Computational system for virtual experimentation with optical tweezers on biological materials.

Microscopic manipulation of cells and synthetic biological structures requires highly complex equipment capable of accurate submicrometric action, such as optical tweezers. They in turn require expensive microscopes and highly trained operators. In this context, inexpensive computational methods that allow for the simulation of the phenomenon being studied greatly improve the efficiency of the physical experiment and helps in the interpretation of the results. The main goal of this subproject is the development of such a computational system, to allow for virtual single-cell experiments. The system will be called VCM-3D (Virtual Cell Manipulation 3D).

Impact

Calibration of physical and mathematical models. Exploration of parameter ranges beyond the capabilities of available equipment. Help in diagnosis through inverse problem solution, possibly coupled to regression algorithms and expert input assimilation. Study of membrane related pathologies, such as spherocytosis, malaria and sickle cell anemia.

Methodology

Finite element based modular code based on polynomial approximations. Deformable meshes with adaptive remeshing. Automatic time step control. Interfaces to and from geometric modelers and visualization tools. Possibility of direct interaction with the model through forces and restrictions. Open source code. Incremental development.

Specifications and outputs

• Equilibrium shapes as obtained from energy minimization.
• Relaxation dynamics considering viscoelasticity, inextensibility, osmosis, interactions.
• Manipulation through virtual tweezers, controlling velocity, displacement or force.
• Modeling of adhesion to tissues.
• Transport, diffusion and reaction of biochemical agents on the membrane and its surroundings. 
• Extension of VCM-3D from single-cell problems to collective behavior, as it becomes computationally feasible.