mi> <mo>→</mo> </mover> </semantics></math>, as indicated. In the continuous long wave-length limit, this configuration carries nonzero torsion. Figure taken from [<a href="#B66-universe-09-00516" class="html-bibr">66</a>].</p>
Full article ">Figure 6
<p>Idealised <span class="html-italic">time-loop</span>. At <math display="inline"><semantics> <mrow> <mi>t</mi> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math>, the hole (yellow) and the particle (black) start their movements from <math display="inline"><semantics> <mrow> <mi>y</mi> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math>, in opposite directions. At <math display="inline"><semantics> <mrow> <mi>t</mi> <mo>=</mo> <msup> <mi>t</mi> <mo>*</mo> </msup> <mo>&gt;</mo> <mn>0</mn> </mrow> </semantics></math>, the hole is at position <math display="inline"><semantics> <mrow> <mo>−</mo> <msup> <mi>y</mi> <mo>*</mo> </msup> </mrow> </semantics></math>, while the particle is at position <math display="inline"><semantics> <mrow> <mo>+</mo> <msup> <mi>y</mi> <mo>*</mo> </msup> </mrow> </semantics></math>, (the blue portion of the circuit). Then they come back to their original position, <math display="inline"><semantics> <mrow> <mi>y</mi> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math>, at <math display="inline"><semantics> <mrow> <mi>t</mi> <mo>=</mo> <mn>2</mn> <msup> <mi>t</mi> <mo>*</mo> </msup> </mrow> </semantics></math> (red portion of the circuit). On the far right, is depicted an equivalent <span class="html-italic">time-loop</span>, where the hole moving forward in time is replaced by a particle moving backward. Figure taken from [<a href="#B69-universe-09-00516" class="html-bibr">69</a>].</p>
Full article ">Figure 7
<p>A grain boundary (<b>left</b>), and a possible modelling of its effects in a continuum (<b>right</b>). This is the prototypical GB, where grain A and grain B are related via a parity (<math display="inline"><semantics> <mrow> <mi>x</mi> <mo>→</mo> <mo>−</mo> <mi>x</mi> </mrow> </semantics></math>) transformation. With this, the right-handed frame in grain A is mapped to the left-handed frame in grain B, so that the net effect of a GB is that two orientations coexist on the membrane, and a discontinuous change happens at the boundary. If one wants to trade this discontinuous change for a continuous one, an equivalent coexistence is at work in the non-orientable Möbius strip. One way to quantify the effects of different <math display="inline"><semantics> <mi>θ</mi> </semantics></math>s is to relate a varying <math display="inline"><semantics> <mi>θ</mi> </semantics></math> to a varying radius <math display="inline"><semantics> <mrow> <mi>R</mi> <mo>(</mo> <mi>θ</mi> <mo>)</mo> </mrow> </semantics></math> of the Möbius strip. Notice that the third spatial axis is an abstract coordinate, <math display="inline"><semantics> <mover accent="true"> <mi>z</mi> <mo>˜</mo> </mover> </semantics></math>, whose relation with the real <span class="html-italic">z</span> of the embedding space is not specified. Figure taken from [<a href="#B66-universe-09-00516" class="html-bibr">66</a>].</p>
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<p>The effective potential of the torsion-induced gravitino condensate <math display="inline"><semantics> <mrow> <msub> <mi>σ</mi> <mi>c</mi> </msub> <mo>=</mo> <mrow> <mo>〈</mo> <msub> <mover> <mi>ψ</mi> <mo>¯</mo> </mover> <mi>μ</mi> </msub> <mspace width="0.166667em"/> <msup> <mi>ψ</mi> <mi>μ</mi> </msup> <mo>〉</mo> </mrow> </mrow> </semantics></math> in the dynamical breaking of <math display="inline"><semantics> <mrow> <mi>N</mi> <mo>=</mo> <mn>1</mn> </mrow> </semantics></math> SUGRA scenario of [<a href="#B99-universe-09-00516" class="html-bibr">99</a>], in which, for simplicity, the one-loop-corrected cosmological constant <math display="inline"><semantics> <mrow> <mo>Λ</mo> <mo>→</mo> <msup> <mn>0</mn> <mo>+</mo> </msup> </mrow> </semantics></math> (for an analysis with <math display="inline"><semantics> <mrow> <mo>Λ</mo> <mo>&gt;</mo> <mn>0</mn> </mrow> </semantics></math> see [<a href="#B100-universe-09-00516" class="html-bibr">100</a>] and references therein). The figures show schematically the effect of tuning the inverse-proper-time (renormalisation-group like) scale <math display="inline"><semantics> <mi>μ</mi> </semantics></math> and the scale of SUSY breaking <span class="html-italic">f</span>, whilst holding, respectively, <span class="html-italic">f</span> and <math display="inline"><semantics> <mi>μ</mi> </semantics></math> fixed. The arrows in the respective axes correspond to the direction of increasing <math display="inline"><semantics> <mi>μ</mi> </semantics></math> and <span class="html-italic">f</span>. The reader should note (see left panel) that the double-wall shape of the potential, characteristic of the super-Higgs effect (dynamical SUGRA breaking), appears for values of <math display="inline"><semantics> <mi>μ</mi> </semantics></math> larger than a critical value, in the direction of increasing <math display="inline"><semantics> <mi>μ</mi> </semantics></math>, that is as we flow from Ultraviolet (UV) to infrared (IR) regions. Moreover, as one observes from the right panel of the figure, tuning <span class="html-italic">f</span> allows us to shift the value of the effective potential <math display="inline"><semantics> <msub> <mi>V</mi> <mi>eff</mi> </msub> </semantics></math> appropriately so as to attain the correct vacuum structure, that is, non-trivial minima <math display="inline"><semantics> <msub> <mi>σ</mi> <mi>c</mi> </msub> </semantics></math> such that <math display="inline"><semantics> <mrow> <msub> <mi>V</mi> <mi>eff</mi> </msub> <mfenced separators="" open="(" close=")"> <msub> <mi>σ</mi> <mi>c</mi> </msub> </mfenced> <mo>=</mo> <mo>Λ</mo> <mo>→</mo> <msup> <mn>0</mn> <mo>+</mo> </msup> </mrow> </semantics></math>. Picture taken from [<a href="#B99-universe-09-00516" class="html-bibr">99</a>].</p>
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<p>Schematic representation of the RVM cosmological evolution of the contorted cosmological model of [<a href="#B133-universe-09-00516" class="html-bibr">133</a>,<a href="#B134-universe-09-00516" class="html-bibr">134</a>,<a href="#B135-universe-09-00516" class="html-bibr">135</a>,<a href="#B136-universe-09-00516" class="html-bibr">136</a>]. The figure depicts the evolution of the Hubble parameter with the scale factor of an expanding stringy-RVM Universe, involving two torsion-induced inflationary eras, interpolated by a stiff KR-axion “matter” epoch: a first hill-top first inflation, which exists immediately after the Big-Bang, and is due to dynamical breaking of SUGRA, as a result of gravitino-torsion-induced condensates of the gravitino field, and second an RVM inflation, due to gravitational anomaly condensates, that are coupled to the torsion-induced KR axion field <math display="inline"><semantics> <mrow> <mi>b</mi> <mo>(</mo> <mi>x</mi> <mo>)</mo> </mrow> </semantics></math>. The latter can also play the role of a dark matter component during post-RVM inflationary eras. Picture taken from [<a href="#B136-universe-09-00516" class="html-bibr">136</a>].</p>
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16 pages, 4084 KiB  
Article
The Supersymmetry Genetic Code Table and Quadruplet Symmetries of DNA Molecules Are Unchangeable and Synchronized with Codon-Free Energy Mapping during Evolution
by Marija Rosandić and Vladimir Paar
Genes 2023, 14(12), 2200; https://doi.org/10.3390/genes14122200 - 12 Dec 2023
Cited by 2 | Viewed by 1150
Abstract
The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: (1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)] and (2) of bases in the [...] Read more.
