scholarly journals Approximate Bound State Solutions for Certain Molecular Potentials

2021 ◽  
Vol 09 (04) ◽  
pp. 736-750
Author(s):  
Mahmoud Farout ◽  
Mohammed Yasin ◽  
Sameer M. Ikhdair
2014 ◽  
Vol 29 (09) ◽  
pp. 1450042 ◽  
Author(s):  
Amlan K. Roy

Accurate ro-vibrational energies, eigenfunctions, radial densities, expectation values are presented for the exponential-type Manning–Rosen (MR) potential. Bound states, accurate up to ten significant figure are obtained by employing a simple, reliable generalized pseudospectral (GPS) method. All 55 eigenstates with n ≤10 are treated for arbitrary values of potential parameters, covering a wide range of interaction, through a non-uniform, optimal spatial radial discretization. A detailed investigation has been made on energy changes with respect to screening and other potential parameters. A systematic estimation of critical screening parameters is given for these eigenstates. Special emphasis has been given to higher states and in the vicinity of critical screening region. A thorough comparison with literature results is made wherever possible. This surpasses the accuracy of all other existing methods currently available. Several new states are reported for the first time. In short, a simple, efficient scheme for accurate calculation of this and other molecular potentials is offered.


2009 ◽  
Vol 20 (03) ◽  
pp. 361-372 ◽  
Author(s):  
SAMEER M. IKHDAIR ◽  
RAMAZAN SEVER

The point canonical transformation (PCT) approach is used to solve the Schrödinger equation for an arbitrary dimension D with a power-law position-dependent effective mass (PDEM) distribution function for the pseudoharmonic and modified Kratzer (Mie-type) diatomic molecular potentials. In mapping the transformed exactly solvable D-dimensional (D ≥ 2) Schrödinger equation with constant mass into the effective mass equation by using a proper transformation, the exact bound state solutions including the energy eigenvalues and corresponding wave functions are derived. The well-known pseudoharmonic and modified Kratzer exact eigenstates of various dimensionality is manifested.


Open Physics ◽  
2008 ◽  
Vol 6 (3) ◽  
Author(s):  
Sameer Ikhdair ◽  
Ramazan Sever

AbstractMaking an ansatz to the wave function, the exact solutions of the D-dimensional radial Schrödinger equation with some molecular potentials, such as pseudoharmonic and modified Kratzer, are obtained. Restrictions on the parameters of the given potential, δ and ν are also given, where η depends on a linear combination of the angular momentum quantum number ℓ and the spatial dimensions D and δ is a parameter in the ansatz to the wave function. On inserting D = 3, we find that the bound state eigensolutions recover their standard analytical forms in literature.


Author(s):  
John Trinickt ◽  
Howard White

The primary force of muscle contraction is thought to involve a change in the myosin head whilst attached to actin, the energy coming from ATP hydrolysis. This change in attached state could either be a conformational change in the head or an alteration in the binding angle made with actin. A considerable amount is known about one bound state, the so-called strongly attached state, which occurs in the presence of ADP or in the absence of nucleotide. In this state, which probably corresponds to the last attached state of the force-producing cycle, the angle between the long axis myosin head and the actin filament is roughly 45°. Details of other attached states before and during power production have been difficult to obtain because, even at very high protein concentration, the complex is almost completely dissociated by ATP. Electron micrographs of the complex in the presence of ATP have therefore been obtained only after chemically cross-linking myosin subfragment-1 (S1) to actin filaments to prevent dissociation. But it is unclear then whether the variability in attachment angle observed is due merely to the cross-link acting as a hinge.We have recently found low ionic-strength conditions under which, without resorting to cross-linking, a high fraction of S1 is bound to actin during steady state ATP hydrolysis. The structure of this complex is being studied by cryo-electron microscopy of hydrated specimens. Most advantages of frozen specimens over ambient temperature methods such as negative staining have already been documented. These include improved preservation and fixation rates and the ability to observe protein directly rather than a surrounding stain envelope. In the present experiments, hydrated specimens have the additional benefit that it is feasible to use protein concentrations roughly two orders of magnitude higher than in conventional specimens, thereby reducing dissociation of weakly bound complexes.


