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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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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Molecular Modeling of the Neurohypophyseal Receptor/Atosiban Complexes
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Modeling of performance of a AUV vehicle towards limiting the hydro-acoustic field.
PublicationSome results of research devoted to the modeling of a AUV-Stealth vehicle performance towards limiting its hydro-acoustic field are presented in the paper. At the beginning the AUV-Stealth autonomous underwater vehicle concept is described. Then the method of research is introduced. Next the key design drivers of the AUV-Stealth vehicle are presented. Between them are the AUV-Stealth hull form, arrangement of internal spaces,...
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Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models
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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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Nonlinear Modeling in Time Domain Numerical Analysis of Stringed Instrument Dynamics
PublicationMusical instruments are very various in terms of sound quality with their timbre shaped by materials and geometry. Materials' impact is commonly treated as dominant one by musicians, while it is unclear whether it is true or not. The research proposed in the study focuses on determining influence of both these factors on sound quality based on their impact on harmonic composition. Numerical approach has been chosen to allowed independent...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA 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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Modeling Dynamics of Autonomous Underwater Vehicle.
PublicationArtykuł dotyczy budowy modelu autonomicznego pojazdu podwodnego do celów syntezy układu sterowania pojazdem. Rozważany pojazd ma długośc ok. 1 m i 30 cm średnicy. Wyposażony jest w 5 pędników, które pozwalają na sterowanie w pięciu stopniach swobody. Do badań wykorzystano model o 4 stopniach swobody. Dokonano identyfikacji parametrycznej modelu. Model zrealizowano w środowisku programowym Matlab/Simulink.
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
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Modeling water exchange in the Oder River mouth area
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Molecular Modeling of Meta II Rhodopsin
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THE CONCEPT OF MODELING OF SNOW IMPACT ON THE STRUCTURE OF THE SUSPENDED TAURON ARENA ROOF IN CRACOW
PublicationThe article presents studies and numerical simulations on modeling snow influence on TAURON ARENA suspended roof structure in Cracow. The scope of work includes experimental tests, functions solutions taking into account various cases of snow impact according to PN and EC, as well as numerical simulations for the sport and entertainment arena in the Czyzyny district. The FEM roof structure model developed in the SOFISITK software...
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Smart Modeling of Maritime Vessels
PublicationCurrently, the market offers many visualization tools available to graphic designers, engineers, managers and academics working on maritime environments. The practice of visualization involves making and manipulating images that convey novel phenomena and ideas. Visual communication, together with virtual reality environments, is an emerging and rapidly evolving discipline. It brings great advantage over written word or voice alone,...
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Structure of the interlayer between Au thin film and Si-substrate: Molecular Dynamics simulations
PublicationInteraction between 2, 3, 5 and 7 atomic layers of gold and a (111) silicon surface was investigated with the molecular dynamics simulation method. The simulation of the diffusion interaction between gold and silicon in the temperature range 425-925 K has been carried out. The peculiarities of the concentration changes of the interacting components and the atomic density at the boundary...
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Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
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Sparse autoregressive modeling
PublicationIn the paper the comparison of the popular pitch determination (PD) algorithms for thepurpose of elimination of clicks from archive audio signals using sparse autoregressive (SAR)modeling is presented. The SAR signal representation has been widely used in code-excitedlinear prediction (CELP) systems. The appropriate construction of the SAR model is requiredto guarantee model stability. For this reason the signal representation...
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Fundamentals of Physics-Based Surrogate Modeling
PublicationChapter 1 was focused on data-driven (or approximation-based) modeling methods. The second major class of surrogates are physics-based models outlined in this chapter. Although they are not as popular, their importance is growing because of the challenges related to construction and handling of approximation surrogates for many real-world problems. The high cost of evaluating computational models, nonlinearity of system responses,...
