A DFTB-Based Molecular Dynamics Investigation of an Explicitly Solvated Anatase Nanoparticle

We performed a self-consistent charge density functional tight-binding molecular dynamics (SCC DFTB-MD) simulation of an explicitly solvated anatase nanoparticle. From the 2 ps trajectory, we were able to calculate both dynamic and static properties, such as the energies of interaction and the formation of water layers at the surface, and compare them to the observed behaviour reported elsewhere. The high degree of agreement between our simulation and other sources, and the additional information gained from employing this methodology, highlights the oft-overlooked viability of DFTB-based methods for electronic structure calculations of large systems.

Quantum harmonic free energies for biomolecules and nanomaterials

Obtaining the free energy of large molecules from quantum mechanical energy functions is a longstanding challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the thermodynamics of molecular systems of unprecedented size, with modest cost. Using this approach, we compute the vibrational thermodynamics of a series of diamond nanocrystals, and show that the error per atom decreases with system size in the limit of large systems. We further show that we can obtain the vibrational contributions to the binding free energies of prototypical protein-ligand complexes where the exact computation is too expensive to be practical. Our work raises the possibility of routine quantum mechanical estimates of thermodynamic quantities in complex systems.

Explicit Stable Finite Difference Methods for Diffusion-Reaction Type Equations

By the iteration of the theta-formula and treating the neighbors explicitly such as the unconditionally positive finite difference (UPFD) methods, we construct a new 2-stage explicit algorithm to solve partial differential equations containing a diffusion term and two reaction terms. One of the reaction terms is linear, which may describe heat convection, the other one is proportional to the fourth power of the variable, which can represent radiation. We analytically prove, for the linear case, that the order of accuracy of the method is two, and that it is unconditionally stable. We verify the method by reproducing an analytical solution with high accuracy. Then large systems with random parameters and discontinuous initial conditions are used to demonstrate that the new method is competitive against several other solvers, even if the nonlinear term is extremely large. Finally, we show that the new method can be adapted to the advection–diffusion-reaction term as well.

Simulation Methods for the Analysis of Complex Systems

Everyday systems like communication, transportation, energy and industrial systems are an indispensable part of our daily lives. Several methods have been developed for their reliability assessment—while analytical methods are computationally more efficient and often yield exact solutions, they are unable to account for the structural and functional complexities of these systems. These complexities often require the analyst to make unrealistic assumptions, sometimes at the expense of accuracy. Simulation-based methods, on the other hand, can account for these realistic operational attributes but are computationally intensive and usually system-specific. This chapter introduces two novel simulation methods: load flow simulation and survival signature simulation which together address the limitations of the existing analytical and simulation methods for the reliability analysis of large systems.

Dipolar Order Parameters in Large Systems With Fast Spinning

Order parameters are a useful tool for quantifying amplitudes of molecular motions. Here we measure dipolar order parameters by recoupling heteronuclear dipole-dipole couplings under fast spinning. We apply symmetry based recoupling methods to samples spinning under magic angle at 60 kHz by employing a variable flip angle compound inversion pulse. We validate the methods by measuring site-specific 15N-1H order parameters of a microcrystalline protein over a small temperature range and the same protein in a large, precipitated complex with antibody. The measurements of the order parameters in the complex are consistent with the observed protein undergoing overall motion within the assembly.

Data-Driven Computational Fluid Dynamics Model for Predicting Drag Forces on Truck Platoons

Fuel-consumption reduction in the truck industry is significantly beneficial to both energy economy and the environment. Although estimation of drag forces is required to quantify fuel consumption of trucks, computational fluid dynamics (CFD) to meet this need is expensive. Data-driven surrogate models are developed to mitigate this concern and are promising for capturing the dynamics of large systems such as truck platoons. In this work, we aim to develop a surrogate-based fluid dynamics model that can be used to optimize the configuration of trucks in a robust way, considering various uncertainties such as random truck geometries, variable truck speed, random wind direction, and wind magnitude. Once trained, such a surrogate-based model can be readily employed for platoon-routing problems or the study of pavement performance.

Probing the gluon plasma with charm balance functions

Recent theoretical explanations for how hydrodynamic-like flow can build up quickly in small collision systems (hydrodynamization) has led to a microscopic picture of flow building up in a gluon-dominated phase before chemical equilibrium between quarks and gluons has been attained. The goal of this contribution to Offshell-2021 is to explore consequence of assuming a long-lived gluon-dominated phase, which we shall denote a gluon plasma (GP). As these consequences are naturally enhanced in a large systems, we assume and explore the extreme scenario in which a GP would be created in AA collisions and exist for significant time before the formation of a chemically-equilibrated quark-gluon plasma (QGP). The GP and its formation would be impossible to probe with light-quark hadrons, which are first produced later in this scenario. As charm quarks are produced early in the collision, they can circumvent the limitations of light quarks and we propose charm balance functions as an effective tool to test this idea and constrain the dynamics of the GP.