The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: (1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)] and (2) of bases in the form of codons; (3) direct–complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns; (4) A + T-rich and C + G-rich alternate codons in the same row between both columns of the genetic code; (5) the same position between divided and undivided codon boxes in relation to horizontal mirror symmetry axis. The SSyGC table has a unique physicochemical purine–pyrimidine symmetry net which is as the core symmetry common for all, with more than thirty different nuclear and mitochondrial genetic codes. This net is present in the SSyGC table of all RNA and DNA living species. None of these symmetries are present in the Standard Genetic Code (SGC) table which is constructed on the alphabetic horizontal and vertical U-C-A-G order of bases. Here, we show that the free energy value of each codon incorporated as fundamentally mapping the “energy code” in the SSyGC table is compatible with mirror symmetry. On the other hand, in the SGC table, the same free energy values of codons are dispersed and a mirror symmetry between them is not recognizable. At the same time, the mirror symmetry of the SSyGC table and the DNA quadruplets together with our classification of codons/trinucleotides are perfectly imbedded in the mirror symmetry energy mapping of codons/trinucleotides and point out in favor of maintaining the integrity of the genetic code and DNA genome. We also argue that physicochemical symmetries of the SSyGC table in the manner of the purine–pyrimidine symmetry net, the quadruplet symmetry of DNA molecule, and the free energy of codons have remined unchanged during all of evolution. The unchangeable and universal symmetry properties of the genetic code, DNA molecules, and the energy code are decreasing disorder between codons/trinucleotides and shed a new light on evolution. Diversity in all living species on Earth is broad, but the symmetries of the Supersymmetry Genetic Code as the code of life and the DNA quadruplets related to the “energy code” are unique, unchangeable, and have the power of natural laws. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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Figure 1

Figure 1
<p>(<b>a</b>) The Standard Genetic Code table is structured horizontally and vertically on the alphabetically U-C-A-G-based manner and suffers from an inability to show the complete physicochemical symmetry between codons. There is only partial mirror symmetry between purines (0) and pyrimidines (1) in the first and second columns as well as in the third and fourth columns. A + U-rich (black) and C + G-rich (red) codons are not in an alternate range regularity in each row. There is not direct and complement (codon 5′3′ ↔ anticodon 3′5′) altering ranging of the codon boxes. (<b>b</b>) The Supersymmetry Genetic Code table with double mirror symmetry and horizontal and vertical mirror symmetry axis. There are, in the same row, A + U-rich and C + G-rich alternate codons between two columns. Both columns have the same distribution of purine–pyrimidine profile; simultaneously, the same profile distribution pairs of codon rows within each box. There is a purine–pyrimidine symmetry between the bases and codons, and direct–complement symmetry (codon 5′3′ ↔ anticodon 3′5′ as well as Watson–Crick pairing) of codons between direct and complement codon boxes. In such a way, for the first time, the sextets for Serine, Arginine, and Leucine, each with six codons, are positioned in continuity. It is interesting that the AUG start signal is at the beginning of the Supersymmetry Genetic Code table. It is important that the purine–pyrimidine symmetry net is in a central position in the code as the “golden rule”; this is common for all RNA and DNA species and unchangeable during evolution. Note: 0 pu—purine; 1 py—pyrimidine; black—A + U-rich codons; red—C + G-rich codons. (<b>c</b>) The center point mirror symmetry for the first base in the whole SSyGC table. First base in each box from the left and right column of the SSyGC table. The 1st, 2nd, 3rd, 4th, 5th, 6th, 7th, and 8th base in the left column correspond to the 8th, 7th, 6th, 5th, 4th, 3rd, 2nd, and 1st base, respectively; all connecting lines pass through the center point. Each base represents a whole box because the first and second bases of the four codons in each box of code are identical.</p>
Full article ">Figure 1 Cont.
