Dissipative particle dynamics (DPD) is a particle-based computational method that provides an efficient way to simulate the dynamic behavior of complex fluids and multi-component mixtures. Unlike more atomic molecular dynamics (MD) simulations, DPD beads represent molecular clusters. Similar to MD simulations, DPD captures the time evolution of many systems through numerical integration of Newton's equations of motion. An advantageous feature of DPD is that it exploits soft repulsive interactions between beads. Therefore, much larger time steps can be used between successive iterations than are required for MD simulations. This approach can be used to simulate physical phenomena that occur on temporal and spatial scales many orders of magnitude larger than those captured by MD. CD BioSciences use computer-aided methods to provide biofilm formation simulation service to help customers complete biofilm related research.

Specific Biofilm Formation Simulation Approaches We Offer

• CD BioSciences used dissipative particle dynamics (DPD) simulation methods to simulate the salient features of biofilm formation.
• We model cells as particles containing hundreds of DPD beads and assign p, the probability of breaking bonds between particles and surfaces or between particles. In the early stages of film growth, we set p = 1, allowing all bonding interactions to be reversible. Once the bound cluster reaches a critical size, we will investigate the case of p = 0 so that the incoming species form irreversible bonds, and the case of p in the range 0.1-0.5. Using this method, we can study nascent biofilm development.
• In addition, we provide professional results analysis, image processing, data aggregation and other services.

Provided by Customers

Please inform us of your specific biofilm formation simulation service details, and we can provide customized solutions for different projects.

Service Process

Our Features

Deliverables

1. Related experimental results raw data
2. Simulation results
3. Image and result analysis
4. Interaction and movement details
5. Summary of relevant calculation parameters

Why Choose Us?

CD BioSciences is a professional biofilm technology provider, supporting a variety of biofilm services. We are able to perform individual tests at the most precise level, as well as design and complete a suite of services as a solution to the subject project. CD BioSciences has accumulated years of quintessence in the field of biofilm modeling, helping our clients accelerate drug discovery and development and improve the overall success rate of their projects. Please feel free to contact us for more detailed information, our scientists will tailor the most reasonable plan for your project.  

Reference

1. Hanfeng Zhai, et al. Multiscale Computational Modeling of Biofilm. 2022

• Biofilm Computational Construction Service
• Biofilm Molecular Dynamics Simulation Service
• Stability Test of Biofilm System
• RMSF Analysis of Biofilm System
• Gyration Radius Analysis of Biofilm System
• Binding Mode Analysis of Biofilm System
• Secondary Structure Analysis of Biofilm System
• Energy Analysis of Biofilm System
• Hydrophobic Interaction Analysis of Biofilm System
• Free Energy Landscape Analysis of Biofilm System
• Biofilm Conformational Principal Component Analysis
• Biofilm Ramachandran Plots Analysis
• Cluster Analysis of Biofilm System
• SAS Analysis Service of Biofilm System
• Energy Decomposition Analysis of Biofilm System
• Electrostatic Interaction Analysis of Biofilm System
• Biofilm Virtual Screening Service
• Computational Modeling of Early-Stage Biofilm Formation
• Biofilm CGMD Service
• Biofilm DPD Service
• Biofilm DEM Service
• Biofilm SPH Service
• Biofilm XFEM Service
• Other Biofilm MD Serivce
• Biofilm Homology Modeling Serivce
• Gram-negative Bacterial Outer Membrane Construction Service
• Construction Services for Discrete Difference Models
• Modeling Services for Geometric Heterogeneity in Biofilms
• Computational Simulation Service for Biofilm Development
• Computational Modeling Service for Synthetic Biofilms
• Biofilm MD Results Analysis Services
• Biofilm Multiscale Computational Modeling Service
• Biofilm Modeling Service