A bactericide evaluation method based on coarse-grained molecular dynamics simulation

Abstract

The application discloses a bactericide evaluation method based on coarse-grained molecular dynamics simulation and relates to the technical field of oilfield development. The bactericide evaluation method based on coarse-grained molecular dynamics simulation comprises the following steps: S1, constructing coarse-grained models of water molecules, bactericide molecules and bacterial cell membrane lipid molecules in a Materials Studio software; S2, modifying interaction parameters and force field types of the coarse-grained models of the water molecules, the bactericide molecules and the bacterial cell membrane lipid molecules; S3, constructing a water-bactericide-bacterial cell membrane mixed model according to the coarse-grained models of the water molecules, the bactericide molecules and the bacterial cell membrane lipid molecules; S4, performing geometric structure optimization on the water-bactericide-bacterial cell membrane mixed model and then performing coarse-grained molecular dynamics simulation; and S5, evaluating the bactericidal effect of the bactericide. The application solves the problems of large bactericide restriction, complex evaluation process, high requirement for equipment and many interference factors.

Description

Technical Field

[0001] This invention relates to the field of oilfield development technology, and specifically to a method for evaluating bactericides based on coarse-grained molecular dynamics simulation. Background Technology

[0002] In the field of oil and gas engineering, particularly in oilfield reinjection water treatment and unconventional gas production systems, the use of bactericides is a key measure to prevent microbial growth and maintain the efficiency of the production system. These systems have complex aquatic environments rich in organic matter, providing ideal growth conditions for microorganisms. If left uncontrolled, microbial proliferation can lead to equipment corrosion, pipe blockage, and reduced water treatment efficiency. Therefore, the selection and evaluation of bactericides is a crucial step.

[0003] Currently, the industry generally follows standards such as SY / T 5757-2010 "General Technical Conditions for Bactericides in Oilfield Injection Water", SY / T6397-1999 "Evaluation Methods for Bactericides for Drilling Fluids", and SY / T 5329-2022 "Technical Requirements and Analytical Methods for Water Quality Indicators in Clastic Rock Reservoirs". The erasure dilution method recommended in these standards is a classic evaluation method. This method determines the bactericidal effect by gradually diluting and culturing water samples. Although it can provide accurate bacterial survival data, the process is time-consuming, requiring a culturing period of up to 14 days, and has extremely high requirements for the aseptic environment. Once the culture medium is contaminated or an operational error occurs, the process must be repeated, which greatly reduces the efficiency of screening and evaluation and limits the ability to quickly respond to market demands.

[0004] Furthermore, to address this issue, some attempts have been made to adopt faster evaluation methods, such as the rapid evaluation method for bactericides in oilfield reinjection water described in patent publication number CN 106770076A, which uses ATP detection technology to assess the bactericidal effect. Although this method can shorten the evaluation time, it relies on complex equipment, has high requirements for sample pretreatment, and non-target sources of ATP in the environment may introduce interference, affecting the accuracy of the results.

[0005] Given the limitations of existing technologies, especially the need to improve evaluation efficiency and accuracy, the development of a new evaluation method is particularly urgent. This new method needs to be able to accurately predict the performance of fungicides while significantly reducing experimental workload and accelerating the fungicide research and development process. Summary of the Invention

[0006] The technical problem to be solved by the present invention is that some conventionally used fungicide evaluation methods have significant limitations on the screening and development of fungicides, while others have problems such as complex evaluation processes, high equipment requirements, and large interference factors. The purpose is to provide a fungicide evaluation method based on coarse-grained molecular dynamics simulation, which solves the problems of large restrictions on fungicides, complex evaluation processes, high equipment requirements, and large interference factors.

[0007] This invention is achieved through the following technical solution:

[0008] A method for evaluating fungicides based on coarse-grained molecular dynamics simulations, including

[0009] S1. Construct coarse-grained models of water molecules, bactericide molecules, and bacterial cell membrane lipid molecules in Materials Studio software;

[0010] S2. Modify the interaction parameters and force field type of the coarse-grained model of water molecules, bactericide molecules, and bacterial cell membrane lipid molecules;

[0011] S3. Construct a water-bactericide-bacterial cell membrane hybrid model based on a coarse-grained model of water molecules, bactericide molecules, and bacterial cell membrane lipids;

[0012] S4. Optimize the geometric structure of the water-bactericide-bacterial cell membrane hybrid model, and then perform coarse-grained molecular dynamics simulation.

