Papers by Narayan Adhikari
Journal of Biomolecular Structure and Dynamics
Earth and Planetary Science Letters, 1993
Journal of Nepal Physical Society
Considering the significance of natural gas, such as methane, and the difficulties in storing it,... more Considering the significance of natural gas, such as methane, and the difficulties in storing it, research is increasingly focusing on developing materials for solid-state methane storage. Two-dimensional materials have a large number of possible adsorption sites for gas molecules due to their high surface-to-volume ratio. However, the two-dimensional structure is chemically inactive and attracts nonpolar gases rather weakly. We investigated the methane gas adsorption capabilities of silicene by activating it with different defects. According to our density functional theory calculations, the mono-vacancy (MV) defect is advantageous in increasing the binding strength of energy-carrying gases such as methane. In MV defective silicene, methane adsorption energy is detected in the order of the internationally specified energy regime.
AIP Advances
Transportation of amino acids throughout the body is an essential mechanism to support life proce... more Transportation of amino acids throughout the body is an essential mechanism to support life processes. Transportation phenomena such as diffusion, viscosity, etc., of amino acids in an aqueous medium are useful to understand their inter- and intra-molecular interactions. In this work, we performed classical molecular dynamics simulation to study the transportation properties of γ-aminobutyric acid (GABA) in an aqueous environment. Self-diffusion coefficients of both GABA and water molecules as well as their binary diffusion coefficient were estimated at different temperatures. This work was further extended to estimate the effect of system size on diffusion coefficients and the viscosity coefficients of the solvent. In addition, the temperature dependence of the diffusion coefficient was studied utilizing an Arrhenius plot. The outcomes were compared with previously reported values. Furthermore, the number of hydrogen bonds between the solute and the solvent as well as the solvent a...
Cornell University - arXiv, Jun 17, 2017
Diffusion, transport of mass in response to concentration and thermal energy gradient, is an impo... more Diffusion, transport of mass in response to concentration and thermal energy gradient, is an important transport property, vital in material science and life science. In the present work classical molecular dynamics study of diffusion of zwittterion glycine, zwitterion diglycine and zwitterion triglycine in water have been carried out. Self and binary diffusion coefficients of aqueous solution of these molecules have been calculated using Einstein method. Our results agree with experimental data reported in literatures. Temperature dependency of diffusion of glycine in water have been explored using estimated values of self and binary diffusion coefficients at four different temperatures. Effect of peptide bond formation in diffusion has been studied using peptide chain composed of up to three monomers of glycine. The structure of the system is analyzed using radial distribution function of different atom.
BIBECHANA
Methylation at O6 atom of guanine is a type of DNA damage which can cause a cancer. This damage a... more Methylation at O6 atom of guanine is a type of DNA damage which can cause a cancer. This damage at O6 atom of guanine in a DNA can be transferred to SG atom of cysteine in O6-alkylguanine-DNA alkyltransferase (AGT). Flipping out of methylated guanine from its base stack is essential to give off the methyl adduct (CH3) to AGT. AGT receives the methyl adduct at cysteine leaving guanine demethylated, but still in flipped out orientation. The repair mechanism of DNA would be completed only when the extrahelically flipped guanine returns back into the base stack, which is considered as the final step of the DNA repair mechanism. Here, the intrahelical flipping mechanism of repaired guanine has been studied. The work is further extended to examine the stability of hydrogen bonds between guanine and its pair partner cytosine. The overall result shows that intrahelical rotation of repaired guanine is possible and the base pairing is stable as the ordinary hydrogen bonding. BIBECHANA 19(2022...
BIBECHANA
Methylation at O6 atom of guanine is a type of DNA damage which can cause a cancer. This damage a... more Methylation at O6 atom of guanine is a type of DNA damage which can cause a cancer. This damage at O6 atom of guanine in a DNA can be transferred to SG atom of cysteine in O6-alkylguanine-DNA alkyltransferase (AGT). Flipping out of methylated guanine from its base stack is essential to give off the methyl adduct (CH3) to AGT. AGT receives the methyl adduct at cysteine leaving guanine demethylated, but still in flipped out orientation. The repair mechanism of DNA would be completed only when the extrahelically flipped guanine returns back into the base stack, which is considered as the final step of the DNA repair mechanism. Here, the intrahelical flipping mechanism of repaired guanine has been studied. The work is further extended to examine the stability of hydrogen bonds between guanine and its pair partner cytosine. The overall result shows that intrahelical rotation of repaired guanine is possible and the base pairing is stable as the ordinary hydrogen bonding. BIBECHANA 19 (202...
