A universal force field coarse-graining model for rod-shaped nanoparticles and its establishment method

Abstract

The present invention proposes a universal force field rod-shaped nanoparticle coarse-graining model and an establishment method thereof, and belongs to the field of nanochemical calculation technology; specifically, the model is divided into a central bead cluster and an outer cylindrical shell-shaped beads, the outermost beads arranged at both ends are hemispherical shells, and the outermost beads arranged in the middle section are cylindrical shells; two types of beads are defined in the force field used, the molar mass and potential action parameters are assigned, and key connections are used in the connection between the central bead cluster and the outermost beads to ensure that they are not deformed or collapsed during molecular dynamics simulation, and the overall properties are kept unchanged; the entire coarse-graining model only has the outermost beads and the central bead cluster, which greatly reduces the number of beads, can ensure the accuracy of molecular dynamics calculations while greatly reducing the amount of calculations, improves the speed of calculations, and avoids the waste of computing power.

Description

Technical Field

[0001] The invention belongs to the field of nanochemical calculation, and specifically relates to a processing calculation of rod-shaped nanoparticles, and specifically is a coarse-graining model of rod-shaped nanoparticles suitable for a general force field and an establishment method thereof. Background Art

[0002] Nanoscience and technology was born in the late 1980s and is still being improved and developed. It means to understand and create new materials by directly operating and controlling the arrangement of atoms and molecules at the nanoscale. Since the performance of nanoparticles in terms of electrical, magnetic, optical, thermal properties and surface stability is significantly different from that of ordinary materials, they have been applied in many industrial fields such as biology, medicine, physics, chemistry, environment, plastics, etc.

[0003] The study of nanoparticles can be simulated using molecular dynamics. Molecular dynamics simulation is a computer simulation method for solving multi-body problems at the atomic and molecular levels, and can predict the dynamic characteristics of materials at the mesoscopic scale. The microstructure, rheological data, and data change laws obtained by molecular dynamics numerical simulation can guide the industrial application of nanoparticles, and can also theoretically analyze the mechanism of action of nanoparticles. Since nanoparticles are cross-scale, it is necessary to establish a universal nanoparticle model, that is, to achieve length scale normalization and energy scale normalization of the nanoparticle system. Length scale normalization means first selecting a universal basic coarse-grained unit of the system, and constructing different substances in the system from the basic coarse-grained unit. Energy scale normalization means calling universal force field parameters on the basis of length scale normalization, and assigning the same potential function to coarse-grained beads of the same type.

[0004] When studying the relevant action modes of nanoparticles at the mesoscopic scale, the shape and size of the nanoparticles are important factors that lead to different results of different nanoparticles. The overall translocation rate of nanoparticles varies greatly with their size and shape. Among them, rod-shaped nanoparticles with high aspect ratios have greatly improved sensitivity to the environment compared to spherical nanoparticles, and can play a better role in imaging, biology, medicine, detection and other fields. For the construction of rod-shaped nanoparticle models, if the existing traditional force field is used under larger size conditions, there are problems such as too many beads required, it is difficult to modify the size and shape once determined, it is difficult to maintain the shape during the calculation process, and the force field parameter settings are complicated, which leads to serious waste of manpower and computing power. In the existing models of rod-shaped nanoparticles, the number of beads is mostly around a few hundred, and the size is mostly between 2-4nm, which cannot meet the research needs of larger rod-shaped nanoparticles. Summary of the invention

[0005] The present invention overcomes the shortcomings of the prior art and proposes a rod-shaped nanoparticle coarse-graining model suitable for a universal force field and its establishment method, so that when establishing large-diameter rod-shaped nanoparticles, the number of coarse-grained beads constituting the rod-shaped nanoparticles is greatly reduced, while satisfying the unchanged dynamic properties. While simplifying the modeling of rod-shaped nanoparticles, the size universality and material system universality are improved, thereby improving the calculation rate of molecular dynamics numerical simulation and solving the problem of computing power waste.

