Journal of Nepal Physical Society

Molecular Interactions of Zinc Finger Protein Kaiso with Hemimethylated DNA

2023-08-12T10:40:40+00:00

DNA methylation is an epigenetic modification that is involved in various essential cellular processes. Methyl CpG binding proteins (MBPs), such as zinc finger protein Kaiso, bind with methylated DNA and mediate to translate methylation signal into the transcription process. To have mechanistic understanding of how these proteins recognize and interpret the DNA methylation signal is important because of their critical role in regulation of gene expression in both normal and diseased cells. In this study, we performed molecular dynamics (MD) simulation to investigate the recognition and binding of hemimethylated (methylation in one strand of double stranded DNA) sequences by Kaiso to assess the role of methylation in each strand. We investigated the major interactions involved in the complex formation as well as the contact area and binding free energy of the Kaiso-DNA complexes. Our results show that the number and strength of hydrogen bonds as well as other non-bonded interactions are greater in Kaiso-DNA complex with methylated CpG sites in non-coding strand. Similarly, the contact area at the Kaiso-DNA interface and binding free energy of Kaiso is also higher in hemimethylated sequence having methylation in non-coding strand. Therefore, methylated CpG sites in non-coding strand play important role in the binding of Kaiso with methylated DNA sequences.

Responses of Total Electron Content to Solar Flares over Low and Mid-Latitude Regions during Sun Halo Day

2023-08-12T08:48:50+00:00

The responses of total electron content (TEC) to solar flares over low- and mid-latitude regions during the sun halo days were investigated. The research is based on GPS data obtained from Bangalore (13.02117°N, 77.57038°E) on May 24, 2021; Cape Town (-33.918861°N, 18.423300°E) on October 26, 2020; and North Dakota (46.55756°N, -96.472300°E) on December 27, 2021, during the solar halo days. The results of this study demonstrate that the values of TEC increased at Bangalore and Cape Town stations during solar halo days as compared to other days. However, over the North Dakota station, TEC during the sun halo day was greater than that on the days before and after the halo day from around 19:00 UT to 23:59 UT hours. During the sun halo over Bangalore and Cape Town stations, positive relative changes in TEC prevail, suggesting that the action of the interplanetary electric field, the prompt penetration electric field, and the disturbance dynamo electric field lead to higher TEC values. However, during the sun halo over North Dakota station, negative relative changes in TEC prevail, which might be related to the consequence that low solar activity with no earth’s field disturbances (a positive Dst) leads to lower ionospheric TEC values. Stations that have greater relative changes in TEC have shown greater power spectrum and global wave spectrum energy. Cape Town has a greater relative change in TEC, a greater power spectrum, and a larger global wave spectrum than Bangalore and North Dakota stations. The values of TEC over three stations are different due to the latitudinal and longitudinal differences in addition to the universal time effects. Finally, solar flares have a major influence on ionosphere electrodynamics, and the upward drift velocity of ionospheres at the low latitude station is more strongly influenced by solar flares due to the effects of the ExB drifts, which induce TEC disturbances during the halo days over the suggested stations.

Plastic: A Boon but Also a Curse to the Environment

2023-08-12T09:10:41+00:00

Besides being a significant part of our daily lives, plastic has a detrimental negative environmental impact thanks to its non-degradable nature. The dependency and impacts of plastics have been carefully analyzed in order to investigate their effects on the environment. The paper studies large scale production, use and the impacts of plastics on the environment. Investigation on the ways plastics affect soil, atmosphere, water and health of living being have been done. Similarly, the statistical data about their use and effects have been presented and future projections have been made.

Numerical Solution of Schrödinger Equation by using Crank-Nicolson Method

2023-08-12T09:23:31+00:00

The Schrödinger equation is a fundamental equation in quantum mechanics that describes how wave functions evolve over time. The study explored specific focus on the Crank-Nicolson scheme, which is widely used and efficient method. By applying these methods to the one-dimensional Schrödinger equation, the work provided insights into the behavior of these systems. To confirm the accuracy and reliability of this method, a test problem is solved. The result obtained from numerical method is compared with analytical solution. The graph of compared result is shown with the help of computational software. The test demonstrates that the method is effective for solving the Schrödinger equation, even when an analytical solution is not possible or too difficult to obtain. Overall, the Crank-Nicolson difference scheme is a valuable tool for understanding the behavior of quantum systems and solving problems.