AIP Advances
Graphene (G) and hexagonal Boron Nitride (h-BN) are structurally similar materials but have very ... more Graphene (G) and hexagonal Boron Nitride (h-BN) are structurally similar materials but have very different electronic and magnetic properties. Heterostructures formed by the combination of these materials are of great research interest. To assess the role played by the crystalline defects in such heterostructures is also of crucial importance owing to their novel properties. In the present work, we study the structural, electronic, and magnetic properties of the G/h-BN heterostructure and the different possible point defects of B and N atoms in it by using first-principles calculations based on the spin-polarized density functional theory (DFT) method within the van der Waals correction DFT-D2 approach. The structural analysis of these systems shows that they are stable two dimensional van der Waals heterostructure materials. Band structure calculations of these materials reveal their semimetallic nature. On the basis of density of states and partial density of states calculations, the defective systems are magnetic materials. The magnetic moment obtained in these defective systems is due to the unpaired up-spin and down-spin states in the orbitals of C, B, and N atoms created by the vacancy defects. On the other hand, the G/h-BN heterostructure has an approving condition for ferromagnetism due to the presence of flat bands in the neighborhood of the Fermi energy.
Journal of Molecular Modeling
Heterostructures (HS), vacancy defects in HS, and molecular adsorption on defected HS of 2D mater... more Heterostructures (HS), vacancy defects in HS, and molecular adsorption on defected HS of 2D materials are fervently inspected for a profusion of applications because of their aptness to form stacked layers that confer approach to an amalgamation of favorable electronic and magnetic properties. In this context, graphene (Gr), hexagonal boron nitride (h-BN), HS of graphene/h-BN (Gr/h-BN), and molecular adsorption on Gr/h-BN offer promising prospects for electronic, spintonic, and optoelectronic devices. In this study, we investigated the structural, electronic, and magnetic properties of C sites vacancy defects in Gr/h-BN HS and adsorption of water molecule on defected Gr/h-BN HS materials by using first-principles calculations based on spin-polarized density functional theory method within van der Waals (vdW) corrections DFT-D2 approach. We found that these considered materials are stable 2D vdW HS. Based on band structure calculations, they are semimetallic, and on density of states and partial density of states analysis, they are magnetic materials. The magnetic moment developed in these defected systems is due to the unpaired up-spin and down-spin states in the orbitals of atoms present in the materials created by the vacancy defects.
AIP Advances, 2022
This work focuses on identifying the conformational stability and binding components in sickle an... more This work focuses on identifying the conformational stability and binding components in sickle and normal hemoglobin to explore the elastic properties and realize the stiffness by using molecular dynamics simulation. Our investigation shows that a larger force is required to separate the beta chain of normal hemoglobin in comparison to the sickle hemoglobin by using steered molecular dynamic. In sickle hemoglobin protein (HbS), the hydrogen bond binding force of the beta chain is 7073.74–12 646.80 pN for pulling velocities of 0.000 20–0.000 40 nm/ps with the spring constant of 800 kcal mol−1 nm−2. Similarly, in normal hemoglobin protein, the hydrogen bond binding force in the beta chain ranges from 12 005.00 to 17 753.70 pN for the same values of pulling velocities and spring constant. This indicates that the normal hemoglobin is stiffer than sickle hemoglobin. We have also analyzed the solvent accessible surface area (SASA) of both proteins, and our investigation shows that the SAS...
Journal of Nepal Physical Society, 2020
Human growth hormone (hGH) is synthesized, stored and secreted by somatotropic cells within the l... more Human growth hormone (hGH) is synthesized, stored and secreted by somatotropic cells within the lateral wings of the anterior lobe of pituitary glands; and is transported to other organs of human body. Study of intra-molecular structure and its binding mechanisms within the molecule gives more insight of structural stability of the molecule and is also essential in drug designing. In this article, we have investigated the various bonded and non-bonded interactions that contribute for the conformation of entire structure of the hGH molecule using molecular dynamics (MD) simulation. The MD outcomes show that the molecule is hydrophobic in nature. In its conformation, several types of interactions exist, such as disulphide bridges (bonded) and nonbonded: hydrogen bond, hydrophobic, aromatic-aromatic, ionic, aromatic-sulphur, cation-pi.
