arXiv subjects

Liaofu Luo

Publications and source records attributed to Liaofu Luo.

23 records · Page 2Linked to original sources

arXiv2009

Protein Folding as a Quantum Transition Between Conformational States

The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is proposed. The conformational-electronic transition is calculated by non-adiabatic operator method. The protein folding is viewed from conformational quantum transition and the folding rate is calculated. The time-scale of microsecond to millisecond for the fundamental folding event (nucleation, collapse, etc) is deduced. The dependence of transition rate W on N inertial moments is given. It indicates how W increases with the number N of torsion angles and decreases with the inertial moment I of atomic group in cooperative transition. The temperature dependence is also deduced which is different from chemical reaction in high-temperature region. It is demonstrated that the conformational dynamics gives deep insights into the folding mechanism and provides a useful tool for analyzing and explaining experimental facts on the rate of protein folding.

q-bio.BM↗

arXiv2008

Law of Genome Evolution Direction : Coding Information Quantity Grows

The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size 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 from outside. 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 evidences on the evolutionary law about the function-coding information quantity are listed. The needs of function is the motive force for the expansion of coding information quantity and the information quantity expansion is the way to make functional innovation and extension for a species. So, the increase of coding information quantity of a genome is a measure of the acquired new function and it determines the directionality of genome evolution.

q-bio.GN↗

arXiv2008

Entropy Production in a Cell and Reversal of Entropy Flow as an Anticancer Therapy

The entropy production rate of cancer cell is always higher than healthy cell under the case of no external field applied. Different entropy production between two kinds of cells determines the direction of entropy flow among cells. The entropy flow is the carrier of information flow. The entropy flow from cancer to healthy cell takes along the harmful information of cancerous cell, propagating its toxic action to healthy tissues. We demonstrate that a low-frequency and low-intensity electromagnetic field or ultrasound irradiation may increase the entropy production rate of a cell in normal tissue than that in cancer, consequently reverse the direction of entropy current between two kinds of cells. The modification of PH value of cells may also cause the reversal of the direction of entropy flow between healthy and cancerous cells. So, the biological tissue under the irradiation of electromagnetic field or ultrasound or under the appropriate change of cell acidity can avoid the propagation of harmful information from cancer cells. We suggest that this entropy mechanism possibly provides a basis for a novel approach to anticancer therapy.

q-bio.CB↗

arXiv2003

Quasireplicas and universal lengths of microbial genomes

Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their universality give powerful clues to the way microbial genomes are grown. We show that the observed genomic properties are explained by a model for genome growth in which primitive genomes grew mainly by maximally stochastic duplications of short segments from an initial length of about 200 nucleotides (nt) to a length of about one million nt typical of microbial genomes. The relevance of the result of this study to the nature of simultaneous random growth and information acquisition by genomes, to the so-called RNA world in which life evolved before the rise of proteins and enzymes and to several other topics are discussed.

physics.bio-ph↗

arXiv2003

Evidence for growth of microbial genomes by short segmental duplications

We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to obey Poisson distributions. It is noticed that for words less than nine letters the average width of the distributions for complete microbial genomes is many times that of a Poisson distribution. We interpret this phenomenon as follows: the genome is a large system that possesses the statistical characteristics of a much smaller ``random'' system, and certain textual statistical properties of genomes we now see are remnants of those of their ancestral genomes, which were much shorter than the genomes are now. This interpretation suggests a simple biologically plausible model for the growth of genomes: the genome first grows randomly to an initial length of approximately one thousand nucleotides (1k nt), or about one thousandth of its final length, thereafter mainly grows by random segmental duplication. We show that using duplicated segments averaging around 25 nt, the model sequences generated possess statistical properties characteristic of present day genomes. Both the initial length and the duplicated segment length support an RNA world at the time duplication began. Random segmental duplication would greatly enhance the ability of a genome to use its hard-to-acquire codes repeatedly, and a genome that practiced it would have evolved enormously faster than those that did not.

physics.bio-ph↗