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Application of the Monte Carlo algorithm for solving volume integral equation in light scattering simulations
PublicationVarious numerical methods were proposed for analysis of the light scattering phenomenon. Important group of these methods is based on solving the volume integral equation describing the light scattering process. The popular method from this group is the discrete dipole approximation (DDA). DDA uses various numerical algorithms to solve the discretized integral equation. In the recent years, the application of the Monte Carlo (MC)...
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Förster Resonance Energy Transfer and Trapping in Selected Systems: Analysis by Monte-Carlo Simulations
PublicationMetoda symulacji Monte Carlo została opisana i zastosowana jako efektywne narzędzie do analizy wyników pomiarów transferu energii w wybranych układach, dla których zastosowanie podejścia analitycznego jest ograniczone lub nawet niemożliwe. Pokazano, że symulacja Monte Carlo pozwala obliczyć tzw. czynnik orientacyjny dla układów częściowo uporządkowanych oraz szereg innych wielkości ważnych do opisu zjawiska transferu energii, które...
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Numerical simulations of sand behavior using DEM with 2 different descriptions of grain roughness
PublicationW rozdziale przedstawiono wyniki dyskretnych symulacji jednorodnego trójosiowego ściskania piasku przy zastosowaniu metody elementów dyskretnych. Obliczenia wykonano stosując 2 różne opisy szorstkości ziaren: kule z uwzględnieniem momentów kontaktu oraz grona kul. Obliczono energię sprężystą i dysypację plastyczną. Wyniki symulacji numerycznych porównano z wynikami doświadczalnymi.
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Nanomechanical Properties of Metallic fcc Nanorods from Molecular Simulations with the Sutton-Chen Potential
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Monte Carlo simulations of the fracture resistance degradation of asphalt concrete subjected to environmental factors
PublicationThe paper presents the results of laboratory tests of SCB (semi-circular beam) samples of asphalt concrete, subjected to the destructive effect of water and frost as well as the aging processes. The determined values of material parameters show significant dispersions, which makes the design of mixtures difficult. Statistical analysis of the test results supplemented by computer simulations made with the use of the proprietary...
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Expedited Trust-Region-Based Design Closure of Antennas by Variable-Resolution EM Simulations
PublicationThe observed growth in the complexity of modern antenna topologies fostered a widespread employment of numerical optimization methods as the primary tools for final adjustment of the system parameters. This is mainly caused by insufficiency of traditional design closure approaches, largely based on parameter sweeping. Reliable evaluation of complex antenna structures requires full-wave electromagnetic (EM) analysis. Yet, EM-driven...
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Novel strategies to enhance hydrodynamic cavitation in a circular venturi using RANS numerical simulations
PublicationHydrodynamic cavitation is a popular advanced oxidation technique and it has received wide range of applications from waste water treatment to the nanoparticles synthesis in recent years. The enhancement of the intensity of the hydrodynamic cavitation is always been an emerging field of research. Within this framework, we have proposed and investigated three distinct strategies to enhance the intensity of cavitation in a circular...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Ampacity of power cables exposed to solar radiation – recommendations of standards vs. CFD simulations
PublicationThe aim of the paper is to evaluate the ampacity of a low-voltage single power cable according to: 1) recommendations of the standard IEC 60287, 2) a Computational Fluid Dynamics method, implemented in Ansys software; and comparison of the results obtained for these two cases. Moreover, limitations of recommendations of the above mentioned standard are indicated.
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Using On-line Measurement by Electronic Nose and Computer Simulations for Real-time Control at WWTP
PublicationContinuous investigation of wastewater quality can be carried out by a device called an e-nose. One important feature of the proposed real-time control system for WWTP is that using on-line measurements by e-nose together (Figure 1) with technological sets picked on this basis by means of computer models, it is possible to change treatment process parameters, depending on the current quality of wastewater. It can be used for the...
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Fracture simulations in concrete beam under bending using a mesoscopic model with cohesive elements
PublicationThe main aim of this paper was to investigate a complex fracture process in a concrete beam subjected to 3-point bending test by means of the 2D meso-scale FEM with 4-node cohesive elements embedded in the initial mesh of 3-node solid elements. The material heterogeneity was taken into account by considering 3 different phases (aggregate, cement matrix, ITZs) on the basis of randomly generated internal structure of concrete and...
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Numerical simulations of triaxial test with sand using DEM. Archives of Hydro-Engineering and Environmental
PublicationW artykule przedstawiono wyniki symulacji badania trójosiowego dlamateriałów granulowanych. Obliczenia wykonano przy zastosowaniu metodyDEM. Pokazano wpływ momentów kontaktowych na wytrzymałoć próbki. Zbadanowpływ parametrów mikroskopowych na zachowanie się materiału. Wynikiporównano z doswiadczeniami.
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Effect of steel fibres on concrete behavior in 2D and 3D simulations using lattice model.