[0006] In order to achieve the above object, the present invention is implemented through the following technical solutions.

[0007] A general force field coarse-grained model of rod-shaped nanoparticles comprises a bead cluster formed by a number of beads at the center of the model and a number of outermost beads evenly arranged on the surface of the model; the outermost beads arranged at both ends are hemispherical shells, and the outermost beads arranged in the middle section are arranged in cylindrical shells; the bead cluster in the center and the outermost beads, the outermost beads, and the beads in the center are all bonded; the number of the outermost beads is determined according to the size of the rod-shaped nanoparticles, and the mass of the rod-shaped nanoparticles is evenly distributed to the outermost beads.

[0008] Preferably, the bond length between the central bead cluster and the outermost beads, the bond length between the outermost beads, and the bond length between the central beads are all determined according to the particle size of the rod-shaped nanoparticles.

[0009] Preferably, the mass of the central bead is negligible.

[0010] The method for establishing the coarse-grained model of rod-shaped nanoparticles comprises the following steps:

[0011] S1. Calculate the mass of the required rod-shaped nanoparticles based on the required size of the rod-shaped nanoparticles and the average density of the nanoparticles.

[0012] S2. Determine the number of beads in the outermost layer according to the particle size of the rod-shaped nanoparticles, and evenly distribute the mass of the required rod-shaped nanoparticles to the beads in the outermost layer.

[0013] S3. According to the particle size of the rod-shaped nanoparticles, determine the bond length between the central bead cluster and the outermost beads, the bond length between the outermost beads, the bond length between the central beads, and the bond energy parameters required to maintain structural rigidity.

[0014] S4. Define the types of the central beads and the outermost beads in the force field used, and modify various parameters of the defined beads in the force field used according to the molar mass of the central beads and the outermost beads.

[0015] Further, the bond energy parameter in step S3 is the bond energy parameter K of the bond energy expression of the bond action in the force field used.r .

[0016] Furthermore, the bond energy parameter K in the force field used is r Increase proportionally from the general value.

[0017] Furthermore, the non-bonded interaction force parameters in the used force field were modified according to the molar mass size of the outermost beads.

[0018] The beneficial effects of the present invention compared with the prior art are as follows:

[0019] The present invention proposes a coarse-graining model and establishment method for constructing rod-shaped nanoparticles suitable for a general force field, and establishes a coarse-graining model for large rod-shaped nanoparticles, which is divided into a central bead cluster and an outer cylindrical shell bead. Since in thermal motion, generally only the interaction between the beads on the surface of the nanoparticles and the external force is considered, this model can ensure that the overall dynamic properties of the rod-shaped nanoparticles remain unchanged.

[0020] Two types of beads are defined in the force field used, and the molar mass and potential action parameters are assigned according to the actual application. Key connection is used to connect the central bead cluster and the outer cylindrical shell beads. At the same time, by establishing a series of central bead clusters, it is ensured that the columnar surface beads are always at a comparable distance to a bead in the central bead cluster, and the length of the rod-shaped nanoparticles can always be controlled by changing the number of central beads.

[0021] By changing the bond energy parameters, the structural rigidity of the rod-shaped nanoparticles is ensured, so that they can remain unchanged without deformation or collapse during molecular dynamics simulations, and the overall properties remain unchanged. The entire coarse-grained model only has the outermost beads and the central bead cluster, which greatly reduces the number of beads. This can greatly reduce the amount of calculation while ensuring the accuracy of molecular dynamics calculations, improve the speed of calculations, and avoid the waste of computing power. BRIEF DESCRIPTION OF THE DRAWINGS

[0022] In order to make the technical problems, technical solutions and beneficial effects to be solved by the present invention more clearly understood, the following drawings are provided for explanation:

[0023] Figure 1 The configuration views of the rod-shaped nanoparticle coarse-grained model along the axial and tangential directions in the visualization software OVITO, where (a) is the configuration view along the axial direction; (b) is the configuration view along the tangential direction;

