Molecular Dynamics Simulations in Photosynthesis

Molecular Dynamics Simulations in Photosynthesis

Molecular dynamics (MD) simulations have become an essential tool for studying the structure-function relationships of proteins with known crystal structures. CD BioSciences is committed to developing the application of MD simulations in photosynthesis research to achieve structural insights into the complex photosynthetic processes in thylakoid membranes.


Photosynthesis is a complex physiological process regulated by dynamic interactions between proteins, pigments, lipids, enzymes and cofactors. With the rapid development of high-performance computer clusters and efficient parallel molecular modeling software, MD simulations provide a powerful toolkit to study the dynamics of (bio)molecular ensembles at different scales. Thus, MD simulations are well suited to solve various problems arising in the field of photosynthesis research.

Photosynthetic systems contain a variety of large photoactive pigment-protein complexes (PPCs) that convert the energy of absorbed light into electronic excitations and electrochemical potential gradients in photosynthetic organisms. PPCs have been the subject of numerous experimental and theoretical studies, however, understanding the function of PPCs at the atomic level is still a challenge to be overcome. The development of MD simulation techniques enables the characterization of energy transfer and electron transfer processes, which provide potential strategies for researchers in the field of photosynthesis.

Schematic of the thylakoid membrane and of the light reactions.Fig.1 Schematic of the thylakoid membrane and of the light reactions. (Liguori, 2020)

Our Services

To help our customers predict and characterize the charge transfer, spectral and optical properties of PPC, we developed a method that combines MD simulations, quantum chemical calculations and quantum many-body theory. The method consists of the following three steps:

  • Tracking the conformational dynamics of the protein matrix embedded in a fully solventized lipid bilayer by classical MD simulations.
  • Determination of the lowest energy quantum state of each pigment molecule along the MD track by quantum chemical calculations.
  • Determination of the transport rate and optical spectra from a lineshape function, which can be calculated from the results of quantum chemical calculations in the case of cumulative approximations.

In addition, we provide classical MD to study the kinetics of proteins, lipids and cofactors in thylakoid membranes from (sub)nanosecond to ~ microsecond time scales, providing valuable quantitative information for interpreting experiments.

Advantages of Us

  • Ph.D. level experienced technicians
  • World-class biophysical analysis platform
  • Rigorous experimental control system
  • Powerful and advanced data analysis tools

Relying on our professional biophysical analysis platform, CD BioSciences provides reliable services for MD simulations in photosynthesis. We are competent to provide you with a full range of services and to draw up the best experimental protocol for you. If you need technical support in the field of photosynthesis research, please feel free to contact us.


  1. Liguori, N.; et al. Molecular dynamics simulations in photosynthesis. Photosynthesis research. 2020, 144(2): 273-295.
For research use only, not intended for any clinical use.
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CD BioSciences is a biotechnology company focused on biophysical services. We are proficient in both chemistry and biophysics, and have a comprehensive biophysical platform containing a wide range of advanced technologies.

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