Simulation method for improving target positioning efficiency of macromolecular chain in limited space

Abstract

The invention discloses a simulation method for improving the target recognition efficiency of a macromolecular chain in a limited space. The method comprises the following steps: establishing a macromolecular chain model; establishing a limited space; performing Langevin dynamics simulation on the limited macromolecular chain influenced by the limited surface adsorption strength; and carrying out simulation calculation on search time. By adopting the technical scheme of the invention, the target identification efficiency of the macromolecular chain in the limited space is remarkably improved by utilizing the adsorption strength, and the target can be positioned and identified more quickly and accurately in a complex environment.

Description

Technical Field

[0001] The invention belongs to the technical field of polymer scientific computing, and in particular relates to a simulation method for improving target recognition efficiency of polymer chains in a confined space. Background Art

[0002] In the field of polymer science and chemical engineering computing, the movement and target recognition behavior of polymer chains in confined space has always been the focus of research. Such as polymer separation, DNA sequencing, virus invasion of cells, and controlled drug delivery. The search process of confined polymers is a common phenomenon in life activities, and the non-equilibrium dynamics behind it is an important part of the theory of soft matter physics. However, considering the inherent complex dynamics of polymer chains, it becomes extremely difficult to study the dynamics of confined polymers through theoretical and experimental methods. Therefore, establishing a reasonable physical model from a microscopic perspective and studying the relationship between the search efficiency and adsorption strength of molecular chains in confined space not only provides the necessary physical basis for understanding life processes, but also provides a theoretical basis for the study of molecular non-equilibrium dynamics.

[0003] In the prior art, researchers have tried to enhance the target recognition ability of polymer chains in confined spaces through various methods, such as changing the chemical structure of the polymer chain, optimizing the spatial geometry, or regulating the movement of the polymer chain through external physical fields (such as electric fields or magnetic fields). However, these methods often face the problems of low efficiency, complex operation, and difficulty in implementation in practical applications. In addition, the complexity and diversity of confined spaces make it difficult for existing technologies to achieve consistent effects in different application scenarios. Adsorption, as an important molecular interaction mechanism, has been widely used in fields such as molecular recognition, catalytic reactions, and material surface modification. However, how to use the adsorption mechanism in confined spaces to improve the target recognition efficiency of polymer chains is still a challenge that has not been fully resolved. Existing adsorption methods are generally difficult to achieve efficient target positioning and recognition in confined spaces at the nanoscale. Summary of the invention

[0004] The technical problem to be solved by the present invention is to provide a method for improving the target recognition efficiency of a polymer chain in a confined space by adjusting the adsorption strength, and to improve the search efficiency by dynamically adjusting the adsorption strength between the polymer chain and the confining plane (especially the lower plate with the target small hole). The method includes establishing a simulation environment confined by two parallel plates, with a small hole at the center of the lower plate. By changing the adsorption strength between the polymer chain and the lower plate, the chain can be "guided" to the vicinity of the small hole, thereby reducing unnecessary movement, thereby optimizing the search process and improving the search efficiency.

[0005] To achieve the above object, the present invention adopts the following technical solution:

[0006] A simulation method for improving target recognition efficiency of a polymer chain in a confined space, comprising:

[0007] Step S1, establishing a polymer chain model;

[0008] Step S2, establishing a confined space;

[0009] Step S3, simulating the Langevin dynamics of the confined polymer chain affected by the adsorption strength of the confined surface according to the polymer chain model and the confined space;

[0010] Step S4: Simulation calculation of search time.

[0011] Preferably, in step S1, the polymer is represented by a coarse-grained bead-spring chain model, where each chain consists of N beads with a friction coefficient ξ=1, and each bead has a diffusion coefficient k B T / ξ Brownian particle, where k B is the Boltzmann constant, T is the temperature; two consecutive beads are connected by a spring, the bond potential energy U b Follows Hooke's law.

[0012] Preferably, in step S1, the excluded volume interaction between any two beads is simulated using a truncated and shifted Lennard-Jones (LJ) potential.

[0013] Preferably, in step S2, the polymer is confined in parallel plates, and the confined space is simulated as setting two plates at positions Z=0 and Z=H using integrated LJ potential energy, and considering periodic boundary conditions in the x and y directions.

