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A comparative study has been carried out to understand the concentration dependence of thermodynamic properties such as, free energy of mixing, heat of mixing, entropy of mixing, activity and microscopic properties, such as concentration fluctuation in long wavelength limit and Warren-Cowley short range order parameter of In-based three liquid alloys (In-Pb , In-Tl and In-Zn) on the basis of self-association model. The analysis reveals that self-association model successfully explains the observed properties of the liquid alloys. Positive deviation of the thermodynamic properties of the alloys from the Raoultian solution behaviour indicates that the alloys are weakly segregating in nature. The comparative assessment of the interaction energy and the microscopic properties suggests that the degree of segregation is greatest in In-Zn alloy and comparable in In-Pb and In-Tl alloys. BIBECHANA 13 (2016) 60-71

The concentration fluctuations in long wavelength limit, Scc(0) and the Warren-Cowley short range order parameter (α1) are important microscopic functions which provide valuable information about the local arrangements of the constituent atoms in the alloy melts. In order to investigate the nature of atomic ordering in Sn-Tl alloy in the molten state at 723K, we have computed these functions using theoretical models. The models satisfactorily explain the small asymmetry observed in the experimental data of free energy of mixing of the alloy. The comparative study further reveals that the energy interaction parameters are temperature dependent and the Sn-Tl alloy is weakly interacting segregating system. DOI: http://dx.doi.org/10.3126/bibechana.v11i0.10379 BIBECHANA 11(1) (2014) 46-52

In this work, thermodynamic and microscopic properties of Ni-Pd liquid alloy at 1873 K have been studied using a simple theory of mixture. In thermodynamic properties, free energy of mixing, heat of mixing and entropy of mixing have been studied. To understand the structural behaviour of the alloy concentration fluctuation in long wavelength limit and chemical short range order parameter have been computed. The Ni-Pd melt at 1873 K is found to be slightly deviated from regular behaviour. The best estimated value of energy parameter is found to be positive. The alloy is found to be weakly segregating system. The symmetric behaviour of all functions has been well explained by the simple theory of mixing. DOI: http://dx.doi.org/10.3126/bibechana.v10i0.9341 BIBECHANA 10 (2014) 108-114

We report thermodynamic, microscopic and surface properties of Cd-Ga alloys in molten state at 700 K. We use quasi-chemical approximation for the computation of thermodynamic and microscopic properties. For the computation of surface we use Butler’s approach and quas-chemical approach. We also calculate the surface concentration of the individual component. DOI: http://dx.doi.org/10.3126/bibechana.v10i0.9079 BIBECHANA 10 (2014) 9-19

We report surface tension of two weakly segregating alloys Al-Ga and Cd-In in molten state at temperatures of 1023 K and 800 K respectively using different approaches. Our analysis based on different assumptions reveal that the metal with lower surface tension tends to segregate on the surface of molten alloy and the metal with higher surface tension tends to segregate in the bulk. Different approaches predict consistency in the values of the surface tension of Al-Ga liquid alloy that increases with increase in bulk concentration of aluminium in the alloy with all values smaller than the ideal values. In Cd-In alloy the models reveal no such regularity in the surface tension; it varies slightly from the ideality. DOI: http://dx.doi.org/10.3126/bibechana.v9i0.7183 BIBECHANA 9 (2013) 103-112

The concentration dependent asymmetry in mixing properties of Mg-Tl liquid alloys at 923 K has been investigated on the basis of regular associated solution model. The concentration of ApB type complex in a regular associated solution of Mg and Tl have been determined. We have then used the concentration of complex to calculate the free energy of mixing, enthalpy of mixing, entropy of mixing, activity, concentration fluctuations in long wavelength limit SCC(0) and the Warren Cowley short-range parameter 1 α .The analysis suggests that heterocoordination leading to the formation of chemical complex Mg2Tl is likely to exist in the melt. The analysis reveals that there is a tendency of unlike atom pairing (Mg-Tl) in Mg-Tl alloy whole range of concentration. Keywords: Mg-Tl alloy; microscopic structure; pairwise interaction energy; chemical short range order DOI: http://dx.doi.org/10.3126/bibechana.v8i0.5692 BIBECHANA 8 (2012) 81-89

