A crucial goal for increasing thermal energy harvesting will be to progress towards atomistic design strategies for smart nanodevices and nanomaterials. This requires the combination of computationally efficient atomistic methodologies with quantum transport based approaches. Here, we review our recent work on this problem, by presenting selected applications of the PHONON tool to the description of phonon transport in nanostructured materials. The PHONON tool is a module developed as part of the Density-Functional Tight-Binding (DFTB) software platform. We discuss the anisotropic phonon band structure of selected puckered two-dimensional materials, helical and horizontal doping effects in the phonon thermal conductivity of boron nitride-carbon heteronanotubes, phonon filtering in molecular junctions, and a novel computational methodology to investigate time-dependent phonon transport at the atomistic level. These examples illustrate the versatility of our implementation of phonon transport in combination with density functional-based methods to address specific nanoscale functionalities, thus potentially allowing for designing novel thermal devices.Entropy 2019, 21, 735 2 of 29 applications in nanoelectronics [7,8], renewable energy harvesting [9,10], nano-and optomechanical devices [11], quantum technologies [12,13], and therapies, diagnostics, and medical imaging [14].An important milestone in the field was the theoretically predicted [15] and subsequently measured quantization of the phononic thermal conductance in mesoscopic structures [16] at low temperatures, this result building the counterpart of the well-known quantization of the electrical conductance in quantum point contacts and other nanostructures (with conductance quantum given by e 2 /h, e being the electron charge and h Planck constant). Thermal conductance quantization has also been found in smaller nanostructures, such as gold wires, where quantized thermal conductance at room temperature was shown down to single-atom junctions [17,18]. The issue is, however, still a subject of debate (see, e.g., [19] for a recent discussion). In contrast to the electrical conductance quantization, the quantum of thermal conductance κ 0 depends, however, on the absolute temperature T through: κ 0 = π 2 k 2 B T/3h, with k B being the Boltzmann constant. This highlights a first important difference between charge and phonon transport. The second one is related to the different energy windows determining the corresponding transport properties: for electrons, the important window lies around the Fermi level, while, for phonons, the conductance results from an integral involving the full vibrational spectrum. Working with a broad spectrum of excitations poses major challenges when it comes to designing thermal devices such as cloaks and rectifiers [2,4], or for information processing in phonon-based computing [6].From the experimental perspective, it is obviously more difficult to tune heat flow than electrical currents. Unlike electrons, phonons are quasi-particle...