[0013] S5. After the simulation process is completed, the radius of gyration of the bacterial cell membrane structure in the system with each bactericide added is calculated at each time point, and the evolution law of the radius of gyration of the bacterial cell membrane structure in the system with each bactericide added is analyzed to evaluate the bactericidal effect of the bactericide.

[0014] As one possible design, step S1 above specifically involves using the mesoscopic system construction tool Coarse Grain in Materials Studio software to construct water molecules and bactericide molecules, and using Bead Types to construct a coarse-grained model of bacterial cell membrane lipid molecules.

[0015] As one possible design, the process of constructing coarse-grained models of water molecules and bactericide molecules using the mesoscopic system construction tool Coarse Grain, and bacterial cell membrane molecules using Bead Types, includes:

[0016] S11. Construct the molecular structures of water and disinfectants in Materials Studio software;

[0017] S12. Optimize the molecular structures of water and disinfectants using the Geometry Optimization task of the Forcite module;

[0018] S13. The molecular structures of water and bactericides were divided into multiple motion units using the Motion groups method of Coarse Grain, a mesoscopic system construction tool.

[0019] S14. By defining and classifying the types of motion units, a coarse-grained model of water molecules and bactericide molecules is constructed.

[0020] S15. Use the mesoscopic system construction tool Bead Types to define bead properties, and set the atomic mass and radius of the beads;

[0021] S16. Use the Build Mesomolecule function to construct a coarse-grained model of bacterial cell membrane lipid molecules.

[0022] As one possible design, step S2 specifically involves opening the MS Martini file in the Project menu and modifying the bond angle parameters of the interactions; then, in the Mesocite Preparation Option function, modifying the MS Martini force field type of the coarse-grained models for water, bactericides, and bacterial cell membranes. After the coarse-grained models are built, the geometry is optimized using the Mesocite Geometry Optimization function to bring the model to a low-energy state.

[0023] As one possible design, step S2 above includes:

[0024] S21. Use the Mesocite Forcefield Manager feature to import the MS Martini file into the current project;

[0025] S22. Open the MS Martini.off file in the Project and modify the bond angle parameters of the interaction between beads inside the bacterial cell membrane lipid coarse-grained model;

[0026] S23. In the Forcefield of Mesocite Calculation, select the MS Martini.off file in the Project and modify the force field type for all beads.

[0027] S24. Define the head and tail of the coarse-grained bacterial cell membrane model in Bead Packing Options. Specifically, open the MS Martini file in the Project menu and modify the interaction parameters, including the angle of contact and bond strength; modify the MS Martini force field type for water molecules, bacterial cell membrane molecules, and bactericide molecules in the Mesocite Preparation Option function.

[0028] Step S3 includes:

[0029] S31. Build the basic simulation framework using the Build Mesostructure Template function;

[0030] S32. Add the coarse-grained model from step S2 to the basic simulation framework to obtain a water-bactericide-bacterial cell membrane hybrid model.

[0031] As a possible design, the geometry optimization process in step S4 above includes: in the Geometry Optimization task of the Mesocite module, the constructed coarse-grained model is iteratively optimized by sequentially or in combination using the steepest descent method, Newton's iteration method and quasi-Newton method to achieve the goal of minimizing the model energy.

[0032] As one possible design, the coarse-grained molecular dynamics simulation in step S4 above includes: relaxing the water-bactericide-bacterial cell membrane mixture model using the NPT ensemble for 200 ps, ​​and then using the NVT ensemble to perform coarse-grained molecular dynamics simulation on the water-bactericide-bacterial cell membrane mixture model for 5000 ps.

[0033] As one possible design, the analysis of the evolution of the bacterial cell membrane structure radius of gyration in the system of each bactericide in step S5 above is specifically as follows: the structural parameters include the bacterial cell membrane structure radius of gyration and the difference between the gyration radii.

[0034] The specific method for evaluating the bactericidal effect of a bactericide based on its structural parameters is as follows:

[0035] The difference in gyration radius is obtained based on the gyration radius. The gyration radius and the difference in gyration radius are plotted separately. First, the fluctuation difference is compared in the bacterial cell membrane gyration radius plot, and then the change in the curve value is compared in the gyration radius difference plot.

