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Wyniki wyszukiwania dla: MOLECULAR DOCKING SIMULATIONS
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublikacjaStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublikacjaGraphene-like nanosheets are the key elements of advanced materials and systems. The mechanical behavior of the structurally perfect 2D nanostructures is well documented, but that of polycrystalline ones is less understood. Herein, we applied molecular dynamics simulation (MDS) to take the fracture fingerprint of polycrystalline SiC nanosheets (PSiCNS), where monocrystalline SiC nanosheets (MSiCNS) was the reference nanosheet....
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Molecular picture of hydroxide anion hydration in aqueoussolutions studied by FT-IR ATR spectroscopy
PublikacjaHydratacja anionu hydroksylowego w wodnych roztworach wodorotlenków metali alkalicznych (LiOH, NaOH, KOH) została zbadana metodą spektroskopii oscylacyjnej FT-IR całkowitego wewnętrznego odbicia (ATR). Widma oscylacyjne wody dostarczają cennych informacji na temat stanu strukturalnego cząsteczek wody w sferach hydratacyjnych, wynikających ze sprzężeń oscylatorów w układzie. Wykazano, że drganie normalne rozciągające cząsteczki...
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublikacjaRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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Communication and Load Balancing Optimization for Finite Element Electromagnetic Simulations Using Multi-GPU Workstation
PublikacjaThis paper considers a method for accelerating finite-element simulations of electromagnetic problems on a workstation using graphics processing units (GPUs). The focus is on finite-element formulations using higher order elements and tetrahedral meshes that lead to sparse matrices too large to be dealt with on a typical workstation using direct methods. We discuss the problem of rapid matrix generation and assembly, as well as...
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Application of gas chromatographic data and 2D molecular descriptors for accurate global mobility potential prediction
PublikacjaMobility is a key feature affecting the environmental fate, which is of particular importance in the case of persistent organic pollutants (POPs) and emerging pollutants (EPs). In this study, the global mobility classification artificial neural networks-based models employing GC retention times (RT) and 2D molecular descriptors were constructed and validated. The high usability of RT was confirmed based on the feature selection...
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublikacjaAmphotericin 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...
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Time-of-flight electron scattering from molecular hydrogen: Benchmark cross sections for excitation of the X1Σ+g→b3Σ+u transition
PublikacjaThe electron impact X1Σ+g to b3Σ+u transition in molecular hydrogen is one of the most important dissociation pathways to forming atomic hydrogen atoms, and is of great importance in modeling astrophysical and industrial plasmas where molecular hydrogen is a substantial constituent. Recently it has been found that the convergent close-coupling (CCC) cross sections of Zammit et al. [Phys. Rev. A 95, 022708 (2017)] are up to a factor...
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Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations
PublikacjaWe present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss...
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LS-DYNA simulations of the impacts of a 38-ton Heavy Goods Vehicle into a road cable barrier
PublikacjaNowadays, more and more attention is being paid to safety on roads and motorways. It is due to the continuous development of road and motorway network and a significant increase of the number of vehicles on roads. To meet the expectations of improving road safety in Poland, the Road Innovations Development (RID) research programme was implemented in 2016. The aim of the RID 3A - Road Safety Equipment (RoSE) project is a comprehensive...
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Novel 2-alkythio-4-chloro-N-[imino(heteroaryl)methyl]benzenesulfonamide Derivatives: Synthesis, Molecular Structure, Anticancer Activity and Metabolic Stability
PublikacjaA series of novel 2-alkythio-4-chloro-N-[imino-(heteroaryl)methyl]benzenesulfonamide derivatives, 8–24, were synthesized in the reaction of the N-(benzenesulfonyl)cyanamide potassium salts 1–7 with the appropriate mercaptoheterocycles. All the synthesized compounds were evaluated for their anticancer activity in HeLa, HCT-116 and MCF-7 cell lines. The most promising compounds, 11–13, molecular hybrids containing benzenesulfonamide...
