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Wyniki wyszukiwania dla: MOLECULAR DOCKING SIMULATIONS
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Molecular basis of TRF proteins and their interactions with peptides
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Molecular Modelling of the Neurophysin II/Vasopressin Complex
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Molecular dynamics simulation of polymerization of p-xylylene
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Comment on “Molecular Origin of Anticooperativity in Hydrophobic Association”
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Molecular simulation study of cooperativity in hydrophobic association
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Professor Edward Borowski and molecular aspects of chemotherapy.
PublikacjaPrzedstawiono sylwetkę naukową i krótkie podsumowanie najważniejszych osiągnięć badawczych profesora Edwarda Borowskiego. Profesor Borowski jest autorem lub współautorem około 800 publikacji naukowych oraz 70 patentów, a jego prace były cytowane ponad 1100 razy. Do najważniejszych osiągnięć prof. Borowskiego i Jego zespołu naukowego należy zaliczyć: izolację i charakterystykę antybiotyków peptydowych, tetainy i edeiny oraz antybiotyków...
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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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Adolfo Poma
OsobyDr. Adolfo Poma (see my biosketch) is the group leader of the Multiscale Modelling of Complex Systems divison. In 2008, he got a MSc. degree in computational physics from the State University of Campinas (Brazil). Then he moved to Germany and under the supervision of Prof. Kurt Kremer (head of the polymer theory group, Max Planck Institute for Polymer Research) and Prof. Luigi Delle Site (Frei University of Berlin) got a PhD degree...
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Tuning of the plasmon resonance location in Au nanostructures coated with a ultrathin film of Al2O3 – Optical measurements and FDTD simulations
PublikacjaThe Au nanostructures have been coated with an ultra-thin films of amorphous aluminium oxide. Optical absorption spectra show the influence of the thickness of Al2O3 on plasmon resonance wavelength. The observed red-shift of the resonance location with the increase of the thickness of the Al2O3 film, can be explained by the change in the dielectric function of this film. It allows control of the optical spectra of the coated particles....
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublikacjaA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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NUMERICAL SIMULATIONS OF HONING PROCESS OF THIN WALL CYLINDER LINERS, WITH CONSTANT AND WITH VARIABLE THICKNESS OF WALL OF HONED PARTS
PublikacjaNumerical simulations of honing process of thin-wall cylinder liners, with constant and with variable thickness of the wall of honed workpieces can improve and can help to conduct the experimental research of honing process and can improve the honing process. A very valuable research assumption, before performing the numerical analysis of computer simulation of honing process, is the measurement of the real geometry of the honing...
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublikacjaIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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Molecular biaxiality determines the helical structure – infrared measurements of the molecular order in the nematic twist-bend phase of difluoro terphenyl dimer
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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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Multi-fidelity EM simulations and constrained surrogate modelling for low-cost multi-objective design optimisation of antennas
PublikacjaIn this study, a technique for low-cost multi-objective design optimisation of antenna structures has been proposed. The proposed approach is an enhancement of a recently reported surrogate-assisted technique exploiting variable-fidelity electromagnetic (EM) simulations and auxiliary kriging interpolation surrogate, the latter utilised to produce the initial approximation of the Pareto set. A bottleneck of the procedure for higher-dimensional...
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Quantitative assessment of the influence of tensile softening of concrete in beams under bending by numerical simulations with XFEM and cohesive cracks
PublikacjaResults of the numerical simulations of the size effect phenomenon for concrete in comparison with experimental data are presented. In-plane geometrically similar notched and unnotched beams under three-point bending are analyzed. EXtended Finite Element Method (XFEM) with a cohesive softening law is used. Comprehensive parametric study with the respect to the tensile strength and the initial fracture energy is performed. Sensitivity...
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Molecular Catalysis
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublikacjaOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Solubility of dapsone in deep eutectic solvents: Experimental analysis, molecular insights and machine learning predictions
PublikacjaBackground. Dapsone (DAP) is an anti-inflammatory and antimicrobial active pharmaceutical ingredient used to treat, e.g., AIDS-related diseases. However, low solubility is a feature hampering its efficient use. Objectives. First, deep eutectic solvents...