The binary mixtures of cabontetrachloride with isobutylmethylketone and benzaldehyde were studied at 308.15 by measuring viscosities and densities. The derived and excess viscosities, activation energy of flow and Grunberg-Nissan parameters have been calculated. It was found that these parameters are satisfactorily used to predict the strength and nature of molecular interactions. It was found that the strength of interactions in the systems studied is in the following order: CCl4 + IBMK>CCl4 + BD Keywords: Binary liquid; benzaldehyde; carbontetrachloride DOI: 10.3126/bibechana.v6i0.3932 BIBECHANA Vol. 6, March 2010 pp.9-14

This study was conducted to investigate the activity concentrations of 226Ra, 232Th and 40K in the sand samples and the health hazards associated with them utilizing a NaI (Tl) gamma spectrometer. The average activity concentrations of 226Ra, 232Th and 40K were found to be 24.8 ± 10.1, 39.8 ± 16.4 and 531.3 ± 52.8 Bq kg-1, respectively. The calculated radiological hazard parameters, including radium equivalent activity, absorbed gamma dose and effective dose rate, were found to be 122.7 ± 34.0 Bq kg-1, 57.7 ± 14.9 nGy h-1 and 0.3 ± 0.1 mSv y-1, respectively. Notably, these results were observed to be below the recommended thresholds. Other measured hazard indices were also lower than the prescribed values. From a radiological perspective, the present study concludes that the sand samples do not pose any threat to human health when utilized as a building material., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Methyl damage to DNA bases is common in the cell nucleus. O6-alkylguanine-DNA alkyl transferase (AGT) may be a promising candidate for direct damage reversal in methylated DNA (mDNA) at the O6 point of the guanine. Indeed, atomic-level investigations in the contact region of AGT-DNA complex can provide an in-depth understanding of their binding mechanism, allowing to evaluate the silico-drug nature of AGT and its utility in removing methyl damage in DNA. In this study, molecular dynamics (MD) simulation was utilized to examine the flipping of methylated nucleotide, the binding mechanism between mDNA and AGT, and the comparison of binding strength prior and post methyl transfer to AGT. The study reveals that methylation at the O6 atom of guanine weakens the hydrogen bond (H-bond) between guanine and cytosine, permitting for the flipping of such nucleotide. The formation of a H-bond between the base pair of methylated nucleotide (i.e., cytosine) and the intercalated arginine of AGT also forces the nucleotide to rotate. Following that, electrostatics and van der Waals contacts as well as hydrogen bonding contribute to form the complex of DNA and protein. The stronger binding of AGT with DNA before methyl transfer creates the suitable condition to transfer methyl adduct from DNA to AGT., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

This comprehensive study examines the concentration of natural radionuclides in bricks from the Terai region of the Koshi province, aiming to assess the radioactivity levels and associated radiological hazards, ultimately quantifying the dose limit. The average concentrations of 226 Ra, 232 Th, and 40 K were 27.1 ± 5.7, 42.6 ± 9.8, and 601.5 ± 93.8 Bq/kg, with their respective contributions to total activity being 20.18 %, 45.35 %, 34.48 %,. Despite this, their concentration distribution followed the pattern 40 K >  232 Th >  226 Ra. The elevated presence of 40 K in the bricks is attributed to the use of phosphate fertilizers in the soil to enhance crop productivity. Notably, the calculated values of radiological hazard parameters, including radium equivalent activity, absorbed gamma dose, and effective dose, are well below the recommended safety thresholds. Consequently, this study suggests that bricks, when used in substantial quantities, pose no significant radiological risks and are considered safe for use as a building material. The extension of such investigations nationwide is recommended to assess the overall radioactivity levels and establish dose limits., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Arun Kumar Shrestha reports University Grants Commission Nepal provided a Ph.D. fellowship and research support grant including a travel reimbursement. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

