A pinboard by
Mona Mohamed

Teaching Assistant, University of Science and Technology at Zewail City


We are theoretically studying the interaction of nucleic acids with Gold Nanoparticles for drug delivery purposes . Both DNA and RNA are known as nucleic acids. They have made up of structures called nucleotides, themselves comprising a number of components, bond together to form the double-helix. A primary DNA or RNA structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. Understanding of the behaviour of nucleic acids in different medium, along with their structure stabilities, are important for developing DNA materials in nano-bio-technology. Also, nanoparticles show great promises in biomedical applications, in electronic diagnostics tool for the chemical and drug delivery inside the living cell, as a respiratory drug carrier system, so on. The nucleic acid binding with NPs can help in understanding the interactions between NPs and DNA thereby promoting the NP-based drug or chemical carrier systems.  


A molecular dynamic model for analyzing concentrations of electrolytes: Fractional molar dependences of microstructure properties

Abstract: Aqueous electrolyte solutions play an important role in many electrophysical and chemical processes in aerospace technology and industrial applications. As noncovalent interactions, the interactions between ions are crucially important for biomolecular structures as well (protein structure folding, molecular level processes followed by ionic pair correlations, the formation of flexible hydrate shells, and so on). Specifically, ions (cations and anions with the same valence charges) can form stable pairs if their sizes match. The formation of ionic pairs can substantially affect the thermodynamic stabilities of proteins in the alkali salts physiologically present in the human body. Research aims and problems impose severe demands on readjustments of the ionic force fields and potential parameters developed to describe aqueous solutions and electrolytic systems. Ionic solutions and their interaction with biomolecules have been observed for over 100 years [1], but the behavior of such solutions remains poorly studied today. New data obtained in this work deals with parameterization strategies and adjustments for the ionic force fields of the alkali cations and halide anions that should be helpful in biomolecular research. Using molecular dynamics (MD) models, four electrolytic systems (HCl-H2O, LiCl-H2O, NaCl-H2O, and KCl-H2O) are investigated as binary mixtures of water and cations and anions, respectively. The intermolecular interaction parameters are varied for two of the four model electrolytes (HCl-H2O and NaCl-H2O) to simulate the possibility of different ionic shells forming during interaction with water. It is found that varying the potential parameters strongly affects the dynamic and structural characteristics of electrolyte systems. MD simulations are performed in the temperature range of 300 to 600 K with a step of 50 K. MD simulations for all electrolyte models (HCl-H2O, LiCl-H2O, NaCl-H2O, KCl-H2O) are also conducted for different molar fractions of electrolyte concentration: 16, 8, and 1 mol/kg. Energies of diffusion activation are calculated using the Arrhenius equation, thereby constructing temperature dependence graphs of diffusion coefficients for all four electrolyte systems. The observed diffusion properties of the electrolyte systems are found to correlate well with the energy and structural radial distribution data.

Pub.: 06 Nov '14, Pinned: 12 Nov '17

On Correlation Effect of the Van-der-Waals and Intramolecular Forces for the Nucleotide Chain - Metallic Nanoparticles - Carbon Nanotube Binding.

Abstract: The tertiary system of nucleotide chain (NC) - gold nanoparticles (NPs) - carbon nanotube (CNT) represents a great interest in the modern research and application of the bio-nano-technologies. The application aspects include, for example, the development of electronic mobile diagnostic facilities, nanorobotic design for a drug delivery inside living cell, and so on. The small NC chain represents an important stage in the understanding of the interaction mechanism of a full DNA or RNA molecule with NP and CNT. In this regard, one has to mention the development of the DNA-CNT devices for the purposes of diagnostic applications in the chemical or drug delivery.For the NC-NP-CNT system, we have built up a series of the molecular dynamics (MD) models with different NC-NP configurations and performed their MD analysis. The entire system (the NC chain, gold NPs and CNT) was allowed to interact with each other by the only VdW forces. The Lennard-Jones short-ranged interaction was assumed between the NC, NP and CNT. For the CNT a many body Tersoff potential having a quantum-chemistry nature was used. So far, the so-called hybrid MD approach was realized, where the quantum-chemistry potential in combination with a classical trajectory calculation applied .The peculiarities of the NC-NP interaction and bond formation inside of a CNT matrix were investigated along with the structural and dynamical behavior. The correlation effects between the weak Van der Waals (VdW) forces and intramolecular vibrations were enlighten for the molecular system consisting of a small nucleotide chain (NC), gold nanoparticles (NPs) and carbon nanotube (CNT) using molecular dynamics (MD) simulation method.The NC intermolecular motions were estimated from MD data thereby building the distance distributions, the angular and dihedral (torsional) bond energy graphs versus simulation time at different temperatures from T=100 K up to 300 K. The MD simulation results have shown that depending on the relative NC-NP position a different scenario of bonding between the NC-NP, within CNT matrix, is possible. We have observed the possibilities of formation of weak, strong and intermediate bonds between the NP-NC, which are overestimated by a presence of CNT matrix as confined environment. The NC chain can form with a particular gold atom a close contact, while with another under the same positional and temperature conditions the weak resultant bonding formation might be possible. We estimated the fluctuations in the NP-NC bonding processes for a single gold atomic case (models 1-3, NC-1NP-CNT), for the two (model 4-6, NC-2NP-CNT) and three (model 7, NC-3NP-CNT) gold particle ones. Thus, a concurrent effect between the NC intramolecular vibrations and a weak VdW interaction between the NC and gold NP were studied in detail.

Pub.: 22 Apr '16, Pinned: 12 Nov '17