Hanon McShea, Catherine Weibel, Sawsan Wehbi, Peter Goodman, Jennifer E James, Andrew L Wheeler, Joanna Masel
{"title":"The effectiveness of selection in a species affects the direction of amino acid frequency evolution.","authors":"Hanon McShea, Catherine Weibel, Sawsan Wehbi, Peter Goodman, Jennifer E James, Andrew L Wheeler, Joanna Masel","doi":"10.1101/2023.02.01.526552","DOIUrl":"10.1101/2023.02.01.526552","url":null,"abstract":"<p><p>Nearly neutral theory predicts that species with higher effective population size (<i>N</i> <sub><i>e</i></sub> ) are better able to purge slightly deleterious mutations. We compare evolution in high-<i>N</i> <sub><i>e</i></sub> vs. low-<i>N</i> <sub><i>e</i></sub> vertebrates to reveal which amino acid frequencies are subject to subtle selective preferences. We take three complementary approaches, two measuring flux and one measuring outcomes. First, we fit non-stationary substitution models of amino acid flux using maximum likelihood, comparing the high-<i>N</i> <sub><i>e</i></sub> clade of rodents and lagomorphs to its low-<i>N</i> <sub><i>e</i></sub> sister clade of primates and colugos. Second, we compare evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies and <i>N</i> <sub><i>e</i></sub> . Third, we dissect the details of flux in human, chimpanzee, mouse, and rat, as scored by parsimony - this also enables comparison to a historical paper. All three methods agree on which amino acids are preferred under more effective selection. Preferred amino acids tend to be smaller, less costly to synthesize, and to promote intrinsic structural disorder. Parsimony-induced bias in the historical study produces an apparent reduction in structural disorder, perhaps driven by slightly deleterious substitutions. Within highly exchangeable pairs of amino acids, arginine is strongly preferred over lysine, and valine over isoleucine, consistent with more effective selection preferring a marginally larger free energy of folding. These two preferences match differences between thermophiles and mesophilic relatives. These results reveal the biophysical consequences of mutation-selection-drift balance, and demonstrate the utility of nearly neutral theory for understanding protein evolution.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"08 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11212923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86208429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Superluminal geometrodynamics of braneworld hyperdrive via brane–bulk interaction","authors":"Anuar Alias, Azman Jalar","doi":"10.1142/s0217732324500329","DOIUrl":"https://doi.org/10.1142/s0217732324500329","url":null,"abstract":"<p>Alcubierre’s warp-drive was the first to introduce superluminal travel from different approaches. Instead of creating a shortcut through spacetime via a wormhole, geometrodynamics of simultaneously contracting and expanding spacetime were conjectured. However, both methods require exotic matter that violates energy conditions. In this paper, we employ the concept of braneworld that naturally influences spacetime geometrodynamics. Starting from defining and developing the spacetime metric of the braneworld warp bubble, the expression for energy densities as a function of relevant parameters which contributes to the braneworld approach of superluminal travel by hyperspace-drive was derived.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"42 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141188570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A review on correlations among the multiplicities of charge particles at SPS, RHIC and LHC energies","authors":"Shreya Bhattacharjee, Prabir Kr. Haldar","doi":"10.1142/s0217732324300039","DOIUrl":"https://doi.org/10.1142/s0217732324300039","url":null,"abstract":"<p>Correlation study among the charge particle multiplicities plays an important role to analyze the heavy-ion interactions. Different observables like charged particle multiplicities, azimuthal anisotropy among the multiplicity of charge particles, transverse momentum of the multiplicities, etc. can correlate and these help to comprehend the various phases of heavy-ion collisions. We have reviewed two- and three-particle correlations, azimuthal correlations and Bose–Einstein correlations among the multiplicities of charge particles. We have also studied the forward-backward correlation technique to investigate the correlations among the charged multiplicities. Here, we have discussed various kinds of correlations at SPS energy, RHIC energy and LHC energy.