Shyam Badu

Thermoelectromechanical effects in relaxed-shape graphene and band structures of graphene quantum dots

We investigate the in-plane oscillations of the relaxed shape graphene due to externally applied tensile edge stress along both the armchair and zigzag directions. Thermo-electromechanical effects are treated via pseudomorphic vector potentials to analyze the influence of these coupled effects on the bandstructures of bilayer graphene quantum dots (QDs). We show that the total elastic energy density is enhanced with temperature for the case of applied tensile edge stress along the zigzag direction. We report that the level crossing between ground and first excited states in the localized edge states can be achieved with the accessible values of temperature. In particular, the level crossing point extends to higher temperatures with decreasing values of externally applied tensile edge stress along the armchair direction. Such kind of level crossing is absent in the states formed at the center of the graphene sheet due to the presence of three fold symmetry.

Discrete-to-continuum models for biomedical applications of RNA nanotubes

RNA macromolecular structures are very important in the currently boosting field of bionanotechnology, including a range of biomedical applications. In order to expand the applications of these RNA nanoclusters obtained from the self assembly of the ribonucleic acid (RNA) building blocks, it is critical to be able to better understand and predict their properties. Therefore, we model the RNA nanotubes of different sizes using molecular dynamics simulations and then study the mechanical properties of such nanotubes with continuum models implemented with the finite element methodology. We present details of our novel discrete-to-continuum models, and explain how the atomistic models in this field can be used to develop the continuum macroscopic models which would allow to calculate elastic properties of RNA nanotubes using the finite element method. By using the elastic constants available for nucleic acids, we demonstrate how to obtain the distribution of the displacement field due to stress along different directions of the RNA nanotube. These new results pave the road to our better understanding of RNA nanotube stability in biomedical applications.

NMR properties of Fenna-Matthews-Olson light harvesting complex: Photosynthesis and its biomedical applications

In this article we study the structural properties of the bacteriochlorophyll taken from the Fenna-Matthews-Olson (FMO) light harvesting complex found in the green sulphur bacteria. This study is motivated by a range of applications of photosynthetic complexes, including their increasing role in biomedicine, where our better understanding of their properties become critical. Specifically, in our current study we present the nulcear magnetic resonance (NMR) spectrum of the bacteriochlorophyll that is directly taken from the FMO complex, as well as the spectrum for this system for its optimized geometry. We use density functional theory to calculate the optimized geometry and the NMR spectra of the bacteriochlorophyll. From our calculations we found that the chemical shift values are slightly lower for the optimized geometry of the bacteriochlorophyll than the values obtained for the unoptimized bacteriochlorophyll. The differences observed between these two spectra are due to the fact that the unoptimized structure of the bacteriochlorophyll possess the influence of the protein environment of FMO complex.

Modelling Biological Polymeric Nanostructures in Physiological Fluids: Focus on Ribonucleic Acid Nanotubes

In this paper, we study bilogical polymeric molecular nanostructures, focusing on ribonucleic acids (RNA) and their behaviour in fluids, in particular in physiological solutions. First, we give a brief overview of the most recent results in this field related to the properties of these structures that can be characterised by root mean square deviation, radius of gyration and radial distribution function. Among other things, we provide insight into typical distributions of 23Na+and 35Cl−ions around the RNA nanotubes as a function of time within a distance of 5 Å from their surface. Finally, we provide details of the recent achievements in the coarse grain modeling of the such bilogical nanotubes.

Transport Properties of RNA Nanotubes Using Molecular Dynamics Simulation

We present novel molecular dynamics studies of transport properties of RNA nanotubes. Specifically, we determine the velocity trajectories for the phosphorous atom at the phosphate backbone of the RNA nanotube, the oxygen atom at sugar ring, and the 23Na + and 35Cl −ions in physiological solutions. At the constant temperature simulation it has been found that the fluctuation of the velocities is small and consistent with simulation time. We have also presented the velocity autocorrelation function for the phosphorous atom in RNA nanotubes that provides better insight into the diffusion direction of the system in physiological solution. We compare our results calculated computationally with the available experimental results.

Studying properties of RNA nanotubes via molecular dynamics

RNA molecules are very flexible in nature. This feature allows us to build various motifs which are essential in bionanotechnological applications. Based on our earlier developed models of RNA nanoclusters, in this contribution we analyze the structure and properties of RNA nanotubes in physiological solutions at different concentrations. Our major tool here is the molecular dynamics (MD) method that was implemented by using the NAMD and VMD packages, with which we study the structural and thermal properties of the nanotubes in physiological solutions. In particular, we have analyzed such characteristics as the Root Mean Square Deviation (RMSD), the radius of gyration, the number of hydrogen bonds per base pairs, and the radial distribution function (RDF) of a RNA nanotube at different concentrations of the physiological solution. Furthermore, the number of 23Na+ and 35Cl−ions around the nanotubes within the distance of 5 Å at two different concentrations has also been analyzed in detail. It has been found that the number of ions accumulated around the nanotubes within the particular distance is growing by small amount while the concentrations of the 23Na+ and 35Cl−ions are substantially increased.

RNA Nanostructures in Physiological Solutions: Multiscale Modeling and Applications

In this review chapter we focus on the nucleic acid nanotechnology research and its application in the biomedical field. We also describe some of our most recent results on the modeling of ribonucleic acid (RNA ) nanotubes and their characteristics in physiological solution s. This includes the properties that can be characterised by root mean square deviation (RMSD ), radius of gyration and radial distribution function (RDF ) for the RNA nanocluster s, paying special attention to RNA nanotube s. We describe the distribution of \(^{23} {\text{Na}}^{ + }\) and \(^{35} {\text{Cl}}^{ - }\) ions around the tube as a function of time within a distance of 5 \({\AA}\) from the surface of the tube. The results obtained from our computational studies are compared with available experimental results in the literature. The current developments in the coarse grain modeling of the RNA nanoclusters and other biomolecules are also highlighted.