"… I seem […] only like a boy playing on the sea-shore, and diverting myself in now and then finding a smoother pebble or a prettier shell than ordinary, whilst the great ocean of truth lay all undiscovered before me". – Isaac Newton.
In the fall of 1972 President Nixon announced that the rate of increase of inflation was decreasing. This was the first time a sitting president used the third derivative to advance his case for reelection.
Hugo Rossi. Mathematics Is an Edifice, Not a Toolbox, Notices of the AMS, v. 43, no. 10, October 1996.
Welcome to the third part is the third part of the essential introduction to the FORTRAN programming series. In this part, we will introduce the use of functions and subroutines to structure the programs. Then we use them to make a program to calculate numerical derivatives of mathematical functions.
Silica is an essential component of many everyday materials. We use silica in containers, appliances, and electronic devices such as smartphones, computers, and tablet screens. These surfaces come into frequent contact with our skin, providing ample opportunities for pathogens, viruses, and microbes to accumulate. Therefore, it is crucial to study the adsorption mechanisms of these microorganisms on silica surfaces.
In collaboration with experimental groups at the University of Lincoln, the University of Greenwich, and Diamond Light Source, we investigate the adsorption mechanisms of isolated RBD regions of the COVID-19 spikes on silica nanoparticles. Our study proposes a simple geometrical model for packing protein particles on spherical silica nanoparticles, which aligns well with the available experimental data. This model revealed a surface occupancy of 32% relative to the maximum theoretical RBD packing, indicating significant adsorption.
My computational contribution to this study involved using molecular dynamics (MD) simulations to explore the binding modes and orientations of the protein adsorbed on a model silica surface. The model consisted of a flat patch of silica surface, which serves as a good approximation of the nanoparticle surface used in the experimental part of this study, given their size. Our findings showed that up to 25% of the RBD’s secondary structures underwent conformational changes as a result of adsorption onto silica nanoparticles.
These insights enhance our understanding of the principles governing protein-surface interactions and can contribute to strategies for controlling the spread of SARS-CoV-2 through contaminated objects.
MD simulations of RBD-silica interaction. (A) Representation of the RBD adsorbed on silica in a representative configuration at the end point of simulation 1. The rectangle highlights the area of contact detailed in panel B. (B) Detailed representation of three residues in close contact with silica: arginine 346 (R346), lysine 356 (K356) and glutamic acid 340 (E340) from left to right. The distances between hydrogen and oxygen atoms at the interface are indicated and are compatible with the hydrogen bonds length.
REFERENCE
Soloviev, M., Siligardi, G., Roccatano, D. and Ferrari, E., 2022. Modelling the adsorption of proteins to nanoparticles at the solid-liquid interface. Journal of Colloid and Interface Science, 605, pp.286-295.
For Schrödinger, the atom was an oscillating system — like the string of a musical instrument — for which there exist a number of modes of oscillation (fundamentals and overtones) which are interpreted as the atom’s energy states.
Armin Hermann. Werner Heisenberg 1901-1976.
This set of slides is from one of my courses in Computational Chemistry. It covers the one-dimensional solution of the Schrödinger equation using Numerov’s method. The material for this article was mainly taken from the excellent Levin textbook in the reference. If you are interested in more details, please like it and subscribe to my website. This way, I will be motivated to add more of these contents.
In college, before video games, we would amuse our- selves by posing programming exercises. One of the favorites was to write the shortest self-reproducing program. Since this is an exercise divorced from reality, the usual vehicle was FORTRAN. Actually, FORTRAN was the language of choice for the same reason that three-legged races are popular.
Ken Thompson, Communications of the ACM. 27 (8), 761–763, 1984.
This is the second part of the basic introductin to FORTRAN programming series.
Control Statements
Relational operators
Relational operators are used for comparison between variables
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