[0014] Preferably, in step S2, the polymer is confined in the upper and lower plates, and a WCA potential is used between the polymer beads and virtual beads of size σ distributed on the upper plate, and is defined as U wall (r);

[0015]

[0016] Where r represents the vertical distance between the bead and the upper plate boundary, that is, r = H-|r i |, cutoff distance

[0017]

[0018] Preferably, in step S2, the polymer is confined in the upper and lower plates, and an attractive potential is applied between the polymer beads and virtual beads of size σ distributed on the lower plate, and is defined as U wall ;

[0019]

[0020] Among them, ε s represents the adsorption strength of the surface, and z represents the vertical distance from the monomer to the surface.

[0021] The present invention has the following beneficial effects:

[0022] 1. The present invention utilizes adsorption strength to significantly improve the target recognition efficiency of polymer chains in confined spaces, and can locate and identify targets more quickly and accurately in complex environments;

[0023] 2. The present invention is also applicable to confined spaces in spherical cavities;

[0024] 3. The present invention does not require complicated chemical modification or external control. It can effectively regulate the motion behavior of polymer chains by optimizing the adsorption potential energy. The operation is simple and easy to implement.

[0025] 5. The present invention has potential application value in multiple fields such as nanotechnology, material science, molecular probe design, and drug delivery systems, and can improve the performance and efficiency of related technologies in these fields;

[0026] 6. The present invention improves the stability and controllability of the system by precisely regulating the adsorption between the polymer chain and the target molecule, which helps to obtain more reliable results in practical applications. BRIEF DESCRIPTION OF THE DRAWINGS

[0027] In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings required for use in the embodiments or the description of the prior art will be briefly introduced below. Obviously, the drawings described below are only embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on the provided drawings without paying creative work.

[0028] Figure 1 A flow chart of a simulation method for improving target recognition efficiency of a polymer chain in a confined space according to an embodiment of the present invention;

[0029] Figure 2 It is a three-dimensional schematic diagram of the polymer chain of the present invention in a confined space;

[0030] Figure 3 This is a search time distribution change diagram of an adsorption intensity of 0.2 obtained by simulation calculation of the present invention;

[0031] Figure 4 This is a search time distribution change diagram of an adsorption intensity of 0.4 obtained by simulation calculation in the present invention;

[0032] Figure 5 This is a search time distribution change diagram of the adsorption intensity of 0.6 obtained by simulation calculation of the present invention;

[0033] Figure 6 This is a search time distribution change diagram of an adsorption intensity of 0.8 obtained by simulation calculation of the present invention;

[0034] Figure 7 This is a search time distribution change diagram of the adsorption intensity of 1.0 obtained by simulation calculation of the present invention;

[0035] Figure 8 This is a search time distribution change diagram of an adsorption intensity of 1.2 obtained by simulation calculation in the present invention;

[0036] Fig. 9 This is a search time distribution change diagram of an adsorption intensity of 1.4 obtained by simulation calculation in the present invention;

[0037] Fig.10 This is a search time distribution change diagram of an adsorption intensity of 1.6 obtained by simulation calculation in the present invention;

[0038] Fig.11 This is a graph showing the variation of the average search time under different adsorption intensities of the present invention. DETAILED DESCRIPTION

[0039] The following will be combined with the drawings in the embodiments of the present invention to clearly and completely describe the technical solutions in the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention.

[0040] In order to make the above-mentioned objects, features and advantages of the present invention more obvious and easy to understand, the present invention is further described in detail below with reference to the accompanying drawings and specific embodiments.

[0041] Embodiment 1:

[0042] like Figure 1 As shown, the embodiment of the present invention provides a simulation method for improving the target recognition efficiency of a polymer chain in a confined space. In a simulation environment, by adjusting the adsorption strength between the polymer chain and the surface of the confined space, its influence on the target positioning efficiency can be studied; by optimizing the adsorption conditions through calculation and simulation, the target positioning efficiency of the polymer chain in the confined space is improved, which specifically includes:

[0043] Step S1: Establishment of polymer chain model

[0044] (a) The polymer is represented by a coarse-grained bead-spring chain model. Each chain consists of N beads with a friction coefficient of ξ = 1. Each bead is considered to have a diffusion coefficient k B T / ξ Brownian particle, where k Bis the Boltzmann constant, and T is the temperature. Two consecutive beads are connected by a spring, and the bond potential energy U b Follows Hooke's law.

[0045]

[0046] Where k is the spring constant, r i is the position of bead No. i, r 1 With r N Represent the two end beads of the molecular chain.

[0047] (b) The excluded volume interaction between any two beads is modeled using a truncated and shifted Lennard-Jones (LJ) potential.

