Programmed algorithm for simulating molecular chemistry trend motion

A technology of molecular chemistry and program algorithm, applied in the field of finite element analysis of complex chemical fluids, can solve problems such as differences in bonding methods, discrepancies in enzyme-substrate specific recognition, deviations, etc.

Active Publication Date: 2020-12-29
NANJING UNIV OF SCI & TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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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 r

Method used

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  • Programmed algorithm for simulating molecular chemistry trend motion
  • Programmed algorithm for simulating molecular chemistry trend motion
  • Programmed algorithm for simulating molecular chemistry trend motion

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Experimental program
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Embodiment 1

[0048] This embodiment provides a figure 1 A hydrodynamic approach to the receptor / ligand association in the modeling scenario shown. Specific steps are as follows:

[0049] Step 1: Following the McMillan-Mayer solution theory detailed in Hill's "An Introduction to Statistical Thermodynamics" and Schellman's "Macromolecular Binding" papers, we analyze the equilibrium state of a region of space Properties, its volume is V, larger than the molecular scale, but smaller on the macroscopic scale, and maintains a constant temperature T.

[0050] In addition to being open to the environment and the chemical potential μ s In addition to the constant solvent (to simplify the model, only one solvent is set at present, but the whole formal system is fully applicable to multi-solvent conditions), the volume is open to the fluid of three solute species u={P 0 , L 0 ,PL}, corresponding to free receptor, free ligand, and receptor-ligand complex, respectively. Then we can get the thermod...

Embodiment 2

[0093] This embodiment provides a program algorithm for numerical simulation figure 1 Chemotaxis behavior due to dynamic coupling of molecules in the shown microchannel. Based on the above model, the code was written and compiled in the development environment of FORCE 2.0 FORTRAN Editor (free download link http: / / force.lepsch.com). The specific algorithm flow is as follows:

[0094] Step 1: Equilibrium approximation. At position R, the instantaneous association and dissociation between the substrate and the product is the premise assumption, which means that the lateral diffusion of the reactant becomes the rate-determining step, which ensures that the numerical simulation evolves towards the chemical equilibrium state with the passage of time:

[0095] k f · c P (R)·c L (R)=k b · c PL (R) (22)

[0096] Based on mass conservation, there is c P (R)=c P0 (R)-c PL (R), where c P0 (R) corresponds to the initial concentration of the receptor, k f and k b are the forwa...

Embodiment 3

[0119] This embodiment provides a method for simulating figure 1 The optimization algorithm for ligand association-induced receptor chemotaxis in the scenario shown, the matching simulation program was generated in the development environment of Wolfram Mathematica v10.2, and the specific steps are as follows:

[0120] Step 1: Consider a three-diluted component: free receptor (R 0 ), free ligand (L 0 ) and a solution of the receptor-ligand (RL) complex. Assuming that at each space point in solution, R, ligand and receptor are in bonding equilibrium, their equilibrium dissociation constant, K D :

[0121]

[0122] in, is a dimensionless association constant, and c 0 is a reference concentration.

[0123] definition and as the total concentration of receptor and ligand respectively; define μ R and μ L is the corresponding effective chemical potential, taking into account c R and c L equilibrium distribution. For each substance as a whole, α=R or L, the effecti...

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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...

Claims

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Application Information

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IPC IPC(8): G06F30/23G06F30/28G16C10/00G06F111/10G06F113/08G06F119/14
CPCG06F30/23G06F30/28G16C10/00G06F2111/10G06F2113/08G06F2119/14
Inventor 邓盛元杨萌李大力李元生马科锋
Owner NANJING UNIV OF SCI & TECH
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