Filters
total: 656
filtered: 586
Search results for: Molecular docking and simulation study
-
Interaction of amphotericin B with phospholipids in the model membrane - molecular dynamics study.
PublicationAmfoterycyna B jest antybiotykiem używanym w leczeniu układowych infekcji grzybowych. Jej mechanizm działania polega na tworzeniu kanałów wewnątrz błon lipidowych. W przedstawianej pracy publikowane są wyniki symulacji przeprowadzonej dynamiką molekularną monomerycznej i dimerycznej formy antybiotyku wewnątrz błony lipidowej zbudowanej z cząsteczek DMPC. Wyniki te wskazują, że powinowactwo cząsteczek amfoterycyny wewnątrz dimeru...
-
Study of the transport properties of a molecular junction as a function of the distance between the leads
Publication -
Molecular Dynamics Study of the Internal Water Molecules in Vasopressin and Oxytocin Receptors
Publication -
Interactions of amphotericin B derivatives with lipid membranes - a molecular dynamics study
PublicationW pracy analizowano oddziaływanie dwóch nisko-toksycznych pochodnych amfoterycyny B (związki SAmE i PAmE) z modelami błon lipidowych. Badania wykonane zostały za pomocą dynamiki molekularnej. Modele błon oprócz fosfolipidów DMPC zawierały odpowiednio cholesterol (model błony zwierzęcej) lub ertosterol (model błony grzybowej). Analiza wyników wykazała, że obie pochodne amfoterycyny B zachowują się inaczej w błonie cholesterolowej...
-
Molecular Dynamics study of short and medium range order in modified BGO glasses.
PublicationArtykuł przedstawia wyniki symulacji dynamiczno-molekularnychniemodyfikowanych i modyfikowanych szkieł BGO o różnych stechiometriach. Otrzymane wyniki dokładnie przedyskutowano pod kątem blisko- i średnio-zasięgowego uporządkowania atomów i porównano z innymi dostępnymi danymi literaturowymi.
-
A study of electron impact excitation of molecular oxygen at a scattering angle of 180 st.
PublicationZbadano wzbudzenie tlenu cząsteczkowego w zderzeniu z elektronem dla rozproszenia do tyłu, pod kątem 180 st. Do pomiarów wykorzystano nowe źródło lokalnego pola magnetycznego o geometrii stożkowej.
-
A general approach to study molecular fragmentation and energy redistribution after an ionizing event
PublicationWe propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron–photoion coincidence experiments and...
-
Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides
Publication -
Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
Publication -
Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
Publication -
Anticancer properties of low molecular weight oat beta-glucan – An in vitro study
Publication -
Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study
Publication -
Design, synthesis and biological evaluation of novel N-phosphorylated and O-phosphorylated tacrine derivatives as potential drugs against Alzheimer’s disease
PublicationIn this work, we designed, synthesised and biologically investigated a novel series of 14N- and O-phosphorylated tacrine derivatives as potential anti-Alzheimer’s disease agents. In the reaction of 9-chlorotacrine and corresponding diamines/aminoalkylalcohol we obtained diamino and aminoalkylhydroxy tacrine derivatives. Next, the compounds were acid to give final products 6–13 and 16–21 that were characterised by 1H, 13 C, 31P...
-
Study on population dynamics for triple-linked food chain using a simulation-based approach
PublicationThe procedures based on simulation have become a feasible testing method that does not require investing valuable resources to create a concrete prototype, especially with the increasing computational power of computers. Thus, design changes can be adopted and design errors can be fixed before it is too late. Simulation turns to be a cheap, safe and often more acceptable from an ethical perspective. In our work we summarize the...
-
Prediction of Overall In Vitro Microsomal Stability of Drug Candidates Based on Molecular Modeling and Support Vector Machines. Case Study of Novel Arylpiperazines Derivatives
PublicationOther than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach its therapeutic site of action. Despite many recent excellent achievements in the field of computational methods supporting drug metabolism studies, a well-recognized procedure to model...
-
Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
-
Synthesis and steroid sulfatase inhibitory activities of N-alkanoyl tyramine phosphates and thiophosphates
PublicationA series of phosphate and thiophosphate analogs based on the frameworks of N-alkanoyl tyramines have been synthesized and biologically evaluated. Their binding modes have been modeled using docking techniques. The inhibitory effects of the synthesized compounds were tested on STS isolated from the human placenta as well as the MCF-7, MDA-MB-231 and SkBr3 cancer cell lines. Most of the new STS inhibitors possessed potent activity...
-
Synthesis and steroid sulfatase inhibitory activities of N-phosphorylated 3-(4-aminophenyl)-coumarin-7-O-sulfamates
PublicationIn the present work, we report convenient methods for the synthesis and biological evaluation of N-phosphorylated derivatives of 3-(4-aminophenyl)-coumarin-7-O-sulfamate as potential steroid sulfatase (STS) inhibitors. Their binding modes were modeled using docking techniques. The inhibitory effects of the synthesized compounds were tested on STS isolated from human placenta. All of the newly synthesised coumarin derivatives were...