[0036] As one possible design, the aforementioned radius of gyration is calculated using the following formula:

[0037]

[0038] In the formula,

[0039] S: Radius of gyration of the molecule;

[0040] mi: the mass of the i-th atom in the molecule;

[0041] Si: The distance from the i-th atom to the center of molecular mass;

[0042] N: The number of atoms in the molecule;

[0043] The difference in the radius of gyration is obtained by subtracting the value at the starting point of time from the value of the radius of gyration at each time point:

[0044] S t =S-S0 (2)

[0045] In the formula,

[0046] S: Radius of gyration in the coarse-grained model of cell membrane lipids;

[0047] St: The distance from the lipid molecule to the mass center of the coarse-grained lipid model of the cell membrane at time t;

[0048] S0: The distance from the lipid molecule to the mass center of the coarse-grained lipid model of the cell membrane at the initial moment.

[0049] Compared with the prior art, the present invention has the following advantages and beneficial effects:

[0050] This invention accurately predicts the bactericidal performance of bactericides by analyzing their molecular structural characteristics, thereby significantly reducing experimental workload and accelerating the screening and development process of bactericides. It can analyze the interaction between bactericides and bacterial cell membranes under given parameters, and analyze the magnitude of the influence of each variable; reducing the workload of bactericide evaluation and quickly obtaining evaluation results; providing theoretical support for bactericide screening; and understanding the changes in bacterial cell membranes under different initial conditions through frame-by-frame analysis and calculation results.

[0051] The inventors have discovered that bacterial cell membranes, under normal conditions, have relatively stable morphology and size, and therefore a relatively stable radius of gyration. However, when bactericide molecules act on the bacterial cell membrane, they interact with the membrane structure. If the bactericide disrupts the interactions between lipid molecules, such as hydrophobic interactions or hydrogen bonds, the arrangement of lipid molecules becomes disordered. This disorder alters the spatial expansion or contraction of the membrane structure, correspondingly increasing or decreasing the radius of gyration. For example, if the bactericide inserts into the phospholipid bilayer, increasing the intermolecular spacing and making the structure looser, the radius of gyration will increase; conversely, if the bactericide causes lipid molecules to aggregate or the membrane to collapse, the radius of gyration will decrease. Therefore, the degree of damage to the membrane by the bactericide can be determined by observing changes in the radius of gyration. Therefore, by comparing the fluctuation differences in the bacterial cell membrane radius of gyration diagram of the simulated process, this invention can determine the degree of disturbance of membrane lipid molecules by different bactericide molecules; by comparing the changes in the radius of gyration of the membrane structure at the initial time and at each stage in the bacterial cell membrane radius of gyration difference diagram of the simulated process, the invention can determine the degree of damage to membrane lipid molecules by different bactericide molecules. Attached Figure Description

[0052] To more clearly illustrate the technical solutions of the exemplary embodiments of the present invention, the accompanying drawings used in the embodiments will be briefly described below. It should be understood that the following drawings only show some embodiments of the present invention and should not be considered as a limitation of the scope. For those skilled in the art, other related drawings can be obtained based on these drawings without creative effort. In the drawings:

[0053] Figure 1 The diagram shows the radius of gyration of the bacterial cell membrane structure (a) and the difference in the radius of gyration of the bacterial cell membrane in the system after adding various bactericides during the simulation process in Example 1 of the present invention (b).

[0054] Figure 2 This is the water-bactericide-bacterial cell membrane mixture model in Example 1 of the present invention;

[0055] Figure 3 This refers to the test results of the blank group (without bactericide) in Experiment Example 1 of this invention;

[0056] Figure 4 The results of the test for bactericide No. 1 in Experimental Example 1 of this invention;

[0057] Figure 5 The results of the test for bactericide No. 2 in Experimental Example 1 of this invention;

[0058] Figure 6 The results of the test for bactericide No. 3 in Experimental Example 1 of this invention;

[0059] Figure 7 The results are from the test of bactericide No. 4 in Experimental Example 1 of this invention. Detailed Implementation

[0060] To make the objectives, technical solutions, and advantages of this invention clearer, the invention will be further described in detail below with reference to embodiments and accompanying drawings. The illustrative embodiments and descriptions of this invention are for explanation only and are not intended to limit the invention. Unless otherwise specified in the embodiments, conventional conditions or conditions recommended by the manufacturer shall apply. Reagents or instruments whose manufacturers are not specified are all commercially available conventional products.

