Engineering topics

Yu, Qi

Publications and source records attributed to Yu, Qi.

5 records

DOE OSTI2024

The development of thermodynamically consistent and physics-informed equation-of-state model through machine learning

Ab initio molecular dynamics (AIMD) simulations have become an important tool used in the construction of equations of state (EOS) tables for warm dense matter. Due to computational costs, only a limited number of system state conditions can be simulated, and the remaining EOS surface must be interpolated for use in radiation-hydrodynamic simulations of experiments. In this work, we develop a thermodynamically consistent EOS model that utilizes a physics-informed machine learning approach to implicitly learn the underlying Helmholtz free-energy from AIMD generated energies and pressures. The model, referred to as PIML-EOS, was trained and tested on warm dense polystyrene producing a fit within a 1% relative error for both energy and pressure and is shown to satisfy both the Maxwell and Gibbs–Duhem relations. In addition, we provide a path toward obtaining thermodynamic quantities, such as the total entropy and chemical potential (containing both ionic and electronic contributions), which are not available from current AIMD simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

GLIDR promotes the progression of glioma by regulating the miR-4677-3p/MAGI2 axis

Gliomas are the most common and fatal primary brain tumors. Growing evidence suggests that long non-coding RNAs (lncRNAs) constitute novel and potential therapeutic targets for glioma. However, the biological role of glioblastoma down-regulated RNA (GLIDR) in glioma remains largely elusive. In the current study, we used quantitative real-time polymerase chain reaction (qRT-PCR) to detect GLIDR expression in glioma cells. Cell counting kit 8 (CCK-8) assay, colony formation assay, JC-1 staining, and flow cytometry were used to evaluate the role of GLIDR in proliferation and apoptosis of glioma cells. Western blotting was performed to assess the effect of GLIDR on the level of apoptosis-related proteins. In addition, bioinformatics prediction, RNA immunoprecipitation (RIP), RNA pull-down, and luciferase reporter gene assays were used to study the regulatory mechanisms of GLIDR in glioma. GLIDR was found to be highly expressed in glioma cells and silencing of GLIDR inhibited cell proliferation and promoted apoptosis. Functionally, GLIDR bound to miR-4677-3p that directly targeted membrane-associated guanylate kinase, WW, and PDZ domain-containing protein 2 (MAGI2). Our data showed that GLIDR affects the proliferation and apoptosis of glioma cells by targeting miR-4677-3p to regulate the expression of MAGI2. In conclusion, our study determined the oncogenic role of GLIDR in glioma, which may provide a new perspective for the treatment of glioma.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Crossover from hydrogen to chemical bonding

Hydrogen bonds (H-bonds) can be interpreted as a classical electrostatic interaction or as a covalent chemical bond if the interaction is strong enough. As a result, short strong H-bonds exist at an intersection between qualitatively different bonding descriptions, with few experimental methods to understand this dichotomy. The [F-H-F] − ion represents a bare short H-bond, whose distinctive vibrational potential in water is revealed with femtosecond two-dimensional infrared spectroscopy. It shows the superharmonic behavior of the proton motion, which is strongly coupled to the donor-acceptor stretching and disappears on H-bond bending. In combination with high-level quantum-chemical calculations, we demonstrate a distinct crossover in spectroscopic properties from conventional to short strong H-bonds, which identify where hydrogen bonding ends and chemical bonding begins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Decoding the 2D IR spectrum of the aqueous proton with high-level VSCF/VCI calculations

The aqueous proton is a common and long-studied species in chemistry, yet there is currently intense interest devoted to understanding its hydration structure and transport dynamics. Typically described in terms of two limiting structures observed in gas-phase clusters, the Zundel H 5 O 2 + and Eigen H 9 O 4 + ions, the aqueous structure is less clear due to the heterogeneity of hydrogen bonding environments and room-temperature structural fluctuations in water. The linear infrared (IR) spectrum, which reports on structural configurations, is challenging to interpret because it appears as a continuum of absorption, and the underlying vibrational modes are strongly anharmonically coupled to each other. Recent two-dimensional IR (2D IR) experiments presented strong evidence for asymmetric Zundel-like motifs in solution, but true structure–spectrum correlations are missing and complicated by the anharmonicity of the system. In this study, we employ high-level vibrational self-consistent field/virtual state configuration interaction calculations to demonstrate that the 2D IR spectrum reports on a broad distribution of geometric configurations of the aqueous proton. We find that the diagonal 2D IR spectrum around 1200 cm –1 is dominated by the proton stretch vibrations of Zundel-like and intermediate geometries, broadened by the heterogeneity of aqueous configurations. There is a wide distribution of multidimensional potential shapes for the proton stretching vibration with varying degrees of potential asymmetry and confinement. In conclusion, we find specific cross peak patterns due to aqueous Zundel-like species. These studies provide clarity on highly debated spectral assignments and stringent spectroscopic benchmarks for future simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2015

The Structure, Anharmonic Vibrational Frequencies, and Intensities of NNHNN+

A semi-global potential energy surface (PES) and quartic force field (QFF) based on fitting high-level electronic structure energies are presented to describe the structures and spectroscopic properties of NNHNN+. The equilibrium structure of NNHNN+ is linear with the proton equidistant between the two nitrogen groups and thus of D(sub ∞h) symmetry. Vibrational second-order perturbation theory (VPT2) calculations based on the QFF fails to describe the proton “rattle” motion, i.e., the antisymmetric proton stretch, due to the very flat nature of PES around the global minimum, but performs properly for other modes with sharper potential wells. Vibrational self-consistent field/virtual state configuration interaction (VSCF/VCI) calculations using a version of MULTIMODE without angular momentum terms successfully describe this motion and predict the fundamental to be at 759 cm(exp -1). This is in good agreement with the value of 746 cm(exp -1) from a fixed-node diffusion Monte Carlo calculation and the experimental Ar-tagged result of 743 cm(exp -1). Other VSCF/VCI energies are in good agreement with other experimentally reported ones. Both double-harmonic intensity and rigorous MULTIMODE intensity calculations show the proton transfer fundamental has a very strong intensity.

Astrochemistry↗