A mapping of a macromolecule is a prescription to construct a simplified representation of the system in which only a subset of its constituent atoms is retained. As the specific choice of the mapping affects the analysis of all-atom simulations as well as the construction of coarse-grained models, the characterisation of the mapping space has recently attracted increasing attention. We here introduce a notion of scalar product and distance between reduced representations, which allows the study of the metric and topological properties of their space in a quantitative manner. Making use of a Wang–Landau enhanced sampling algorithm, we exhaustively explore such space, and examine the qualitative features of mappings in terms of their squared...
All-atom Molecular Dynamics (MD) is the standard approach to perform in silico simulations of biomol...
International audienceUnderstanding the dynamics of biomolecules is the key to understanding their b...
A phase-space approach is proposed for molecular dynamics simulations, which serve as a bridge betwe...
The success of any physical model critically depends upon adopting an appropriate representation for...
Increasingly, it is recognized that new automated forms of analysis are required to understand the h...
Algorithms for quantifying the differences between two lattices are used for Bravais lattice determi...
Efficient, physically-inspired descriptors of the structure and composition of molecules and materia...
When examining complex problems, such as the folding of proteins, coarse grained descriptions of the...
Complex systems are characterised by a tight, nontrivial interplay of their constituents, which give...
In order to characterize molecular structures we introduce configurational fingerprint vectors which...
Dimension reduction is often necessary when attempting to reach longer length and time scales in mol...
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by t...
The computational resources required by atomistic simulations of biomolecular systems still limit th...
In this paper we develop a formal definition of chemical space as a discrete metric space of molecul...
Great computational effort is invested in generating equilibrium states for molecular systems using,...
All-atom Molecular Dynamics (MD) is the standard approach to perform in silico simulations of biomol...
International audienceUnderstanding the dynamics of biomolecules is the key to understanding their b...
A phase-space approach is proposed for molecular dynamics simulations, which serve as a bridge betwe...
The success of any physical model critically depends upon adopting an appropriate representation for...
Increasingly, it is recognized that new automated forms of analysis are required to understand the h...
Algorithms for quantifying the differences between two lattices are used for Bravais lattice determi...
Efficient, physically-inspired descriptors of the structure and composition of molecules and materia...
When examining complex problems, such as the folding of proteins, coarse grained descriptions of the...
Complex systems are characterised by a tight, nontrivial interplay of their constituents, which give...
In order to characterize molecular structures we introduce configurational fingerprint vectors which...
Dimension reduction is often necessary when attempting to reach longer length and time scales in mol...
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by t...
The computational resources required by atomistic simulations of biomolecular systems still limit th...
In this paper we develop a formal definition of chemical space as a discrete metric space of molecul...
Great computational effort is invested in generating equilibrium states for molecular systems using,...
All-atom Molecular Dynamics (MD) is the standard approach to perform in silico simulations of biomol...
International audienceUnderstanding the dynamics of biomolecules is the key to understanding their b...
A phase-space approach is proposed for molecular dynamics simulations, which serve as a bridge betwe...