PublicationW artykule przedstawiono wyniki numerycznej symulacji betonu zbrojonego włóknami stalowymi. Beton został opisany w skali mezo jako materiał 3-fazowy przy zastosowaniu modelu sieciowego. Obliczenia wykonano dla rozciągania jednoosiowego. Porównano ze sobą wyniki dwu- i trójwymiarowe.
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Discrete simulations of shear zone patterning in sand in earth pressure problems of a retaining wall
PublicationW artykule przedstawiono wyniki doświadczalne i teoretyczne naporu piasku na ściankę szczelną. Obliczenia wykonano stosując metodę elementów dyskretnych. Wyniki porównano z wynikami uzyskanymi metodą elementów skończonych na bazie mikropolarnego hipoplastycznego prawa materiałowego oraz z wynikami doświadczalnymi uzyskanymi metodą korelacji obrazów cyfrowych. Wykonano obszerne studia parametryczne.
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Simulations of Shear Zones and Cracks in Engineering Materials Using eXtended Finite Element Method
PublicationNumerical simulations of cracks and shear zones in quasi-brittle materials are presented. Extended Finite Element Method is used to describe both cracks and shear zones. In a description of tensile cracks, a Rankine criterion is assumed. A discrete Mohr-Coulomb law is adopted for simulations of shear zones. Results of simple numerical tests: unixial tension, bending and biaxial compression are demonstrated.
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Numerical simulations of localization of deformation in quasibrittle materials within non-local softening plasticity.
PublicationW artykule przedstawiono model sprężysto-plastyczny z nielokalnym osłabieniem do obliczeń lokalizacji odkształceń w materiałach kruchych. Analizę przeprowadzono dla jednoosiowego ściskania i rozciągania. Obliczenia wykonano dla różnych długości charakterystycznych.
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Improved-Efficacy EM-Based Antenna Miniaturization by Multi-Fidelity Simulations and Objective Function Adaptation
PublicationThe growing demands for integration of surface mount design (SMD) antennas into miniatur-ized electronic devices have been continuously imposing limitations on the structure dimen-sions. Examples include embedded antennas in applications such as on-board devices, picosatel-lites, 5G communications, or implantable and wearable devices. The demands for size reduction while ensuring a satisfactory level of the electrical and field...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Speed estimation of a car at impact with a W-beam guardrail using numerical simulations and machine learning
PublicationThis paper aimed at developing a new method of estimating the impact speed of a passenger car at the moment of a crash into a W-beam road safety barrier. The determination of such a speed based on the accident outcomes is demanding, because often there is no access to full accident data. However, accurate determination of the impact speed is one of the key elements in the reconstruction of road accidents. A machine learning algorithm...
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Surrogate modeling of impedance matching transformers by means of variable‐fidelity electromagnetic simulations and nested cokriging
PublicationAccurate performance evaluation of microwave components can be carried out using full‐wave electromagnetic (EM) simulation tools, routinely employed for circuit verification but also in the design process itself. Unfortunately, the computational cost of EM‐driven design may be high. This is especially pertinent to tasks entailing considerable number of simulations (eg, parametric optimization, statistical analysis). A possible...
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Rapid Yield Optimization of Miniaturized Microwave Passives by Response Features and Variable-Fidelity EM Simulations
PublicationThe operation of high-frequency devices, including microwave passive components, can be impaired by fabrication tolerances but also incomplete knowledge concerning operating conditions (temperature, input power levels) and material parameters (e.g., substrate permittivity). Although the accuracy of manufacturing processes is always limited, the effects of parameter deviations can be accounted for in advance at the design phase...
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Approximate analytical boundary conditions for efficient finite difference frequency domain simulations in cylindrical coordinates
PublicationW artykule zaprezentowano prostą technikę analizy rezonatora otwartego. Algorytm łączy w sobie metodę różnic skończonych i rozwinięć funkcyjnych , umożliwiając implementację warunków brzegowych symulujących otwartą przestrzeń. Metoda testowana była w analizie rezonatorów o różnych wymiarach,a otrzymane wyniki dobrze zgadzały się z rezultatami innych metod.
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Measurements of glucose content in scattering media with time-of-flight technique: comparison with Monte Carlo simulations.
PublicationZbadano możliwości pomiaru koncentracji glukozy w materiale silnie rozpraszającym światło z wykorzystaniem techniki czasu przelotu. Badania przeprowadzono wykorzystując ''Intralipid'' będącym fantomem tkanki. Stężenie glukozy wynosiło 100, 200, 300, 500, 1000, 2000,4000 lub 8000 mg/dl. Wyniki pomiarów porównano z wynikami uzyskanymi na drodze modelowania matematycznego.
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Experimental and numerical simulations of flow and heat transfer in heatexchanger elements using liquid crystal thermography.
