GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems

Micro-second time-resolved X-ray single-molecule internal motions of SARS-CoV-2 spike variants

Single-molecule intramolecular dynamics were successfully measured for three variants of SARS-CoV-2 spike protein, alpha: B.1.1.7, delta: B.1.617, and omicron: B.1.1.529, with a time resolution of 100 μs using X-rays. The results were then compared with respect to the magnitude and directions of motions for the three variants. The largest 3-D intramolecular movement was observed for the omicron variant irrespective of ACE2 receptor binding. A more detailed analysis of the intramolecular motions revealed that the distribution state of intramolecular motion for the three variants was completely different with and without ACE2 receptor binding. The molecular dynamics for the trimeric spike protein of the omicron variant increased when ACE2 binding occurred. At that time, the diffusion constant increased from 71.0 [mrad2/ms] to 91.1 [mrad2/ms].

Beyond Conventional Density Functional Theory: Advanced Quantum Dynamical Methods for Understanding Degradation of Per- and Polyfluoroalkyl Substances

Computational chemistry methods, such as density functional theory (DFT), have now become more common in environmental research, particularly for simulating the degradation of per- and polyfluoroalkyl substances (PFAS). However, the vast majority of PFAS computational studies have focused on conventional DFT approaches that only probe static, time-independent properties of PFAS near stationary points on the potential energy surface. To demonstrate the rich mechanistic information that can be obtained from time-dependent quantum dynamics calculations, we highlight recent studies using these advanced techniques for probing PFAS systems. We briefly discuss recent applications ranging from ab initio molecular dynamics to DFT-based metadynamics and real-time time-dependent DFT for probing PFAS degradation in various reactive environments. These quantum dynamical approaches provide critical mechanistic information that cannot be gleaned from conventional DFT calculations. We conclude with a perspective of promising research directions and recommend that these advanced quantum dynamics simulations be more widely used by the environmental research community to directly probe PFAS degradation dynamics and other environmental processes.

Velocity-Gauge Real-Time Time-Dependent Density Functional Tight-Binding for Large-Scale Condensed Matter Systems

We present a new velocity-gauge real-time, time-dependent density functional tight-binding (VG-rtTDDFTB) implementation in the open-source DFTB+ software package (https://dftbplus.org) for probing electronic excitations in large, condensed matter systems. Our VG-rtTDDFTB approach enables real-time electron dynamics simulations of large, periodic, condensed matter systems containing thousands of atoms with a favorable computational scaling as a function of system size. We provide computational details and benchmark calculations to demonstrate its accuracy and computational parallelizability on a variety of large material systems. As a representative example, we calculate laser-induced electron dynamics in a 512-atom amorphous silicon supercell to highlight the large periodic systems that can be examined with our implementation. Taken together, our VG-rtTDDFTB approach enables new electron dynamics simulations of complex systems that require large periodic supercells, such as crystal defects, complex surfaces, nanowires, and amorphous materials.