23 citations · 79 across the 10 of their papers we have counts for
10 papers
Derivation of the Sample-Size Scaling of TWO-NN Intrinsic-Dimension Estimates from Molecular Dynamics Trajectories
Riccardo Capelli
The intrinsic dimension of a dataset is the number of independent directions needed to describe the space occupied by its data. Estimators based on nearest neighbors infer this num…
Kinetic rates calculation via non-equilibrium dynamics
Bruno Stegani, Riccardo Capelli
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand com…
The standard coil or globule phases cannot describe the denatured state of structured proteins and intrinsically disordered proteins
F. Righini, G. Potel, R. Capelli +1
The concepts of globule and random coil were developed to describe the phases of homopolymers and then used to characterize the denatured state of structured cytosolic proteins and…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Ephemeral ice-like local environments in classical rigid models of liquid water
Riccardo Capelli, Francesco Muniz-Miranda, Giovanni M. Pavan
Despite great efforts over the past 50 years, the simulation of water still presents significant challenges and open questions. At room temperature and pressure, the collective mol…
Automatic Multi-Objective Optimization of Coarse-Grained Lipid Force Fields Using SwarmCG
Charly Empereur-mot, Riccardo Capelli, Mattia Perrone +3
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving corr…
Exhaustive Search of Ligand Binding Pathways via Volume-based Metadynamics
Riccardo Capelli, Paolo Carloni, Michele Parrinello
Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics…
Exact value for the average optimal cost of bipartite traveling-salesman and 2-factor problems in two dimensions
Riccardo Capelli, Sergio Caracciolo, Andrea Di Gioacchino +1
We show that the average cost for the traveling-salesman problem in two dimensions, which is the archetypal problem in combinatorial optimization, in the bipartite case, is simply…
An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations
Riccardo Capelli, Guido Tiana, Carlo Camilloni
Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimen…
Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale
R. Capelli, C. Paissoni, P. Sormanni +1
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, s…