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تسجيل مستخدم جديدMachine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
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Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting valuable information from the enormous amounts of data generated by simulation of complex systems. We provide here a review of our current understanding of goals, benefits, and limitations of machine learning techniques for computational studies on atomistic systems, focusing on the construction of empirical force fields from ab-initio databases and the determination of reaction coordinates for free energy computation and enhanced sampling.
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Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such computationally expen
sive simulations is the definition of coarse-grained molecular models. Existing coarse-graining approaches define an effective interaction potential to match defined properties of high-resolution models or experimental data. In this paper, we reformulate coarse-graining as a supervised machine learning problem. We use statistical learning theory to decompose the coarse-graining error and cross-validation to select and compare the performance of different models. We introduce CGnets, a deep learning approach, that learns coarse-grained free energy functions and can be trained by a force matching scheme. CGnets maintain all physically relevant invariances and allow one to incorporate prior physics knowledge to avoid sampling of unphysical structures. We show that CGnets can capture all-atom explicit-solvent free energy surfaces with models using only a few coarse-grained beads and no solvent, while classical coarse-graining methods fail to capture crucial features of the free energy surface. Thus, CGnets are able to capture multi-body terms that emerge from the dimensionality reduction.
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P kernels fail to provide faithful force estimates, despite succeeding in bulk Ni systems. However, both 3- and many-body kernels predict forces within a $sim$0.1 eV/$text{AA}$ average error even for small training datasets, and achieve high accuracy even on out-of-sample, high temperature, structures. While training and testing on the same structure always provides satisfactory accuracy, cross-testing on dissimilar structures leads to higher prediction errors, posing an extrapolation problem. This can be cured using heterogeneous training on databases that contain more than one structure, which results in a good trade-off between versatility and overall accuracy. Starting from a 3-body kernel trained this way, we build an efficient non-parametric 3-body force field that allows accurate prediction of structural properties at finite temperatures, following a newly developed scheme [Glielmo et al. PRB 97, 184307 (2018)]. We use this to assess the thermal stability of Ni$_{19}$ nanoclusters at a fractional cost of full ab initio calculations.
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machine learning force fields results key for modelling metallic nanoparticles, as their fluxionality and multi-funneled energy landscape needs to be sampled over long time scales. In this review, we first formally introduce the most commonly used machine learning algorithms for force field generation, briefly outlining their structure and properties. We then address the core issue of training database selection, reporting methodologies both already used and yet unused in literature. We finally report and discuss the recent literature regarding machine learning force fields to sample the energy landscape and study the catalytic activity of metallic nanoparticles.
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are coupled. He
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