<p>(<b>a</b>) The Standard Genetic Code table is structured horizontally and vertically on the alphabetically U-C-A-G-based manner and suffers from an inability to show the complete physicochemical symmetry between codons. There is only partial mirror symmetry between purines (0) and pyrimidines (1) in the first and second columns as well as in the third and fourth columns. A + U-rich (black) and C + G-rich (red) codons are not in an alternate range regularity in each row. There is not direct and complement (codon 5′3′ ↔ anticodon 3′5′) altering ranging of the codon boxes. (<b>b</b>) The Supersymmetry Genetic Code table with double mirror symmetry and horizontal and vertical mirror symmetry axis. There are, in the same row, A + U-rich and C + G-rich alternate codons between two columns. Both columns have the same distribution of purine–pyrimidine profile; simultaneously, the same profile distribution pairs of codon rows within each box. There is a purine–pyrimidine symmetry between the bases and codons, and direct–complement symmetry (codon 5′3′ ↔ anticodon 3′5′ as well as Watson–Crick pairing) of codons between direct and complement codon boxes. In such a way, for the first time, the sextets for Serine, Arginine, and Leucine, each with six codons, are positioned in continuity. It is interesting that the AUG start signal is at the beginning of the Supersymmetry Genetic Code table. It is important that the purine–pyrimidine symmetry net is in a central position in the code as the “golden rule”; this is common for all RNA and DNA species and unchangeable during evolution. Note: 0 pu—purine; 1 py—pyrimidine; black—A + U-rich codons; red—C + G-rich codons. (<b>c</b>) The center point mirror symmetry for the first base in the whole SSyGC table. First base in each box from the left and right column of the SSyGC table. The 1st, 2nd, 3rd, 4th, 5th, 6th, 7th, and 8th base in the left column correspond to the 8th, 7th, 6th, 5th, 4th, 3rd, 2nd, and 1st base, respectively; all connecting lines pass through the center point. Each base represents a whole box because the first and second bases of the four codons in each box of code are identical.</p>
Full article ">Figure 1 Cont.
<p>(<b>a</b>) The Standard Genetic Code table is structured horizontally and vertically on the alphabetically U-C-A-G-based manner and suffers from an inability to show the complete physicochemical symmetry between codons. There is only partial mirror symmetry between purines (0) and pyrimidines (1) in the first and second columns as well as in the third and fourth columns. A + U-rich (black) and C + G-rich (red) codons are not in an alternate range regularity in each row. There is not direct and complement (codon 5′3′ ↔ anticodon 3′5′) altering ranging of the codon boxes. (<b>b</b>) The Supersymmetry Genetic Code table with double mirror symmetry and horizontal and vertical mirror symmetry axis. There are, in the same row, A + U-rich and C + G-rich alternate codons between two columns. Both columns have the same distribution of purine–pyrimidine profile; simultaneously, the same profile distribution pairs of codon rows within each box. There is a purine–pyrimidine symmetry between the bases and codons, and direct–complement symmetry (codon 5′3′ ↔ anticodon 3′5′ as well as Watson–Crick pairing) of codons between direct and complement codon boxes. In such a way, for the first time, the sextets for Serine, Arginine, and Leucine, each with six codons, are positioned in continuity. It is interesting that the AUG start signal is at the beginning of the Supersymmetry Genetic Code table. It is important that the purine–pyrimidine symmetry net is in a central position in the code as the “golden rule”; this is common for all RNA and DNA species and unchangeable during evolution. Note: 0 pu—purine; 1 py—pyrimidine; black—A + U-rich codons; red—C + G-rich codons. (<b>c</b>) The center point mirror symmetry for the first base in the whole SSyGC table. First base in each box from the left and right column of the SSyGC table. The 1st, 2nd, 3rd, 4th, 5th, 6th, 7th, and 8th base in the left column correspond to the 8th, 7th, 6th, 5th, 4th, 3rd, 2nd, and 1st base, respectively; all connecting lines pass through the center point. Each base represents a whole box because the first and second bases of the four codons in each box of code are identical.</p>
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<p>Our quadruplet classification of 61 codons and 3 stop signals (with U-uracil) for genetic code, or trinucleotides (with T-thymine instead of uracil) for RNA and DNA genomes with incorporated the free energy of codons (reading unidirectionally from 5′ to 3′). Each quadruplet is unique and consists of codons or trinucleotides denoted as direct D, and reverse complement from direct RC(D), complement from direct C(D), and reverse from direct R(D). The ten A + U-rich (group I) and ten C + G-rich (group II) quadruplets are organized in three subgroups. The Ia subgroup consists of nonsymmetrical codons/trinucleotides containing four different nucleotides; the Ib subgroup consists of nonsymmetrical codons/trinucleotides containing two different nucleotides; the Ic subgroup consists of symmetrical codons/trinucleotides which contain duplicated codons/trinucleotides labeled with an asterisk (D = RC, C = R). The first four A + U-rich quadruplets we generated with start/stop signals: AUG, UGA, UAG, and UAA. The C + G-rich trinucleotides correspond to purine–purine and pyrimidine–pyrimidine transformations of A + U-rich codons/trinucleotides. Three symmetries are present in our codon/trinucleotide classification: (1) purine–pyrimidine symmetries in each quadruplet; (2) purine–pyrimidine symmetries within and between A + U-rich and C + G-rich quadruplets in the same row of the classification; (3) mirror symmetry between direct–reverse and complement–reverse complement in the same quadruplet. For clarity, the white and grey rows are alternating, to emphasize pairs of A + T-rich and C + G-rich codons. Note: 0—purine; 1—pyrimidine. Namely, it is irrelevant which codon/trinucleotide in the quadruplet is direct, because the other three are accordingly adapted.</p>
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<p>An example of symmetries in one A + T-rich quadruplet from the DNA molecule with the incorporated free energy of trinucleotides. The free energy value follows quadruplet symmetries in bidirectional form (top strand 5′3′, bottom strand 3′5′). There are three quadruplet symmetries: purine–pyrimidine symmetry, direct–complement symmetry, both on the principle of Watson–Crick pairing between DNA strands, and important mirror symmetry between both DNA strands in Qbox<sub>D-RC</sub> as well as Qbox<sub>c–R</sub>, and between both boxes. Their mirror symmetry with complementary base pairing leads directly to Chargaff’s second parity rule (see the text). The free energy of trinucleotides follows mirror symmetry. The same symmetries exist in the SSyGC table. D—direct; RC—reverse complement; C—complement; R—reverse; C(D)—complement from direct of four trinucleotides; R(D)—reverse from direct; RC(D)—reverse complement from direct; <span class="html-fig-inline" id="genes-14-02200-i001"><img alt="Genes 14 02200 i001" src="/genes/genes-14-02200/article_deploy/html/images/genes-14-02200-i001.png"/></span> mirror symmetry. The inputted measured free energy values are from [<a href="#B8-genes-14-02200" class="html-bibr">8</a>,<a href="#B9-genes-14-02200" class="html-bibr">9</a>].</p>
