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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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Numerical modeling of the nonlinear wave propagation in a bubble layer
PublicationRozważano zagadnienie propagacji fali wewnątrz warstwy z pęcherzykami. Omówiono model matematyczny, przedstawiono przykładowe wyniki badań teoretycznych. Analizowano zmiany ciśnienia wewnątrz warstwy, falę odbitą i bieżącą w ośrodku otaczającym, badano gęstość widmową mocy. Badania teoretyczne przeprowadzono dla różnych grubości warstwy, koncentracji pęcherzyków i wartości parametrów fali padającej.
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Modeling organic nitrogen conversions in activated sludge bioreactors
PublicationOpracowano model przemian azotu organicznego (Norg)jako rozszerzenie Modelu Osadu Czynnego Nr 2d (ASM2d). Nowy model zawiera trzy frakcje Norg: rozpuszczoą, koloidalną i zawesinową. Każda frakcja została podzielona na dwie podfrakcje - rozkładalną i nierozkładalną. Model został zweryfikowany w oparciu o wyniki badań eksperymentalnych w oczyszczalni ścieków Gdańsk-Wschód.
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Modeling of the acoustic waves propagation in non-homogeneous medium
PublicationRozważano zagadnienie propagacji fal w ośrodku niejednorodnym. Przedstawiono model matematyczny i przykładowe wyniki badań numerycznych. Model matematyczny zbudowano w oparciu o równanie KZK. Do rozwiązania zagadnienia zastosowano metodę różnic skończonych. Badano zmiany ciśnienia i zmiany widma odpowiednio w ośrodku jednorodnym i niejednorodnym.
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Numerical modeling in open channel hydraulics / R. Szymkiewicz
Publicationksiążka poświęcona jest zagadnieniom modelowania matematycznego przepływów w kanałach otwartych.oprócz wyprowadzenia podstawowych równań przepływów oraz transportu masy i energii, w książce omówiono metody numeryczne użyteczne w hydraulice kanałów.przedstawiono liczne przykłady ich aplikacji do rozwiązania równań przepływu ustalonego i nieustalonego. opisowi metod rozwiązania towarzyszą analizy dokładności oraz stabilności numerycznej.
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AAM toolkit: a system for visual object appearance modeling
PublicationAktywne modele wyglądu (AAM) mogą być traktowane jako zaawansowana metoda analizy informacji multimedialnych, pozwalająca na lokalizowanie i rozpoznawanie obiektów w obrazach statycznych i sekwencjach wideo. Pomimo tego że ukazało się wiele publikacji dotyczących AAM, przejście od koncepcji teoretycznych do działającej implementacji stanowi nadal duże wyzwanie. W pracy przedstawiono przygotowany przez autorów pakiet oprogramowania...
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M-Split Estimation in Laser Scanning Data Modeling
PublicationPublikacja traktuje o wykorzystaniu estymacji M-Split do modelowania danych pozyskanych w wyniku skaningu laserowego. Autorzy prezentują rozwiązanie w oparciu o detekcję krawędzi dwóch płaszczyzn.
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Transient modeling in common DC link of power converters
PublicationПредмет исследования. Представлена математическая модель силовых преобразователей электропривода, питающихся от общего звена постоянного тока, на примере тяговых электроприводов карьерного самосвала БЕЛАЗ-90 мощностью 280 кВт. Модель выполнена в пакете MATLAB/Simulink. Новизна предложенной модели заключается в применении новой топологии силовой схемы для исследования работы двух инверторов, под- ключенных к одному звену постоянного...
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Modeling of strain localization in granular and quasi-brittle materials
PublicationW artykule przedstawiono wyniki symulacji lokalizacji odkształceń w materiałach granulowanych i kruchych. Zasosowano różne modele w ramach mechaniki ośrodków ciągłych i dyskretnych. Wyniki obliczeń porównano z doswiadczeniami.
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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
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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Michał Michna dr hab. inż.
PeopleMichal Michna received the M.Sc. and Ph.D. degrees in electrical engineering from the Gdansk University of Technology (GUT), Gdansk, Poland, in 1998 and 2005, respectively. Since 2004, he was employed at the Department of Power Electronics and Electrical Machines of the Gdańsk University of Technology (assistant, assistant professor, senior lecturer). In 2010-2015 he was a deputy of head of the Department of Power Electronics and...
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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International Journal of Modeling Simulation and Scientific Computing
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International Journal of Information System Modeling and Design
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SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL
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Modeling a Traffic Remapping Attack Game in a Multi-hop Ad Hoc Network
PublicationIn multi-hop ad hoc networks, selfish nodes may unduly acquire high quality of service (QoS) by assigning higher priority to source packets and lower priority to transit packets. Such traffic remapping attacks (TRAs) are cheap to launch, impossible to prevent, hard to detect, and harmful to non-selfish nodes. While studied mostly in single-hop wireless network settings, TRAs have resisted analysis in multi-hop settings. In this paper...
