arXiv subjects

Papia Chowdhury

Publications and source records attributed to Papia Chowdhury.

10 recordsLinked to original sources

arXiv2020

Repurposing the Combination Drug of Favipiravir, Hydroxychloroquine and Oseltamivir as a Potential Inhibitor against SARS-CoV-2: A Computational Study

The virus SARS-CoV-2 has created a situation of global emergency all over the world from the last few months. We are witnessing a helpless situation due to COVID-19 as no vaccine or drug is effective against the disease. In the present study, we have tested the applicability of some combination drugs against COVID-19. We have tried to understand the mechanism of action of some repurposed drugs: Favipiravir (F), Hydroxychloroquine (H) and Oseltamivir (O). The ADME analysis have suggested strong inhibitory possibility of F, H, O combination towards receptor protein of $3CL^{pro}$ of SARS-CoV-2 virus. The strong binding affinity, number of hydrogen bond interaction between inhibitor, receptor and lower inhibition constant computed from molecular docking validated the better complexation possibility of F+H+O: $3CL^{pro}$ combination. Various thermodynamical output from Molecular dynamics (MD) simulations like potential energy ($E_g$), temperature (T), density, pressure, SASA energy, interaction energies, Gibbs free energy ($ΔG_{bind}$) etc., also favored the complexation between F+H+O and CoV-2 protease. Our In-Silico results have recommended the strong candidature of combination drugs Favipiravir, Hydroxychloroquine and Oseltamivir as a potential lead inhibitor for targeting SARS-CoV-2 infections.

physics.bio-ph↗

arXiv2020

Ivermectin and Doxycycline Combination as a Promising Drug Candidate Against SARS-CoV-2 Infection: A Computational Study

In the present study, we have described how by using molecular docking and molecular dynamic (MD) simulation studies the combination drug of ivermectin and doxycycline can be used as a potential inhibitor for SARS-CoV-2 virus. In lieu of unavailability of specific cure of COVID-19 till now various possibilities for individual and combination drugs have been explored by the medical practitioners/scientists for the remedial purpose of CoV-2 infections. $3CL^{pro}$ is the main protease of SARS-CoV-2 virus which plays an essential role in mediating viral replication in the human body. $3CL^{pro}$ protein can serve as an attractive drug target. In this work, we have studied drug: $3CL^{pro}$ interactions by in silico molecular docking and MD simulation approaches. Common and easily available antiviral drugs ivermectin, doxycycline and their combination have been proved their valid candidature to be used as potential drug candidates against SARS-CoV-2 infections.

physics.bio-ph↗

arXiv2020

Studies on optical signal due to oxygen effect on hydrogenated amorphous/crystalline silicon thin-films

We have studied the effects of oxygen on hydrogenated amorphous/crystalline silicon films in terms of their structural and optical properties. Different hydrogenated silicon oxide (SiO:H) and silicon (Si:H) films are fabricated between microcrystalline and amorphous transition region. X-ray diffraction, Raman, FTIR and UV-Vis emission spectrometry have been used to characterize different films. A comparison of the results with those of different types of films like hydrogenated amorphous silicon oxide (a-SiO:H), hydrogenated amorphous silicon (a-Si:H) and microcrystalline silicon ($μ$c-Si:H) films reveal their superiority as an excellent substance for solar cell. X-ray diffraction, FTIR and Raman spectral analysis show that difference of the H dilution effect has a major effect on the structure of the film and the optical properties. Photoluminescence analysis of amorphous silicon-oxygen and silicon-hydride alloy films has established their efficient application appropriate as Si based light emitting devices. A large optical band gap of 1.83 eV and appearance of strong photo luminescence at 2.0 eV validates the applicability of a-SiO:H film as a better alternative for the solar cells.