Interdisciplinary Research in Education, 2021
This study aimed to find out the pedagogical approaches for effective classroom management. The s... more This study aimed to find out the pedagogical approaches for effective classroom management. The study is also undertaken to explore the teacher's opinions on effective classroom management. The study has addressed the research question ''how teachers can effectively manage a classroom with a wide range of learning abilities and styles, in a student-centered way''. It is adopted the qualitative research design. Qualitative data were taken from in-depth interviews. Thematic analysis and verbatim analysis have been done. Data were analyzed on the themes of student-centered classroom management, reactive and proactive classroom management strategies, cooperative discipline, culturally responsive teaching teacher’s role, and classroom management. The study's findings entail that a well-managed classroom is a powerful motivator for students’ learning. Reactive and proactive classroom, cooperative and collaborative learning atmosphere, culturally responsive teaching...
Grenzflächeneigenschaften von zwei unverträglichen Polymeren unterschiedlicher Steifigkeiten werd... more Grenzflächeneigenschaften von zwei unverträglichen Polymeren unterschiedlicher Steifigkeiten werden mittels gitterfreies Kugel-Stab-Modell und Monte-Carlo-Techniken untersucht. Die Bestimmung der Grenzflächenspannung erfolgt durch Anwendung des Virialsatzes und aus einer Analyse des Kapillarwellenspektrums. Grenzflächenprofile für Segment- und Kettenorientierung werden im Detail untersucht. Die Ergebnisse zeigen, daß die Grenzflächenspannung mit der Steifigkeit der semiflexiblen Komponente anwächst und mit wachsender Steifigkeit schnell in einen konstanten Wert einmündet. Dieser konstante Wert wird bereits deutlich unterhalb der Steifigkeit erreicht, bei der die semiflexiblen Polymere einen Übergang vom isotropen zum nematischen Zustand erfahren. Im tatsächlich semiflexiblen Bereich ergibt sich bei Berücksichtigung der Effekte endlicher Kettenlänge eine gute Übereinstimmung mit den Mean-Field-Resultaten. Die Ergebnisse zeigen, daß χc mit zunehmender Steifigkeit der semiflexiblen Kom...
Journal of Nepal Physical Society, 2021
In this work, we have carried out Molecular Dynamics Simulation technique to study the diffusion ... more In this work, we have carried out Molecular Dynamics Simulation technique to study the diffusion coefficients, radial distribution functions and solvation free energy of sucrose (C12H22O11) at different temperatures ranging from 298.15 K to 318.15 K. We have taken 2 molecules of sucrose in 1343 molecules of extended simple point charge (SPC/E) water model. The self-diffusion coefficients are obtained by applying linear best fit to the mean squaredisplacement (MSD) plot and binary diffusion coefficients are obtained by using Darken’s relation. Arrhenius equation has been used to show a linear relationship between natural logarithm of binary diffusion coefficient and reciprocal of temperature. The structural analysis of the solution has been carried out with the help of radial distribution functions (RDFs) of its constituents. The solvation free energy of sucrose is studied at 300 K by using free energy perturbation method like Bennett Acceptance Ratio (BAR). The results of binary dif...
The binary alloys formed from the elements of Fe and Pd like FePd and Fe3Pd, have the strange ele... more The binary alloys formed from the elements of Fe and Pd like FePd and Fe3Pd, have the strange electronic and magnetic properties, generally used in shape memory alloys, Computational chips, Medical purposes as well as modern technological uses. We used TB-LMTO-ASA Approach for the study of band structure and density of states of the transitional elements Fe and Pd and their ordered alloys FePd and Fe3Pd. We analyzed metallic and nonmetallic character and occupation of s, p and d electrons from the band structures and magnetic properties through the plot of density of states. Our findings show that all the elements and alloys bear metallic nature whereas bulk Palladium shows non magnetic behavior. Similarly Fe and both the ordered alloys FePd and Fe3Pd are found to be magnetic in nature with values B 19. 2 µ , B 49. 3 µ and B 01. 3 µ respectively. These well agree with experimental as well as previous theoretical calculations.
First – principles calculations to study thermal and electrical properties of pristine and calciu... more First – principles calculations to study thermal and electrical properties of pristine and calcium filled skutterudite Ir4Sb12 has been carried out. Density of states (DOS) and band-structure calculations are based on Density Functional Theory (DFT) within Generalized Gradient Approximation (GGA). Transport properties are calculated using BoltzTrap software packages. Volume optimization is carried out on the basis of Murnaghan equation of states. The optimized lattice parameter of pristine Ir4Sb12 is found to be 9.4243 Å and that of calcium filled Ir4Sb12 is found to be 9.4949 Å. Our calculation shows that pristine Ir4Sb12 is a p-type of semiconductor with a narrow PBE-GGA band gap of 0.25 eV. After filling calcium, the band gap is reduced to zero showing the metallic behavior of filled compound. Band structure, density of states, variations of electrical and thermal conductivities with temperature and Seebeck coefficient show that calcium filled Ir4Sb12 has a metallic character. At...