-
Synthesis of bicoumarin thiophosphate derivatives as steroid sulfatase inhibitors
PublicationBased on the frameworks of 7-hydroxy-2,3-dihydro-1H-cyclopenta[c]chromen-4-one, 3-hydroxy- 7,8,9,10-tetrahydro-6H-benzo[c]chromen-6-one and 3-hydroxy-8,9,10,11-tetrahydro-7H-cyclohepta[c] chromen-6-one, a series of bicoumarin thiophosphate analogs have been synthesized and biologically evaluated. Additionally, their binding modes have been modeled using docking techniques. The inhibitory properties of the synthesized compounds...
-
Derecho Evolving from a Mesocyclone—A Study of 11 August 2017 Severe Weather Outbreak in Poland: Event Analysis and High-Resolution Simulation
PublicationThis study documents atmospheric conditions, development, and evolution of a severe weather outbreak that occurred on 11 August 2017 in Poland. The emphasis is on analyzing system morphology and highlighting the importance of a mesovortex in producing the most significant wind damages. A derecho-producing mesoscale convective system (MCS) had a remarkable intensity and was one of the most impactful convective storms in the history...
-
Impact of Low Switching-to-Fundamental Frequency Ratio on Predictive Current Control of PMSM: A simulation study
PublicationPredictive current control algorithms for permanent magnet synchronous (PMSM) drives rely on an assumption that within short intervals motor currents can be approximated with linear functions. This approximation may result either from discretizing the motor model or from simplifications applied to the continuous-time model. As the linear current approximation has been recognized as inaccurate in case when the drive operates with...
-
Simplified simulation technique of rotating, induction heated, calender rolls for study of temperature field control
Publication -
Experimental study and numerical simulation of low calorific fuel combustion at different oxygen content in the oxydizer
PublicationW pracy przedstawiono wyniki badań eksperymentalnych oraz obliczeń numerycznych procesu spalania paliwa gazowego niskokalorycznego w utleniaczu o podwyższonej temperaturze i zmiennej zawartości tlenu. Badanym paliwem był gaz o składzie zbliżonym do paliwa pochodzącego z gazyfikacji biomasy. Spalanie przeprowadzano dla zmiennej wartości temperatury utleniacza oraz zawartości tlenu. Obliczenia numeryczne wykonano z wykorzystaniem...
-
Two-dimensional diffusion wave model for numerical simulation of inundation - Upper Narew case study
PublicationPrzedstawiono zastosowanie uproszczonego modelu matematycznego przepływu wody ze swobodną powierzchnią, zwanego falą dyfuzyjną, do numerycznej symulacji zalewu powodziowego doliny rzeki. Równania modelu rozwiązano metodą objętości skończonych. Model w dwuwymiarowej wersji wykorzystano do odtworzenia przejścia fali powodziowej przez fragment doliny Górnej Narwi między miejscowościami Suraż i Łapy.
-
Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublicationW pracy przedstawiono wyniki symulacji wczesnych etapów kondensacji z fazy gazowej w układzie xH2O (1-x)N2. Przeanalizowano całkowitą liczbę klastrów, średni rozmiar klastra i rozmiar klastra maksymalnego w funkcji czasu.
-
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...
-
A DSC and NMR-Relaxation study of the molecular mobility of water protons interacting with chemically modified starches
PublicationChanges in the mobility of water protons in the chemically modified starches (CMS)–water system are studied by differential scanning calorimetry and NMR relaxation. The amounts of unfrozen water at negative temperatures and additional (after gelation) unfrozen for CMS are lower than those for native starch. The proton spin–spin relaxation time T2 for CMS samples, conventionally attributed to the water fraction in starch granules,...
-
Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives
Publication -
Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
-
MARSTRUCT benchmark study on nonlinear FE simulation of an experiment of an indenter impact with a ship side-shell structure
PublicationThis paper presents a benchmark study on collision simulations that was initiated by the MARSTRUCT Virtual Institute. The objective was to compare assumptions, finite element models, modelling techniques and experiences between established researchers within the field. Fifteen research groups world-wide participated in the study. An experiment involving a rigid indenter penetrating a ship-like side structure was used as the case...
-
Numerical Simulation of Catastrophic Flood: the Case Study of Hypothetical Failure of the Bielkowo Hydro–Power Plant Reservoir
PublicationThe numerical modeling of flood wave propagation following the hypo-thetical breaks of the embankments of the Bielkowo hydro–power plant storage reservoir (Kolbudy II Reservoir) on the Radunia River in Poland have been presented. The results of computations were used to estimate the parameters of the flood waves, which are indispensable for the flood zone determination and mapping and then for the flood risk analysis. When estimating...
-
A Comparative Numerical Simulation Study of Turbulent Non-premixed CO/H2/N2 Syngas Jet Flames
PublicationIn the present work, numerical simulations of turbulent non-premixed syngas flame have been performed in Reynolds-Averaged Naver-Stokes turbulence approach using four turbulence-chemistry interaction models. To this aim, we used assumed beta PDF approach, Steady Laminar Flamelet model, Eddy Dissipation Concept and Partially Stirred Reactor model. Numerical results are compared and analysed with respect to two experiments from the...