[0061] A method for evaluating fungicides based on coarse-grained molecular dynamics simulations, comprising:

[0062] S1. Construct coarse-grained models of water molecules, bactericide molecules, and bacterial cell membrane lipid molecules in Materials Studio software;

[0063] By constructing the model, a basic structure is provided for subsequent simulations, and coarse-grained representations of bacterial cell membranes, water molecules, and bactericide molecules are generated, simplifying atomic-level details and making it easier to focus on key interactions.

[0064] In some embodiments of the present invention, step S1 specifically involves using the mesoscopic system construction tool Coarse Grain in Materials Studio software to construct water molecules and bactericide molecules, and using Bead Types to construct a coarse-grained model of bacterial cell membrane lipid molecules.

[0065] Initialize using the default parameters of the MS Martini force field to ensure that all beads have uniform physical properties, which facilitates simulation consistency and simplifies complexity.

[0066] In some embodiments of the present invention, the process of constructing water molecules and bactericide molecules using the mesoscopic system construction tool Coarse Grain, and constructing coarse-grained models of bacterial cell membrane molecules using Bead Types, includes:

[0067] S11. Construct the molecular structures of water and disinfectants in Materials Studio software;

[0068] S12. Optimize the molecular structures of water and disinfectants using the Geometry Optimization task of the Forcite module;

[0069] S13. The molecular structures of water and bactericides were divided into multiple motion units using the Motion groups method of Coarse Grain, a mesoscopic system construction tool.

[0070] S14. By defining and classifying the types of motion units, a coarse-grained model of water molecules and bactericide molecules is constructed.

[0071] S15. Use the mesoscopic system construction tool Bead Types to define bead properties, and set the atomic mass and radius of the beads;

[0072] S16. Use the Build Mesomolecule function to construct a coarse-grained model of bacterial cell membrane lipid molecules.

[0073] The aforementioned beads are basic units in simplified models of coarse-grained molecular dynamics simulations, representing a group of atoms or molecules. These beads are not single atoms, but rather represent collections of multiple atoms, and their properties (such as mass and radius) are based on the average characteristics of the represented atoms or molecules. Defining beads can significantly reduce the computational burden of simulations, enabling simulations on larger time and spatial scales; it helps in understanding the behavior of macromolecules such as proteins and lipids in biological membranes; and it reduces computational resource requirements while maintaining a description of the system's key physical properties. This invention, by defining beads, ensures model consistency and physical realism, as well as consistency during simulation. The selection of these parameters is based on empirical data and theoretical models to ensure that, while simplifying, the key physicochemical properties affecting bactericidal efficacy are captured. In this way, researchers can effectively simulate how bactericidal molecules interact with bacterial cell membranes, thereby evaluating their bactericidal efficacy.

[0074] In some embodiments of the present invention, after the above coarse-grained model is constructed, the geometric structure is optimized by the Mesocite GeometryOptimization function to make the model reach a low-energy state.

[0075] Optionally, the lipid molecules in the bacterial cell membrane refer to dipalmitoylphosphatidylcholine (DPPC), and the description of the bacterial cell membrane in this invention is similar.

[0076] Dipalmitoylphosphatidylcholine (DPPC) plays a crucial role in the structure of biological membranes, and its structural characteristics make it an ideal choice for simulating bacterial cell membranes: First, due to its long-chain saturated fatty acid (palmitic acid), DPPC can simulate the hydrophobic tail interactions of phospholipids and the hydrophilicity of phospholipid heads in bacterial cell membranes, which is essential for understanding the stability of lipid bilayers; Second, it exhibits good orderliness; Third, DPPC can exhibit phase transition behavior at different temperatures, from liquid to solid, which helps to simulate the dynamic changes of cell membranes under different conditions; Fourth, using a single type of phospholipid such as DPPC can reduce the variables in the simulation, facilitating the study of how bactericides affect the structure and stability of membranes.

[0077] S2. Modify the interaction parameters and force field type of the coarse-grained model of water molecules, bactericide molecules, and bacterial cell membrane lipid molecules.

[0078] By modifying the interaction parameters and force field type, the simulation can more accurately reflect actual chemical and physical interactions, helping to capture subtle differences in the interaction between bactericides and cell membranes.

[0079] In some embodiments of the present invention, step S2 specifically involves opening the MS Martini file in the Project menu, modifying the bond angle parameters of the interactions, and modifying the MS Martini force field type of water molecules, bacterial cell membrane molecules, and bactericide molecules in the Mesocite Preparation Option function.