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Quantum structure in competing lizard communities
PublicationAlmost two decades of research on applications of the mathematical formalism of quantum theory as a modeling tool in domains different from the micro-world has given rise to many successful applications in situations related to human behavior and thought, more specifically in cognitive processes of decision-making and the ways concepts are combined into sentences. In this article, we extend this approach to animal behavior, showing...
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Reliable low-cost surrogate modeling and design optimisation of antennas using implicit space mapping with substrate segmentation
PublicationAbstract: In this work, a reliable methodology for fast simulation-driven design optimisation of antenna structures is proposed. The authors’ approach exploits implicit space mapping (ISM) technology. To adopt it for handling antenna structures, they introduce substrate segmentation with separate dielectric permittivity value assigned for each segment as ISM preassigned parameters. At the same time, the coarse model for space mapping...
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Structure of the scalar field around unidirectional circular cylinders
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Lattice dynamics of Mg2SiO4
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Stress Relaxation Behaviour Modeling in Rigid Polyurethane (PU) Elastomeric Materials
PublicationPolyurethane (PU) has been used in a variety of industries during the past few years due to its exceptional qualities, including strong mechanical strength, good abrasion resistance, toughness, low-temperature flexibility, etc. More specifically, PU is easily “tailored” to satisfy particular requirements. There is a lot of potential for its use in broader applications due to this structure–property link. Ordinary polyurethane items...
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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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Interactions of amphotericin B derivatives with lipid membranes - a molecular dynamics study
PublicationW pracy analizowano oddziaływanie dwóch nisko-toksycznych pochodnych amfoterycyny B (związki SAmE i PAmE) z modelami błon lipidowych. Badania wykonane zostały za pomocą dynamiki molekularnej. Modele błon oprócz fosfolipidów DMPC zawierały odpowiednio cholesterol (model błony zwierzęcej) lub ertosterol (model błony grzybowej). Analiza wyników wykazała, że obie pochodne amfoterycyny B zachowują się inaczej w błonie cholesterolowej...
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Interaction of amphotericin B with phospholipids in the model membrane - molecular dynamics study.
PublicationAmfoterycyna B jest antybiotykiem używanym w leczeniu układowych infekcji grzybowych. Jej mechanizm działania polega na tworzeniu kanałów wewnątrz błon lipidowych. W przedstawianej pracy publikowane są wyniki symulacji przeprowadzonej dynamiką molekularną monomerycznej i dimerycznej formy antybiotyku wewnątrz błony lipidowej zbudowanej z cząsteczek DMPC. Wyniki te wskazują, że powinowactwo cząsteczek amfoterycyny wewnątrz dimeru...
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Separation of variables in molecular-dynamics simulations: A criterion to estimate the quality of the approximation
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Release of Encapsulated Bioactive Compounds from Active Packaging/Coating Materials and Its Modeling: A Systematic Review
PublicationThe issue of achieving controlled or targeted release of bioactive compounds with specific functional properties is a complex task that requires addressing several factors, including the type of bioactive, the nature of the delivery system, and the environmental conditions during transportation and storage. This paper deals with extensive reporting for the identification of original articles using Scopus and Google Scholar based...
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Selected Problems of Machine Dynamics II
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Selected Problems of Machine Dynamics - advances
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Selected Problems of Machine Dynamics - advances
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Determination of free tyrosine in equestrian supplements by LC–MS/MS and comparison of its quantity with total free amino acids content in view of doping control
PublicationThe reports on the probable beneficial impact of tyrosine (TYR) supplementation on performance enhancement have contributed to the growth of interest in TYR in equestrian sports field and related industries, such as the manufacture of dietary and nutritional supplements. In this study, the first attempt to the assessment of horses exposure to TYR during nutritional supplementation was demonstrated by quantification of unbound TYR...
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Inverse Modeling and Optimization of CSRR-based Microwave Sensors for Industrial Applications
PublicationDesign optimization of multivariable resonators is a challenging topic in the area of microwave sensors for industrial applications. This paper proposes a novel methodology for rapid re-design and parameter tuning of complementary split-ring resonators (CSRRs). Our approach involves inverse surrogate models established using pre-optimized resonator data as well as analytical correction techniques to enable rapid adjustment of geometry...
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Decoherence-free communication over multiaccess quantum channels
PublicationIn this paper we consider decoherence-free communication over multiple access and k-user quantum channels. First, we concentrate on a hermitian unitary noise model U for a two-access bi-unitary channel and show that in this case a decoherence-free code exists if the space of Schmidt matrices of an eigensubspace of U exhibits certain properties of decomposability. Then, we show that our technique is also applicable for generic random unitary...
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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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Exchange-Traded Funds in Europe
PublicationExchange-Traded Funds in Europe provides a single point of reference on a diverse set of regional ETF markets, illuminating the roles ETFs can play in risk mitigation and speculation. Combining empirical data with models and case studies, the authors use diffusion models and panel/country-specific regressions—as well as graphical and descriptive analyses— to show how ETFs are more than conventional, passive investments. With new...
