Programmed algorithm for simulating molecular chemistry trend motion

Abstract

The invention discloses a programmed algorithm for simulating molecular chemical trend motion, which comprises the following steps of: establishing a finite element model related to receptor and ligand cross diffusion, and strictly deducing an analytical equation for unifying molecular chemotaxis behaviors from a statistical thermodynamics basic framework; developing a core algorithm capable of deducing the special motion process, flow field configuration and fluid properties serving as input parameters, giving numerical simulation to the molecular chemotaxis system, and using the molecular chemotaxis system for predicting and checking experiment results. According to the method, the first principle is followed, a dominance equation for describing molecular chemotaxis is completely derivedfrom the basis of a basic statistical thermodynamics theorem, trial mathematical expression and empirical parameter definition are not needed, and a general model is established; a motion equation isconverted into a core algorithm of a program, the motion trend and related effects of a specific molecular binding system are efficiently simulated on the basis of the properties of an actual system,and a quantitative prediction result is output and used for data mining and comparison.

Description

technical field [0001] The invention belongs to the field of finite element analysis of complex chemical fluids, in particular to a program algorithm for simulating molecular chemical tendency movement. Background technique [0002] The spontaneous migration of enzyme molecules to their substrates in microfluidic chips has been widely reported, but the mechanism of the catalyzed chemical tendency movement has not been resolved so far, leading to many controversial views in this field, and some research conclusions are even contradictory. For example, in 2015, Nature reported that using single-molecule fluorescence correlation spectroscopy, it was found that in the intrinsic exothermic catalytic process of urease, laccase, and alkaline phosphatase, the self-diffusion coefficient gradually increased, and was related to the substrate concentration and time. There is a linear correlation, and the fitting slope is related to the conversion frequency of each enzyme to the substrat...

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Problems solved by technology

On the other hand, although the enthalpy change of the catalytic reaction is generally more significant, Professor Golestanian of the Max Planck Institute in Germany has found that the temperature of the actual reaction micro-zone has only increased by less than 1 / 1000K; he also found that in the glycolytic metabolism The diphosphofructase catalyzes the endothermic reaction of fructose-1,6-bisphosphate, and also has all the chemotactic behavior characteristics catalyzed by exothermic enzymes

However, such as diffusion swimming, diffusion osmosis, etc. are non-equilibrium migration in nature, which is inconsistent with the specific recognition of enzyme-substrate dominated by chemical equilibrium; There are significant differences in the way

In the final analysis, it is precisely because of the lack of understanding of the nature of the molecular motion picture that tentatively introducing concepts such as "enhanced diffusion"; The center of mass of the impulse and conformation shifts, and then imagines the instantaneous differential stress of the solvent (the so-called "chemical acoustic surface wave"), etc., in this way, a series of micromechanical models are assumed, so that the predicted results are all in line with the actual observations. large deviation

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