[0080] In some embodiments of the present invention, step S2 above includes:

[0081] S21. Use the Mesocite Forcefield Manager feature to import the MS Martini file into the current project;

[0082] S22. Open the MS Martini.off file in the Project and modify the bond angle parameters for the interaction between beads;

[0083] S23. In the Forcefield of Mesocite Calculation, select the MS Martini.off file in the Project and modify the force field type for all beads.

[0084] S24. Define the head and tail of the coarse-grained model in the Bead Packing Options.

[0085] S3. Construct a water-bactericide-bacterial cell membrane hybrid model based on a coarse-grained model of water molecules, bactericide molecules, and bacterial cell membrane lipid molecules.

[0086] By constructing a hybrid model, a comprehensive simulation environment can be created, thereby realistically simulating the interaction between bactericides and bacterial cell membranes in aqueous solutions, which facilitates the acquisition of the penetration mechanism of bactericides and the response of cell membranes.

[0087] In some embodiments of the present invention, step S3 above includes:

[0088] S31. Build the basic simulation framework using the Build Mesostructure Template function;

[0089] S32. Add the coarse-grained model from step S2 to the basic simulation framework to obtain a water-bactericide-bacterial cell membrane hybrid model.

[0090] S4. Optimize the geometric structure of the water-bactericide-bacterial cell membrane hybrid model, and then perform coarse-grained molecular dynamics simulation.

[0091] By combining geometric optimization and coarse-grained molecular dynamics simulation, dynamic processes under real-world conditions can be simulated.

[0092] In some embodiments of the present invention, the geometric optimization process in step S4 above includes: in the Geometry Optimization task of the Mesocite module, the constructed coarse-grained model is iteratively optimized by comprehensively applying the steepest descent method, Newton's iteration method and quasi-Newton method to achieve the goal of minimizing model energy.

[0093] In some embodiments of the present invention, the coarse-grained molecular dynamics simulation in step S4 above includes: relaxing the water-bactericide-bacterial cell membrane mixture model using the NPT ensemble for 200 ps, ​​and then using the NVT ensemble to perform coarse-grained molecular dynamics simulation on the water-bactericide-bacterial cell membrane mixture model for 5000 ps.

[0094] The NPT and NVT ensembles simulate isobaric and isothermal conditions, respectively, which are closer to the actual state of biological systems and help to evaluate the long-term effects and stability of fungicides.

[0095] S5. After the simulation process is completed, the radius of gyration of the bacterial cell membrane structure in the system with each bactericide added is calculated at each time point, and the evolution law of the radius of gyration of the bacterial cell membrane structure in the system with each bactericide added is analyzed to evaluate the bactericidal effect of the bactericide.

[0096] In some embodiments of the present invention, the evolution of the radius of gyration of the bacterial cell membrane structure in the system with each bactericide added in step S5 is specifically as follows:

[0097] The difference in gyration radius is obtained based on the gyration radius. The gyration radius and the difference in gyration radius are plotted separately. First, the fluctuation difference is compared in the bacterial cell membrane gyration radius plot, and then the change in the curve value is compared in the gyration radius difference plot.

[0098] Changes in the radius of gyration reflect structural disturbances in the cell membrane and are one of the indicators for assessing bactericidal activity. Data analysis can scientifically determine the efficiency and mechanism of action of bactericides.

[0099] In some embodiments of the present invention, the above-mentioned radius of gyration is calculated by the following formula:

[0100]

[0101] In the formula,

[0102] S: Radius of gyration of the molecule;

[0103] mi: the mass of the i-th atom in the molecule;

[0104] Si: The distance from the i-th atom to the center of molecular mass;

[0105] N: The number of atoms in the molecule;

[0106] The difference in the radius of gyration is obtained by subtracting the value at the starting point of time from the value of the radius of gyration at each time point:

[0107] S t =S-S0 (2)

[0108] In the formula,

[0109] S: Radius of gyration in the coarse-grained model of cell membrane lipids;

[0110] S t : The distance from the lipid molecule to the center of mass of the coarse-grained lipid model of the cell membrane at time t;

[0111] S0: The distance from the lipid molecule to the mass center of the coarse-grained lipid model of the cell membrane at the initial moment.

[0112] By analyzing the changes in the radius of gyration of the bacterial cell membrane in the trajectory file of the simulation process, the relationship between the perturbation and deformation of the DPPC structure by different bactericide molecules can be characterized, thereby predicting the structure-activity relationship of different bactericide molecules. Four bactericides were selected (refer to...). Figure 2 The bactericidal effect of each bactericide is determined by the evaluation method provided in this invention, and the reliability of the method is verified by comparing it with the bactericidal performance test data.

