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Search results for: PROTEIN STRUCTURE PREDICTION, MULTISCALE MODELING, UNRES FORCE FIELD, FREE AND BIOINFORMATICS-ASSISTED MODELING, REPLICA-EXCHANGE MOLECULAR DYNAMICS
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Modeling of shear localization during confined granular flow in silos within non-local hypoplasticity.
PublicationW artykule przedstawiono wyniki numerycznej analizy lokalizacji odkształceń w materiałach granulowanych podczas przepływu w silosach. Obliczenia wykonano przy zastosowaniu metody elementów skończonych i mikropolarnego modelu hipoplastycznego. Zastosowano podejście ALE. Pokazano wpływ szorstkości ścian silosu i zagęszczenia materiału sypkiego na typ lokalizacji.
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Modeling of a cyclic plane strain compression-extension test in granular bodies within a polar hypoplasticity
PublicationW artykule przedstawiono wyniki numerycznej analizy wpływu cyklicznego ściskania-rozciągania na lokalizację odkształceń stycznych w materiałach granulowanych. Obliczenia wykonano stosując metodę elementów skończonych i mikropolarne hipoplastyczne prawo konstytutywne. Analizę przeprowadzono dla piasku zagęszczonego i luźnego dla różnych amplitud obciążenia.
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Equivalent Single Layer Models in Free Vibration Analysis of Laminated Multi-Layered Plates
PublicationThe performance of selected equivalent single-layer (ESL) models is evaluated within several classical benchmark tests for small amplitude free vibration analysis of multi-layered plates. The authors elaborated their own Finite Element software based on the first-order shear deformation (FOSD) theory with some modifications incorporated including a correction of the transverse shear stiffness and an application of zigzag type functions....
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Enhancing capabilities of Atomic Force Microscopy by tip motion harmonics analysis
PublicationMotion of a tip used in an atomic force microscope can be described by the Lennard-Jones potential, approximated by the van der Waals force in a long-range interaction. Here we present a general framework of approximation of the tip motion by adding three terms of Taylor series what results in non-zero harmonics in an output signal. We have worked out a measurement system which allows recording of an excitation tip signal and its...
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Power System Dynamics. Stability and Control. 3rd edition
PublicationComprehensive, state-of-the-art review of information on the electric power system dynamics and stability. It places the emphasis first on understanding the underlying physical principles before proceeding to more complex models and algorithms. The book explores the influence of classical sources of energy, wind farms and virtual power plants, power plants inertia and control strategy on power system stability. The book cover...
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ARIMA vs LSTM on NASDAQ stock exchange data
PublicationThis study compares the results of two completely different models: statistical one (ARIMA) and deep learning one (LSTM) based on a chosen set of NASDAQ data. Both models are used to predict daily or monthly average prices of chosen companies listed on the NASDAQ stock exchange. Research shows which model performs better in terms of the chosen input data, parameters and number of features. The chosen models were compared using...
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Structure-rheology relationship of fully bio-based linear polyester polyols for polyurethanes - Synthesis and investigation
PublicationThe synthesis of polyols from renewable substances as an alternative for petrochemical-based polyols play important matter in the polyurethane industry. In this work, the fully bio-based linear polyester polyols with different catalyst amounts were synthesized via two-step polycondensation method. The effect of various catalyst content on the structure and rheological behavior were established. Fourier Transform Infrared Spectroscopy,...
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Optical fiber aptasensor for label-free bacteria detection in small volumes
PublicationHighly sensitive devices for fast bacteria detection are sought to be developed with the task of quantifying the worldwide problem of pathogenic bacteria and thus helping to take control over spreading bacterial infections. This work concerns a sensing solution based on microcavity in-line Mach-Zehnder interferometer (μIMZI) induced in an optical fiber. Such a device exhibits ultrahigh sensitivity to refractive index changes...
