Accelerating the density-functional tight-binding method using graphical processing units

Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility (OLCF) with 1 to 6 NVIDIA Volta V100 GPUs per computer node, and (2) an in-house Intel Xeon computer with 1 to 2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2- and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters

Polish Soil Classification, 6th edition – principles, classification scheme and correlations

The sixth edition of the Polish Soil Classification (SGP6) aims to maintain soil classification in Poland as a modern scientific system that reflects current scientific knowledge, understanding of soil functions and the practical requirements of society. SGP6 continues the tradition of previous editions elaborated upon by the Soil Science Society of Poland in consistent application of quantitatively characterized diagnostic horizons, properties and materials; however, clearly referring to soil genesis. The present need to involve and name the soils created or naturally developed under increasing human impact has led to modernization of the soil definition. Thus, in SGP6, soil is defined as the surface part of the lithosphere or the accumulation of mineral and organic materials permanently connected to the lithosphere (through buildings or permanent constructions), coming from weathering or accumulation processes, originated naturally or anthropogenically, subject to transformation under the influence of soilforming factors, and able to supply living organisms with water and nutrients. SGP6 distinguishes three hierarchical categories: soil order (nine in total), soil type (basic classification unit; 30 in total) and soil subtype (183 units derived from 62 unique definitions; listed hierarchically, separately in each soil type), supplemented by three non-hierarchical categories: soil variety (additional pedogenic or lithogenic features), soil genus (lithology/parent material) and soil species (soil texture). Non-hierarchical units have universal definitions that allow their application in various orders/types, if all defined requirements are met. The paper explains the principles, classification scheme and rules of SGP6, including the key to soil orders and types, explaining the relationships between diagnostic horizons, materials and properties distinguished in SGP6 and in the recent edition of WRB system as well as discussing the correlation of classification units between SGP6, WRB and Soil Taxonomy

Understanding Beam Induced Electronic Excitations in Materials

A time dependent self consistent field based method for determining the rates of electronic excitations induced in materials by the presence of external point charges is presented. The method utilizes the full scalar potential of the external point charge in the interaction Hamiltonian instead of relying on multipolar expansions thereof. A general method is presented for determining the conditions under which dipole selection rules are adequate to describe the electronic response of the material to perturbation by external point charges. The position dependence of point charge induced transition rates between the ground and lowest few excited electronic states was resolved for a small polybenzoid. Notably, electronic excitations that are optically forbidden can be strongly allowed for particular positions of the perturbing point charge. Application of the methods detailed here can lead to an improved understanding of the electronic response of materials under irradiation by beams of charged particles

Computational approaches to delivery of anticancer drugs with multidimensional nanomaterials

Functionalized nanotubes (NTs), nanosheets, nanorods, and porous organometallic scaffolds are potential in vivo carriers for cancer therapeutics. Precise delivery through these agents depends on factors like hydrophobicity, payload capacity, bulk/surface adsorption, orientation of molecules inside the host matrix, bonding, and nonbonding interactions. Herein, we summarize advances in simulation techniques, which are extremely valuable in initial geometry optimization and evaluation of the loading and unloading behavior of encapsulated drug molecules. Computational methods broadly involve the use of quantum and classical mechanics for studying the behavior of molecular properties. Combining theoretical processes with experimental techniques, such as X-ray crystallography, NMR spectroscopy, and bioassays, can provide a more comprehensive understanding of the structure and function of biological molecules. This integrated approach has led to numerous breakthroughs in drug discovery, enzyme design, and the study of complex biological processes. This short review provides an overview of results and challenges described from erstwhile investigations on the molecular interaction of anticancer drugs with nanocarriers of different aspect ratios