[0113] Example 1

[0114] A method for evaluating fungicides based on coarse-grained molecular dynamics simulations includes the following steps:

[0115] S1. In Materials Studio software, beads are defined using Bead Type, and a coarse-grained model of the bactericide molecule is constructed using the MS Copolymer function. First, the molecular structures of water and the bactericide are constructed in Materials Studio. Second, the molecular structures of water and the bactericide are optimized using the Geometry Optimization task in the Forcite module. Then, the Motion groups method of the Coarse Grain mesoscopic system construction tool is used to divide the molecular structures of water and the bactericide into multiple motion units. Finally, by defining and classifying the types of each motion unit, a coarse-grained model of the water molecule and the bactericide molecule is constructed.

[0116] S2. First, use the Mesocite Forcefield Manager function to save the MS Martini.off file and modify the bond angle between the beads to 120°. Then, in the Forcefield of Mesocite Calculation, select the MS Martini.off file in the Project and modify the force field type for all beads. Finally, define the head and tail of the coarse-grained model in BeadPacking Options.

[0117] S3. Construct a "water-bactericide-bacterial cell membrane hybrid model" (refer to...) Figure 6 Use the Build MesostructureTemplate function to build the most basic simulation framework; finally, add the corresponding coarse-grained model on the built framework.

[0118] S4. First, the geometric structure of the "water-bactericide-bacterial cell membrane hybrid model" constructed in step S3 is optimized by comprehensively applying the steepest descent method, Newton's iteration method, and quasi-Newton method. Second, the "water-bactericide-bacterial cell membrane hybrid model" with modified MSMartini force field is relaxed using the NPT ensemble for 200 ps. Finally, the "water-bactericide-bacterial cell membrane hybrid model" is simulated using the NVT ensemble with coarse-grained molecular dynamics for 5000 ps.

[0119] S5. Analyze the simulation results, calculate the radius of gyration and the difference in radius of gyration of the bacterial cell membrane, and determine the effect of the fungicide: Analyze the Relative Concentration data using the Mesocite Analysis function and import the data into Excel; obtain the radius of gyration of each fungicide using the radius of gyration calculation formula; subtract the value at the starting point from the value at each time point to obtain the difference in radius of gyration.

[0120] Plot all curves on a single graph and compare them using a two-step method: First, compare the fluctuation differences in the bacterial cell membrane radius of gyration diagram (see...). Figure 1 a) The second step is to compare the changes in the curve values ​​in the radius of gyration difference graph (refer to...). Figure 1 b).

[0121] from Figure 1 (a) It can be seen that the fluctuation range of fungicides No. 2 and No. 4 is significantly greater than that of fungicides No. 1 and No. 3. Therefore, the fungicidal effect of fungicides No. 2 and No. 4 is better than that of fungicides No. 1 and No. 3.

[0122] from Figure 1 (b) It can be seen that the curve of fungicide No. 3 is higher than that of fungicide No. 1. Therefore, fungicide No. 3 is better than fungicide No. 1. Similarly, fungicide No. 4 is better than fungicide No. 2.

[0123] In summary, the order of bactericidal effect is: Bactericide No. 4 ≥ Bactericide No. 2 ≥ Bactericide No. 3 > Bactericide No. 1.

[0124] Experimental Example 1

[0125] The bactericidal performance of four bactericides was tested:

[0126] Sterilization of test items: Before the test, all heat-resistant devices and consumables were sterilized in an autoclave. The procedure was as follows: the items to be sterilized were placed in the autoclave and heated; when the temperature reached 105℃, the pressure relief valve was opened to release the cold air inside the autoclave, then the pressure relief valve was closed and heating continued; when the pressure rose to 1.15MPa, the pressure relief valve was opened to reduce the pressure to 1.05MPa, and sterilization was carried out under these conditions for 20 minutes. For some items that could not be sterilized in an autoclave, ultraviolet light sterilization for more than 30 minutes should be used.