Structural, Electronic & Magnetic Properties of Pristine and Defected ZnO Monolayer: First-Principles Study

2023-08-12T12:31:15+00:00

Electronic and magnetic properties of materials are appealing properties and have budding applications in the devices. In this work, we have investigated the structural, electronic and magnetic properties of pristine Zinc-Oxide (ZnO) and Oxygen-defected Zinc-Oxide (ZnO_O) materials by spin-polarized density functional theory (DFT) method. Structural properties are studied by calculating their total ground state energy, and found that both are stable 2D materials. It is also found that ZnO have higher stability than of ZnO_O material. Electronic properties of considered materials are examined by analyzing of their band structure, density of states (DOS) calculations and found that ZnO is a direct band gap, n-type semiconductor material in its pristine form and an indirect band gap, p-type semiconductor material in its Oxygen-defected form (ZnO_O). Magnetic properties of pristine and defected ZnO are investigated by analyzing their density of states (DOS) and partial density of states (PDOS) calculations, they revealed that ZnO and ZnO_O have non-magnetic properties.

Radiation Shielding Properties of Oxides (Al2O3, PbO and Fe2O3) based on Klein-Nishina Cross-section

2023-08-13T15:37:11+00:00

In this study, we investigate the Klein-Nishina differential cross-section equation for total cross-section and extend it to calculate the total molecular cross-section for compounds Al₂O₃, PbO, and Fe₂O₃. Our findings reveal that the total molecular cross-section of these compounds is significantly larger, with values 5 times greater than the total atomic cross-section. Furthermore, we determine that the molecular cross-section of Al₂O₃, PbO, and Fe₂O₃ is 73, 132, and 118 times greater than the total electronic cross-section, respectively, while the atomic cross-section of these compounds is 15, 66, and 24 times greater. At low energy levels ranging from 1-5 MeV, the entire molecular, atomic, and electronic cross-section dominates due to Compton scattering. However, as the photon energy increases, Compton scattering becomes negligible, and a slight contribution from pair production scattering is observed. We also establish the adequate atomic numbers for Al₂O₃, PbO, and Fe₂O₃, which are determined to be 15, 66, and 24, respectively. These results highlight the significance of mass attenuation, cross-section, and adequate atomic number in the selection of radiation shielding materials for various protection purposes. The findings from this study provide valuable insights into the properties and behavior of these compounds, enabling informed decisions in radiation shielding applications.

Prediction of Solar Radiation using Empirical Models over Lowland Region Nepal

2023-08-13T15:49:52+00:00

Renewable energy sources are becoming more and more popular as a result of the world's rapidly rising energy needs and the depletion of fossil fuel stocks. Solar energy significantly increases the need for electricity. Due to high energy demands, solar energy most viable out among all of energy sources. Before choosing a location for a solar-powered power plant, it is necessary to predict or anticipate solar energy. For the estimation of the solar energy we use meteorological parameters such as sunshine hour, temperature and relative humidity on selected empirical models to find the empirical coefficients at the study site Biratnagar (Lat. 26° 27' 15" E, Long. 87° 16' 47" N, and alt. 72 m) Nepal. Regression technique is utilized on meteorological parameters including global solar radiation at different models viz. Angstrom-Prescott (A-P) model, Ogunlade model, Gopinathan model and Hargreaves model. Among the four models, the A-P model is better than other models by analyzing the statistical tools. Finally, the empirical constants of A-P model and are found. The finding coefficients can be used to estimate the solar radiation and solar energy at similar geographical locations of Nepal.

