6 research outputs found
Recent advances in describing and driving crystal nucleation using machine learning and artificial intelligence
With the advent of faster computer processors and especially graphics
processing units (GPUs) over the last few decades, the use of data-intensive
machine learning (ML) and artificial intelligence (AI) has increased greatly,
and the study of crystal nucleation has been one of the beneficiaries. In this
review, we outline how ML and AI have been applied to address four outstanding
difficulties of crystal nucleation: how to discover better reaction coordinates
(RCs) for describing accurately non-classical nucleation situations; the
development of more accurate force fields for describing the nucleation of
multiple polymorphs or phases for a single system; more robust identification
methods for determining crystal phases and structures; and as a method to yield
improved course-grained models for studying nucleation.Comment: 15 pages; 1 figur
Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms
14 pagesRegulatory protein access to the DNA duplex 'interior' depends on local DNA 'breathing' fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson-Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.This research was supported by a grant from the National
Institute of Child Health and Human Development (5R01HD081
362-05) awarded to L.S. and N.B.A. The funding sources had no role
in the study design, data collection and analysis, or submission
process
Large Scale Benchmark of Materials Design Methods
Lack of rigorous reproducibility and validation are major hurdles for
scientific development across many fields. Materials science in particular
encompasses a variety of experimental and theoretical approaches that require
careful benchmarking. Leaderboard efforts have been developed previously to
mitigate these issues. However, a comprehensive comparison and benchmarking on
an integrated platform with multiple data modalities with both perfect and
defect materials data is still lacking. This work introduces
JARVIS-Leaderboard, an open-source and community-driven platform that
facilitates benchmarking and enhances reproducibility. The platform allows
users to set up benchmarks with custom tasks and enables contributions in the
form of dataset, code, and meta-data submissions. We cover the following
materials design categories: Artificial Intelligence (AI), Electronic Structure
(ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For
AI, we cover several types of input data, including atomic structures,
atomistic images, spectra, and text. For ES, we consider multiple ES
approaches, software packages, pseudopotentials, materials, and properties,
comparing results to experiment. For FF, we compare multiple approaches for
material property predictions. For QC, we benchmark Hamiltonian simulations
using various quantum algorithms and circuits. Finally, for experiments, we use
the inter-laboratory approach to establish benchmarks. There are 1281
contributions to 274 benchmarks using 152 methods with more than 8 million
data-points, and the leaderboard is continuously expanding. The
JARVIS-Leaderboard is available at the website:
https://pages.nist.gov/jarvis_leaderboar
Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation
Ligand unbinding is mediated by its
free energy change, which has
intertwined contributions from both energy and entropy. It is important,
but not easy, to quantify their individual contributions to the free
energy profile. We model hydrophobic ligand unbinding for two systems,
a methane particle and a C60 fullerene, both unbinding
from hydrophobic pockets in all-atom water. Using a modified deep
learning framework, we learn a thermodynamically optimized reaction
coordinate to describe the hydrophobic ligand dissociation for both
systems. Interpretation of these reaction coordinates reveals the
roles of entropic and enthalpic forces as the ligand and pocket sizes
change. In both cases, we observe that the free-energy barrier to
unbinding is dominated by entropy considerations. Furthermore, the
process of methane unbinding is driven by methane solvation, while
fullerene unbinding is driven first by pocket wetting and then fullerene
wetting. For both solutes, the direct importance of the distance from
the binding pocket to the learned reaction coordinate is present,
but low. Our framework and subsequent feature important analysis thus
give useful thermodynamic insight into hydrophobic ligand dissociation
problems that are otherwise difficult to glean