[0024] Figure 2 for Figure 1 , wherein (a) is a cross-sectional view along the axial direction; (b) is a cross-sectional view along the tangential direction;

[0025] Figure 3It is a schematic cross-sectional view of the coarse-grained model of rod-shaped nanoparticles along the axial direction;

[0026] Figure 4 It is a schematic cross-sectional view of the coarse-grained model of rod-shaped nanoparticles along the tangent direction;

[0027] Among them, SP is the surface bead; CP is the central bead; SB is the short bond; LB is the long bond. DETAILED DESCRIPTION

[0028] In order to make the technical problems, technical solutions and beneficial effects to be solved by the present invention clearer, the present invention is further described in detail in conjunction with the embodiments and the accompanying drawings. It should be understood that the specific embodiments described herein are only used to explain the present invention and are not intended to limit the present invention. The technical solutions of the present invention are described in detail below in conjunction with the embodiments and the accompanying drawings, but the scope of protection is not limited thereto.

[0029] A method for establishing a coarse-grained model of rod-shaped nanoparticles suitable for a general force field specifically comprises the following steps:

[0030] S1. Calculate the mass of the model rod-shaped nanoparticle coarse particles:

[0031] In this example, a rod-shaped gold nanoparticle with a length of 8 nm and a diameter of 4 nm is used for model configuration. The force field used is the Martini coarse-grained force field. The volume of the rod-shaped gold nanoparticle can be calculated to be 8.37810 -20 cm 3 The average density of gold is 19.32 g / cm 3 , it can be obtained that the mass of the constructed rod-shaped gold nanoparticle model is about 1.61810 -18 g.

[0032] S2. Determine the number of beads and evenly distribute the mass of gold:

[0033] The coarse-grained model of the rod-shaped gold nanoparticle with a length of 8nm and a diameter of 4nm is divided into two types of beads, the first type is the central beads, and the second type is the outer shell beads. According to the size of the model, the number of beads in the outermost spherical shell is finally determined to be 424, and the number of central beads is 9. The total number of coarse-grained beads in the entire rod-shaped gold nanoparticle coarse-grained model is 433. The mass of a rod-shaped gold nanoparticle model constructed by S1 is about 1.61810 -18 g, evenly distributed to the outermost beads, that is, the mass of each outermost bead is 3.8110 -21 g, the mass of the central bead can be ignored, (refer to Figure 1-4 ).

[0034] S3. Determine the bond length and bond energy parameters between coarse-grained beads:

[0035] The central bead and the outermost bead, the outermost beads, and the central beads are all connected by bonds. According to the actual size of the model, the bond between the central bead and the outermost bead is LB (Long Bond), with a bond length of 2nm; the bond between the outermost beads and the central beads is SB (Short Bond), with a bond length of 0.47nm. In the Martini force field, the bond energy expression of the bond and action is: In order to maintain the structural rigidity of the rod-shaped gold nanoparticles, the bond energy parameter K is set to r It is expanded 2.2 times from the general value of 1250 KJ / mol to 2750 KJ / mol.

[0036] S4. Define the bead type and modify various parameters of the defined beads in the Martini force field:

[0037] Two types of beads are defined in the Martini force field, CP (Central Particle) and SP (Surface Particles), where SP represents the outermost beads with large mass, and CP represents the central beads with almost zero mass. Since gold nanoparticles are polar particles, the two types of beads defined have similar properties to the polar beads Q0. The molar mass of the Q0 particle in the Martini force field is 72 g / mol, which is determined by the Avogadro constant N A , and the mass of each outermost bead, the molar mass of the outermost bead, i.e., the SP bead, can be calculated to be 2293 g / mol, while the molar mass of the central bead, CP, is defined as 0.01 g / mol, which is almost negligible. The van der Waals potential force parameters in the Martini force field can be modified according to the mass of the beads. The central bead CP and the outermost bead SP are mainly bonded, and the non-bonded force parameters are all 0.

