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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Multi-state multi-reference Møller-Plesset second-order perturbation theory for molecular calculations
PublicationThis work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order...
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Excited state properties of a series of molecular photocatalysts investigated by time dependent density functional theory.
PublicationTime dependent density functional theory calculations are applied on a series of molecular photocatalysts of the type [(tbbpy)2M1(tpphz)M2X2]2+ (M1 = Ru, Os; M2 = Pd, Pt; X = Cl, I) in order to provide information concerning the photochemistry occurring upon excitation of the compounds in the visible region. To this aim, the energies, oscillator strengths and orbital characters of the singlet and triplet excited states are investigated....
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublicationThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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The exposure to UV filters: Prevalence, effects, possible molecular mechanisms of action and interactions within mixtures
PublicationSubstances that can absorb sunlight and harmful UV radiation such as organic UV filters are widely used in cosmetics and other personal care products. Since humans use a wide variety of chemicals for multiple purposes it is common for UV filters to co-occur with other substances either in human originating specimens or in the environment. There is increasing interest in understanding such co-occurrence in form of potential synergy, antagonist,...
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Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
PublicationThe increasing interest in polyurethane materials has raised the question of the environmental impact of these materials. For this reason, the scientists aim to find an extremely difficult balance between new material technologies and sustainable development. This work attempts to validate the possibility of replacing petrochemical polyols with previously synthesized bio-polyols and their impact on the structure and properties...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Selected symmetrically substituted carbazoles: Investigation of anticancer activity and mechanisms of action at the cellular and molecular levels
PublicationDNA topoisomerases play a critical role as essential enzymes in controlling alterations in the topology of DNA. They achieve this by orchestrating the coordinated process of breaking and rejoining DNA strands, which is crucial for maintaining the proper structure of DNA during regular cellular development. The search for and development of new potential anticancer drugs is a challenging yet immensely important area of research...
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Quasirelativistic potential energy curves and transition dipole moments of NaRb
PublicationWe report on extensive calculations of quasi-relativistic potential energy curves and, for the first time, transition dipole moments including spin-orbit and scalar-relativistic effects of the NaRb molecule. The calculated curves of the 0+, 0-, 1, 2 and 3 molecular states correlate for large internuclear separation with the fourteen lowest atomic energies up to the Na(3s ^2S_{1/2}) + Rb(7s ^2S_{1/2}) atomic limit. Several new features...
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CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
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Advances In Atomic Molecular and Optical Physics
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International Journal of Molecular and Cellular Medicine
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Statistical Applications in Genetics and Molecular Biology
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International Journal of Molecular Epidemiology and Genetics
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Hormone Molecular Biology and Clinical Investigation
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MOLECULAR AND QUANTUM ACOUSTICS. ANNUAL JOURNAL
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Methods in molecular biology (Clifton, N.J.)
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Malaysian Journal of Biochemistry and Molecular Biology
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Molecular Therapy-Methods & Clinical Development
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European Journal of Molecular and Clinical Medicine
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Plant Cell Biotechnology and Molecular Biology
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JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY
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Chinese Journal of Biochemistry and Molecular Biology
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NATURE REVIEWS MOLECULAR CELL BIOLOGY
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International Review of Cell and Molecular Biology
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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
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JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC
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Progress in Molecular Biology and Translational Science
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Effect of biodynamic preparations on the content of some mineral elements and starch in tubers of three coloured potato cultivars
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Theoretical designing of selenium heterocyclic non-fullerene acceptors with enhanced power conversion efficiency for organic solar cells: a DFT/TD-DFT-based prediction and understanding
PublicationIn this study, we have designed and explored a new series of non-fullerene acceptors for possible applications in organic solar cells. We have designed four molecules named as APH1 to APH4 after end-capped modification of recently synthesized Y6-Se-4Cl molecule. Density functional theory and time dependent-density functional theory have been employed for computing geometric and photovoltaic parameters of the designed molecules....