A Comparative Analysis of Force Fields of Drug-Like Molecules: Omeprazole, Favipiravir and Amoxicillin by using Bonded and Non-Bonded Potential Distributions

2023-08-13T16:09:31+00:00

This research aims to compare and analyze the force field parameters of drug-like compounds generated by the online servers CGenFF, SwissParam, and LigParGen. CHARMM27, OPLS-AA, and CHARMM36 force fields of amoxicillin, favipiravir, and omeprazole have been examined by bonded and non-bonded energy distributions of the potential function. The local terms of the force field function are bond length, bond angle, and dihedral potentials, while the non-local terms are van der Waals and pairwise electrostatic interactions. The parabolic curves of bond length potential appear to internally bend because of the larger values of force constants. The bond length and angle energies are lowest at reference values for each of the corresponding atom pairs in the molecules. The higher values of the bending force constant positively deflect the sinusoidal curve from the equilibrium position according to the dihedral angle energy distribution. The Lennard-Jones interaction exhibits the same repellent nature at closer ranges and the same attracting nature at farther ranges whereas a mildly differentiated interaction is seen at the intermediate state as a result of changing well-depth parameters. Depending on the size of the optimized partial charges, it is discovered in electrostatic interaction that the distributions of end-to-end lengths of identical atom pairs are more exponentially skewed from one another. The main cause of inconsistency in the results of MD simulations for the same protein-ligand system is due to the shifted topology and parameters.

Optical and Electrical Properties of Homo and Heterojunction Formed by the ZnO/FTO and CuO/ZnO/FTO Nanostructures

2023-08-13T16:22:31+00:00

The most common materials used to create electrical and optoelectronic devices for a variety of applications including transistor, sensor and detector are semiconductor nanostructures. Combining the nanostructures can result semiconductor homostructure and heterostructure. The homojunction of ZnO/FTO and heterojunction of CuO/ZnO/FTO coated glass substrate are formed using spray pyrolysis technique. The optical band gap for the FTO, ZnO, ZnO/FTO and CuO/ZnO/FTO films calculated using data from UV-visible spectroscopy are 3.629 eV, 3.236 eV, 3.113 eV and 1.456 eV respectively. The observed ohmic behavior of ZnO/FTO homojunction is due to the close band gap of FTO (i.e. E_g = 3.629 eV) and ZnO (E_g = 3.236 eV) whereas the non-ohmic behavior of CuO/ZnO/FTO heterojunction is due to the significant different in band gap energy of CuO (i.e. E_g = 1.456 eV) and ZnO (E_g = 3.236 eV). The photocurrent for ZnO/FTO homojunction increases from 232 μA to 350 μA for visible light illumination and from 232 μA to 400 μA for UV light illumination at bias voltage of 2.5 V. There is no significantly changed in the threshold voltage in visible region. For the CuO/ZnO/FTO heterojunction, the photocurrent increases from 280 μA to 390 μA for visible illumination and from 280 μA to 480 μA for UV illumination at 2.5 V. The enhancement of channel current in both sample (i.e. homojunction and heterojunction) under visible illumination is due to detrapping the charge carriers from mid gap states and released to the conduction band. The large enhancement of photocurrent under UV illumination is due to band gap absorption. Threshold voltage for CuO/ZnO/FTO non-ohmic device is shifted negatively from 1 V to 0 V with increasing the frequency of incident radiation. It suggests that the heterojunction formed by CuO/ZnO/FTO structure is applicable for broad band photo detector.

Molecular Dynamics Study of Peptide in Water at Different Temperature

2023-08-13T16:36:19+00:00

Molecular dynamics approach has been carried out to study the structural properties of peptide to estimate the self-diffusion coefficients of water at different temperatures 290 K, 300 K, and 310 K respectively. The energy profiles show the stability of system which ensures a well-balanced molecular structure of the system. The radial distribution functions (RDFs) of the solvent-solvent, solute-solute, and solute-solvent show the distribution of system within the required references. The self-diffusion coefficients of water have been determined using respective mean square displacement (MSD) curves through the Einstein’s relation. The self-diffusion coefficients of water at different temperatures are 0.44 ×10^-5 cm²s^-1, 0.48 ×10^-5 cm²s^-1, and 0.50 ×10^-5 cm²s^-1 respectively. Calculations show that the MSD of water throughout the system is increasing on increasing temperature. The results are also valid with the theoretical as well as available experimental data.

First-Principles Study of Structural, Electronic and Magnetic Properties of Lithium Doped Hexa]gonal Boron Nitride Monolayer (h-BN)

2023-08-17T08:43:50+00:00

We examine the structural, electronic, and magnetic properties of pure and lithium doped hexagonal boron nitride (h-BN) monolayer using density functional theory (DFT) based on first-principles calculations. LiB site is more conducive to doping than LiN site, according to the values of formation energy, which are found to be 13.06 eV and 18.50 eV, respectively. Metallic behavior may be seen in the band structures for both the Li_B site and Li_N in nature. At both sites, the density of states (DOS) is asymmetric for spin-up and spin-down electrons. This suggests that systems with Li doping on h-BN are magnetic.