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"19 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141188600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Addendum — Inertia modified by electromagnetic Abelian gauge transformations","authors":"Alcides Garat","doi":"10.1142/s0217732324910012","DOIUrl":"https://doi.org/10.1142/s0217732324910012","url":null,"abstract":"<p>In this paper, we will analyze the relationship between both potentials in vacuum electrodynamics and their local gauge transformations.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"54 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141188574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Y. S. Solanke, T. D. Nakade, D. D. Pawar, V. J. Dagwal
{"title":"Kaluza–Klein cosmological model with strange-quark-matter in f(R,T) theory of gravity","authors":"Y. S. Solanke, T. D. Nakade, D. D. Pawar, V. J. Dagwal","doi":"10.1142/s0217732324500561","DOIUrl":"https://doi.org/10.1142/s0217732324500561","url":null,"abstract":"<p>This work deals with the Kaluza–Klein cosmological model with strange-quark-matter in <span><math altimg=\"eq-00002.gif\" display=\"inline\"><mi>f</mi><mo stretchy=\"false\">(</mo><mi>R</mi><mo>,</mo><mi>T</mi><mo stretchy=\"false\">)</mo></math></span><span></span> theory of gravity, where <i>R</i> is the Ricci scalar and <i>T</i> is the trace of the energy–momentum tensor. To determine the solution of the field equation, we have assumed that scalar expansion <span><math altimg=\"eq-00003.gif\" display=\"inline\"><mi>θ</mi></math></span><span></span> is proportional to shear scalar <span><math altimg=\"eq-00004.gif\" display=\"inline\"><msup><mrow><mi>σ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span><span></span> which leads to <span><math altimg=\"eq-00005.gif\" display=\"inline\"><mi>R</mi><mo>=</mo><msup><mrow><mi>A</mi></mrow><mrow><mi>m</mi></mrow></msup></math></span><span></span>, where <i>R</i> and <i>A</i> are metric potentials and <i>m</i> is constant. The cosmological parameters are investigated with the help of the equation of state strange-quark-matter (SQM) is <span><math altimg=\"eq-00006.gif\" display=\"inline\"><mi>p</mi><mo>=</mo><mfrac><mrow><mi>ρ</mi><mo>−</mo><mn>4</mn><msub><mrow><mi>B</mi></mrow><mrow><mi>c</mi></mrow></msub></mrow><mrow><mn>3</mn></mrow></mfrac></math></span><span></span>, where <span><math altimg=\"eq-00007.gif\" display=\"inline\"><msub><mrow><mi>B</mi></mrow><mrow><mi>c</mi></mrow></msub></math></span><span></span> is Bag constant. We have concentrated on the distances of cosmology such as the look-back time, proper distance, luminosity distance, angular-diameter distance and distance modulus which are presented graphically by using suitable data of <span><math altimg=\"eq-00008.gif\" display=\"inline\"><msub><mrow><mi>H</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span><span></span>. The physical and geometrical properties of models are also discussed.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"50 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141188568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ijaz Ahmed, Mashal Shakar, M. U. Ashraf, Jamil Muhammad, Taimoor Khurshid
{"title":"Effect of polarized colliding beam on Higgs boson production at the lepton collider","authors":"Ijaz Ahmed, Mashal Shakar, M. U. Ashraf, Jamil Muhammad, Taimoor Khurshid","doi":"10.1142/s0217732324500470","DOIUrl":"https://doi.org/10.1142/s0217732324500470","url":null,"abstract":"<p>Different production processes involving the Higgs boson, such as annihilation and W/Z boson fusion, will be observed in the International Linear Collider (ILC). The ILC operates at a center-of-mass (CM) energy of <span><math altimg=\"eq-00001.gif\" display=\"inline\" overflow=\"scroll\"><msqrt><mrow><mi>s</mi></mrow></msqrt><mo>=</mo><mn>2</mn><mn>0</mn><mn>0</mn></math></span><span></span>–1000<span><math altimg=\"eq-00002.gif\" display=\"inline\" overflow=\"scroll\"><mspace width=\".17em\"></mspace></math></span><span></span>GeV. The study reveals that the production cross-section can either be enhanced or reduced depending on the CM energy and the specific combination used, which has implications for selecting appropriate production processes. Additionally, this investigation highlights that by polarizing beams, the number of measurable observables increases. These observables, such as left–right asymmetry, detailed effective polarization, and adequate effective luminosity, are crucial to ascertain contemporary physical parameters in physics models absurdly the Standard Model (SM).