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Liaofu Luo

Publications and source records attributed to Liaofu Luo.

At least 19 recordsLinked to original sources
arXiv2026

Stochastic mutation as a mechanism for the emergence of SARS-CoV-2 new variants -- A Scientific Conjecture on Artificial Intelligence Paradigm

The article summaries authors' researches on spreading dynamics of COVID 19 by use of the method of continuously asking and answering questions. Scientific conjecture provides the logical starting point and the important driving force of scientific research. The present article also proposes a scientific conjecture on the development of artificial intelligence: Question answering AI is highly efficient and low cost as compared with AI agent.

q-bio.QM↗
arXiv2022

Application of Generalized Quaternion in Physics

The applications of quaternion in physics are discussed with an emphasis on elementary particle symmetry and interaction. Three colours of the quark and the quantum chromodynamics (QCD) can be introduced directly from the invariance of basic equations under the quaternion phase transformation (quaternion gauge invariance). The generalized quaternions obey the SU(3) symmetry. QCD is essentially the quantum quaternion dynamics. The further generalization of SU(3) quaternion to G2 octonion is worked out. We demonstrate that the G2 octonion contains seven tri-generator sets of SU(2) symmetry and three of them form SU(3) subgroup. A model of the elementary particle classification and interaction based on octonion gauge theory is proposed. The model unifies the colour and flavour of all particles. It provides a framework for the unified description of four kinds of elementary particles (quarks, leptons, gauge fields and Higgs bosons) and their interactions.

hep-ph↗
arXiv2022

Phylogenetic Study of 2019-nCoV by Using Alignment Free Method (Evolutionary Bifurcation of Novel Coronavirus Mutants)

The phylogenetic tree of SARS-CoV-2 (nCov-19) viruses is reconstructed according to the similarity of genome sequences. The tree topology of Betacoronavirus is remarkably consistent with biologist's systematics. Because the tree construction contains enough information about virus mutants, it is suitable to study the evolutionary relationship between novel coronavirus mutants transmitted among humans. The emergences of 14 kinds of main mutants are studied and these strains can be classified as eight bifurcations of the phylogenetic tree. It is found that there exist three types of virus mutations, namely, the mutation among sub-branches of the same branch, the off-root mutation and the root-oriented mutation between large branches of the tree. From the point of the relation between viral mutation and host selection we found that individuals with low immunity provide a special environment for the positive natural selection of virus evolution. It gives a mechanism to explain why large mutations between two distant branches generally occur in the nCov-19 phylogenetic tree. The finding is helpful to formulate strategies to control the spread of COVID-19.

q-bio.GN↗
arXiv2021

Theoretical Model on Meridian Conduction

The physical mechanism on meridians (acupuncture lines) is studied and a theoretical model is proposed. The meridians are explained as an alternating system responsible for the integration and the regulation of life in addition to the neuro-humoral regulation. We proposed that the meridian conduction is a kind of mechanical waves (soliton) of low frequency along the slits of muscles. The anatomical-physiological and experimental evidences are reviewed. It is demonstrated that the stabilization of the soliton is guaranteed by the coupling between muscle vibration and cell activation. Therefore the propagation of mechanical wave dominates the excitation of cell groups along the meridian. The meridian wave equations and its solution are deduced and how these results can be used in studying human healthy is briefly discussed .