Winter-time Hydraulic Jump over the Pokhara Valley, Nepal

2023-08-19T03:55:47+00:00

The Pokhara Valley is set to be one of the aviation hubs of Nepal with the opening of an international airport. The complex mid-hill mountainous topography of the Gangi-Himalaya and the characteristic wind system of the valley make safe aviation rather challenging over the valley. This study using the Weather Research and Forecasting modeling system shows that hydraulic jump-like phenomena occur regularly during winter in the western and central part of the Pokhara Valley during late afternoon/early evening when the airport may remain relatively busy. The jump occurs over the western part of the valley when the regional southwesterly plain to mountain wind via the Putalibazar Valley intrudes into the Valley crossing the Deurali-Mattikhan hill. The jump-like flow is accompanied by the formation of a mild reverse roller above the jump region and the head-on convergence with the northeasterly katabatic/drainage wind from Parche-Namarjung along the southeast–northwest oriented valley axis generating an updraft of as much as 0.4 to 0.8 m s^-1. The southwesterly overrides northeasterly generating clockwise vertical rotors and high turbulence over the northeastern region of the valley. An early prediction of possible wind hazards at high spatiotemporal resolutions are highly desired to make aviation activities in the region safer for civil aviation.

Impact of Plasma Treatment on Lady’s Finger Seeds for Germination and its Growth

2023-08-19T04:07:40+00:00

Atmospheric pressure plasma has emerged as a promising technology in various fields, including plasma medicine, agriculture, food safety and storage, and food manufacturing. Plasma treatment has proven to be beneficial in plasma agriculture, as it enhances seed germination, plant growth, and resilience against both abiotic and biotic stresses. Additionally, it can aid in the removal of pesticides, increase biomass, and improve yield. However, the molecular mechanisms underlying the effects of plasma treatment on seed germination and plant growth are not yet fully understood. Therefore, in this study, the authors aimed to investigate the physical and chemical properties of Lady’s finger seeds treated with cold plasma, characterized by 2.86 W dissipative power at 7 kV in an argon environment and electron density of 4.53×10¹⁰ cm^–3 under atmospheric conditions. The FTIR technique was used to identify the functional groups present in the seed before and after treatment, revealing the presence of C-H, C=O, C-O, and N-O functional groups, as indicated by their corresponding absorption peaks at different wave numbers. The stretching of bonds between elements of the functional groups was observed based on transmittance. Moreover, the treated seeds were germinated, and the physical growth of different parts (root, shoot, and leaf) was measured. The results showed that the growth rate of different parts was higher in the treated seeds than in the untreated.

Pollution Threat by Face Mask after COVID-19 in Nepal

2023-08-19T04:24:22+00:00

The COVID-19 pandemic has led to a significant increase in the production and use of disposable face masks, contributing to the growing global waste problem. While face masks were initially used primarily by healthcare professionals who knew how to dispose of them properly, their widespread adoption by the general public has raised concerns regarding the correct management of discarded masks. This issue is particularly significant as new types of pollutants, including microplastics, are being introduced into the environment. In underdeveloped nations like Nepal, misconceptions about the composition of face masks and a lack of awareness about their environmental impact are prevalent. To gain insight into the particle constituents of commonly used face masks, namely normal, surgical, and KN95 masks favored by residents of Nepal's Kathmandu Valley, we conducted Fourier Transform Infrared Spectroscopy (FTIR) analysis using an IRTracer-100 spectrometer. Our analysis identified the functional group and revealed that the primary material found in these masks is polypropylene microplastic polymers, rather than biodegradable fibers.