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Prediction of cast-in-place concrete strength of the extradosed bridge deck based on temperature monitoring and numerical simulations
PublikacjaThe work is devoted to the implementation of a monitoring system for high performance concrete embedded in the span of an extradosed bridge deck using a modified maturity method augmented by numerical simulations conducted by the authors’ FEM code. The paper presents all research stages of bridge construction and considers the conclusions drawn from the results of laboratory tests, field measurements, and numerical calculations....
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Cost‐efficient performance‐driven modelling of multi‐band antennas by variable‐fidelity electromagnetic simulations and customized space mapping
PublikacjaElectromagnetic (EM) simulations have become an indispensable tool in the design of contemporary antennas. EM‐driven tasks, for example, parametric optimization, entail considerable computational efforts, which may be reduced by employing surrogate models. Yet, data‐driven modelling of antenna characteristics is largely hindered by the curse of dimensionality. This may be addressed using the recently reported domain‐confinement...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublikacjaCRISPR-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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The molecular function of kallikrein‐related peptidase 14 demonstrates a key modulatory role in advanced prostate cancer
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Excited state properties of a series of molecular photocatalysts investigated by time dependent density functional theory.
PublikacjaTime 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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A Proposed Molecular Mechanism of High-Dose Vitamin D3 Supplementation in Prevention and Treatment of Preeclampsia
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Fast tolerance-aware design optimization of miniaturized microstrip couplers using variable-fidelity EM simulations and re-sponse features
PublikacjaManufacturing tolerances and other types of uncertainties may considerably affect operation and performance of microwave components and systems. Quantification of these effects is therefore an important part of the design process. It is even more important to obtain designs whose sensitivity to parameter deviations is reduced as much as possible. All of these require statistical analysis carried out at the level of electromagnetic...
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Objective selection of minimum acceptable mesh refinement for EMC simulations
PublikacjaOptimization of computational electromagnetics (CEM) simulation models can be costly in both time and computing resources. Mesh refinement is a key parameter in determining the number of unknowns to be processed. In turn, this controls the time and memory required for a simulation. Hence, it is important to use only a mesh that is good enough for the objectives of the simulation, whether for direct handling of high-fidelity EM...
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Reduction of Computational Complexity in Simulations of the Flow Process in Transmission Pipelines
PublikacjaThe paper addresses the problem of computational efficiency of the pipe-flow model used in leak detection and identification systems. Analysis of the model brings attention to its specific structure, where all matrices are sparse. With certain rearrangements, the model can be reduced to a set of equations with tridiagonal matrices. Such equations can be solved using the Thomas algorithm. This method provides almost the same values...
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Numerical Simulations of Laser and Hybrid S700MC T-Joint Welding
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Computational Techniques in Numerical Simulations of Arc and Laser Welding Processes
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Measurements and numerical simulations of laser hardening and remelting thermal cycles
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APPLICATION OF NUMERICAL SIMULATIONS ON X10CRWMOVNB9-2 STEEL MULTILAYER WELDING
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Numerical heat transfer model in skin burn depth simulations
PublikacjaW artykule przedstawiono numeryczny model wymiany ciepła zachodzącej w tkance skórnej . Wyniki symulacji na modelu zostały porównane z wynikami pomiarów In vivo na zwierzętach.
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Hydroacoustic signals simulations in workstation for training asw helicopter navigators
PublikacjaPolska Marynarka Wojenna użytkuje śmigłowce wyposażone w systemy pokładowe zmoderni-zowane w ostatnich latach a przeznaczone do wykrywania i śledzenia okrętów podwodnych: sonary z opuszczaną anteną, odbiorniki do nasłuchu i analizy sygnałów z radiohydroboi oraz magnetometry. W artykule przedstawiono pokrótce strukturę trenażera nawigatorów - operatorów tych systemów, wykorzystywanego również jako stanowisko do analizy danych zebranych...
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Polymerization and Structure of Opposing Polymer Brushes Studied by Computer Simulations
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Simulations of impact force spectrum for earthquake-induced structural pounding.