PublicationPrzedstawienie koncepcji badań eksperymentalnych i numerycznych oraz ich wyników podczas wymiany ciepła w modelach klasycznych i płytowych wymienników ciepła w warunków przepływów przejściowych i turbulentnych.
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Experimental tests and numerical simulations of full scale composite sandwich segment of a foot- and cycle- bridge
PublicationIn the paper experimental tests and numerical simulations of a full cross-section segment of ultimately designed foot-and cycle-bridge are presented. The experimental tests were conducted on element with length reduced to 3 m and unchanged (target) cross-section dimensions. The external skin of structure is GFRP laminate while internal core is PET foam. Several quasi-static tests were performed using hydraulic cylinder to generate...
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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LS-DYNA simulations of the impacts of a 38-ton Heavy Goods Vehicle into a road cable barrier
PublicationNowadays, 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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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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Simulations of freshwater lens recharge and salt/freshwater interfaces using the HYDRUS and SWI2 packages for MODFLOW
PublicationThe paper presents an evaluation of the combined use of the HYDRUS and SWI2 packages for MODFLOW as a potential tool for modeling recharge in coastal aquife rs subject to saltwater intrusion. The HYDRUS package for MODFLOW solves numerically the one-dimensional form of the Richards equation describing water flow in variably- saturated media. The code computes groundwater recharge to or...
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Communication and Load Balancing Optimization for Finite Element Electromagnetic Simulations Using Multi-GPU Workstation
PublicationThis 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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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Comparison of Absorbed and Intercepted Fractions of PAR for Individual Trees Based on Radiative Transfer Model Simulations
PublicationThe fraction of absorbed photosynthetically active radiation (fAPAR) is a key parameter for estimating the gross primary production (GPP) of trees. For continuous, dense forest canopies, fAPAR, is often equated with the intercepted fraction, fIPAR. This assumption is not valid for individual trees in urban environments or parkland settings where the canopy is sparse and there are well-defined tree crown boundaries. Here, the distinction...
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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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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublicationThe four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most...
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Homogeneous nucleation rate of methane hydrate formation under experimental conditions from seeding simulations
PublicationIn this work, we shall estimate via computer simulations the homogeneous nucleation rate for the methane hydrate at 400 bars for a supercooling of about 35 K. The TIP4P/ICE model and a Lennard-Jones center were used for water and methane, respectively. To estimate the nucleation rate, the seeding technique was employed. Clusters of the methane hydrate of different sizes were inserted into the aqueous phase of a two-phase gas–liquid...
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FE-simulations of dynamic shear localization in granular bodies using an Arbitrary Lagrangian-Eulerian formulation.
PublicationW artykule przedstawiono wyniki symulacji lokalizacji odkształceń w materiałach granulowanych. Obliczenia wykonano przy zastosowaniu nielokalnego modelu hipoplastycznego dla 2 różnych problemów: sciskania dwuosiowego i przepływu silosowego. W obliczeniach wykorzystano sformułowanie ALE.
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Local response surface approximations and variable-fidelity electromagnetic simulations for computationally efficient microwave design optimisation
PublicationIn this study, the authors propose a robust and computationally efficient algorithm for simulation-driven design optimisation of microwave structures. Our technique exploits variable-fidelity electromagnetic models of the structure under consideration. The low-fidelity model is optimised using its local response surface approximation surrogates. The high-fidelity model is refined by space mapping with polynomial interpolation of...
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Reduced-Cost Microwave Design Closure by Multi-Resolution EM Simulations and Knowledge-Based Model Management
PublicationParameter 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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Towards improved energy efficiency of future smart ships by application of advanced CFD simulations – case study
PublicationThe international trade plays crucial role in today’s globally developed world’s economy. Many people are unaware of the unimaginable volume of cargo being transported every year by oceans and seas. For most of the time invisible from land the shipping industry preserves its strong position of the most cost-efficient and environmental friendly mean of transport. However during last years the shipping industry is under great pressure...
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Simulations of hydro-fracking in rock mass at meso-scale using fully coupled DEM/CFD approach
PublicationThe paper deals with two-dimensional (2D) numerical modelling of hydro-fracking (hydraulic fracturing) in rocks at the meso-scale. A numerical model was developed to characterize the properties of fluid-driven fractures in rocks by combining the discrete element method (DEM) with computational fluid dynamics (CFD). The mechanical behaviour of the rock matrix was simulated with DEM and the behaviour of the fracturing fluid flow...
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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
PublicationThe 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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Combining X-ray tomogrpahy imaging and DEM simulations to investigate granular material flow during silo discharging
PublicationEven 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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Use of Innovative and Advanced Computer Simulations of Chemical Speciation of Heavy Metals in Soils and Other Environmental Samples
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Experiments and Numerical Simulations of the Annealing Temperature Influence on the Residual Stresses Level in S700MC Steel Welded Elements
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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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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