Star Formation Rate of Eight Nearby Dwarf Galaxies within 85 Mpc Distance

2023-08-19T04:38:08+00:00

This study examines the star formation rates (SFR) of eight dwarf galaxies, namely IC 700, MRK 0225, NGC 3440, NGC 5089, PGC 026162, PGC 051103, UM 158, and UM 454. The SFR estimators include the luminosities of the H alpha and [OII] emission lines, as well as the ultraviolet continuum. The data is obtained from GALEX and SDSS spectral observations. Of the eight galaxies, seven are classified as starburst dwarfs, while PGC 026162 is identified as a Seyfert galaxy. The highest H alpha SFR is observed in MRK 0225, measuring 0.30466 solar masses per year, whereas IC 0700 exhibits the lowest value of 0.00096 without accounting for extinction. However, upon correcting for extinction, the values become 0.84543 and 0.00177, respectively. In terms of OII SFR, MRK 0225 demonstrates the highest value of 0.32111, while IC 0700 displays the lowest at 0.00232. Additionally, MRK 0225 also exhibits the highest NUV SFR with a value of 0.19725, whereas IC 0700 shows the lowest NUV SFR at 0.06462. Upon applying the extinction correction, these values become 0.47936 and 0.10162, respectively. Analysis reveals that MRK 0225 and UM 158 have experienced recent increases in SFR, indicating a significant presence of newly formed stars. Conversely, UM 454 has maintained a relatively constant SFR for approximately 100 million years. Finally, NGC 3440, IC 700, NGC 5089, and PGC 051103 demonstrate a recent decline in SFR, suggesting a depletion of gaseous content available for star formation. The study also examines the line metallicity by assessing the ratio of NII to H alpha, identifying two galaxies, UM 158 and UM 454, with notably low line metallicity values of 8.11 and 8.13, respectively. Our samples also reveal a consistent trend: galaxies located at greater distances exhibit a notably higher rate of star formation. Overall, the findings indicate that these dwarf galaxies align with the trends observed in local-volume, star-forming galaxies.

Determination of Variation of Mass with Gravity

2023-08-19T04:51:15+00:00

The paper demonstrates that the theory of mass and gravity in the existing normally acknowledged version of theory of gravitational red-shift is completely erroneous. What makes it erroneous is that the frequency of particle in a gravitational field is considered to change depending on its location while mass of particle is treated as constant parameter. This paper predicts that a body in a gravitational field of escape velocity V_e will be more massive by a factor of 1 + (V_e²/C²) , where C is the speed of light, as compared to mass of a similar body outside the field. It manifests that mass of a body measured at earth surface is different than actual mass because of the influence of gravity. If m' and m denote mass of body within and beyond the gravitational field respectively, then the mass (m') measured at earth surface as compared to actual mass (m) is given by the formula m' = m (1+1.39 × 10^-9). It reveals that an actual relative mass change at earth m' - m/m = 1.39 × 10^-9) is extremely small, with change measure in nanogram. Based on this postulate of variation of mass with gravity, the correct criteria for a particle to be inside black hole turns out to be m'>2m. Therefore, a gravitational field is a black hole if the mass of a body inside the field will be more than two times of its actual mass. In this highly interesting topic, the particular purpose is to present a succinct and carefully reasoned account of new aspect of gravitational red shift which properly allows to determine the change of mass with gravity.

Structural, Morphological, and Textural Properties of Coprecipitated CaTiO3 for Anion Exchange in the Electrolyzer

2023-08-19T04:59:00+00:00

The limitation in fossil fuel and the emission of greenhouse gases (GHG) resulting in global warming is one of the global challenging issues. Similarly, efficient and cost-effective renewable energy resources are always in demand for the overcome of the limitation. One of the best alternatives to fossil fuels based on renewable energy sources is hydrogen fuel. The main component of the hydrogen fuel generator is the Electrolyzer. Among different types of electrolyzers, the incorporation of an anion exchange membrane is one approach. In this work, we are focusing on the preparation, characterization, and analysis of anion exchange material CaTiO₃ used for the electrolyzer. A co-precipitation method was used for the preparation of CaTiO₃ XRD shows the orthorhombic structure of the CaTiO₃. FT-IR shows the vibrational spectra of CaTiO₃. The particles were spherical and crystalline with an average size of 200 nm when viewed through the Scanning Electron Microscope (SEM), Transmission Electron Microscopy (TEM), and High-Resolution Transmission Electron Microscopy (HRTEM). The SAED pattern verifies the single crystalline nature of the sample. In this way, the CaTiO₃, the anion exchange agent was synthesized and characterized successfully.

Editorial Vol.9(1)

2023-08-19T08:11:12+00:00

No abstract available.