126 citations · 877 across the 41 of their papers we have counts for
9 papers · 1 filter
Three-level multilevel simulation of the neuroreceptor function of NMDA
Francesco Di Palma, Sauro Succi, Fabio Sterpone +3
We present a new multiscale method to study the N-Methyl-D-Aspartate (NMDA) neuroreceptor starting from the reconstruction of its crystallographic structure. Thanks to the combinat…
Modulation of current through a nanopore induced by a charged globule: implications for DNA-docking
Mauro Chinappi, Carlo Massimo Casciola, Fabio Cecconi +2
The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a dist…
Quantized biopolymer translocation through nanopores: departure from simple scaling
Simone Melchionna, Massimo Bernaschi, Maria Fyta +2
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of f…
Numerical simulation of conformational variability in biopolymer translocation through wide nanopores
Maria Fyta, Simone Melchionna, Massimo Bernaschi +2
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular…
Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations
Maria Fyta, Simone Melchionna, Sauro Succi +1
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule…
Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows
Maria Fyta, Simone Melchionna, Efthimios Kaxiras +1
We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of s…
Multiscale modeling of biopolymer translocation through a nanopore
Maria Fyta, Simone Melchionna, Efthimios Kaxiras +1
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (M…
Exploring DNA translocation through a nanopore via a multiscale Lattice-Boltzmann Molecular-Dynamics methodology
Simone Melchionna, Maria Fyta, Efthimios Kaxiras +1
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are…
Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore
Maria G. Fyta, Simone Melchionna, Efthimios Kaxiras +1
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a me…