Department of Bioscience and Nutrition

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From atomistic details to coarse-grained description

Biomolecular Modelling

Alessandra Villa

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 isfundamental to understanding their function. 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.

Current and Past projects


Alessandra Villa: Le Grand Jorasses