Engineering topics

Nguyen, Phuong

Publications and source records attributed to Nguyen, Phuong.

3 records

DOE OSTI2025

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗

DOE OSTI2024

Phase Transitions and Thermal Equation of State of Fe‐9wt.%Si Applied to the Moon and Mercury

Abstract Accurate knowledge of the phase transitions and thermoelastic properties of candidate iron alloys, such as Fe‐Si alloys, is essential for understanding the nature and dynamics of planetary cores. The phase diagrams of some Fe‐Si alloys between 1 atm and 16 GPa have been back‐extrapolated from higher pressures, but the resulting phase diagram of Fe 83.6 Si 16.4 (9 wt.% Si) is inconsistent with temperature‐induced changes in its electrical resistivity between 6 and 8 GPa. This study reports in situ synchrotron X‐ray diffraction (XRD) measurements on pre‐melted and powder Fe 83.6 Si 16.4 samples from ambient conditions to 60 GPa and 900 K using an externally heated diamond‐anvil cell. Upon compression at 300 K, the bcc phase persisted up to ∼38 GPa. The hcp phase appeared near 8 GPa in the pre‐melted sample, and near 17 GPa in the powder sample. The appearance of the hcp phase in the pre‐melted sample reconciles the reported changes in electrical resistivity of a similar sample, thus resolving the low‐pressure region of the phase diagram. The resulting high‐temperature Birch‐Murnaghan equation of state (EoS) and thermal EoS based on the Mie‐Gruneisen‐Debye model of the bcc and hcp structures are consistent with, and complement the literature data at higher pressures. The calculated densities based on the thermal EoS of Fe‐9wt.%Si indicate that both bcc and hcp phases agree with the reported core density estimates for the Moon and Mercury.

Berrada, Meryem↗

DOE OSTI2024

An artificial intelligence accelerated virtual screening platform for drug discovery

Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we develop a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screen multi-billion compound libraries against two unrelated targets, a ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel Na V 1.7. For both targets, we discover hit compounds, including seven hits (14% hit rate) to KLHDC2 and four hits (44% hit rate) to Na V 1.7, all with single digit micromolar binding affinities. Screening in both cases is completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.

Science & Technology - Other Topics↗