PublikacjaCelem artykułu jest analiza możliwości zastosowanie tzw. spektrum siły zderzenia przy projektowaniu sąsiadujących ze sobą konstrukcji budowlanych na terenach sejsmicznych, w przypadku zbyt małej przerwy dylatacyjnej między nimi. W artykule przedstawiono wyniki symulacji numerycznych przeprowadzonych dla różnych wartości parametrów dynamicznych konstrukcji.
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Representation of magnetic hysteresis in single-phase transformer for circuit simulations
PublikacjaThe paper presents a mathematical model for the hysteresis phenomenon in a multi-winding single-phase core type transformer. In the circuit transformer model, it is assumed that there is a flux common Φ to all windings as nonlinear and hysteretic function of the total currents Θ (Ampere turns) of all windings. To simulate magnetic behaviour of the iron core the feedback scalar Preisach model of hysteresis is developed. The Preisach...
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OpenGL accelerated method of the material matrix generation for FDTD simulations
PublikacjaThis paper presents the accelerated technique of the material matrix generation from CAD models utilized by the finite-difference time-domain (FDTD) simulators. To achieve high performance of these computations, the parallel-processing power of a graphics processing unit was employed with the use of the OpenGL library. The method was integrated with the developed FDTD solver, providing approximately five-fold speedup of the material...
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Simulations of fracture in concrete elements using continuous and discontinuous models
PublikacjaArtykuł przedstawia wyniki symulacji MES w elementach betonowych przy zastosowaniu modeli ciągłych i nieciągłych. Stosując modele ciągłe symulowano proces lokalizacji odkształceń. Stosując modele nieciągłe symulowano proces zarysowania. Obliczenia wykonano dla różnych typów obciążeń.
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A material model of asphalt mixtures based on Monte Carlo simulations
PublikacjaThe paper aims to numerically reflect mineral-asphalt mixture structure by a standard FEM software. Laboratory test results are presented due to bending tests of circular notched elements. The result scatter is relatively high. An attempt was made to form a random aggregate distribution in order to obtain various results corresponding to laboratory tests. The material structure calibration, its homogenization and finite element...
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Electromagnetic Simulations with 3D FEM and Intel Optane Persistent Memory
PublikacjaAbstract—Intel Optane persistent memory has the potential to induce a change in how high-performance calculations requiring a large system memory capacity are conducted. This article presents what this change may look like in the case of factorization of large sparse matrices describing electromagnetic problems arising in the 3D FEM analysis of passive highfrequency components. In numerical tests, the Intel oneAPI MKL PARDISO was...
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Discrete simulations of shear zone pattern in earth pressure problems
PublikacjaW artykule przedstawiono wyniki dyskretnych symulacji naporu piasku na ściankę szczelną. Obliczenia wykonano stosując metodę elementów dyskretnych z kulami uwzględnieniem momentów kontaktu. Wyniki symulacji numerycznych porównano z wynikami doświadczalnymi.
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Numerical simulations of granular material flow in silos with and without insert
PublikacjaArtykuł omawia wyniki naporu materiału sypkiego podczas przepływu w silosach z i bez wkładek. Obliczenia wykonano wykorzystując sformułowanie ale na bazie prawa sprężysto-plastycznego według druckera-pragera. Zbadano wpływ kształtu i położenia wkładki na wielkość naporu i rodzaj przepływu.
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FE-simulations of size effects in granular and quasi-brittle materials
PublikacjaW artykule przedstawiono symulacje efektów skali w materiałach granulowanych i kruchych. Obliczenia wykonano dla ściskania dwuosiowego i fundamentu w przypadku materiałów granulowanych oraz belek zginanych w przypadku materiałów kruchych. Do obliczeń wykorzystano mikropolarne prawo hipoplastyczne i sprężysto-plastyczne prawo z nielokalnym osłabieniem.