cond-mat.mtrl-sci↗

arXiv2020

Studies on Size Dependent Structures and Optical Properties of CdSeS Clusters

The size-dependent structures and optical properties of CdSeS nanoclusters in water medium are investigated. The stability of different size-dependent Cd$_n$Se$_m$S$_p$ nanoclusters (up to n=6) is studied using density functional theory/time-dependent density functional theory (DFT/TDDFT). The computed results for ground (S$_0$) and excited (S$_1$, S$_2$, S$_3$) states are experimentally verified through UV-Vis spectroscopy. Computed ab initio results suggest that CdSeS clusters are significantly more hyperpolarizable compared to CdX (X= S, Se, Te) clusters. Structure dependent response properties are also observed, especially for n>3. Larger hyperpolarizabilities ($β$ and$γ$), charge variation and orbital analysis establish Cd$_4$Se$_m$S$_p$ clusters, as nonlinear optically active quantum dots (QDs).

cond-mat.mtrl-sci↗

arXiv2020

Optical and Electronic Properties of CdTe Quantum Dots in their Freezed Solid Matrix Phase and Solution Phase

The present work deals with the comparison of sizes, optical and electronic properties of COOH functionalized CdTe quantum dots (QDs) in freezed solid polymeric (polyvinyl alcohol (PVA) matrix and in solution phase (water). PVA has been chosen as host material for guest CdTe QDs because of its unique properties like hydrophilicity, good thermo stability, and easy process ability. Experimental absorption, emission, X-Ray diffraction spectra and electronic band gap have been studied by UV-Vis absorption, luminescence and X-Ray diffraction spectroscopy. The smaller size of CdTe QDs in solid PVA polymer matrix (~ 6 nm) and larger band gap of ~9.5 eV validates their quantum confinement regime in freezed solid phase. The smaller particle size in solid phase compared to that of the particle size in its solution phase (8 nm) validates the non existence of agglomeration in solid phase. Appearance of high intense and wide luminescence emission in solid form proves the strong candidature of CdTe QDs as promising sensors for today's optoelectronic and biomedical industry.

cond-mat.mtrl-sci↗

arXiv2020

Nonlinear optical responses of organic based indole derivative: an experimental and computational study

The nonlinear optical (NLO) properties of the Indole-7-carboxyldehyde (I7C) have been investigated by computational and experimental (UV-VIS, Raman) data analysis. Mulliken charge analysis, molecular electrostatic potential, and UV-VIS absorption and vibrational Raman studies have been used to analyze the intra-molecular charge transfer occurrence in the probe system. Observed high value of dipole moment, linear polarizability and first order hyperpolarizability values suggest that the indole derivative may indeed have possibility to show good NLO behaviour.

cond-mat.mtrl-sci↗

arXiv2020

Neuroprotective Immunity by Essential Nutrient "Choline" for the Prevention of SARS CoV2 Infections: An in Silico Study by Molecular Dynamics Approach

Prenatal COVID infection is one of the worst affected and least attended aspects of the COVID-19 disease. Like other coronaviruses, CoV2 infection is anticipated to affect fetal development by maternal inflammatory response on the fetus and placenta. Studies showed that higher prenatal choline level in mother's body can safeguard the developing brain of the fetus from the adverse effects of CoV2 infection. Choline is commonly used as food supplement. By virtual screening, molecular docking and molecular dynamics techniques, we have established a strong inhibitory possibility of choline for SARS $\rm{3CL^{pro}}$ protease which may provide a lead for prenatal COVID-19 treatment.

physics.bio-ph↗

arXiv2020

Functionalized CdTe Fluorescence Nanosensor for the Sensitive Detection of Water Borne Environmentally Hazardous Metal Ions

