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.
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.
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds and stretching-bending vibrations the molecular torsion has the lowest energy and can be looked as the slow variable of the system. Simultaneously, from the multi-minima property of torsion potential the local conformational states are well defined. Following the idea that the slow variables slave the fast ones and using the nonadiabaticity operator method we deduce the Hamiltonian describing conformational change. It is proved that the influence of fast variables on the macromolecule can fully be taken into account through a phase transformation of slow variable wave function. Starting from the conformation- transition Hamiltonian the nonradiative matrix element is calculated in two important cases: A, only electrons are fast variables and the electronic state does not change in the transition process; B, fast variables are not limited to electrons but the perturbation approximation can be used. Then, the general formulas for protein folding rate are deduced. The analytical form of the formula is utilized to study the temperature dependence of protein folding rate and the curious non-Arrhenius temperature relation is interpreted. The decoherence time of quantum torsion state is estimated and the quantum coherence degree of torsional angles in the protein folding is studied by using temperature dependence data. The proposed folding rate formula gives a unifying approach for the study of a large class problems of biological conformational change.
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.
The large-molecules conformational transitions problem (the 'protein folding problem') is an open issue of vivid current science research work of fundamental importance for a number of modern science disciplines as well as for nanotechnology. Here, we elaborate the recently proposed quantum-decoherence-based approach to the issue. First, we emphasize a need for detecting the elementary quantum mechanical processes (whose combinations may give a proper description of the realistic experimental situations) and then we design such a model. As distinct from the standard approach that deals with the conformation system, we investigate the optically induced transitions in the molecule electrons system that, in effect, may give rise to a conformation change in the molecule. Our conclusion is that such a model may describe the comparatively slow conformational transitions.
We investigate the irreversible evolution of a small system in which a chemical reaction takes place.We have two main goals: the first requires to find an equation to produce a time-irreversible behavior,the second consists in introducing a simple exactly solvable model in order to understand basic facts in chemical kinetics.Our basic tool is the transition function counting the number of paths joining two points in the reactive coordinates system.An exact quantum Smoluchowski equation is derived for the reactive system in vacuum, in the presence of a solvent in equilibrium at any time with the reactive system a new Smoluchowski equation is obtained.The transition from a quantum regime to a classical one is discussed.The case of a reactive system not in equilibrium with its neighborhood is investigated in terms of path integral and via a partial differential function.Memory effects and closure assumptions are discussed.Using a simple potential model, the chemical rate constant is exactly calculated and questions such as the meaning of the activation energy or the physical content of the so-called prefactor are investigated.
Our recently proposed quantum approach to biomolecular recognition processes is hereby additionally supported by biomolecular Resonant Recognition Model and by quantum-chemical theory of biomolecular non-radiative resonant transitions. Previously developed general quantumdecoherence framework for biopolymer conformational changes in very selective ligandproteins/ target-receptors key/lock biomolecular recognition processes (with electron-conformational coupling, giving rise to dynamical modification of many-electron energy-state hypersurface of the cellular quantum-ensemble ligand-proteins/target-receptors biomolecular macroscopic quantum system, with revealed possibility to consider cellular biomolecular recognition as a Hopfield-like quantum-holographic associative neural network) is further extended from nonlocal macroscopicquantum level of biological cell to nonlocal macroscopic-quantum level of biological organism, based on long-range coherent microwave excitations (as supported by macroscopic quantum-like microwave resonance therapy of the acupuncture system) - which might be of fundamental importance in understanding of underlying macroscopic quantum (quantum-holographic Hopfieldlike) control mechanisms of embryogenesis/ontogenesis and morphogenesis, and their backward influence on the expression of genes.
The rapid development of the chemical industry and science and new challenges in the field of health care put forward increased demands for the development of the theory of organic and inorganic chemistry, biochemistry and biophysics, the search and implementation of new modelling and analysis methods, and the improvement of technological processes. One of the safe and fast methods of researching the properties and behavior of new materials and tools is the modelling of relevant experiments, in particular, computer molecular modelling based on mathematical models. Modelling the interactions between micro and macromolecules at the quantum level allows us to manipulate the substances’ electronic, magnetic, optical and other characteristics and consider the possibilities of creating new chemical bonds, molecular structures, phase transitions, quantum states, and so on. Accordingly, the main idea of our research is to apply the technology of algebraic modelling and quantum-chemical apparatus for the simulation and verification of experiments in physics, chemistry, and biology areas. The use of formal algebraic methods allows proving properties and finding relevant scenarios for the effective analysis of the behavior of various objects in real-time, considering not individual scenarios but sets of possible behaviors. At this research stage, we have developed a methodology for formalization complex organic and inorganic substances, chemical processes and reactions based on the formalization of the interaction of atoms and molecules at the level of quantum interactions.