</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"3 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140927064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Further prediction on the possible double-peak structure of the X17 particle","authors":"Hua-Xing Chen","doi":"10.1142/s0217732324500573","DOIUrl":"https://doi.org/10.1142/s0217732324500573","url":null,"abstract":"<p>The <span><math altimg=\"eq-00003.gif\" display=\"inline\" overflow=\"scroll\"><mi>X</mi><mn>1</mn><mn>7</mn></math></span><span></span> particle, discovered by [A. J. Krasznahorkay <i>et al.</i>, <i>Phys. Rev. Lett.</i><b>116</b>, 042501 (2016), doi:10.1103/PhysRevLett.116.042501] at ATOMKI, was recently confirmed in the <span><math altimg=\"eq-00004.gif\" display=\"inline\" overflow=\"scroll\"><mi>γ</mi><mi>γ</mi></math></span><span></span> invariant mass spectra by [K. U. Abraamyan, C. Austin, M. I. Baznat, K. K. Gudima, M. A. Kozhin, S. G. Reznikov and A. S. Sorin, arXiv:2311.18632] at JINR. We notice with surprise and interest that the <span><math altimg=\"eq-00005.gif\" display=\"inline\" overflow=\"scroll\"><mi>X</mi><mn>1</mn><mn>7</mn></math></span><span></span> seems to have a double-peak structure. This is in a possible coincidence with our QCD sum rule study of [H.-X. Chen, arXiv:2006.01018], where we interpreted the <span><math altimg=\"eq-00006.gif\" display=\"inline\" overflow=\"scroll\"><mi>X</mi><mn>1</mn><mn>7</mn></math></span><span></span> as a tetraquark state composed of four bare quarks (<span><math altimg=\"eq-00007.gif\" display=\"inline\" overflow=\"scroll\"><mi>u</mi><mi>ū</mi><mi>d</mi><mover accent=\"true\"><mrow><mi>d</mi></mrow><mo>̄</mo></mover></math></span><span></span>), and claimed that “A unique feature of this tetraquark assignment is that we predict two almost degenerate states with significantly different widths”. These two different tetraquark states are described by two different chiral tetraquark currents <span><math altimg=\"eq-00008.gif\" display=\"inline\" overflow=\"scroll\"><msub><mrow><mi>ū</mi></mrow><mrow><mi>L</mi></mrow></msub><msub><mrow><mi>γ</mi></mrow><mrow><mi>μ</mi></mrow></msub><msub><mrow><mi>d</mi></mrow><mrow><mi>L</mi></mrow></msub><mspace width=\"0.35em\"></mspace><msub><mrow><mover accent=\"true\"><mrow><mi>d</mi></mrow><mo>̄</mo></mover></mrow><mrow><mi>L</mi></mrow></msub><msup><mrow><mi>γ</mi></mrow><mrow><mi>μ</mi></mrow></msup><msub><mrow><mi>u</mi></mrow><mrow><mi>L</mi></mrow></msub></math></span><span></span> and <span><math altimg=\"eq-00009.gif\" display=\"inline\" overflow=\"scroll\"><msub><mrow><mi>ū</mi></mrow><mrow><mi>L</mi></mrow></msub><msub><mrow><mi>γ</mi></mrow><mrow><mi>μ</mi></mrow></msub><msub><mrow><mi>d</mi></mrow><mrow><mi>L</mi></mrow></msub><mspace width=\"0.35em\"></mspace><msub><mrow><mover accent=\"true\"><mrow><mi>d</mi></mrow><mo>̄</mo></mover></mrow><mrow><mi>R</mi></mrow></msub><msup><mrow><mi>γ</mi></mrow><mrow><mi>μ</mi></mrow></msup><msub><mrow><mi>u</mi></mrow><mrow><mi>R</mi></mrow></msub></math></span><span></span>. To verify whether the tetraquark assignment is correct or not, we replace the up and down quarks by the strange quarks, and apply the QCD sum rule method to study the other four chiral tetraquark currents <span><math altimg=\"eq-00010.gif\" display=\"inline\" overflow=\"scroll\"><msub><mrow><mi>ū</mi></mrow><mrow><mi>L</mi></mrow></msub><msub><mrow><mi>γ</mi></mrow><mrow><mi>μ</mi></","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"4 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140926997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Degeneracy pressure in the presence of maximum length for non-interacting electrons","authors":"S. Parsamehr, N. Fatahi","doi":"10.1142/s0217732324500391","DOIUrl":"https://doi.org/10.1142/s0217732324500391","url":null,"abstract":"<p>Combining