In this work, we have investigated the possibility of using COOH functionalized CdTe quantum dots (QDs) as fluorescent nanosensor for the detection of some environmentally hazardous metal ions ($\rm{Cr^{3+}}$, $\rm{Pb^{2+}}$, $\rm{Cu^{2+}}$, $\rm{Zn^{2+}}$ and $\rm{Co^{2+}}$) in aqueous phase. COOH-CdTe QDs are prepared in aqueous medium and characterized by UV-visible, photo luminescence and FTIR spectrometry. Optical response of CdTe nanosensor is observed to be time and temperature dependent. A strong "Turn-Off" fluorescence response of CdTe is observed in presence of all metals ions ($\rm{X^{n+}}$). The output of Stern volmer relation, graphical Job's plot and FTIR data established the existence of strong 1:1 complexation ($\rm{X^{n+}: ^{-}OOC-CdTe)}$ between CdTe and metal ions. CdTe shows its efficient sensing ability for $\rm{Pb^{2+}}$, $\rm{Cr^{3+}}$ and $\rm{Cu^{2+}}$ ions up to concentration $\rm{10^{-14}}$ M which was established by its low detection of limit (LOD)validation. Further, strong appearance of $\frac{F-F_{0}}{F_{0}}$ establishes the better sensing capability of CdTe QDs for $\rm{Cr^{3+}}$, $\rm{Pb^{2+}}$, $\rm{Cu^{2+}}$ ions which are far better than the existing fluorescent sensors available in industry. The proposed optical techniques and principal component analysis of sensing were successfully applied for testing of dissolved metal ions in real samples like: paint, river water, rain water etc which validates the applicability of COOH functionalized CdTe nanosensor as a effective successful optical sensor for water dissolved metal ions which are responsible for water pollution.

physics.chem-ph↗

arXiv2020

In Silico Investigation of Phytoconstituents from Indian Medicinal Herb 'Tinospora cordifolia (Giloy)' against SARS-CoV-2 (COVID-19) by Molecular Dynamics Approach

The recent appearance of COVID-19 virus has created a global crisis due to unavailability of any vaccine or drug that can effectively and deterministically work against it. Naturally, different possibilities (including herbal medicines having known therapeutic significance) have been explored by the scientists. The systematic scientific study (beginning with in silico study) of herbal medicines in particular and any drug in general is now possible as the structural components (proteins) of COVID-19 are already characterized. The main protease of COVID-19 virus is $\rm{M^{pro}}$ or $\rm{3CL^{pro}}$ which is a key CoV enzyme and an attractive drug target as it plays a pivotal role in mediating viral replication and transcription. In the present study, $\rm{3CL^{pro}}$ is used to study drug:3CLpro interactions and thus to investigate whether all or any of the main chemical constituents of Tinospora cordifolia (e.g., berberine $\rm{(C_{20}H_{18}NO_{4})}$, $β$-sitosterol $\rm{(C_{29}H_{50}O)}$, choline $\rm{(C_{5}H_{14}NO)}$, tetrahydropalmatine $\rm{(C_{21}H_{25}NO_{4})}$ and octacosanol $\rm{(C_{28}H_{58}O))}$ can be used as an anti-viral drug against SARS-CoV-2. The in silico study performed using tools of network pharmacology, molecular docking including molecular dynamics have revealed that among all considered phytochemicals in Tinospora cordifolia, berberine can regulate $\rm{3CL^{pro}}$ protein's function due to its easy inhibition and thus can control viral replication. The selection of Tinospora cordifolia was motivated by the fact that the main constituents of it are known to be responsible for various antiviral activities and the treatment of jaundice, rheumatism, diabetes, etc.

q-bio.BM↗

arXiv2010

Study of Proton Transfer Reaction Dynamics in Pyrrole 2-Carboxyldehyde

Photophysical and photochemical dynamics of ground state and excited state proton transfer reaction is reported for Pyrrole 2-Carboxyldehyde (PCL). Steady state absorption and emission measurements are conducted in PCL. The theoretical investigation is done by using different quantum mechanical methods (e.g. Hartree Fock, DFT, MP2, CCSD etc.). The reaction pathway and two dimensional potential energy surfaces are computed in various level of theory. A transition state is also reported in gas phase and reaction filed calculation. It is established that PCL forms different emitting species in different media. A large Stokes shifted emission band, which is attributed to species undergoing excited state intramolecular proton transfer, is observed in hydrocarbon solvent. Intermolecular proton transfer is observed in hydroxylic polar solvent. Experimental observations yield all possible signatures of intramolecular and intermolecular proton transfer in excited state of PCL. The origins of these signatures have been explained successfully using corresponding quantum mechanical theories.

physics.atm-clus↗