-
Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
Publication -
Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
Publication -
Graph Neural Networks and Structural Information on Ionic Liquids: A Cheminformatics Study on Molecular Physicochemical Property Prediction
PublicationIonic liquids (ILs) provide a promising solution in many industrial applications, such as solvents, absorbents, electrolytes, catalysts, lubricants, and many others. However, due to the enormous variety of their structures, uncovering or designing those with optimal attributes requires expensive and exhaustive simulations and experiments. For these reasons, searching for an efficient theoretical tool for finding the relationship...
-
Experimental study and numerical simulation on porosity dependent direct reducibility of high-grade iron oxide pellets in hydrogen
PublicationThe transition to more environmentally friendly steel production methods has intensified research into hydrogen-based direct reduction (HyDR) of iron oxide pellets. The aim of this study is to systematically investigate the kinetics of the reduction process, the evolution of porosity and the resulting microstructural changes on the reduction behavior of high-quality pellets during HyDR of iron ore at different temperatures. A modified...
-
Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5-Bromouracil case study
Publication -
Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5-Bromouracil case study
PublicationABSTRACT Laser illuminated gold nanoparticles (AuNPs) efficiently absorb light and heat up the surrounding medium, leading to versatile applications ranging from plasmonic catalysis to cancer photothermal therapy. Therefore, an in-depth understanding of the thermal, optical, and electron induced reaction pathways is required. Here, the electrophilic DNA nucleobase analog 5-Bromouracil (BrU) has been used as a model compound to...
-
On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
-
Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
Publication -
A comparative study of the molecular lipophilicity indices of vitamins A and E, and of some precursors of vitamin A, estimated by HPLC and by different computation methods
PublicationIndeksy lipofilowości witamin A i E oraz wybranych prekursorów witaminy A zostały obliczone na podstawie wyników badań z wykorzystaniem wysokosprawnej chromatografii cieczowej z odwróconym układem faz (RPHPLC) i kolumn chromatograficznych typu C-8 i C-18.Uzyskano doskonałe współczynniki korelacji (>0,9999) dla wyników uzyskanych dla tych dwóch typów kolumn chromatograficznych.
-
Human serum interactions with phenolic and aroma substances of Kaffir(Citrus hystrix) and Key lime (Citrus aurantifolia) juices
PublicationTo understand the therapeutic application of polyphenols extracted from Kaffir (PolKaf) and Key (PolKey) limesdifferent analytical methods were applied. Based on quantitative analysis by two dimensional gas chromato-graphy (GC×GC) and time of flight mass spectrometry (TOFMS) it can be observed that the biggest differencesin the contents of selected terpenes of Kaffir and Key limes occur in chemical compounds such as limonene, citraland...
-
Comparison of Macintosh and Intubrite laryngoscopes for orotracheal intubation by nurses during resuscitation: preliminary data of a randomized crossover simulation-based study
Publication -
A BODIPY‐Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐resolved Emission and Transient Absorption Spectroscopy
Publication -
Simulation-Based Approach to a More Efficient Handling Strategy for a Container Terminal Storage Yard: Case Study of the Baltic Hub Container Terminal
PublicationThe primary objective of this research was to implement a more efficient handling strategy in the container terminal storage yard at the Baltic Hub Container Terminal (BHCT). Following an analysis of the current logistics system associated with starboard-side mooring, an attempt was made to shift the mooring to the port side. Two routing strategies corresponding to the analysed mooring operations were tested using a developed...
-
Synthesis, Molecular Structure, Anticancer Activity, and QSAR Study of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)Benzenesulfonamide Derivatives
PublicationA series of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)benzenesulfonamides were synthesized from 4-amino-N-(aryl/heteroaryl)benzenesulfonamides and 2,5-dimethoxytetrahydrofuran. All the synthesized compounds were evaluated for their anticancer activity on HeLa, HCT-116, and MCF-7 human tumor cell lines. Compound 28, bearing 8-quinolinyl moiety, exhibited the most potent anticancer activity against the HCT-116, MCF-7, and HeLa cell lines,...
-
Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors—molecular dynamics study of the activated receptor–vasopressin–Gα systems
Publication -
A BODIPY‐Based Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐Resolved Emission and Transient Absorption Spectroscopy
PublicationBODIPY and BODIPY-derived systems are widely applied as fluorophores and as probes for viscosity detection in solvents and biological media. Their orientational and rotational dynamics in biological media are thus of vital mechanistic importance and extensively investigated. In this contribution, polarization-resolved confocal microscopy is used to determine the orientation of an amphiphilic BODIPY-cholesterol derivative in homogeneous...
-
Comment on “Anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond” [J. Chem. Phys. 115, 1414 (2001)]
Publication -
Molecular modeling study of tectoquinone and acteoside from Tectona grandis linn: a new SARS-CoV-2 main protease inhibitor against COVID-19
Publication