[0048]

[0049] Where r = |r i -r j | represents the distance between beads No. i and No. j, ε and σ represent unit energy and unit length respectively. cut ) Ensure U LJ (r) at the cutoff distance r cut Return to zero steadily, set This potential energy is purely repulsive.

[0050] Step S2: Establishment of confined space

[0051] (a) To confine the polymer in parallel plates, the confined space is simulated by setting two plates at Z = 0 and Z = H using the integrated LJ potential, and considering periodic boundary conditions in the x and y directions.

[0052] (b) To confine the polymer in the upper and lower plates, a WCA potential is used between the polymer beads and virtual beads of size σ distributed on the upper plate and defined as U wall (r);

[0053]

[0054] Where r represents the vertical distance between the bead and the upper plate boundary, that is, r = H-|r i |, cutoff distance

[0055]

[0056] (c) To confine the polymer in the upper and lower plates, an attractive potential is applied between the polymer beads and virtual beads of size σ distributed on the lower plate, and is defined as U wall ;

[0057]

[0058] Among them, ε s represents the adsorption strength of the surface, and z represents the vertical distance from the monomer to the surface;

[0059] By changing the attractive interaction potential parameters between the polymer chain and the plate, for example, adjusting ε in the attractive potential s , in order to enhance or weaken the adsorption effect, in the present invention, the adsorption intensity ε s The value range is 0.2-1.6;

[0060] Step S3: Langevin dynamics simulation of the influence of adsorption strength on confined polymer chains

[0061]

[0062] The simulation process of the entire system adopts Langevin dynamics, and its integral equation is as follows:

[0063] The first of these is Inertial force, which means that a particle i with mass m at position r i The second term is the dissipation force, γ is the drag coefficient; the third term is the acceleration at the point (i.e., the inertia force of the particle); is the contribution of various potential energies to particle motion, U b Used to describe the bond potential between polymer chain segments, U LJ (r) is used to describe the interaction force between particles, U wall Used to describe the adsorption of polymer chains on the adsorption surface, U wall (r) describes the repulsive interaction when the polymer chains approach the surface, Gaussian random noise that satisfies the fluctuation dissipation theorem and has a mean of 0 is simulated using a GPU-accelerated server.

[0064] In the present invention, the time step of the Langevin equation is Δt=5×10 -3 τ 0 , where τ 0 is the bond relaxation time. This time step is small enough to ensure the stability and accuracy of the simulation. In the simulation, the height H between the two plates is 8, the length and width of the two plates are 10, 10 respectively, and the polymer chain length is 30. Initialization is to bring all monomers close to the center of the space and stack them together, and collect simulation data after the system is balanced for a time much longer than the relaxation of the entire chain. Each run will terminate after the marked terminal monomer recognizes the positioning target for the first time. The results in the present invention are obtained by averaging the results of at least 4000 runs.

[0065] Step S4: Simulation calculation of search time

[0066] (a) One of the key properties to measure the efficiency of the target positioning of the polymer chain in the confined space is the search time. To determine the average search time, we must first calculate the survival probability S(t) of the monomer in the confined space, that is, the probability that the marked monomer has not found an opening at time t, where S(t) is a statistic of the simulation results, and its calculation formula is:

[0067]

[0068] Among them, N s is the number of statistical samples, t j is the search time for the jth sample, Θ(t) is the Heaviside step function;

[0069] (b) The specific steps for calculating the search time are:

[0070]

[0071] Among them, τ is the search time, S(t) is the survival probability;

[0072] (c) The specific steps of calculating the search time also include:

[0073]

[0074] Where τ is the search time, N s is the number of statistical samples, t j is the search time for the jth sample;

[0075] Based on the simulation results and corresponding data processing, the search mechanism under the control of adsorption intensity is analyzed; specifically:

[0076] As can be seen from Table 1, the average search time decreases with the increase of adsorption intensity, which shows that the interaction force between the polymer chain and the surface is weak during weak adsorption, and the polymer chain searches in three-dimensional space, resulting in low search efficiency. During strong adsorption, the interaction force between the polymer chain and the surface is strong, and the polymer chain sticks to the lower plate and searches in two-dimensional space, which also results in low search efficiency. When the adsorption intensity is moderate, the search efficiency is obviously very high. Because when the adsorption intensity is moderate, the polymer chain switches back and forth between three-dimensional space and two-dimensional surface, and performs an intermittent search, thereby improving the search efficiency. Therefore, the target positioning efficiency of polymer chains in confined space can be improved by adjusting the adsorption intensity.