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Simulations of the Behavior of Granular Bodies Using the Discrete Element Approach
PublikacjaZachowanie niespójnych ciał ziarnistych opisano metodą elementów dyskretnych (DEM) w warunkach quasi-statycznych dwu- i trójwymiarowych. Do symulacji nieregularnego kształtu granulatu wykorzystano kule z momentami kontaktowymi lub skupiska sztywnych kul. Początkowo badano dwa różne problemy dla zagęszczonego materiału ziarnistego: pasywne przemieszczanie ściany oporowej i ściskanie w płaskim stanie odkształceń pod stałym ciśnieniem...
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FE-simulations of direct and simple shearing within a polar hypoplasticity
PublikacjaW artykule przedstawiono wyniki analizy MES dwóch podstawowych testów w mechanice gruntów, mianowicie testu bezpośredniego ścinania i testu prostego ścinania. Obliczenia wykonano stosując metodę elementów skończonych i mikropolarne hipoplastyczne prawo konstytutywne. Szczególną uwagę zwrócono na wpływ warunków brzegowych na lokalizacje odkształceń.
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Simulations of behaviour of granular bodies using a lattice-gas automaton.
PublikacjaW artykule przedstawiono wyniki numerycznej analizy przepływu materiałów granulowanych podczas 3 różnych problemów: przepływu silosowego, przepływu kanałowego i tworzenia się nasypu. W modelu zaczerpniętym z teorii gazów przyjęto kolizje cząsteczek i dysypację energii. Wyniki porównano z doświadczeniami.
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Simulations of flow patterns in silos with a cellular automaton - part 2
PublikacjaW artykule przedstawiono wyniki symulacji przepływów silosowych przy zastosowaniu zaawansowanego aparatu komórkowego, w którym uwzględniono kolizje cząstek i dysypację energii. Obliczenia wykonano dla przepływu masowego i kominowego.
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A Subspace-Splitting Moment-Matching Model-Order Reduction Technique for Fast Wideband FEM Simulations of Microwave Structures
PublikacjaThis article describes a novel model-order reduction (MOR) approach for efficient wide frequency band finite-element method (FEM) simulations of microwave components. It relies on the splitting of the system transfer function into two components: a singular one that accounts for the in-band system poles and a regular part that has no in-band poles. In order to perform this splitting during the reduction process, the projection...
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Two-dimensional simulations of concrete fracture at aggregate level with cohesive elements based on X-ray lCT images
PublikacjaThe paper presents results of two-dimensional meso-scale simulations of fracture in notched concrete beams subjected to three-point bending test. Concrete was assumed as a 4-phase material composed of aggregate grains placed in the cement matrix, interfacial transitional zones (ITZs) and macro-voids. The particle distribution was taken from real concrete beams on the basis of X-ray lCT images. Comprehensive numerical analyses were carried...
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The impact of initial and boundary conditions on severe weather event simulations using a high-resolution WRF model. Case study of the derecho event in Poland on 11 August 2017
PublikacjaPrecise simulations of severe weather events are a challenge in the era of changing climate. By performing simulations correctly and accurately, these phenomena can be studied and better understood. In this paper, we have verified how different initial and boundary conditions affect the quality of simulations performed using the Weather Research and Forecasting Model (WRF). For our analysis, we chose...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublikacjaThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Molecular Classification of Low-Grade Diffuse Gliomas
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Do positrons measure atomic and molecular diameters?
PublikacjaWe report on density functional calculations (DFT) of elastic integral scattering cross-sections for positron collisions with argon, krypton, nitrogen and methane. The long-range asymptotic polarization potential is described using higher-order terms going much beyond an induced dipole potential (−α / r 4) while the short-range interaction is modeled by two different forms of electron – positron correlation potential (Boroński-Nieminen...
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Molecular Modeling of the Neurohypophyseal Receptor/Atosiban Complexes
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Coherent electron transport in hydrocarbon molecular devices
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Hubbard operators approach to the transport in molecular junctions
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Molecular basis of TRF proteins and their interactions with peptides
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