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<p>(<b>a</b>) The energy code incorporated in the SSyGC table, which is adjusted for the mitochondrial human genetic code. Placing the axis of horizontal mirror symmetry in the central position of the SSyGC table, we observed an excellent agreement of the sum free energy of codons between both halves of code (see (<b>d</b>)) and complete symmetry for <b>differences</b> between the free energy of codons in each box which has at the third position C and G (strong) or A end U (weak) nucleotides. Therefore, in the SSyGC table, we see symmetries between differences in codon-free energy in the boxes 1 and 5, 2 and 6, 3 and 7, and 4 and 8, with a slight deviation in the second column. Namely, each box contains four codons with the same first and second bases, and the decisive free energy difference depends only on the third base in each codon. Within each box in the SSyGC table, the codons with G and C third strong base have larger values of free energy than codons with A and U weak third base (see text). Pu—purine; py—pyrimidine; red—codons with C and G third base; blue—codons with A end U third base; S sum. The inputted measured free energy values are from [<a href="#B8-genes-14-02200" class="html-bibr">8</a>,<a href="#B9-genes-14-02200" class="html-bibr">9</a>]. (<b>b</b>) Differences in free energy codons between the A + U-rich weak codons and the C + G-rich strong codons from alternately boxes in both columns of the SSyGC table. There appears horizontal mirror symmetry between differences in codon-free energy in the horizontal pairs of boxes 1 and 8, 2 and 7, 3 and 6, and 4 and 5, with only a slight deviation in the second (right) column. (<b>c</b>) Sum of differences between free energies within each codon with A or U weak third base and codon with C or G strong third base in the same box. Only the third base of codons in each box is different and makes the difference in the free energy between their codons (all four codons in each box have first and second base identical). Energy differences are defined as in (<b>a</b>). Sums of energy differences show the symmetry with respect to the horizontal mirror symmetry axis of the SSyGC table (see (<b>a</b>)). (<b>d</b>) Sum of free energy of all codons in kcal/mol with respect to the horizontal mirror symmetry axis of the SSyGC table is almost identical above and below mirror symmetry axis (127.5 + 129.5 = 257). The difference of 2 between summary values is probable a technical mistake. This free energy mirror symmetry of codons is result of identical purine–pyrimidine symmetry net and identical number of A + T-rich and C + G-rich codons above and below horizontal symmetry axis of code.</p>
Full article ">Figure 4 Cont.
<p>(<b>a</b>) The energy code incorporated in the SSyGC table, which is adjusted for the mitochondrial human genetic code. Placing the axis of horizontal mirror symmetry in the central position of the SSyGC table, we observed an excellent agreement of the sum free energy of codons between both halves of code (see (<b>d</b>)) and complete symmetry for <b>differences</b> between the free energy of codons in each box which has at the third position C and G (strong) or A end U (weak) nucleotides. Therefore, in the SSyGC table, we see symmetries between differences in codon-free energy in the boxes 1 and 5, 2 and 6, 3 and 7, and 4 and 8, with a slight deviation in the second column. Namely, each box contains four codons with the same first and second bases, and the decisive free energy difference depends only on the third base in each codon. Within each box in the SSyGC table, the codons with G and C third strong base have larger values of free energy than codons with A and U weak third base (see text). Pu—purine; py—pyrimidine; red—codons with C and G third base; blue—codons with A end U third base; S sum. The inputted measured free energy values are from [<a href="#B8-genes-14-02200" class="html-bibr">8</a>,<a href="#B9-genes-14-02200" class="html-bibr">9</a>]. (<b>b</b>) Differences in free energy codons between the A + U-rich weak codons and the C + G-rich strong codons from alternately boxes in both columns of the SSyGC table. There appears horizontal mirror symmetry between differences in codon-free energy in the horizontal pairs of boxes 1 and 8, 2 and 7, 3 and 6, and 4 and 5, with only a slight deviation in the second (right) column. (<b>c</b>) Sum of differences between free energies within each codon with A or U weak third base and codon with C or G strong third base in the same box. Only the third base of codons in each box is different and makes the difference in the free energy between their codons (all four codons in each box have first and second base identical). Energy differences are defined as in (<b>a</b>). Sums of energy differences show the symmetry with respect to the horizontal mirror symmetry axis of the SSyGC table (see (<b>a</b>)). (<b>d</b>) Sum of free energy of all codons in kcal/mol with respect to the horizontal mirror symmetry axis of the SSyGC table is almost identical above and below mirror symmetry axis (127.5 + 129.5 = 257). The difference of 2 between summary values is probable a technical mistake. This free energy mirror symmetry of codons is result of identical purine–pyrimidine symmetry net and identical number of A + T-rich and C + G-rich codons above and below horizontal symmetry axis of code.</p>
Full article ">Figure 4 Cont.
<p>(<b>a</b>) The energy code incorporated in the SSyGC table, which is adjusted for the mitochondrial human genetic code. Placing the axis of horizontal mirror symmetry in the central position of the SSyGC table, we observed an excellent agreement of the sum free energy of codons between both halves of code (see (<b>d</b>)) and complete symmetry for <b>differences</b> between the free energy of codons in each box which has at the third position C and G (strong) or A end U (weak) nucleotides. Therefore, in the SSyGC table, we see symmetries between differences in codon-free energy in the boxes 1 and 5, 2 and 6, 3 and 7, and 4 and 8, with a slight deviation in the second column. Namely, each box contains four codons with the same first and second bases, and the decisive free energy difference depends only on the third base in each codon. Within each box in the SSyGC table, the codons with G and C third strong base have larger values of free energy than codons with A and U weak third base (see text). Pu—purine; py—pyrimidine; red—codons with C and G third base; blue—codons with A end U third base; S sum. The inputted measured free energy values are from [<a href="#B8-genes-14-02200" class="html-bibr">8</a>,<a href="#B9-genes-14-02200" class="html-bibr">9</a>]. (<b>b</b>) Differences in free energy codons between the A + U-rich weak codons and the C + G-rich strong codons from alternately boxes in both columns of the SSyGC table. There appears horizontal mirror symmetry between differences in codon-free energy in the horizontal pairs of boxes 1 and 8, 2 and 7, 3 and 6, and 4 and 5, with only a slight deviation in the second (right) column. (<b>c</b>) Sum of differences between free energies within each codon with A or U weak third base and codon with C or G strong third base in the same box. Only the third base of codons in each box is different and makes the difference in the free energy between their codons (all four codons in each box have first and second base identical). Energy differences are defined as in (<b>a</b>). Sums of energy differences show the symmetry with respect to the horizontal mirror symmetry axis of the SSyGC table (see (<b>a</b>)). (<b>d</b>) Sum of free energy of all codons in kcal/mol with respect to the horizontal mirror symmetry axis of the SSyGC table is almost identical above and below mirror symmetry axis (127.5 + 129.5 = 257). The difference of 2 between summary values is probable a technical mistake. This free energy mirror symmetry of codons is result of identical purine–pyrimidine symmetry net and identical number of A + T-rich and C + G-rich codons above and below horizontal symmetry axis of code.</p>
