From atomistic details to coarse-grained description
Cells are a complex network of molecular interactions. Among diverse
molecules, proteins and nucleic acid systems play a major role in regulating
intra and inter cellular functions. Knowing the structure of these molecules
is fundamental to understanding their function. We use simulation techniques to better understand the structure-function relationship.
Simulation techniques can provide detailed three-dimensional structure of molecular systems at atomistic level and link the microscopic information to thermodynamic properties of the system.
The basic challenge of simulation technique is one of describing the macroscopic (experimentally observable) properties of the system in terms of the interactions between atoms or group of atoms. The molecular system is described by a set of potentials (empirical force
fields) based on simple chemical concept. That allows to define the potential
energy of the system in terms of the coordinates of the atoms or groups of atoms. Newton equation of motion is used to predict the time evolution of the system.
It is important that the adopted model is capable of correctly describing and
predicting the biological phenomena at corresponding spatial and temporal
scale. The size and the time scale of some biological process can not be
describe by atomistic models and necessitates the use of low-resolution models,
so-called coarse grained models where several atoms are grouped into larger
units. This approach allows not only to reduce the number of degrees of
freedom in the simulation but also significantly to speed up the inherent timescale of the simulation.