NANO-D - 2017 - Annual activity report

NANO-D

NANO-D - 2017

Project-Team Nano-d

Personnel

Overall Objectives

Overview
Research axes

Research Program

The need for practical design of nanosystems
Challenges of practical nanosystem design
Current simulation approaches
Research axes

New Software and Platforms

SAMSON
HermiteFit
Knodle
RigidRMSD
DockTrina

New Results

Incremental methods for long range interactions
Adaptive Algorithms for Orbital-Free Density Functional Theory
As-Rigid-As-Possible molecular interpolation paths
ART-RRT: As-Rigid-As-Possible Exploration of Ligand Unbinding Pathways
IM-UFF: extending the Universal Force Field for interactive molecular modeling
Exploring Chemical Reaction Paths
Combination of force fields
Simulating nanomaterials
Parallel algorithms for adaptive molecular dynamics simulations
Development of Convex-PL, a scoring function for protein-ligand interactions
Participation in the D3R Grand Challenge 2 with the Convex-PL scoring function
Development of a Normal Modes Analysis SAMSON Element
Development of a Hex SAMSON Element
Development of RDKit Smiles Manager SAMSON Elements
Symmetry mate generator for SAMSON
Development of a symmetry detection software AnAnaS
Integration of AnAnaS to SAMSON
Deep Learning for Symmetry detection
Pepsi-SAXS calculator of small-angle X-ray scattering profiles
NOLB nonlinear normal modes
Applications of the NOLB NMA method to structural biology
Off-grid fitting method
RapidRMSD library
SBROD protein quality assessment method
Symmetry detection methods
SAXS-assisted protein docking
Methods for the estimation of collective motions
Smoothed-force energy optimization
Adaptively Restrained Molecular Dynamics in LAMMPS
Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics
Auto update process for SAMSON & SAMSON-SDK
SAMSON Elements policies
Improvements to our software development pipeline
SAMSON Connect Forum

Partnerships and Cooperations

National Initiatives
European Initiatives
International Initiatives
International Research Visitors

Dissemination

Promoting Scientific Activities
Teaching - Supervision - Juries
Popularization

Bibliography

Publications of the year
References in notes

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2017 Project-Team Activity Report

NANO-D

Algorithms for Modeling and Simulation of Nanosystems

Research centre: Grenoble - Rhône-Alpes

In partnership with: CNRS

In collaboration with: Laboratoire Jean Kuntzmann (LJK)

Field: Applied Mathematics, Computation and Simulation

Theme: Numerical schemes and simulations

Keywords:

Computer Science and Digital Science:

A6. - Modeling, simulation and control
A6.2. - Scientific Computing, Numerical Analysis & Optimization
A9.2. - Machine learning

Other Research Topics and Application Domains:

B1. - Life sciences
B1.1. - Biology
B2. - Health
B5.3. - Nanotechnology
B5.5. - Materials