quantum theory with the fundamental principles of gravity results in the modification of the uncertainty principle. In this study, we employ the extended uncertainty principle (EUP) with the maximum length derived from the cosmological particle horizon. The impact of this specific kind of modification is examined in a non-interacting electron gas system. We analytically derive the generalized relations for the degeneracy pressure and the bulk modulus. An intriguing finding is that the degeneracy pressure is reduced, as confirmed by the observed size of white dwarfs, which is smaller than what is predicted by the standard theory. Nevertheless, it is still capable of providing support against gravitational collapse.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"43 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140926998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Micro-cosmos model of a nucleon","authors":"Michael Cramer Andersen","doi":"10.1142/s0217732324500536","DOIUrl":"https://doi.org/10.1142/s0217732324500536","url":null,"abstract":"<p>This study explores the age-old quest to construct a geometric model of a quantum particle. While static classical particle models have largely been dismissed, the focus has now shifted to intricate dynamic models that hold the promise of reconciling general relativity with quantum mechanics. We propose that matter particles can be described as radiation confined within dynamically curved spacetime regions, without the need for quantization of space and time, and using standard field equations and natural Planck units. Specifically, we investigate a cyclic or oscillating radiation-dominated micro-cosmos undergoing repeated bouncing. Our methodology employs integration, with carefully defined initial conditions. The results include several observable properties characteristic of quantum particles. We calculate the total mass, revealing a compelling inverse proportionality between mass and radius identical with the de Broglie relationship. Applying this model to protons, we discover a profound and surprisingly simple relationship between the proton’s radius and mass expressed in Planck units. This enables a definition of the proton radius that aligns remarkably well with the 2018 CODATA value. Furthermore, our analysis demonstrates that the radial density profile of the proton (or nucleon), averaged over a cycle time, increases toward the center. The problem of embedding the micro-cosmos within a background spacetime is also described. These results underscore the relevance of general relativity in the domain of nuclear physics. Moreover, the model offers a fresh perspective that can stimulate new ideas in the ongoing quest to unify general relativity with quantum physics.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"66 3 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140831320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A novel quantum dialogue without information leakage based on single photons in both polarization and spatial-mode degrees of freedom","authors":"Shen Rao","doi":"10.1142/s0217732324500354","DOIUrl":"https://doi.org/10.1142/s0217732324500354","url":null,"abstract":"<p>This paper puts forward a novel quantum dialogue (QD) protocol without information leakage based on single photons in both polarization and spatial-mode degrees of freedom. In this protocol, the receiver sends his private message to the sender in the way of quantum secure direct communication; and the receiver decodes out the private message of the sender with the help of auxiliary single photons in two degrees of freedom, double controlled-not (CNOT) operations and an auxiliary classical bit sequence sent from the sender. As a result, no information leakage takes place. Moreover, this protocol is proven to defeat the intercept-resend attack, the measure-resend attack, the entangle-measure attack and the Trojan horse attack from an outside eavesdropper. This protocol only employs single photons in two degrees of freedom as quantum resource and needs single-photon measurements. The qubit efficiency of this protocol is as high as 66.7%.</p>","PeriodicalId":18752,"journal":{"name":"Modern Physics Letters A","volume":"154 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140798332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}