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What drives sustainable investing? Adoption determinants of sustainable investing exchange-traded funds in Europe
PublicationDespite the growing interest in various topics related to sustainable (ESG) investing, some issues remain understudied, such as the determinants of their utilization at the macro level. This paper contributes to the state of knowledge two-directionally. First, it shows the development of sustainable investing exchange-traded funds (ETFs) in European countries. Second, it traces the significant determinants of adopting sustainable...
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Expedited Geometry Scaling of Compact Microwave Passives by Means of Inverse Surrogate Modeling
PublicationIn this paper, the problem of geometry scaling of compact microwave structures is investigated. As opposed to conventional structures (i.e., constructed using uniform transmission lines), re-design of miniaturized circuits (e.g., implemented with artificial transmission lines, ATSs) for different operating frequencies is far from being straightforward due to considerable cross-couplings between the circuit components. Here, we...
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Analysis of dynamics of a map-based neuron model via Lorenz maps
PublicationModeling nerve cells can facilitate formulating hypotheses about their real behavior and improve understanding of their functioning. In this paper, we study a discrete neuron model introduced by Courbage et al. [Chaos 17, 043109 (2007)], where the originally piecewise linear function defining voltage dynamics is replaced by a cubic polynomial, with an additional parameter responsible for varying the slope. Showing that on a large...
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Conformation analysis and semiclassical dynamics study of charge exchange process induced by collision of C2+ ions with tetrahydrofuran
PublicationWe present the results of recent investigations of charge transfer processes in the collisions of C²⁺ ions with heterocyclic molecules of tetrahydrofuran.
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Genre-Based Music Language Modeling with Latent Hierarchical Pitman-Yor Process Allocation
PublicationIn this work we present a new Bayesian topic model: latent hierarchical Pitman-Yor process allocation (LHPYA), which uses hierarchical Pitman-Yor pr ocess priors for both word and topic distributions, and generalizes a few of the existing topic models, including the latent Dirichlet allocation (LDA), the bi- gram topic model and the hierarchical Pitman-Yor topic model. Using such priors allows for integration of -grams with a topic model,...
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Genre-Based Music Language Modeling with Latent Hierarchical Pitman-Yor Process Allocation
PublicationIn this work we present a new Bayesian topic model: latent hierarchical Pitman-Yor process allocation (LHPYA), which uses hierarchical Pitman-Yor pr ocess priors for both word and topic distributions, and generalizes a few of the existing topic models, including the latent Dirichlet allocation (LDA), the bi- gram topic model and the hierarchical Pitman-Yor topic model. Using such priors allows for integration of -grams with a topic...
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Enhanced uniform data sampling for constrained data‐driven modeling of antenna input characteristics
PublicationData-driven surrogates are the most popular replacement models utilized in many fields of engineering and science, including design of microwave and antenna structures. The primary practical issue is a curse of dimensionality which limits the number of independent parameters that can be accounted for in the modelling process. Recently, a performance-driven modelling technique has been proposed where the constrained domain of the...
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The effect of sunscreen 4‐methylbenzylidene camphor in different and reproductive models, its bioaccumulation and molecular effects on ligand‐receptor interaction, and protein expression
Publication4-Methylbenzylidene camphor (4-MBC) is a photo-absorbing UV filter prevalently used in cosmetics, which can be absorbed into circulation and cause systemic effects. 4-MBC is continued to be released in the environment despite the growing knowledge about its bioaccumulation and endocrine disrupting effects. Previous reviews have mentioned UV-filter together but this review considers 4-MBC alone, due to its prevalence and concerning...
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Ionic liquid-assisted sol-gel synthesis of Fe2O3-TiO2 for enhanced photocatalytic degradation of bisphenol a under UV illumination: Modeling and optimization using response surface methodology
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Statistical evaluation of the changes in cellulose properties caused by the stepwise solvent exchange and esterification
PublicationThe objective of the research was to empirically confirm the changes in cellulose reactivity caused by the pre-treatment with solvents of different polarity. Therefore, 5 solvents varying in their polar component of surface tension from 0 to 4.6 mN/m were chosen. Their impact on the biopolymer properties was carefully analysed concerning chemical structure, crystallinity and surface characteristics. It was revealed that the length...
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Development of Strategies for AOB and NOB Competition Supported by Mathematical Modeling in Terms of Successful Deammonification Implementation for Energy-Efficient WWTPs
PublicationNovel technologies such as partial nitritation (PN) and partial denitritation (PDN) could be combined with the anammox-based process in order to alleviate energy input. The former combination, also noted as deammonification, has been intensively studied in a frame of lab and full-scale wastewater treatment in order to optimize operational costs and process efficiency. For the deammonification process, key functional microbes include...
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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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...