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An MOR Algorithm Based on the Immittance Zero and Pole Eigenvectors for Fast FEM Simulations of Two-Port Microwave Structures
PublikacjaThe aim of this article is to present a novel model-order reduction (MOR) algorithm for fast finite-element frequency-domain simulations of microwave two-port structures. The projection basis used to construct the reduced-order model (ROM) comprises two sets: singular vectors and regular vectors. The first set is composed of the eigenvectors associated with the poles of the finite-element method (FEM) state-space system, while...
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Molecular transformation of dissolved organic matter in manganese ore-mediated constructed wetlands for fresh leachate treatment
PublikacjaThe organic matter (OM) and nitrogen in Fresh leachate (FL) from waste compression sites pose environmental and health risks. Even though the constructed wetland (CW) can efficiently remove these pollutants, the molecular-level transformations of dissolved OM (DOM) in FL remain uncertain. This study reports the molecular dynamics of DOM and nitrogen removal during FL treatment in CWs. Two lab-scale vertical-flow CW systems were...
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Expedited Globalized Antenna Optimization by Principal Components and Variable-Fidelity EM Simulations: Application to Microstrip Antenna Design
PublikacjaParameter optimization, also referred to as design closure, is imperative in the development of modern antennas. Theoretical considerations along with rough dimension adjustment through supervised parameter sweeping can only yield initial designs that need to be further tuned to boost the antenna performance. The major challenges include handling of multi-dimensional parameter spaces while accounting for several objectives and...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublikacjaDeep 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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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublikacjaF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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Theoretical Design of the Molecular Structure of Bent-Core Mesogens with Large Second-Order Nonlinear Optical Properties
PublikacjaABSTRACT: The first hyperpolarizability of two series of moleculeswith bent-shaped structures has been calculated at the ab initio level.The two series consist of carboxyl derivatives for which somemolecules are known to exhibit banana phases and of their sulfinatehomologues that have not been synthesized yet. The final purpose isto reveal the relevance or not in synthesizing these latter molecules.The strategy is based on reporting...
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Star Polymers vs. Dendrimers: Studies of the Synthesis Based on Computer Simulations
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Modelling of soft fault propagation in sequential circuits by fuzzy-logic simulations
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Numerical simulations of space-time conditional random fields of ground motions
PublikacjaArtykuł przedstawia metodę modelowania stochastycznego efektu propagacji fali sejsmicznej z wykorzystaniem przestrzenno-czasowej funkcji korelacji pola losowego trzęsienia ziemi. Metodę wykorzystano do generacji nieznanych historii czasowych trzęsienia w wybranych punktach na podstawie znanego rejestru w jednym miejscu. Wyniki pokazały, iż zastosowanie zaproponowanej metody prowadzi do relatywnie małych błędów symulacji.
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From flow to jamming: Lattice Gas Automaton simulations in granular materials
PublikacjaWe introduce the first extension of a Lattice Gas Automaton (LGA) model to accurately replicate observed emergent phenomena in granular materials with a special focus on previously unexplored jamming transitions by incorporating gravitational effects, energy dissipation in particle collisions, and wall friction. We successfully reproduce flow rate evolution, density wave formation, and jamming transition observed in experiments....
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A simplified behavioral MOSFET model based on parameters extraction for circuit simulations.
PublikacjaThe paper presents results on behavior modeling of general purpose Metal-Oxide Semiconductor Field-Effect Transistor (MOSFET) for simulation of power electronics systems requiring accuracy both in steady-state and in switching conditions. Methods of parameters extraction including nonlinearity of parasitic capacitances and steady-state characteristics are based on manufacturer data sheet and externally measurable characteristics....
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Verification of geotechnical numerical simulations by model tests using PIV technique
PublikacjaPrzedstawiono metodykę i wyniki badań modelowych stateczności fundamentów bezpośrednich posadowionych w sąsiedztwie kątowych ścian oporowych. Dla takiego złożonego układu fundament - obciążenie - podłoże gruntowe wykonano badania modelowe w płaskim stanie odkształcenia na gruncie naturalnym i analogowym. Trajektorie i izopola przemieszczeń oraz progresywny rozwój kształtu i zasięgu powierzchni poślizgu określono techniką PIV.