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<p>Quadruplet boxes (Q-boxes) of codons (D—direct; RC—reverse complement; C—complement; R—reverse) arranged as in the SSyGC table in the form of DNA quadruplets with mirror symmetry (see also <a href="#genes-14-02200-f002" class="html-fig">Figure 2</a> and <a href="#genes-14-02200-f003" class="html-fig">Figure 3</a>). The corresponding value of free energy is given with each codon. It is necessary to read bases/codons of the Q-box bidirectionally (5′3′ top strand, 3′5′ bottom strand). Full agreement of the identical free energy values for all four members in each Q-box is present. The inputted measured free energy values are from [<a href="#B8-genes-14-02200" class="html-bibr">8</a>,<a href="#B9-genes-14-02200" class="html-bibr">9</a>].</p>
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<p>Degeneracies of free energies vs. codons for human mitochondrial DNA. Codons are ordered in pairs according to the strand symmetry (Chargaff’s second parity rule).</p>
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16 pages, 368 KiB  
Article
Finiteness of N=4 Super-Yang–Mills Effective Action in Terms of Dressed N=1 Superfields
by Igor Kondrashuk and Ivan Schmidt
Particles 2023, 6(4), 993-1008; https://doi.org/10.3390/particles6040063 - 8 Nov 2023
Cited by 7 | Viewed by 2205
Abstract
We argue in favor of the independence on any scale, ultraviolet or infrared, in kernels of the effective action expressed in terms of dressed N=1 superfields for the case of N=4 super-Yang–Mills theory. Under “scale independence” of the effective [...] Read more.
We argue in favor of the independence on any scale, ultraviolet or infrared, in kernels of the effective action expressed in terms of dressed N=1 superfields for the case of N=4 super-Yang–Mills theory. Under “scale independence” of the effective action of dressed mean superfields, we mean its “finiteness in the off-shell limit of removing all the regularizations”. This off-shell limit is scale independent because no scale remains inside these kernels after removing the regularizations. We use two types of regularization: regularization by dimensional reduction and regularization by higher derivatives in its supersymmetric form. Based on the Slavnov–Taylor identity, we show that dressed fields of matter and of vector multiplets can be introduced to express the effective action in terms of them. Kernels of the effective action expressed in terms of such dressed effective fields do not depend on the ultraviolet scale. In the case of dimensional reduction, by using the developed technique, we show how the problem of inconsistency of the dimensional reduction can be solved. Using Piguet and Sibold formalism, we indicate that the dependence on the infrared scale disappears off shell in both the regularizations. Full article
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<p>The only one-loop contribution to the <math display="inline"><semantics> <mrow> <mi>L</mi> <mi>c</mi> <mi>c</mi> </mrow> </semantics></math> vertex.</p>
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<p>One-loop massless scalar triangle in position space. Integration in position space should be carried out over internal points only (See Ref. [<a href="#B76-particles-06-00063" class="html-bibr">76</a>]); however, this diagram does not have internal points at all. The points <math display="inline"><semantics> <mrow> <msub> <mi>x</mi> <mn>1</mn> </msub> <mo>,</mo> </mrow> </semantics></math> <math display="inline"><semantics> <mrow> <msub> <mi>x</mi> <mn>2</mn> </msub> <mo>,</mo> </mrow> </semantics></math> <math display="inline"><semantics> <msub> <mi>x</mi> <mn>3</mn> </msub> </semantics></math> are external points.</p>
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<p>One-loop massless scalar triangle in momentum space.</p>
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53 pages, 698 KiB  
Review
Critical Properties of Three-Dimensional Many-Flavor QEDs
by Simon Metayer and Sofian Teber
Symmetry 2023, 15(9), 1806; https://doi.org/10.3390/sym15091806 - 21 Sep 2023
Viewed by 1120
Abstract
We review several variants of three-dimensional quantum electrodynamics (QED3) with Nf fermion (or boson) flavors, including fermionic (or spinorial) QED3, bosonic (or scalar) QED3, N=1 supersymmetric QED and also models of reduced QED (supersymmetric [...] Read more.
We review several variants of three-dimensional quantum electrodynamics (QED3) with Nf fermion (or boson) flavors, including fermionic (or spinorial) QED3, bosonic (or scalar) QED3, N=1 supersymmetric QED and also models of reduced QED (supersymmetric or not). We begin with an introduction to these models and their flow to a stable infra-red fixed point in the large-Nf limit. We then present detailed state-of-the-art computations of the critical exponents of these models within the dimensional regularization (and reduction) scheme(s), at the next-to-leading order in the 1/Nf expansion and in an arbitrary covariant gauge. We finally discuss dynamical (matter) mass generation and the current status of our understanding of the phase structure of these models. Full article
(This article belongs to the Special Issue Review on Quantum Field Theory)
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<p>Exactly vanishing one-loop bubble diagrams. (<b>a</b>) <math display="inline"><semantics> <msub> <mi>B</mi> <mn>1</mn> </msub> </semantics></math>, (<b>b</b>) <math display="inline"><semantics> <msub> <mi>B</mi> <mn>2</mn> </msub> </semantics></math>, (<b>c</b>) <math display="inline"><semantics> <msub> <mi>B</mi> <mn>3</mn> </msub> </semantics></math>.</p>
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<p>Vanishing one-loop matter triangles in gQED<math display="inline"><semantics> <msub> <mrow/> <mn>3</mn> </msub> </semantics></math>. (<b>a</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>1</mn> </msub> </semantics></math>, (<b>b</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>2</mn> </msub> </semantics></math>, (<b>c</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>3</mn> </msub> </semantics></math>, (<b>d</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>4</mn> </msub> </semantics></math>, (<b>e</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>5</mn> </msub> </semantics></math>, (<b>f</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>6</mn> </msub> </semantics></math>, (<b>g</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>7</mn> </msub> </semantics></math>, (<b>h</b>) <math display="inline"><semantics> <msub> <mi>T</mi> <mn>8</mn> </msub> </semantics></math>.</p>