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Born-Oppenheimer potential energy curves of the NaK molecule
Open Research DataAdiabatic potential energy curves (APEC) of the singlet (s) and triplet (t) Sigma+, Pi, and Delta electronic states have been calculated for the NaK molecule. All results of the presented molecular states have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Linear and nonlinear Stark effect in a triangular molecule
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Electron collision with sulfuryl chloride (SO2Cl2) molecule
PublicationStosując liniową metodę transmisyjną zmierzono całkowite przekroje czynne (TCS) na zderzenie elektronów z drobinami SO2Cl2 w zakresie energii 0.5-150 eV. Stwierdzono obecność głębokiego minimum przy ok. 1.8 eV i szerokiego maksimum w pobliżu 9.5 eV. Przeprowadzono porównanie z dostępnymi wynikami dla innych związków zawierających grupę sulfonową.
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First deep eutectic solvent-based (DES) stationary phase for gas chromatography and future perspectives for DES application in separation techniques
PublicationThe paper presents the first application of deep eutectic solvents (DES) as stationary phases for gas chromatography. DES obtained by mixing tetrabutylammonium chloride (TBAC) as a hydrogen bond acceptor (HBA) with heptadecanoic acid being a hydrogen bond donor (HBD) in a mole ratio of HBA:HBD equal to 1:2 was characterized by its ability to separate volatile organic compounds (VOCs). The Rohrschneider – McReynolds constants determined...
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Separation of Monovinyl and Divinyl Protochlorophyllides Using C30 Reverse Phase High Performance Liquid Chromatography Column: Analytical and Preparative Applications
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Nanostructured polyethersulfone nanocomposite membranes for dual protein and dye separation: Lower antifouling with lanthanum (III) vanadate nanosheets as a novel nanofiller
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Classification of Music Genres Based on Music Separation into Harmonic and Drum Components . Klasyfikacja gatunków muzycznych wykorzystująca separację instrumentów muzycznych
PublicationThis article presents a study on music genre classification based on music separation into harmonic and drum components. For this purpose, audio signal separation is executed to extend the overall vector of parameters by new descriptors extracted from harmonic and/or drum music content. The study is performed using the ISMIS database of music files represented by vectors of parameters containing music features. The Support Vector...
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Optimal conditions of naphthoquinones separation from carnivorous plants extracts using thin-layer chromatography and high performance liquid chromatography
PublicationDroseraceae plants are owned by the family of carnivorous plants, which in an unusual way adapt to environments poor in nutrients. Droseraceae obtain essential nutrients catching insects and other small invertebrantes. Plumbagin, chloroplumbagin, ramentaceon and droseron are naphthoquinones, which could be found in leaves and shoots of plants from Droseraceae family. In the literature there are a lot of information about the pharmacological...
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Capillary gas chromatography using a -cyclodextrin forenantiomeric separation of methylamphetamine, its precursors andchloro intermediates after optimization of the derivatization reaction
PublicationtThe enantiomeric ratio of methylamphetamine (MAMP) is closely related to the optical activity of precur-sors and reagents used for the synthesis and this knowledge can provide useful information concerningthe origins and synthetic methods used for illicit manufacture. The information can be utilized for reg-ulation of the precursors and investigation of the manufacturing sources but this requires analyticalprocedures to determine...
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Musical Instrument Separation Applied to Music Genre Classification . Separacja instrumentów muzycznych w zastosowaniu do rozpoznawania gatunków muzycznych
PublicationThis paper outlines first issues related to music genre classification and a short description of algorithms used for musical instrument separation. Also, the paper presents proposed optimization of the feature vectors used for music genre recognition. Then, the ability of decision algorithms to properly recognize music genres is discussed based on two databases. In addition, results are cited for another database with regard to...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Adhesion of the genome-sequenced Lactococcus lactis subsp. cremoris IBB477 strain is mediated by specific molecular determinants
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Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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