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Numerical simulations of transonic flow with film cooling and jet vortex generators
PublikacjaW pracy przedstawiono wyniki obliczeń przepływu transonicznego na stronie ssącej łopatki turbiny gazowej. Obliczenia wykonano dla geometrii komory pomiarowej w tunelu transonicznym IMP PAN, zaprojektowanej tak, aby odwzorować warunki przepływowe istniejące w palisadzie turbinowej. Przedstawiono wyniki obliczeń przepływu z zastosowaniem otworów chłodzących (film cooling) oraz strumieniowych generatorów wirów. Porównano je z danymi...
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An Enhanced Reduced Basis Method for Wideband Finite Element Method Simulations
PublikacjaIn this paper, we present a novel strategy for selecting expansion points in the reduced basis method. A single computation of the error estimator is used to select a few expansion points in the multi-parameter space simultaneously. The number of selected points is determined adaptively, based on the accuracy of the current reduced model. The reliability and efficiency of this proposed approach are illustrated by numerical tests...
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RMS-based damage detection in reinforced concrete beams: numerical simulations
PublikacjaImage-based damage detection methods using guided waves are well known and widely applied approaches in structural diagnostics. They are usually utilized in detection of surface damages or defects of plate-like structures. The article presents results of the study of applicability of imaging wave-based methods in detection in miniscule internal damage in the form of debonding. The investigations were carried out on numerical models...
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Full scale CFD seakeeping simulations for case study ship redesigned from V-shaped bulbous bow to X-bow hull form
PublikacjaIncreasing propulsion efficiency, safety, comfort and operability are of the great importance, especially for small ships operating on windy sites like the North Sea and the Baltic Sea. Seakeeping performance of ships and offshore structures can be analysed by different methods and the one that is becoming increasingly important is CFD RANS. The recent development of simulation techniques together with rising HPC accessibility...
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Reduced-Cost Microwave Design Closure by Multi-Resolution EM Simulations and Knowledge-Based Model Management
PublikacjaParameter adjustment through numerical optimization has become a commonplace of contemporary microwave engineering. Although circuit theory methods are ubiquitous in the development of microwave components, the initial designs obtained with such tools have to be further tuned to improve the system performance. This is particularly pertinent to miniaturized structures, where the cross-coupling effects cannot be adequately accounted...
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Palladium versus Platinum: The Metal in the Catalytic Center of a Molecular Photocatalyst Determines the Mechanism of the Hydrogen Production with Visible Light
PublikacjaTo develop highly efficient molecular photocatalysts for visible light-driven hydrogen production, a thorough understanding of the photophysical and chemical processes in the photocatalyst is of vital importance. In this context, in situ X-ray absorption spectroscopic (XAS) investigations show that the nature of the catalytically active metal center in a (N^N)MCl2 (M=Pd or Pt) coordination sphere has a significant impact on the...
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublikacjaThe 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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Combining X-ray tomogrpahy imaging and DEM simulations to investigate granular material flow during silo discharging
PublikacjaEven after few decades of research, the study of particle motion taking place during silo discharging hasn’t been fully addressed, both experimentally and numerically, because of nontrivial behaviors that occur during associated flow patterns. For instance, discrete element method (DEM) has shown good qualitative prediction potential of velocity profile, but, on the other hand, frequently failed to match quantitatively experimental...
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Molecular Characterisation of Uterine Endometrial Proteins during Early Stages of Pregnancy in Pigs by MALDI TOF/TOF
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Selection of material for X-ray tomography analysis and DEM simulations: comparison between granular materials of biological and non-biological origins
PublikacjaPhysical properties and X-ray tomography images of five different granular materials: glass bead, glass grit, short grain white rice, sorghum and clay granules (Seramis) are investigated to select the most promising materials for numerical simulations and time-lapse X-ray tomography imaging. The examined materials represent granular materials of non-biological origin (glass bead, glass grit and Seramis) and granular plant materials...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublikacjaUsing 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...
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Role of electronic correlations in the transport characteristics of molecular junctions
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Molecular factors involved in the development of diabetic foot syndrome.
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Shape resonance of the ethylene anion stabilized in a molecular trap
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Low-Molecular-Weight Aldehyde Inhibitors of Cathepsin G
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Lipid-protein interactions in membranes: a molecular modelling study
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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
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Plasma Treatment as an Unconventional Molecular Magnet Engineering Method
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Molecular diagnosis in type I epithelial ovarian cancer
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