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Comparison of mass spectrometry data and bioinformatics predictions to assess the bona fide localization of proteins identified in cell wall proteomics studies
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Impact of the trap–assisted recombination in the perovskite solar cells
PublicationTo achieve the highest performance using perovskite solar cells it is necessary to understand all the dominant mechanisms which affect the operation of solar cell. Here, we have investigated the bulk and interface trap–assisted recombination processes in the solar cells with p–i–n architecture. These studies are based on the numerical and experimental methods to get better understanding of these physical processes. The following results...
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Investigation of the laser generated ablation plasma plume dynamics and plasma plume sound wave dynamics
PublicationWe investigated the dynamics of laser generated ablation plasma plume expanding in ambient air and dynamics of the sound wave generated by the expanding plasma. The ablation plasma plume was generated during nanosecond laser micromachining of the thin metal foil. The time-resolved images of the expanding plasma plume and sound wave were captured at several nanosecond intervals. Using captured images the expansion rate of the plasma...
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BALCONY: an R package for MSA and functional compartments of protein variability analysis
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublicationStaphylococci 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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Deciphering the Molecular Mechanism of Substrate-Induced Assembly of Gold Nanocube Arrays toward an Accelerated Electrocatalytic Effect Employing Heterogeneous Diffusion Field Confinement
PublicationThe complex electrocatalytic performance of gold nanocubes (AuNCs) is the focus of this work. The faceted shapes of AuNCs and the individual assembly processes at the electrode surfaces define the heterogeneous conditions for the purpose of electrocatalytic processes. Topographic and electron imaging demonstrated slightly rounded AuNC (average of 38 nm) assemblies with sizes of ≤1 μm, where the dominating patterns are (111) and...
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Sustainable investing exchange-traded funds: US and European market
PublicationThe key aim of the paper is to examine the diffusion of the sustainable investing exchange-traded funds (ETFs) on the European and US ETFs markets, with the special focus on the market shares of sustainable investing and conventional funds. The model of diffusion of innovation (logistic growth model) is applied. Monthly data on the assets of ETFs in the time period of 2006-2017 are used. Increasing assets of sustainable investing...
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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Molecular Design Using Selected Concentration Effects in Optically Activated Fluorescent Matrices
PublicationMolecular physics plays a pivotal role in various fields, including medicine, pharmaceuticals, and broader industrial applications. This study aims to enhance the methods for producing specific optically active materials with distinct spectroscopic properties at the molecular level, which are crucial for these sectors, while prioritizing human safety in both production and application. Forensic science, a significant socio-economic...
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Evolution towards simplicity in bacterial small heat shock protein system
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two...
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Application of Feed Forward Neural Networks for Modeling of Heat Transfer Coefficient During Flow Condensation for Low and High Values of Saturation Temperatur
PublicationMost of the literature models for condensation heat transfer prediction are based on specific experimental parameters and are not general in nature for applications to fluids and non-experimental thermodynamic conditions. Nearly all correlations are created to predict data in normal HVAC conditions below 40°C. High temperature heat pumps operate at much higher parameters. This paper aims to create a general model for the calculation...
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Crystal structure and electronic structure of CePt2In7
PublicationWe report a corrected crystal structure for the CePt2In7 superconductor, refined from single crystal x-ray diffraction data. The corrected crystal structure shows a different Pt–In stacking along the c-direction in this layered material than was previously reported. In addition, all of the atomic sites are fully occupied with no evidence of atom site mixing, resolving a discrepancy between the observed high resistivity ratio of...
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A critical review on biochar-assisted free radicals mediated redox reactions influencing transformation of potentially toxic metals: Occurrence, formation, and environmental applications
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Antimicrobial molecular nanocarrier–drug conjugates
PublicationMany antimicrobial drugs are poorly active against pathogenic microbes causing intracellular infections, such as Mycobacterium tuberculosis or Plasmodium falciparum. On the other hand, several known antimicrobial agents are not effective enough because of their limited cellular penetration. A common feature of both challenges is the inability of an active agent to cross the biological membrane(s). One of the possible approaches...