physics.med-ph↗
arXiv2021

Spike conformation transition in SARS-CoV-2 infection

A theory on the conformation transition for SARS-CoV-2 spike protein (S) is proposed. The conformation equilibrium between open (up) and closed (down) conformations of receptor binding domain (RBD) of the spike is studied from the first-principle. The conformational state population is deduced from the free energy change in conformation transition of S protein. We demonstrated that the free energy includes two parts, one from the multi-minima of conformational potential and another from the variation of structural elasticity. Both factors are dependent of amino acid mutation. The former is related to the change of affinity of RBD to ACE 2 due to the mutation in the subdomain RBM (receptor binding motif) of RBD. The latter is caused by the change of elastic energy of S protein. When the affinity has increased significantly and/or the elastic energy has been reduced substantially the equilibrium is biased to the open conformation. Only then can the virus infection process continue. Possible new SARS-CoV-2 variants from amino acid mutations in 5-9 sites on RBD interface are predicted. The elastic energy variation needed for conformation transition is estimated quantitatively. Taking the elastic-structural change into account more virus variants are possible. Both the D614G mutation, the K986P mutation and the new variants 501Y in current SARS-CoV-2 pandemic can be interpreted from the presented theory. The comparison of the infectivity of SARS-CoV-2 with SARS-CoV-1 is made from the point of conformation equilibrium. Why the virus entrance takes priority in lower temperature and higher humidity is interpreted by the present theory. The conformational transition influenced by electromagnetic field is also discussed briefly.

q-bio.BM↗
arXiv2020

DNA Torsion-based Model of Cell Fate Phase Transitions

All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate transition can be regarded as a phase transition in DNA supercoiling. However, there has been a dearth of quantitative biophysical models to explain and predict the behaviors of these phase transitions. The generalized Ising model is proposed to define such phase transitions. The model predicts that, apart from temperature-induced phase transitions, there exists DNA torsion frequency-induced phase transitions. Major transitions in epigenetic states, from stem cell activation to differentiation and reprogramming, can be explained by such torsion frequency-induced phase transitions, with important implications for regenerative medicine and medical diagnostics in the future.

q-bio.BM↗
arXiv2019

Quantum patterns of genome size variation in angiosperms

The nuclear DNA amount in angiosperms is studied from the eigen-value equation of the genome evolution operator H. The operator H is introduced by physical simulation and it is defined as a function of the genome size N and the derivative with respective to the size. The discontinuity of DNA size distribution and its synergetic occurrence in related angiosperms species are successfully deduced from the solution of the equation. The results agree well with the existing experimental data of Aloe, Clarkia, Nicotiana, Lathyrus, Allium and other genera. It may indicate that the evolutionary constrains on angiosperm genome are essentially of quantum origin.

q-bio.OT↗
arXiv2015

From Chemically to Physically Induced Pluripotency in Stem Cell

A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the differentiate state to pluripotent state is defined as the quantum transition between conformational states. The transitional rate is calculated and an analytical form for the rate formulas is deduced. Then the dependence of the rate on the number of torsion angles of the gene and the magnitude of the rate can be estimated by comparison with protein folding. The reaction equations of the conformational change of the pluripotency genes in chemical reprogramming are given. The characteristic time of the chemical reprogramming is calculated and the result is consistent with experiments. The dependence of the transition rate on physical factors such as temperature, PH value and the volume and shape of the coherent domain is analyzed from the rate equation. It is suggested that by decreasing the coherence degree of some pluripotency genes a more effective approach to the physically induced pluripotency can be made.

q-bio.BM↗
arXiv2015

A Quantum Model on Chemically-Physically Induced Pluripotency in Stem Cells

A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the differentiate state to pluripotent state is defined as the quantum transition between conformational states. The transitional rate is calculated and an analytical form for the rate formulas is deduced. Then the dependence of the rate on the number of torsion angles of the gene and the magnitude of the rate can be estimated by comparison with protein folding. The reaction equations of the conformational change of the pluripotency genes in chemical reprogramming are given. The characteristic time of the chemical reprogramming is calculated and the result is consistent with experiments. The dependence of the transition rate on physical factors such as temperature, PH value and the volume and shape of the coherent domain is analyzed from the rate equation. It is suggested that by decreasing the coherence degree of some pluripotency genes a more effective approach to the physically induced pluripotency can be made.

