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Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
The atomistic resolution recently achieved by ultrafast spectroscopies demands corresponding theoretical advances. Real-time time-dependent density-functional theory (RT-TDDFT) with Ehrenfest dynamics offers an optimal trade-off between…
In many mechanical, electrical, and general physical systems evolving over time or space, spectral analysis methods as Fast Fourier Transform (FFT), Short Term Fourier Transform (STFT), Power Spectrum Density (PSD) plays a very important…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
Time-resolved absorption spectroscopy as well as magnetic circular dichroism with circularly polarized soft X-rays (XAS and XMCD) are powerful tools to probe electronic and magnetic dynamics in magnetic materials element- and…
The understanding of oxygen reduction reaction (ORR) activity on perovskite oxide surfaces is essential for promising future fuel cell applications. We report a comparative study of ORR mechanisms on La$B$O$_3$ ($B$=Mn, Fe, Cr) surfaces by…
We construct a new reduced nuclear reaction network able to reproduce the energy production due to the photo-disintegration of heavy elements such as Ru, which are believed to occur during superbursts in mixed H/He accreting systems. We use…
The elucidation of fundamental mechanisms underlying ion-induced radiation damage of biological systems is crucial for the advancement of radiotherapy with ion beams and for radiation protection in space. The study of ion-induced biodamage…
We present observations of 12CO J=1-0, 13CO J=1-0, HI, and all four ground-state transitions of the hydroxyl (OH) radical toward a sharp boundary region of the Taurus molecular cloud. Based on a PDR model that reproduces CO and [CI]…
Empirical force fields remain the primary tool for large-scale molecular simulation, yet their limited flexibility and transferability often hinder predictive modeling in chemically complex condensed-phase systems. Here we present ORION, a…
Direct imaging of molecular dynamics is a long-standing goal in physics and chemistry. As an emerging tool, high-harmonic spectroscopy (HHS) enables accessing molecular dynamics on femtosecond to attosecond time scales. However, decoding…
Coherent control of OH-free radicals interacting with the spin-triplet state of a DNA molecule is investigated. A model Hamiltonian for molecular spin singlet-triplet resonance is developed. We illustrate that the spin-triplet state in DNA…
In nuclear reaction experiments, the measured decay energy spectra can give insights into the shell structure of decaying systems. However, extracting the underlying physics from the measurements is challenging due to detector resolution…
Background: Ultra-high-dose-rate (UHDR) radiation therapy has demonstrated promising potential in reducing toxicity to organs-at-risk (OARs). Proton therapy is uniquely positioned to deliver UHDR by leveraging the Bragg peak in conjunction…
Transport of fast electron in overdense plasmas is of key importance in high energy density physics. However, it is challenging to diagnose the fast electron transport in experiments. In this article, we study coherent transition radiation…
We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following earlier work of Wu et al. Phys. Rev.…
We have developed the first laser damage simulation algorithm capable of determining crater and surface modification morphology from microscopic physics. Rapid progress in the field of high intensity ultrafast lasers has enabled its utility…
Resistive random access memories (ReRAMs) with a bilayer TaOx/HfO2 stack structure have shown unique multi-level resistive switching capabilities. However, the physical processes governing their behavior, and specifically the atomistic…
We develop a kinetic reaction model for cells having irradiated DNA molecules due to ionizing radiation exposure. Our theory simultaneously accounts for the time-dependent reactions of the DNA damage, the DNA mutation, the DNA repair, and…
We report on radiative hydrodynamic simulations of M dwarf stellar flares and compare the model predictions to observations of several flares. The flares were simulated by calculating the hydrodynamic response of a model M dwarf atmosphere…