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Modeling external carbon addition in combined N-P activated sludge systems with an extension of the IWA Activated Sludge Models
PublicationThe aim of this study was to expand the IWA Activated Sludge Model No. 2d (ASM2d) to account for a newly defined readily biodegradable substrate that can be consumed by polyphosphate accumulating organisms (PAOs) under anoxic and aerobic conditions, but not under anaerobic conditions. The model change was to add a new substrate component and process terms for its use by PAOs and other heterotrophic bacteria under anoxic and aerobic...
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Modeling external carbon addition in combined N-P activated sludge systems with an extension of the IWA Activated Sludge Models
PublicationThe aim of this study was to expand the IWA Activated Sludge Model No. 2d (ASM2d) to account for a newly defined readily biodegradable substrate that can be consumed by polyphosphate accumulating organisms (PAOs) under anoxic and aerobic conditions, but not under anaerobic conditions. The model change was to add a new substrate component and process terms for its use by PAOs and other heterotrophic bacteria under anoxic and aerobic...
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Structure of the twist-bend nematic phase with respect to the orientational molecular order of the thioether-linked dimers
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Municipal landfill leachate nitrification in RBC biofilm – Process efficiency and molecular analysis of microbial structure
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Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublicationIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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Justifying the prolongation of the service life of the bearing structure of a tank car when using Y25 bogies
PublicationThis paper substantiates the use of Y25 bogies under tank cars in order to prolong their service life. The reported study has been carried out for a tank car with rated parameters, as well as the actual ones, registered during full-scale research. Mathematical modeling was performed to determine the basic indicators of the tank car dynamics. The differential equations of motion were solved by a Runge-Kutta method using the Mathcad...
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Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp: Phosphorus dynamics
PublicationThis is the third paper of the series about “Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp”. In this paper, phosphorus dynamics were investigated under the condition of culturing bighead carp and common carp with added fish food (nitrogen dynamics is discussed in the second paper because their behaviors are so different from each other). Nearly fifty days’ observation results...
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Aerodynamic shape optimization by variable-fidelity computational fluid dynamics models: a review of recent progress
PublicationA brief review of some recent variable-fidelity aerodynamic shape optimization methods is presented.We discuss three techniques that—by exploiting information embedded in low-fidelity computationalfluid dynamics (CFD) models—are able to yield a satisfactory design at a low computational cost, usu-ally corresponding to a few evaluations of the original, high-fidelity CFD model to be optimized. Thespecific techniques considered here...
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Conducted emi identification in power electronic converters : modeling of EMI generation and propagation using circuit simulation and wiener filtering methods.
PublicationThis work presents the circuit simulations and the conventional signal processing technique (Wiener filtering) in order to reconstruct conducted ElectroMagnetic Interferences (EMI), generated and propagated in power electronics converters. In the simulation study, the most accurate presently available models of components of circuit have been used and improved. The proposed Wiener filtering method allows to identifying the transfer...
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Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions
PublicationWe present a method for the calculation of four-centre two-electron repulsion integrals in terms of localised non-orthogonal generalised Wannier functions (NGWFs). Our method has been imple- mented in the ONETEP program and is used to compute the Hartree-Fock exchange energy component of Hartree-Fock and Density Functional Theory (DFT) calculations with hybrid exchange-correlation functionals. As the NGWFs are optimised in situ...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublicationEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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Spin and Orbital Effects on Asymmetric Exchange Interaction in Polar Magnets: M(IO3)2 (M = Cu and Mn)
PublicationMagnetic polar materials feature an astonishing range of physical properties, such as magnetoelectric coupling, chiral spin textures, and related new spin topology physics. This is primarily attributable to their lack of space inversion symmetry in conjunction with unpaired electrons, potentially facilitating an asymmetric Dzyaloshinskii–Moriya (DM) exchange interaction supported by spin–orbital and electron–lattice coupling. However,...
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Multisource model of ship electric field
PublicationA steel-hulled ship in sea water produces an electric field around itself. The source of this field are electrochemical processes and ship's cathodic protection. The analysis of the electric field around the ship is important by the reason of the ship's identification and counter-mine protection. The paper presents a simplified model of the ship's multisource electric field, which allows to calculate the electric field distribution...