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<p>Phase diagrams for dynamical mass generation in: (<b>a</b>) Graphene (QED<math display="inline"><semantics> <msub> <mrow/> <mrow> <mn>4</mn> <mo>,</mo> <mn>3</mn> </mrow> </msub> </semantics></math>) from (<a href="#FD160-symmetry-15-01806" class="html-disp-formula">160</a>) and (<b>b</b>) super-graphene (SQED<math display="inline"><semantics> <msub> <mrow/> <mrow> <mn>4</mn> <mo>,</mo> <mn>3</mn> </mrow> </msub> </semantics></math>) from (<a href="#FD162-symmetry-15-01806" class="html-disp-formula">162</a>). Note that the relevant case for (super-)graphene is <math display="inline"><semantics> <mrow> <msub> <mi>N</mi> <mrow> <mspace width="-1.13809pt"/> <mi>f</mi> </mrow> </msub> <mo>=</mo> <mn>2</mn> </mrow> </semantics></math>. Insulator refers to an excitonic insulating phase, while metal refers to a semimetallic phase.</p>
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<p>All results obtained in this article for the critical number of fermion flavors below which a dynamical mass is generated in various QED models. The darker it is, the more likely the corresponding model is massive for a given <math display="inline"><semantics> <msub> <mi>N</mi> <mrow> <mspace width="-1.13809pt"/> <mi>f</mi> </mrow> </msub> </semantics></math>. Note that the case of interest is generally <math display="inline"><semantics> <mrow> <msub> <mi>N</mi> <mrow> <mspace width="-1.13809pt"/> <mi>f</mi> </mrow> </msub> <mo>=</mo> <mn>1</mn> </mrow> </semantics></math> for all the QED<math display="inline"><semantics> <msub> <mrow/> <mn>3</mn> </msub> </semantics></math> variants. For graphene (QED<math display="inline"><semantics> <msub> <mrow/> <mrow> <mn>4</mn> <mo>,</mo> <mn>3</mn> </mrow> </msub> </semantics></math>) and super-graphene (SQED<math display="inline"><semantics> <msub> <mrow/> <mrow> <mn>4</mn> <mo>,</mo> <mn>3</mn> </mrow> </msub> </semantics></math>), the case of interest is usually <math display="inline"><semantics> <mrow> <msub> <mi>N</mi> <mrow> <mspace width="-1.13809pt"/> <mi>f</mi> </mrow> </msub> <mo>=</mo> <mn>2</mn> </mrow> </semantics></math>.</p>
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20 pages, 711 KiB  
Article
Emergent Strings at an Infinite Distance with Broken Supersymmetry
by Ivano Basile
Astronomy 2023, 2(3), 206-225; https://doi.org/10.3390/astronomy2030015 - 14 Sep 2023
Cited by 4 | Viewed by 1073
Abstract
We investigate the infinite-distance properties of families of unstable flux vacua in string theory with broken supersymmetry. To this end, we employ a generalized notion of distance in the moduli space and we build a holographic description for the non-perturbative regime of the [...] Read more.
We investigate the infinite-distance properties of families of unstable flux vacua in string theory with broken supersymmetry. To this end, we employ a generalized notion of distance in the moduli space and we build a holographic description for the non-perturbative regime of the tunneling cascade in terms of a renormalization group flow. In one limit, we recover an exponentially-light tower of Kaluza-Klein states, while in the opposite limit, we find a tower of higher-spin excitations of D1-branes, realizing the emergent string proposal. In particular, the holographic description includes a free sector, whose emergent superconformal symmetry resonates with supersymmetric stability, the CFT distance conjecture and S-duality. We compute the anomalous dimensions of scalar vertex operators and single-trace higher-spin currents, finding an exponential suppression with the distance which is not generic from the renormalization group perspective, but appears specific to our settings. Full article
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<p>A heavy stack of D1-branes (in the orientifold models) or NS5-branes (in the heterotic model) sources a spacetime geometry whose near-horizon limit is an <math display="inline"><semantics> <mrow> <mi>AdS</mi> <mo>×</mo> <mi>S</mi> </mrow> </semantics></math> throat [<a href="#B37-astronomy-02-00015" class="html-bibr">37</a>,<a href="#B45-astronomy-02-00015" class="html-bibr">45</a>]. One can expect branes on conical singularities to produce similar Freund–Rubin compactifications in this limit.</p>
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<p>The interaction between branes in the presence of string-scale supersymmetry breaking is mediated by the gravitational tadpole. As as a result, the effective charge-to-tension ratio is renormalized by a <math display="inline"><semantics> <mrow> <mi mathvariant="script">O</mi> <mo>(</mo> <mn>1</mn> <mo>)</mo> </mrow> </semantics></math> factor, and like-charge branes exert mutually repulsive forces [<a href="#B37-astronomy-02-00015" class="html-bibr">37</a>,<a href="#B45-astronomy-02-00015" class="html-bibr">45</a>].</p>
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<p>The proposed holographic dual of the cascade of flux tunneling processes in the gravitational EFT is an RG flow in the boundary field theory [<a href="#B71-astronomy-02-00015" class="html-bibr">71</a>]. Depending on the size, location and number of nucleation events, the trajectory can vary, approaching different fixed points. As <math display="inline"><semantics> <mrow> <mi>N</mi> <mo>≫</mo> <mn>1</mn> </mrow> </semantics></math> increases, the flows ought to approach the fixed points more closely, since the dual <math display="inline"><semantics> <mi>AdS</mi> </semantics></math> vacua are closer to stability [<a href="#B45-astronomy-02-00015" class="html-bibr">45</a>].</p>
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<p>The fixed points approached by the holographic RG flow can arise from the IR dynamics of the worldvolume gauge theory living on D1-brane stacks. The final state corresponds to the IR dynamics of a single D1-brane, which features a free sector with conserved single-trace higher-spin currents dual to massless single-particle higher-spin states. Furthermore, the Sugimoto model of [<a href="#B28-astronomy-02-00015" class="html-bibr">28</a>] features emergent supersymmetry on account of <math display="inline"><semantics> <mrow> <mi>Spin</mi> <mo>(</mo> <mn>8</mn> <mo>)</mo> </mrow> </semantics></math> triality.</p>
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<p>The IR dynamics of the worldvolume gauge theories living on <math display="inline"><semantics> <mrow> <mi>N</mi> <mo>=</mo> <mn>2</mn> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <mi>N</mi> <mo>=</mo> <mn>1</mn> </mrow> </semantics></math> D1-branes can be described via NL<math display="inline"><semantics> <mi>σ</mi> </semantics></math>M and WZW coset constructions. The RG flow connecting the corresponding CFTs is triggered by the target-space metric, which is marginally irrelevant in the IR and yields an infinite distance along the flow.</p>
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9 pages, 934 KiB  
Communication
Supersymmetric AdS Solitons, Ground States, and Phase Transitions in Maximal Gauged Supergravity
by Antonio Gallerati
Particles 2023, 6(3), 762-770; https://doi.org/10.3390/particles6030048 - 12 Aug 2023
Viewed by 887
Abstract
We review some recent soliton solutions in a class of four-dimensional supergravity theories. The latter can be obtained from black hole solutions by means of a double Wick rotation. For special values of the parameters, the new configurations can be embedded in the [...] Read more.