[0127] Culture medium preparation: The SRB strain used in the experiment was isolated from formation water in an injection well of a shale gas field in China. SRB liquid culture medium was prepared according to NACE TMO 194-94 standard. The composition of the culture medium was: 1g yeast extract, 0.1g ascorbic acid, 4mL sodium lactate, 0.01g K₂HPO₄, 0.2g MgSO₄·7H₂O, 10g NaCl, 0.2g ferrous ammonium sulfate, and 1000mL deionized water. The culture medium needed to be sterilized using an autoclave. Heat-sensitive chemicals were added after a period of cooling following sterilization, and contact with chemicals was avoided as much as possible after removal to ensure sterility. During the sterilization process, the temperature was maintained at 120℃ for 20 minutes, followed by deoxygenation with N₂ for 2 hours.

[0128] SRB culture: A 10% (v / v) concentration of SRB bacterial culture was inoculated into the culture medium and then placed in a constant temperature water bath at 35°C. After 5 days, the number of SRB reached its peak and remained stable.

[0129] Formation water preparation: Based on the composition of produced water from a gas field in China, the simulated formation water composition should be 5.2g KCl, 18g NaCl, 0.8g CaCl2, 0.3g Na2SO4, 0.1g MgCl2, and 0.5g NaHCO3.

[0130] Test solution preparation: The test solution is prepared by adding 10% culture medium solution to simulated formation water.

[0131] Sterilization test: Take 200 mL of cultured bacterial solution and add different sterilizing agents at a concentration of 100 ppm. Count the bacteria 24 hours after adding the sterilizing agent. The SRB counting method adopts the erasure dilution method (triple replication method), with a total of 10 dilution levels. Each dilution level has three identical vials containing 9 mL of SRB culture medium. Take 1 mL of the test sample and inject it into the level 0 vial. Shake well, then take 1 mL of the solution from the level 0 vial and inject it into the level 1 vial. The syringe used for each liquid collection is disposable to avoid affecting the final result. Continue in this manner until the 9th dilution level is reached. Incubate all vials at 35°C for 14 days.

[0132] The principle for determining growth indicators is as follows: Starting from the dilution level where a negative sample appears, select three dilution levels sequentially. Count the number of positive samples at each dilution level to obtain an index (if the index is 000, advance one level; if there are fewer than three dilution levels, advance until three levels are reached). Multiply the index by the water sample's dilution factor 10n (where n is the number of dilutions before the index level) to obtain the growth indicator (summarized according to section 5.6.5.3 of SY / T 5329—1994). Consult the corresponding bacterial count table, substitute the bacterial count obtained from the index, and you will get the content of that bacterium in the water sample (cells / mL).

[0133] The experimental results are shown in Table 1. Bottles 1 through 10 in the table are all vials containing 9 mL of SRB culture medium. Levels 0-9 represent dilution levels, with level 0 being undiluted and each level representing a 10-fold dilution. Take 1 mL of the sample to be tested into bottle 1 (level 0); use a new syringe to take 1 mL from bottle 1 into bottle 2 (level 1); use another new syringe to take 1 mL from bottle 2 into bottle 3 (level 2), and so on, until 1 mL from bottle 9 into bottle 10 (level 9). "+" represents a positive bottle, and "-" represents a negative bottle. Figure 3-7 As shown, the white bottle is the negative bottle, which contains no SRB, and the black bottle is the positive bottle, which contains SRB.

[0134] Table 1. Results of bactericidal performance test

[0135]

[0136]

[0137] As can be seen from the table above, the order of bactericidal effect is: Bactericide No. 4 > Bactericide No. 2 > Bactericide No. 3 > Bactericide No. 1. Clearly, the test results of the bactericides are consistent with the simulation results of Example 1, and the bactericidal test results verify that the method provided by this invention has good accuracy.

[0138] The specific embodiments described above further illustrate the purpose, technical solution, and beneficial effects of the present invention. It should be understood that the above description is only a specific embodiment of the present invention and is not intended to limit the scope of protection of the present invention. Any modifications, equivalent substitutions, improvements, etc., made within the spirit and principles of the present invention should be included within the scope of protection of the present invention.

Claims

1. A method for evaluating bactericides based on coarse-grained molecular dynamics simulation, characterized in that, include S1. Construct coarse-grained models of water molecules, bactericide molecules, and bacterial cell membrane lipid molecules in Materials Studio software; S2. Modify the interaction parameters and force field type of the coarse-grained model of water molecules, bactericide molecules, and bacterial cell membrane lipid molecules; S3. Construct a water-bactericide-bacterial cell membrane hybrid model based on a coarse-grained model of water molecules, bactericide molecules, and bacterial cell membrane lipids; S4. Optimize the geometric structure of the water-bactericide-bacterial cell membrane hybrid model, and then perform coarse-grained molecular dynamics simulation. S5. After the simulation process is completed, the radius of gyration of the bacterial cell membrane structure in the system with each bactericide added is calculated at each time point, and the evolution law of the radius of gyration of the bacterial cell membrane structure in the system with each bactericide added is analyzed to evaluate the bactericidal effect of the bactericide.

2. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 1, characterized in that, Specifically, step S1 involves using the mesoscopic system construction tool Coarse Grain in Materials Studio software to construct water molecules and bactericide molecules, and using Bead Types to construct a coarse-grained model of bacterial cell membrane lipid molecules.

3. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 2, characterized in that, The process of constructing coarse-grained models of water molecules and bactericide molecules using the mesoscopic system construction tool Coarse Grain, and constructing bacterial cell membrane molecules using Bead Types, includes: S11. Construct the molecular structures of water and disinfectants in Materials Studio software; S12. Optimize the molecular structures of water and disinfectants using the Geometry Optimization task of the Forcite module; S13. The molecular structures of water and bactericides were divided into multiple motion units using the Motion groups method of Coarse Grain, a mesoscopic system construction tool. S14. By defining and classifying the types of motion units, a coarse-grained model of water molecules and bactericide molecules is constructed. S15. Use the mesoscopic system construction tool Bead Types to define bead properties, and set the atomic mass and radius of the beads; S16. Use the Build Mesomolecule function to construct a coarse-grained model of bacterial cell membrane lipid molecules.

4. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 1, characterized in that, Specifically, step S2 involves opening the MS Martini file in the Project menu, modifying the bond angle parameters of the interactions, and modifying the MSMartini force field type of the water, bactericide, and bacterial cell membrane coarse-grained models in the Mesocite Preparation Option function.

5. A method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 1 or 4, characterized in that, Step S2 includes: S21. Use the Mesocite Forcefield Manager feature to import the MS Martini file into the current project; S22. Open the MS Martini.off file in the Project and modify the bond angle parameters of the interaction between beads inside the bacterial cell membrane lipid coarse-grained model; S23. In the Forcefield of Mesocite Calculation, select the MS Martini.off file in the Project and modify the force field type for all beads. S24. Define the head and tail of the bacterial cell membrane coarse-grained model in the Bead Packing Options.

6. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 1, characterized in that, Step S3 includes: S31. Build the basic simulation framework using the Build Mesostructure Template function; S32. Add the coarse-grained model from step S2 to the basic simulation framework to obtain a water-bactericide-bacterial cell membrane hybrid model.

7. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 1, characterized in that, The geometric optimization process in step S4 includes: in the Geometry Optimization task of the Mesocite module, the constructed coarse-grained model is iteratively optimized by sequentially or in combination using the steepest descent method, Newton's iteration method and quasi-Newton method to achieve the goal of minimizing the model energy.

8. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 1, characterized in that, The coarse-grained molecular dynamics simulation in step S4 includes: relaxing the water-bactericide-bacterial cell membrane mixture model using the NPT ensemble for 200 ps, ​​and then performing a coarse-grained molecular dynamics simulation on the water-bactericide-bacterial cell membrane mixture model using the NVT ensemble for 5000 ps.

9. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 1, characterized in that, The specific evolution of the bacterial cell membrane gyration radius in the system with each bactericide added, as analyzed in step S5, is as follows: The difference in gyration radius is obtained based on the gyration radius. The gyration radius and the difference in gyration radius are plotted separately. First, the fluctuation difference is compared in the bacterial cell membrane gyration radius plot, and then the change in the curve value is compared in the gyration radius difference plot.

10. The method for evaluating bactericides based on coarse-grained molecular dynamics simulation according to claim 9, characterized in that, The radius of gyration is calculated using the following formula: In the formula, S: Radius of gyration of the molecule; mi: the mass of the i-th atom in the molecule; Si: The distance from the i-th atom to the center of molecular mass; N: The number of atoms in the molecule; The difference in the radius of gyration is obtained by subtracting the value at the starting point of time from the value of the radius of gyration at each time point: S t =S-S0 (2) In the formula, S: Radius of gyration in the coarse-grained model of cell membrane lipids; St: The distance from the lipid molecule to the mass center of the coarse-grained lipid model of the cell membrane at time t; S0: The distance from the lipid molecule to the mass center of the coarse-grained lipid model of the cell membrane at the initial moment.

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