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Protein overproduction alters exosome secretion in Chinese hamster ovary cells
PublicationDespite the abundance of available cell lines, nearly 70% of all recombinant therapeutic proteins today are produced in Chi-nese hamster ovary (CHO) cells. The impact of protein overproduction on the secretion of exosomes by CHO cells has been investigated here. Increased secretion of extracellular vesicles (EVs) by protein overexpressing CHO cells was demonstrated with protein content assay, nanoparticle tracking analysis, and...
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Efficient Multiscale Finite Difference Frequency Domain Analysis Using Multiple Macromodels with Compressed Boundaries
PublicationW niniejszym artykule zaprezentowany został nowatorski pomysł na zmniejszenie numerycznej złożoności metody różnic skończonych przy użyciu wielu makromodeli. Skuteczność techniki macromodelingu zależy od liczby portów modelu. Aby zwiększyć efektywność algorytmu, próbki pola na granicy makromodeli są zastępowane przez amplitudy wielomianów Legendre'a. Przedefiniowanie problemu w taki sposób powoduje znaczną redukcję czasu analizy....
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The field–dependent interface recombination velocity for organic–inorganic heterojunction
PublicationWe have derived an analytical formula which describes the field–dependent interface recombination velocity for the boundary of two materials characterized by different permittivities. The interface recombination of charge carriers has been considered in the presence of image force Schottky barrier. We suggest that this effect may play an important role in the loss of current for organic–inorganic hybrid heterojunctions. It has...
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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: their in silico assessment as potential ligands for N-protein of SARS-CoV-2
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Analysis of magnetic field of Helmholtz's coils
PublicationThe 3-axis fluxgate magnetometer requires conducting a precise calibration in the magnetic field whose value is determined and which is characterized by the high uniformity of the distribution of the field, especially along the axis of the sensors. The generation of the magnetostatic field characterized by the high uniformity, can be achieved by using the Helmholtz's coils. The requirements of the uniformity of distribution of...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Numerical solution analysis of fractional point kinetics and heat exchange in nuclear reactor
PublicationThe paper presents the neutron point kinetics and heat exchange models for the nuclear reactor. The models consist of a nonlinear system of fractional ordinary differential and algebraic equations. Two numerical algorithms are used to solve them. The first algorithm is application of discrete Grünwald-Letnikov definition of the fractional derivative in the model. The second involves building an analog scheme in the FOMCON Toolbox...
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Multidipoles model of ship's magnetic field
PublicationShips made of ferromagnetic metals interfere with Earth's magnetic field in their surrounding. The disturbance of the magnetic field makes possible localization and even identification of the ship, which could determine a threat to the ship. The measurement of the magnetic field around the ship enables to determine its magnetic signature. The paper presents a multidipoles model of the ship magnetic field, which allows to determine...
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Multidipoles model of ship's magnetic field
PublicationShips made of ferromagnetic metals interfere with Earth's magnetic field in their surrounding. The disturbance of the magnetic field makes possible localization and even identification of the ship, which could determine a threat to the ship. The measurement of the magnetic field around the ship enables to determine its magnetic signature. The paper presents a multidipoles model of the ship magnetic field, which allows to determine...
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Parametric method applicable in assessing breakout force and time for lifting slender bodies from seabed
PublicationThe article presents a parametric method applicable in assessing the suction force of a slender body to the seabed, and prognosing the body extrication time. Along with the body weight in water, the information on the suction force is essential for assessing the force needed to lift the object from the seabed. Based on the Foda theory and the resulting integral equation, which relates the maximum suction force with basic parameters...
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On Bayesian Tracking and Prediction of Radar Cross Section
PublicationWe consider the problem of Bayesian tracking of radar cross section. The adopted observation model employs the gamma family, which covers all Swerling cases in a unified framework. State dynamics are modeled using a nonstationary autoregressive gamma process. The principal component of the proposed solution is a nontrivial gamma approximation, applied during the time update recursion. The superior performance of the proposed approach...
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Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
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