[0038] This method divides the coarse-grained model of the bulky rod-shaped nanoparticles into a central bead cluster and an outermost shell-shaped bead. Since only the outermost layer of the rod-shaped nanoparticle interacts with the outside world during molecular thermal motion, the dynamic performance of the rod-shaped nanoparticles can be guaranteed to remain unchanged by ensuring that the properties of the outermost layer of the rod-shaped nanoparticles remain unchanged. Two types of beads are defined in the Martini force field, and the molar mass and potential action parameters are assigned according to practical applications. In the connection between the central bead cluster and the outermost shell-shaped beads, a bond connection is used, and the bond energy parameters are changed at the same time, which ensures the structural rigidity of the rod-shaped nanoparticles, and can remain unchanged without deformation or collapse during molecular dynamics simulation, and keep the overall properties unchanged. The entire coarse-grained model only has the outermost beads and the central bead cluster, which greatly reduces the number of beads, can greatly reduce the amount of calculation while ensuring the accuracy of molecular dynamics calculations, improve the speed of calculations, and avoid the waste of computing power.

[0039] The above content is a further detailed description of the present invention in combination with a specific preferred embodiment. It cannot be determined that the specific embodiments of the present invention are limited to this. For ordinary technicians in the technical field to which the present invention belongs, several simple deductions or substitutions can be made without departing from the present invention, which should be regarded as belonging to the present invention and the scope of patent protection determined by the submitted claims.

Claims

1. A general force field rod-shaped nanoparticle coarse-graining model, characterized in that: It includes a bead cluster formed by a number of beads located at the center of the model and a number of outermost beads evenly arranged on the surface of the model; the outermost beads arranged at both ends are hemispherical shells, and the outermost beads arranged in the middle section are arranged in cylindrical shells; the bead cluster in the center and the outermost beads, the outermost beads, and the beads in the center are all bonded; the number of the outermost beads is determined according to the size of the rod-shaped nanoparticles, and the mass of the rod-shaped nanoparticles is evenly distributed to the outermost beads; The bond length between the central bead cluster and the outermost beads, the bond length between the outermost beads, and the bond length between the central beads are all determined according to the particle size of the rod-shaped nanoparticles.

2. A general force field rod-shaped nanoparticle coarse-graining model according to claim 1, characterized in that: The mass of the center bead is negligible.

3. The method for establishing a coarse-grained model of rod-shaped nanoparticles according to claim 1 or 2, characterized in that: The following steps are involved: S1. Calculate the mass of the required rod-shaped nanoparticles according to the required size of the rod-shaped nanoparticles and the average density of the nanoparticles; S2. Determine the number of beads in the outermost layer according to the particle size of the rod-shaped nanoparticles, and evenly distribute the mass of the required rod-shaped nanoparticles to the beads in the outermost layer; S3. Determine the bond length between the central bead cluster and the outermost beads, the bond length between the outermost beads, the bond length between the central beads, and the bond energy parameters required to maintain structural rigidity according to the particle size of the rod-shaped nanoparticles; S4. Define the types of the central beads and the outermost beads in the force field used, and modify various parameters of the defined beads in the force field used according to the molar mass of the central beads and the outermost beads.

4. The method for establishing a general force field rod-shaped nanoparticle coarse-graining model according to claim 3, characterized in that: The bond energy parameter described in step S3 is the bond energy parameter K of the bond energy expression of the bond action in the force field used. r .

5. The method for establishing a general force field rod-shaped nanoparticle coarse-graining model according to claim 4, characterized in that: The bond energy parameter K in the force field used r Increase proportionally from 1250 KJ / mol.

6. The method for establishing a general force field rod-shaped nanoparticle coarse-graining model according to claim 4, characterized in that: The non-bonded interaction force parameters in the used force field were modified according to the molar mass size of the outermost beads.

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