A mutation at the sixth residue, glutamic acid to valine, in beta chain of hemoglobin distorts the entire shape of hemoglobin into a sickle shape. The investigation of the binding mechanisms of different chains of hemoglobin under the mutated condition can give an understanding of the molecular distortion. In this work, we have studied the binding mechanism between two chains in the dimer structure of the R-state conformation of carbonmonoxyl sickle hemoglobin and is compared with that of normal hemoglobin by using molecular dynamics simulations. The binding strength between α -chain (PROA) and β -chain (PROB) in hemoglobin dimer has been analyzed by estimating hydrogen bonds, salt bridges, hydrophobic interactions and non-bonded interactions (electrostatics and van der Waals). The quantitative estimation of aforementioned interactions depicts that the structural stability of normal hemoglobin dimer is found to be greater than that of sickle one. The outcomes of such interactions are also supported by the estimated free energy between the chains in R-state conformation of the dimers. The difference of binding free energy, calculated by utilizing the umbrella sampling technique, is found to be ≈ (0.67 ± 0.06) kcal/mol.Communicated by Ramaswamy H. Sarma.

This work helps to identify the source of pollution in water and characterize the water quality which is essential to water management for sustainable development. Therefore, the main objective of this work is to evaluate the spatial distribution of the water quality of Ratuwa river and its tributaries. The water samples were collected from six discrete sampling locations and fifteen parameters were tested using respective well-calibrated equipment and standard APHA methods. The physicochemical analysis, water quality index, and correlation matrix method were employed to evaluate the spatial variation of the water quality of Ratuwa river. Turbidity was the most polluting factor in river water. The results showed the spatial variation of the water quality index (WQI) from 39.3 to 70.5, which fell in the range of "good" to "poor" water quality status. None of the water samples was either "excellent" or "unsuitable for drinking." The water quality was "Poor" upstream and downstream of Ratuwa river due to the high value of turbidity. Chaju river was found to have unpolluted whereas Dipeni river was slightly polluted due to domestic and municipal wastes. Hence, the deterioration of water quality can be attributed to natural and anthropogenic sources., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Shrestha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Methylation induced DNA base-pairing damage is one of the major causes of cancer. O 6 -alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex., (© 2021 Walter de Gruyter GmbH, Berlin/Boston.)

Temperature-dependent interaction parameters of Redlich-Kister (R-K) polynomials for Li-Mg alloy in liquid phase have been optimized using experimental data in the framework of linear and exponential models. These parameters have then been used to compute the thermodynamic properties (excess Gibbs free energy of mixing, enthalpy of mixing and activity) and structural property (concentration fluctuations in the long-wavelength limit) of the alloy at temperatures 1000 K, 1300 K, 1600 K, 1900 K, and 2200 K. The negative values of excess Gibbs free energy of mixing computed using linear T-dependent parameters increases with the rise in the temperature of the system beyond 1000 K while the same physical quantity computed using the exponential T-dependent interaction parameters decreases with the rise in temperatures and does not show any unusual trends up to 2200 K. Similar behavior has been found in the case of other thermodynamic and structural functions. The unusual behavior that appears in the thermodynamic and structural functions computed using linear T-dependent parameters can be eliminated if these functions are computed using exponential T-dependent parameters., Competing Interests: The authors declare no conflict of interest., (© 2021 The Author(s).)

The surface tension and viscosity of Cu-Fe-Si ternary alloys were computed at different temperatures using thermodynamic approaches. The thermodynamic data of the alloy were optimized in the framework of the Redlich-Kister (R-K) polynomials and exponential temperature dependent coefficients of the R-K polynomial were obtained. These coefficients were used to compute the excess Gibbs free energy of mixing of the alloy and the partial excess free energy of the components. The partial excess free energy so obtained was used to compute the surface tension of the ternary Cu-Fe-Si alloy system and its binary sub-systems. The enthalpy of mixing was also optimized and it was used to compute the viscosity of the sub-binary and ternary alloys., (© 2020 The Author(s).)