Author(s):  
Parth Sarthi Sen Gupta ◽  
Satyaranjan Biswal ◽  
Saroj Kumar Panda ◽  
Abhik Kumar Ray ◽  
Malay Kumar Rana

<p>While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by ~5000 folds within 48 hours, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting -10.4 kcal/mol and -9.6 kcal/mol, respectively. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site, with MM/PBSA free energy of -135.2 kJ/mol, almost twice that of Helicase (-76.6 kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration. </p>


Author(s):  
Aditi Rathee ◽  
Anil Panwar ◽  
Seema Kumari ◽  
Sanjay Chhibber ◽  
Ashok Kumar

Introduction:: Enzymatic degradation of peptidoglycan, a structural cell wall component of Gram-positive bacteria, has attracted considerable attention being a specific target for many known antibiotics. Methods:: Peptidoglycan hydrolases are involved in bacterial lysis through peptidoglycan degradation. β-N-acetylglucosaminidase, a peptidoglycan hydrolase, acts on O-glycosidic bonds formed by N-acetylglucosamine and N-acetyl muramic acid residues of peptidoglycan. Aim of present study was to study the action of β-N-acetylglucosaminidase, on methicillin- resistant Staphylococcus aureus (MRSA) and other Gram-negative bacteria. Results:: We investigated its dynamic behaviour using molecular dynamics simulation and observed that serine and alanine residues are involved in catalytic reaction in addition to aspartic acid, histidine, lysine and arginine residues. When simulated in its bound state, the RMSD values were found lesser than crystal form in the time stamp of 1000 picoseconds revealing its stability. Structure remained stably folded over 1000 picoseconds without undergoing any major change further confirming the stability of complex. Conclusion:: It can be concluded that enzymes belonging to this category can serve as a tool in eradicating Gram-positive pathogens and associated infections.


2020 ◽  
Vol 51 (5) ◽  
pp. 979-987 ◽  
Author(s):  
I. Filikhin ◽  
B. Vlahovic

2020 ◽  
Vol 2020 (12) ◽  
Author(s):  
Yudai Ichikawa ◽  
Junko Yamagata-Sekihara ◽  
Jung Keun Ahn ◽  
Yuya Akazawa ◽  
Kanae Aoki ◽  
...  

Abstract We have measured, for the first time, the inclusive missing-mass spectrum of the $^{12}$C$(K^-, p)$ reaction at an incident kaon momentum of 1.8 GeV/$c$ at the J-PARC K1.8 beamline. We observed a prominent quasi-elastic peak ($K^-p \rightarrow K^-p$) in this spectrum. In the quasi-elastic peak region, the effect of secondary interaction is apparently observed as a peak shift, and the peak exhibits a tail in the bound region. We compared the spectrum with a theoretical calculation based on the Green’s function method by assuming different values of the parameters for the $\bar{K}$–nucleus optical potential. We found that the spectrum shape in the binding-energy region $-300 \, \text{MeV} &lt; B_{K} &lt; 40$ MeV is best reproduced with the potential depths $V_0 = -80$ MeV (real part) and $W_0 = -40$ MeV (imaginary part). On the other hand, we observed a significant event excess in the deeply bound region around $B_{K} \sim 100$ MeV, where the major decay channel of $K^- NN \to \pi\Sigma N$ is energetically closed, and the non-mesonic decay modes ($K^- NN \to \Lambda N$ and $\Sigma N$) should mainly contribute. The enhancement is fitted well by a Breit–Wigner function with a kaon-binding energy of 90 MeV and width 100 MeV. A possible interpretation is a deeply bound state of a $Y^{*}$-nucleus system.


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