Journal of Institute of Science and Technology, 2021
Water adsorbed in MoS2 (wad-MoS2), 1S atom vacancy defect in wad-MoS2 (1S-wad-MoS2), 2S atoms vac... more Water adsorbed in MoS2 (wad-MoS2), 1S atom vacancy defect in wad-MoS2 (1S-wad-MoS2), 2S atoms vacancy defects in wad-MoS2 (2S-wad-MoS2), and 1Mo atom vacancy defect in wad-MoS2 (Mo-wad-MoS2) materials were constructed, and their structural, electronic, and magnetic properties were studied by spin-polarized density functional theory (DFT) based first-principles calculations. The wad-MoS2, 1S-wad-MoS2, 2S-wad-MoS2, and Mo-wad-MoS2 materials were found stable. From band structure calculations, wad-MoS2, 1S-wad-MoS2 and 2S-wad-MoS2 materials open energy bandgap of values 1.19 eV, 0.65 eV and 0.38 eV respectively. Also, it was found that the conductivity strength of the material increases with an increase in the concentration of S atom vacancy defects in the structure. On the other hand, the Mo-wad-MoS2 material has metallic properties because energy bands of electrons crossed the Fermi energy level in the band structure. For the investigation of magnetic properties, the density of state...
Bibechana, 2021
Thermodynamic properties of sickled and normal hemoglobin protein are considered within the frame... more Thermodynamic properties of sickled and normal hemoglobin protein are considered within the framework of classical molecular dynamics. Here we have studied the specific heat capacity and RMSD (Root Mean Square Deviation) of both types of hemoglobin protein. Our investigation reveals that the specific heat capacity and RMSD for oxygenated hemoglobin protein is higher than those of de-oxygenated sickle hemoglobin protein. It is also observed that the specific heat capacity and RMSD values of sickle hemoglobin protein decrease with a rise in temperature. BIBECHANA 18 (2021) 140-148
arXiv: Chemical Physics, 2018
In the present work, molecular dynamics study of diffusion of Gamma Aminobutyric acid in water at... more In the present work, molecular dynamics study of diffusion of Gamma Aminobutyric acid in water at different temperatures 298.2 K, 303.2 K, 313.2 K, 323.2 K, 333.2 K have been performed. The solute and solvent is modeled using OPLS AA platform. The structure of the system is analyzed using RDF of different atom or molecule pairs. In all the cases, at least two or more peaks were obtained which suggests appreciable amount of interaction between atoms and molecules. The self diffusion coefficient of GABA and water is calculated from mean square displacement (MSD) plot using Einstein's relation. Binary diffusion coefficient is obtained from self diffusion coefficient using Darken's relation. Binary diffusion coefficient agrees well with the previously reported experimental data within an error of around 7%. The temperature dependence of self diffusion coefficients of GABA in water follows the Arrhenius behaviour. With the help of Arrhenius plot, we estimate the activation energy...
Amrit Research Journal, 2021
In this work, we have studied the electronic and magnetic properties of 1C atom vacancy defects i... more In this work, we have studied the electronic and magnetic properties of 1C atom vacancy defects in graphene (1Cv-d-G), 1N atom impurity defects in graphene (1NI-d-G) and 1O atom impurity defects in graphene (1OI-d-G) materials through first principles calculations based on spin-polarized density functional theory (DFT) method, using computational tool Quantum ESPRESSO (QE) code. From band structure and density of states (DOS) calculations, we found that supercell structure of monolayer graphene is a zero bandgap material. But, electronic bands of 1Cv-d-G, 1NI-d-G and 1OI-d-G materials split around the Fermi energy level and DOS of up & down spins states appear in the Fermi energy level. Thus, 1Cv-d-G, 1NI-d-G and 1OI-d-G materials have metallic properties. We have studied the magnetic properties of pure and defected materials by analyzing density of states (DOS) and partial density of states (PDOS) calculations. We found that graphene and 1OI-d-G materials have non-magnetic properti...
Uploads
Papers by Narayan Adhikari