We review some recent soliton solutions in a class of four-dimensional supergravity theories. The latter can be obtained from black hole solutions by means of a double Wick rotation. For special values of the parameters, the new configurations can be embedded in the gauged maximal N=8 theory and uplifted in the higher-dimensional D=11 theory. We also consider BPS soliton solutions, preserving a certain fraction of supersymmetry. Full article
(This article belongs to the Special Issue Beyond the Standard Models in Particle Physics and Cosmology)
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<p>Rescaled free energy <math display="inline"><semantics><mfrac><mi>F</mi><mfenced separators="" open="|" close="|"><msub><mi>G</mi><mn>0</mn></msub></mfenced></mfrac></semantics></math> as a function of <math display="inline"><semantics><msub><mi>q</mi><mn>1</mn></msub></semantics></math> with the condition <math display="inline"><semantics><mrow><msub><mi>q</mi><mn>2</mn></msub><mo>=</mo><mo>−</mo><msqrt><mn>3</mn></msqrt><mspace width="0.166667em"/><msub><mi>q</mi><mn>1</mn></msub></mrow></semantics></math>. The yellow line represents the hairy supersymmetric solitons. The non-supersymmetric pure Einstein–Maxwell solutions are shown in blue. We can notice that there exist non-susy solutions featuring lower energy than susy configurations for the same boundary conditions and asymptotic charges [<a href="#B33-particles-06-00048" class="html-bibr">33</a>].</p>
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16 pages, 323 KiB  
Review
R-Symmetries and Curvature Constraints in A-Twisted Heterotic Landau–Ginzburg Models
by Richard S. Garavuso
Particles 2023, 6(3), 746-761; https://doi.org/10.3390/particles6030047 - 7 Aug 2023
Viewed by 982
Abstract
In this paper, we discuss various aspects of a class of A-twisted heterotic Landau–Ginzburg models on a Kähler variety X. We provide a classification of the R-symmetries in these models which allow the A-twist to be implemented, focusing on the case in [...] Read more.
In this paper, we discuss various aspects of a class of A-twisted heterotic Landau–Ginzburg models on a Kähler variety X. We provide a classification of the R-symmetries in these models which allow the A-twist to be implemented, focusing on the case in which the gauge bundle is either a deformation of the tangent bundle of X or a deformation of a sub-bundle of the tangent bundle of X. Some anomaly-free examples are provided. The curvature constraint imposed by supersymmetry in these models when the superpotential is not holomorphic is reviewed. Constraints of this nature have been used to establish properties of analogues of pullbacks of Mathai–Quillen forms which arise in the correlation functions of the corresponding A-twisted or B-twisted heterotic Landau–Ginzburg models. The analogue most relevant to this paper is a deformation of the pullback of a Mathai–Quillen form. We discuss how this deformation may arise in the class of models studied in this paper. We then comment on how analogues of pullbacks of Mathai–Quillen forms not discussed in previous work may be obtained. Standard Mathai–Quillen formalism is reviewed in an appendix. We also include an appendix which discusses the deformation of the pullback of a Mathai–Quillen form. Full article
(This article belongs to the Collection High Energy Physics)
19 pages, 5771 KiB  
Review
The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code
by Marija Rosandić and Vladimir Paar
Int. J. Mol. Sci. 2023, 24(15), 12029; https://doi.org/10.3390/ijms241512029 - 27 Jul 2023
Cited by 2 | Viewed by 1738
Abstract
Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form [...] Read more.
Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson–Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons’ relationship as to how to develop the DNA molecule on the principle of Watson–Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system. Full article
(This article belongs to the Section Molecular Biophysics)
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<p>Our quadruplet classification of 64 codons (with U—uracil) for the genetic code, or trinucleotides (with T—thymine instead of uracil) for RNA and DNA genomes. Each quadruplet is unique and consists of four specific codons or trinucleotides denoted as direct D, reverse complement from direct RC(D), complement from direct C(D), and reverse from direct R(D). Ten A + U rich (group I) and ten C + G rich (group II) quadruplets are organized in three subgroups. Ia consisting of nonsymmetrical codons/trinucleotides containing three different nucleotides, Ib consisting of nonsymmetrical codons/trinucleotides containing two different nucleotides, and Ic consisting of symmetrical codons/trinucleotides that contain duplicated codons/trinucleotides labelled with an asterisk (D = RC, C = R). The first four A + U rich quadruplets were generated with start/stop signals: AUG, UGA, UAG, and UAA. The C + G rich trinucleotides correspond to the purine–purine and pyrimidine–pyrimidine transformation of A + U rich codons/trinucleotides. Three symmetries are present in our codon/trinucleotide classification: (1) purine–pyrimidine symmetries in each quadruplet, (2) purine–pyrimidine symmetries within and between A + U rich and C + G rich quadruplets in the same row of the classification, and (3) mirror symmetry between the direct-reverse and complement-reverse complement in the same quadruplet. Mirror symmetry is also present between purines and pyrimidines of the whole A + T rich group and C + G rich group of codons/trinucleotides. For clarity, the white and grey rows are alternating, to emphasize pairs of A + T rich and C + G rich codons. 0, purine; 1, pyrimidine. It is irrelevant which codon/trinucleotide in the quadruplet is direct, because the other three are accordingly adapted: mirror symmetry. From work by Marija Rosandić and Vladimir Paar [<a href="#B11-ijms-24-12029" class="html-bibr">11</a>], published by Elsevier and reproduced with the permission of the publisher.</p>
