Determining the structure of small molecules via their pseudo-electrons and atoms 3D models using FPGA

Abstract

The particle-pair or particle-particle distance problem (ppdistance) appears in several scientific fields. The pp-distance calculation is a computationally demanding task involved, for instance, in the calculation of X-ray spectra, as shown in Fig-1. Fig. 1. Full experiment layout. Protein structure is one of the bases of the biomedicine and nanotechnology. Different methods are used to determine the structures. One of them is X-ray which is usually limited to highly crystalline structures. We propose to extend the method to low crystallinity samples. We solve the pp-distance problem by calculating the theoretical X-Ray spectra for non-crystalline structures and comparing it against the real one. Our C program reduces the computational time using High Performance Computing over FPGA. We use pseudo-electrons 3D models to accelerate the convergence of the computed spectrums to the referenced one, (see Fig-1, subplot 6.a). Then, we use atoms 3D models to determine exactly the structure of the sample of molecules using Debye approximation and equations [4], (see Fig-1, subplot 6.b).