[0077] Table 1

[0078] Adsorption strength 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 Average search time 1130.5 693.8 434.3 300 264.7 320.1 405.0 1560.6

[0079] The restricted polymer chain model in the present invention is as follows Figure 2As shown, a schematic diagram of a real chain confined between parallel plates, with the terminal unit of the polymer chain searching for the target on the lower plate.

[0080] The effect of adjusting the adsorption intensity on the average search time distribution in the implementation column is as follows: Figure 3-10 .

[0081] Adsorption strength is used to improve the efficiency of polymer chain search for targets including:

[0082] The relationship between the polymer chain search time under the control of adsorption intensity, such as Fig.11 As shown in the figure. When the adsorption strength is weak, the average search time is longer. This shows that under weak adsorption strength, the efficiency of the polymer chain in finding the target in the confined space is low. When strongly adsorbed, the chain stays on the surface for a long time and falls into local search, thus reducing the global search efficiency. Therefore, the appropriate adsorption strength will increase the target positioning efficiency of the polymer chain in the confined space.

[0083] The present invention is based on Langevin dynamics simulation, and by controlling the adsorption strength, the polymer chain has different target positioning efficiencies, and the polymer chain is observed to locate the flat target under different adsorption strength potential energies, and the efficiency of the polymer chain target positioning is observed. The motion of the polymer chain in the confined space is modeled, so that the target positioning efficiency of the polymer chain in the confined space becomes simple to judge, and the motion and positioning of the polymer chain in the confined space in the real system can be effectively predicted.

[0084] The embodiments of the present invention enhance the interaction force between the polymer chain and the confined surface by increasing the adsorption potential field, modifying the potential energy of the confined surface, and adjusting the external environmental conditions (such as adsorption strength), thereby significantly improving the directional movement and target search capabilities of the polymer chain in the confined space. The present invention provides a highly controllable and efficient polymer chain target positioning technology, which is suitable for multiple fields such as nanotechnology, pharmaceutical industry, and materials science. The simulation results show that this method has significant advantages over the existing technology and can achieve efficient and accurate target positioning under a variety of confined conditions.

[0085] The embodiments described above are only descriptions of the preferred embodiments of the present invention and are not intended to limit the scope of the present invention. Without departing from the design spirit of the present invention, various modifications and improvements made to the technical solutions of the present invention by ordinary technicians in this field should all fall within the protection scope determined by the claims of the present invention.

Claims

1. A simulation method for improving the target recognition efficiency of a polymer chain in a confined space, characterized in that: include: Step S1, establishing a polymer chain model; Step S2, establishing a confined space; Step S3, simulating the Langevin dynamics of the confined polymer chain affected by the adsorption strength of the confined surface according to the polymer chain model and the confined space; Step S4: Simulation calculation of search time.

2. The simulation method for improving the target recognition efficiency of a polymer chain in a confined space according to claim 1, characterized in that: In step S1, the polymer is represented by a coarse-grained bead-spring chain model, where each chain consists of N beads with a friction coefficient ξ = 1 and each bead has a diffusion coefficient k B T / ξ Brownian particle, where k B is the Boltzmann constant, T is the temperature; two consecutive beads are connected by a spring, the bond potential energy U b Follows Hooke's law.

3. The simulation method for improving the target recognition efficiency of a polymer chain in a confined space as claimed in claim 2, characterized in that: In step S1, the excluded volume interaction between any two beads is simulated using a truncated and shifted Lennard-Jones (LJ) potential.

4. The simulation method for improving target recognition efficiency of polymer chains in confined space according to claim 3, characterized in that: In step S2, the polymer is confined in parallel plates, and the confined space is simulated as setting two plates at the positions of Z=0 and Z=H using the integrated LJ potential energy, and considering periodic boundary conditions in the x and y directions.

5. The simulation method for improving the target recognition efficiency of a polymer chain in a confined space as claimed in claim 4, characterized in that: In step S2, the polymer is confined in the upper and lower plates, and a WCA potential is used between the polymer beads and virtual beads of size σ distributed on the upper plate, which is defined as U wall (r); Where r represents the vertical distance between the bead and the upper plate boundary, that is, r = H-|r i |, cutoff distance 6. The simulation method for improving the target recognition efficiency of a polymer chain in a confined space as claimed in claim 5, characterized in that: In step S2, the polymer is confined in the upper and lower plates, and an attractive potential is applied between the polymer beads and virtual beads of size σ distributed on the lower plate, which is defined as U wall ; Among them, ε s represents the adsorption strength of the surface, and z represents the vertical distance from the monomer to the surface.

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