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2. Deep Potential training data for subcritical and supercritical water
- Author(s):
- Calegari Andrade, Marcos; Ko, Hsin-Yu; Car, Roberto
- Abstract:
- Data set used to train a Deep Potential (DP) model for subcritical and supercritical water. Training data contain atomic forces, potential energy, atomic coordinates and cell tensor. Energy and forces were evaluated with the density functional SCAN. Atomic configurations were extracted from DP molecular dynamics at P = 250 bar and T = 553, 623, 663, 733 and 823 K. Input files used to train the DP model are also provided.
- Type:
- Dataset
- Issue Date:
- 19 August 2020
3. Data from "Homogeneous ice nucleation in an ab initio machine learning model"
- Author(s):
- Piaggi, Pablo
- Abstract:
- This dataset contains input and output files to reproduce the results of the manuscript "Homogeneous ice nucleation in an ab initio machine learning model" by Pablo M. Piaggi, Jack Weis, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, and Roberto Car (arXiv preprint https://arxiv.org/abs/2203.01376). In this work, we studied the homogeneous nucleation of ice from supercooled liquid water using a machine learning model trained on ab initio energies and forces. Since nucleation takes place over times much longer than the simulation times that can be afforded using molecular dynamics simulations, we make use of the seeding technique that is based on simulating an ice cluster embedded in liquid water. The key quantity provided by the seeding technique is the size of the critical cluster (i.e., a size such that the cluster has equal probabilities of growing or shrinking at the given supersaturation). Using data from the seeding simulations and the equations of classical nucleation theory we compute nucleation rates that can be compared with experiments.
- Type:
- Dataset
- Issue Date:
- 4 April 2022
4. Data from "Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point"
- Author(s):
- Piaggi, Pablo M; Gartner, Thomas E; Car, Roberto; Debenedetti, Pablo G
- Abstract:
- The possible existence of a liquid-liquid critical point in deeply supercooled water has been a subject of debate in part due to the challenges associated with providing definitive experimental evidence. Pioneering work by Mishima and Stanley [Nature 392, 164 (1998) and Phys.~Rev.~Lett. 85, 334 (2000)] sought to shed light on this problem by studying the melting curves of different ice polymorphs and their metastable continuation in the vicinity of the expected location of the liquid-liquid transition and its associated critical point. Based on the continuous or discontinuous changes in slope of the melting curves, Mishima suggested that the liquid-liquid critical point lies between the melting curves of ice III and ice V. Here, we explore this conjecture using molecular dynamics simulations with a purely-predictive machine learning model based on ab initio quantum-mechanical calculations. We study the melting curves of ices III, IV, V, VI, and XIII using this model and find that the melting lines of all the studied ice polymorphs are supercritical and do not intersect the liquid-liquid transition locus. We also find a pronounced, yet continuous, change in slope of the melting lines upon crossing of the locus of maximum compressibility of the liquid. Finally, we analyze critically the literature in light of our findings, and conclude that the scenario in which melting curves are supercritical is favored by the most recent computational and experimental evidence. Thus, although the preponderance of experimental and computational evidence is consistent with the existence of a second critical point in water, the behavior of the melting lines of ice polymorphs does not provide strong evidence in support of this viewpoint, according to our calculations.
- Type:
- Dataset
- Issue Date:
- February 2023
5. Raw Data for GrsA Sub-domain Dynamics
- Author(s):
- Sun, Xun; Alfermann, Jonas; Li, Hao; Watkins, Maxwell B.; Chen, Yi-Tsao; Chu, Jhih-Wei; Ando, Nozomi
- Abstract:
- This repository contains the raw photon-by-photon single-molecule FRET (smFRET) trajectories, SAXS data, and MD simulation trajectories, multi-sequence alignment, and gel images for the paper titled "Sub-Domain Dynamics Enables Chemical Chain Reactions in Nonribosomal Peptide Synthetases."
- Type:
- Dataset
- Issue Date:
- 2 August 2023
