Pejov, LJupcho
Preferred name
Pejov, LJupcho
Official Name
Pejov, LJupcho
Translated Name
Pejov, Ljupco
Main Affiliation
Email
ljupcop@pmf.ukim.mk
23 results
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Item type:Publication, Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis(BULGARIAN ACADEMY OF SCIENCES, 2020-12-31); ; - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Quantitative Measurement of Scientific Software Quality: Definition of a Novel Quality Model(World Scientific Pub Co Pte Lt, 2018-03); ; This paper presents a novel quality model, which provides a quantitative assessment of the attributes evaluated at each stage of development of scientific applications. This model is defined by selecting a set of attributes and metrics that affect the quality of applications. It is based on the established quality standards. The practical application and verification of the quality model is confirmed by two case studies. The first is an application for solving one-dimensional and two-dimensional Schrödinger equations, using the discrete variables representation method. The second is an application for calculating an ECG-derived heart rate and respiratory rate. The first application follows a development model for scientific applications, which includes some software engineering practices. The second application does not use a specific development model, rather, it is developed ad hoc. The quality of the applications is evaluated through comparative analyses using the proposed model. Based on software quality metrics, the results of this study indicate that the application for solving one-dimensional and two-dimensional Schrödinger equations produces more desirable results. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Isotropic Magnetic Shielding of Al(OH) − 4 in Aqueous Solution: A Hybrid Monte Carlo - Quantum Mechanical Computational Model(Springer International Publishing, 2016); ; - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Semiempirical Atom-centered Density Matrix Propagation Approach to Temperature-dependent Vibrational Spectroscopy of Irinotecan(Scalable Computing: Practice and Experience, 2018-05-10); ; ; ; <jats:p>In the present study, a molecular dynamics study of irinotecan molecule with the atom-centered density matrix propagation scheme was carried out at AM1 semiempirical level of theory, at series of different temperatures, ranging from 5 K to 300 K. Molecular dynamics simulations were performed within the NVE ensemble, initially injecting (and redistributing among the nuclei) various amounts of nuclear kinetic energies to achieve the desired target temperatures. Subsequently to initial equilibration phase of 2 ps, productive simulations were carried out for 8 ps. The accuracy of simulations and the closeness of the generated trajectory to those at the Born-Oppenheimer surface were carefully followed and analyzed. To compute the temperature-dependent rovibrational density of states spectra, the velocity-velocity autocorrelation functions were computed and Fourier-transformed. Fourier-transformed dipole moment autocorrelation functions were, on the other hand, used to calculate the temperature-dependent infrared absorption cross section spectra. The finite-temperature spectra were compared to those computed by a static approach, i.e. by diagonalization of mass-weighted Hessian matrices at the minima located on the potential energy surfaces. Thermally-induced spectral changes were analyzed and discussed. The advantages of finite-temperature statistical physics simulations based on semiempirical Hamiltonian over the static semiempirical ones in the case of complex, physiologically active molecular systems relevant to intermolecular interactions between drugs and drug carriers were pointed out and discussed.</jats:p> - Some of the metrics are blocked by yourconsent settings
Item type:Publication, - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Magnetic Response Properties of Aqueous Aluminum(III) Ion: A Hybrid Statistical Physics Quantum Mechanical Approach Implementing the Map-Reduce Computational Technique(Springer International Publishing, 2015); ; - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Comparative Study of Two Approaches for Solving the Torsional Schrödinger Equation: Fourier Grid Hamiltonian Method and Hamiltonian Diagonalization Method(Faculty of Computer Science and Engineering, Skopje, North Macedonia, 2015); ; In this study, we have compared the computational performance of two methods implemented to solve the Schrödinger equation for intramolecular torsional motions. The first approach is the Fourier grid Hamiltonian (FGH) operator method, which is based on fragmentation of the total torsional Hamiltonian into kinetic energy part, which is diagonal in momentum representation, and the potential energy part, diagonal in coordinate representation. The second approach is the standard diagonalization technique, based on variational principle of quantum mechanics. Torsional energy eigenvalues are further used to compute the torsional correlation times in the framework of BPP (Bloembergen-Purcell-Pound) approach. The results show that diagonalization technique performs much faster than the FGH algorithm. Besides that, the convergence of eigenvalues with the number of basis functions appears to be achieved faster with Hamiltonian diagonalization. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, On the Choice of Method for Solution of the Vibrational Schrödinger Equation in Hybrid Statistical Physics - Quantum Mechanical Modeling of Molecular Solvation(Springer International Publishing, 2014); ; - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Quantum Vibrational Dynamics of Molecular Species Relevant to Atmospheric Chemistry and ClimateScience. Formic Acid and its Clusters with Benzene(Society of Chemists and Technologists of Macedonia, 2016); ; Vibrational dynamics of formic acid and its noncovalenly bonded complexes with benzene was studied at series of finite temperatures mimicking atmospheric conditions, as well as in the limit of 0 K. Potential energy surfaces (PES) of bare formic acid as well as of its binary noncovalent clusters with benzene were explored employing density functional theory and many-body perturbation theory. Anharmonic OH stretching frequencies of cis- and trans- conformers of formic acid at 0 K were calculated by computing the corresponding anharmonic adiabatic vibrational potentials and subsequently numerically solving the vibrational Schrödinger equations. Similar computations were carried out for the minima located on the benzene – formic acid PESs. The corresponding vibrational frequency shifts with respect to the free monomeric species were compared to the available experimental data. The dynamics of cis → trans and reverse interchange was studied on the basis of computed fully relaxed torsional potentials at the mentioned theoretical levels employing WKB semiclassical methodology. To study the finite-temperature effects on the inter- and intramolecular vibrational dynamics of the studied species, a series of ab initio molecular dynamics (MD) simulations were carried out, employing both Born-Oppenheimer molecular dynamics (BOMD) as well as the atom-centered density matrix propagation scheme (ADMP). All ab initio MD simulations were performed in the NVE ensemble. In parallel, for comparison purposes, also a series of classical Monte Carlo (MC) simulations were performed, using Coulomb + Lennard-Jones interaction potentials. Vibrational spectroscopic properties of monomeric and noncovalently bonded dimeric species were elucidated from dynamical simulations analyzing the corresponding time- correlation functions, i.e. employing time-series analytic methods. For that purpose, both velocity autocorrelation function as well as the atomic position autocorrelation function was computed and subsequently Fourier-transformed. The differences between “static” and dynamic vibrational spectra were noted and discussed. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Computational study of intramolecular oh stretching vibrations in the two rotamers of free formic acid(Editura Academiei Romane, 2018); ;
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