q-bio.OT↗
arXiv2014

Quantum Theory on Glucose Transport Across Membrane

After a brief review of the protein folding quantum theory and a short discussion on its experimental evidences the mechanism of glucose transport across membrane is studied from the point of quantum conformational transition. The structural variations among four kinds of conformations of the human glucose transporter GLUT1 (ligand free occluded, outward open, ligand bound occluded and inward open) are looked as the quantum transition. The comparative studies between mechanisms of uniporter (GLUT1) and symporter (XylE and GlcP) are given. The transitional rates are calculated from the fundamental theory. The monosaccharide transport kinetics is proposed. The steady state of the transporter is found and its stability is studied. The glucose (xylose) translocation rates in two directions and in different steps are compared. The mean transport time in a cycle is calculated and based on it the comparison of the transport times between GLUT1,GlcP and XylE can be drawn. The non-Arrhenius temperature dependence of the transition rate and the mean transport time is predicted. It is suggested that the direct measurement of temperature dependence is a useful tool for deeply understanding the transmembrane transport mechanism.

q-bio.BM↗
arXiv2014

A Model on Genome Evolution

A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the stochastic quantum equation are proposed. It is proved that the classical equation can be put in a form of the least action principle and the latter can be used for obtaining the quantum generalization of the evolutionary law. The wave equation and uncertainty relation for the quantum evolution are deduced logically. It is shown that the classical trajectory is a limiting case of the general quantum evolution depicted in the coarse-grained time. The observed smooth/sudden evolution is interpreted by the alternating occurrence of the classical and quantum phases. The speciation event is explained by the quantum transition in quantum phase. Fundamental constants of time dimension, the quantization constant and the evolutionary inertia, are introduced for characterizing the genome evolution. The size of minimum genome is deduced from the quantum uncertainty lower bound. The present work shows the quantum law may be more general than thought, since it plays key roles not only in atomic physics, but also in genome evolution.

q-bio.OT↗
arXiv2012

A Proposal on Quantum Histone Modification in Gene Expression

A quantum mechanical model on histone modification is proposed. Along with the methyl / acetate or other groups bound to the modified residues the torsion angles of the nearby histone chain are supposed to participate in the quantum transition cooperatively. The transition rate W is calculated based on the non-radiative quantum transition theory in adiabatic approximation. By using W's the reaction equations can be written for histone modification and the histone modification level can be calculable from the equations, which is decided by not only the atomic group bound to the modified residue, but also the nearby histone chain. The theory can explain the mechanism for the correlation between a pair of chromatin markers observed in histone modification. The temperature dependence and the coherence-length dependence of histone modification are deduced. Several points for checking the proposed theory and the quantum nature of histone modification are suggested as follows: 1, The relationship between lnW and 1/T is same as usual protein folding. The non-Arhenius temperature dependence of the histone modification level is predicted. 2, The variation of histone modification level through point mutation of some residues on the chain is predicted since the mutation may change the coherence-length of the system. 3, Multi-site modification obeys the quantum superposition law and the comparison between multi-site transition and single modification transition gives an additional clue to the testing of the quantum nature of histone modification.

q-bio.BM↗
arXiv2011

On the Law of Directionality of Genome Evolution

The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication, expansion of code, and gene transfer between genomes. The function-coding information quantity of a genome consists of two parts, p-coding information quantity which encodes functional protein and n-coding information quantity which encodes other functional elements except amino acid sequence. The relation of the proposed law to the thermodynamic laws is indicated. The evolutionary trends of DNA sequences revealed by bioinformatics are investigated which afford further evidences on the evolutionary law. It is argued that the directionality of genome evolution comes from species competition adaptive to environment. An expression on the evolutionary rate of genome is proposed that the rate is a function of Darwin temperature (describing species competition) and fitness slope (describing adaptive landscape). Finally, the problem of directly experimental test on the evolutionary directionality is discussed briefly.

q-bio.GN↗
arXiv2011

Protein Photo-folding and Quantum Folding Theory

The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein photo-folding processes are compared with common protein folding without interaction of photons (nonradiative folding). It is demonstrated that there exists a common factor (thermo-averaged overlap integral of vibration wave function, TAOI) for protein folding and protein photo-folding. Based on this finding it is predicted that: 1) the stimulated photo-folding rates show the same temperature dependence as protein folding; 2) the spectral line of electronic transition is broadened to a band which includes abundant vibration spectrum without and with conformational transition and the width of the vibration spectral line is largely reduced; 3) the resonance fluorescence cross section changes with temperature obeying the same law (Luo-Lu's law). The particular form of the folding rate - temperature relation and the abundant spectral structure imply the existence of a set of quantum oscillators in the transition process and these oscillators are mainly of torsion type of low frequency, imply the quantum tunneling between protein conformations does exist in folding and photo-folding processes and the tunneling is rooted deeply in the coherent motion of the conformational-electronic system.