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<p>The difference between strand symmetry (CSPR) and quadruplet symmetry for triplets. (<b>A</b>) Strand symmetry includes the same strand direct (D) and reverse complement (RC) of a triplet. Reading bidirectionally, in the direction of the arrow, the same trinucleotides appear in both strands and DNA is reduced to a binary system. However, in this way, quadruplet symmetries among trinucleotides are not evident. (<b>B</b>) Quadruplet symmetry includes all four members of the whole quadruplet of trinucleotides: direct (D) and reverse complement (RC) as well as complement (<b>C</b>) and reverse (R) in both strands of DNA as a quartic system. The quadruplet boxes Qbox <sub>D-RC</sub> and Qbox <sub>C-R.R</sub> have their own mirror symmetry between both strands of DNA. The mirror symmetry is present also between both Qboxes in each strand. Thus, each quadruplet consists of structural physicochemical symmetries, creating an aesthetic form of “butterfly” double mirror symmetry. (<b>C</b>) The same quadruplet mirror symmetries are present in the purine–pyrimidine relationship: 0 is assigned to purines (A, G), and 1 is assigned to pyrimidines (T, C). (<b>D</b>) All four members of the same Qbox have the same frequencies (<span class="html-italic">f</span>D = <span class="html-italic">f</span>RC, respectively, <span class="html-italic">f</span>C = <span class="html-italic">f</span>R), but frequencies between the Qboxes differ mutually. For quadruplets with symmetric trinucleotides, such as AGA or CTC, there is no difference in frequencies between boxes. However, frequencies in both strands of DNA for each individual member of the quadruplet are identical regardless of whether the trinucleotides are symmetric or asymmetric as well as whether the four members of each quadruplet are a mononucleotide, dinucleotide, trinucleotide, or oligonucleotide (<span class="html-italic">f</span>D = <span class="html-italic">f</span>RC = <span class="html-italic">f</span>C = <span class="html-italic">f</span>R). From work by Marija Rosandić and Vladimir Paar [<a href="#B10-ijms-24-12029" class="html-bibr">10</a>], published by MDPI.</p>
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<p>A + T rich and C + G rich trinucleotide quadruplet matrices with relative frequencies of trinucleotides from human chromosome 1. In each quadruplet, the frequency of all four members in both strands is identical (<span class="html-italic">f</span>D = <span class="html-italic">f</span>RC = <span class="html-italic">f</span>C = <span class="html-italic">f</span>R), noted as a plateau on the upper edge of each quadruplet. The plateau shows that the investigated sequence (chromosome, genome) is in accordance with Chargaff’s second parity rule. From work by Marija Rosandić and Vladimir Paar [<a href="#B10-ijms-24-12029" class="html-bibr">10</a>], published by MDPI.</p>
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<p>Examples for the natural law of DNA creation and conservation. According to this law, all mono/oligonucleotides that enter one strand of DNA must enter the second strand regardless of their localization. Binding with a complementary pair, the quadruplet structures with mirror symmetry between both strands and the final CSPR are created. At the same time, the new DNA segment in a bidirectional 5′3′↔3′5′ manner is also created. The total number of bases in both strands is identical. (<b>A</b>) Example with the entrance of 6 oligonucleotide ATGACT into the top strand, its reverse oligonucleotide TCAGTA entering the bottom strand. (<b>B</b>) The same nucleotides may also enter as mononucleotide (A), trinucleotide (TGA), and dinucleotide (CT). The farther process and result is identical, as in (<b>A</b>). (<b>C</b>) The same 6 nucleotides can enter the top strand and the bottom strand individually as mononucleotides. Binding with a complementary pair, the quadruplet structures with mirror symmetry are created, and the final CSPR result is identical as in A and B. From work by Marija Rosandić and Vladimir Paar [<a href="#B10-ijms-24-12029" class="html-bibr">10</a>], published by MDPI.</p>
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<p>The supersymmetry genetic code (SSyGC) table with 2 × 8 boxes. The AUG start signal is at the beginning of the SSyGC table. It has the same distribution of the purine/pyrimidine profile in both columns, and simultaneously the same profile distribution pairs of codon rows within each box. There are five symmetries present: purine–pyrimidine symmetry between bases and codons, direct–complement symmetry of codons between boxes, and A + U rich and C + G rich symmetry of codons between two columns. Superior dominant double mirror symmetry as a core symmetry of the SSyGC table is present between all purines and pyrimidines of the whole genetic code. With the horizontal and vertical central mirror symmetry axis, it created the purine–pyrimidine symmetry net as “the golden rule “for all RNA and DNA species that is unchangeable during evolution. Purines A and G are marked as 0, and pyrimidines C and U are marked as 1. Mirror symmetry with the horizontal symmetry axis is also present between the second and third bases of codons. Mirror symmetry simultaneously generated symmetry between positions of amino acids. In such a way, the sextets for Serine, Arginine, and Leucine, each with six codons, are, for the first time, positioned in continuity—0 pu, purine; 1 py, pyrimidine; bold black line, the axis of the mirror symmetry; dark yellow, two pairs of split boxes with direct–complement symmetry between codons; dark blue, two pairs of no-split boxes with direct–complement symmetry between codons; light yellow, two pairs of split boxes with purine ↔ purine, pyrimidine ↔ pyrimidine transformation between codons of both columns; and light blue, two pairs of non-split boxes with purine ↔ purine, pyrimidine ↔ pyrimidine transformation between codons of both columns as in the whole code.. From work by Marija Rosandić and Vladimir Paar [<a href="#B11-ijms-24-12029" class="html-bibr">11</a>] published by Elsevier and reproduced with the permission of the publisher.</p>
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<p>The mitochondrial invertebrate code incorporated in the SSyGC table. Red: Methionine (M, Met) expands to the neighbouring Isoleucine (Ile) codon AUA; Arginine (Arg) AGA and AGG codons become the 7th and 8th codons for Serine (Ser). In various nuclear and mitochondrial genetic codes, individual amino acids usually capture a codon from a neighbouring amino acid in the SSyGC table [<a href="#B11-ijms-24-12029" class="html-bibr">11</a>]. But the purine–pyrimidine symmetry net always remains unchanged. From work by Marija Rosandić and Vladimir Paar [<a href="#B11-ijms-24-12029" class="html-bibr">11</a>], published by Elsevier and reproduced with the permission of the publisher.</p>
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