q-bio.BM↗
arXiv2011

Temperature Dependence of Protein Folding Deduced from Quantum Transition

A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory is used to study the temperature dependences of folding rate of 15 proteins and their non-Arrhenius behavior can all be deduced in a natural way. A general formula on the rate-temperature dependence has been deduced which is in good accordance with experimental data. These temperature dependences are further analyzed in terms of torsion potential parameters. Our results show it is necessary to move outside the realm of classical physics when the temperature dependence of protein folding is studied quantitatively.

q-bio.BM↗
arXiv2010

Protein Folding as a Quantum Transition Between Conformational States: Basic Formulas and Applications

The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency variation in folding. Then the following problems about the application of the rate theory are discussed: 1) The unified theory on the two-state and multi-state protein folding is given based on the concept of quantum transition. 2) The relationship of folding and unfolding rates vs denaturant concentration is studied. 3) The temperature dependence of folding rate is deduced and the non-Arrhenius behaviors of temperature dependence are interpreted in a natural way. 4) The inertial moment dependence of folding rate is calculated based on the model of dynamical contact order and consistent results are obtained by comparison with one-hundred-protein experimental dataset. 5) The exergonic and endergonic foldings are distinguished through the comparison between theoretical and experimental rates for each protein. The ultrafast folding problem is viewed from the point of quantum folding theory and a new folding speed limit is deduced from quantum uncertainty relation. And finally, 6) since only the torsion-accessible states are manageable in the present formulation of quantum transition how the set of torsion-accessible states can be expanded by using statistical energy landscape approach is discussed. All above discussions support the view that the protein folding is essentially a quantum transition between conformational states.

q-bio.BM↗
arXiv2010

Information-theoretic View of Sequence Organization in a Genome

Sequence organizations are viewed from two points: one is from informational redundancy or informational correlation (IC) and another is from k-mer frequency statistics. Two problems are investigated. The first is how the ICs exceed the fluctuation bound and the order emerges from fluctuation in a genome when the sequence length attains some critical value. We demonstrated that the transition from fluctuation to order takes place at about sequence length 200-300 thousands bases for human and E coli genome. It means that the life emerges from a region between macroscopic and microscopic. The second is about the statistical law of the k-mer organization in a genome under the evolutionary pressure and functional selection. We deduced a sum rule Q(k,N) on the k-mer frequency deviations from the randomness in a N-long sequence of genome and deduced the relations of Q(k,N) with k and N. We found that Q(k,N) increases with length N at a constant rate for most genome sequences and demonstrated that when the functional selection of k-mers is accumulated to some critical value the ordering takes place. An important finding is the sum rule correlated with the evolutionary complexity of the genome.

q-bio.GN↗
arXiv2009

A Unified Theory on Construction and Evolution of the Genetic Code

A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the redundancy distribution of codons in the genetic code obeys MD minimization principle; 2, the hydrophilic-hydrophobic distribution of amino acids on the code table is global MD (GMD) minimal; 3, the standard genetic code can be deduced from the adaptive minimization of GMD; 4, the variants of the standard genetic code can be explained quantitatively by use of GMD formalism and the general trend of the evolution is GMD non-increasing which reflects the selection on the code. We have demonstrated that the redundancy distribution of codons and the hydrophobic-hydrophilic (H-P) distribution of amino acids are robust in the code relative to the mutational parameter, and indicated that the GMD can be looked as a non-fitness function on the adaptive landscape. Finally, an important aspect on the symmetry of the code construction, the Yin-Yang duality is investigated. The Yin-Yang duality among codons affords a sound basis for understanding the H-P structure in the genetic code.

q-bio.OT↗