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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A Maximum-Likelihood Approach to Force-Field Calibration
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Prediction of Stress and Deformation Caused by Magnetic Attraction Force in Modulation Elements in a Magnetically Geared Machine Using Subdomain Modeling
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Billiard in a rotating half-plane: modeling and dynamics
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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublicationThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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Mathematical Modeling of Ice Dynamics as a Decision Support Tool in River Engineering
PublicationThe prediction of winter flooding is a complicated task since it is affected by many meteorological and hydraulic factors. Typically, information on river ice conditions is based on historical observations, which are usually incomplete. Recently, data have been supplemented by information extracted from satellite images. All the above mentioned factors provide a good background of the characteristics of ice processes, but are not...
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Category-Based Workload Modeling for Hardware Load Prediction in Heterogeneous IaaS Cloud
PublicationThe paper presents a method of hardware load prediction using workload models based on application categories and high-level characteristics. Application of the method to the problem of optimization of virtual machine scheduling in a heterogeneous Infrastructure as a Service (IaaS) computing cloud is described.
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Molecular dynamics studies of polyurethane nanocomposite hydrogels
PublicationPolyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...
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Grand Challenges on the Theory of Modeling and Simulation
PublicationModeling & Simulation (M&S) is used in many different fields and has made many significant contributions. As a field in its own right, there have been many advances in methodologies and technologies. In 2002 a workshop was held in Dagstuhl, Germany, to reflect on the grand challenges facing M&S. Ten years on, a series of M& S Grand Challenge activities are marking a decade of progress and are providing an opportunity to reflect...
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Surrogate Modeling and Optimization Using Shape-Preserving Response Prediction: A Review
PublicationComputer simulation models are ubiquitous in modern engineering design. In many cases, they are the only way to evaluate a given design with sufficient fidelity. Unfortunately, an added computa-tional expense is associated with higher fidelity models. Moreover, the systems being considered are often highly nonlinear and may feature a large number of designable parameters. Therefore, it may be impractical to solve the design problem...
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Numerical modeling of force and contact networks in fragmented sea ice
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Global Surrogate Modeling by Neural Network-Based Model Uncertainty
PublicationThis work proposes a novel adaptive global surrogate modeling algorithm which uses two neural networks, one for prediction and the other for the model uncertainty. Specifically, the algorithm proceeds in cycles and adaptively enhances the neural network-based surrogate model by selecting the next sampling points guided by an auxiliary neural network approximation of the spatial error. The proposed algorithm is tested numerically...
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Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
PublicationCoarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...
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Modeling of Human Tissue for Medical Purposes
PublicationThe paper describes the possibilities offered for medicine by modeling of human tissue using virtual and augmented reality. It also presents three proposals of breast modeling for the use in clinical practice. These proposals are the result of arrangements of medical and computer scientists team (the authors) and will be pursued and implemented in the near future. There is included also a brief description of the most popular methods...
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Numerical modeling of GPR field in damage detection of a reinforced concrete footbridge
PublicationThe paper presents a study on the use of the ground penetrating radar (GPR) method in diagnostics of a footbridge. It contains experimental investigations and numerical analyses of the electromagnetic field propagation using the finite difference time domain method (FDTD). The object of research was a reinforced concrete footbridge over a railway line. The calculations of the GPR field propagation were performed on a selected cross-section...
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Fundamentals of Data-Driven Surrogate Modeling
PublicationThe primary topic of the book is surrogate modeling and surrogate-based design of high-frequency structures. The purpose of the first two chapters is to provide the reader with an overview of the two most important classes of modeling methods, data-driven (or approx-imation), as well as physics-based ones. These are covered in Chap-ters 1 and 2, respectively. The remaining parts of the book give an exposition of the specific aspects...
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Computational modeling of molecularly imprinted polymers as a green approach to the development of novel analytical sorbents
PublicationThe development of novel molecularly imprinted polymers (MIP) sorbents for specific chemical compounds require a lot of tedious and time-consuming laboratory work. Significant quantities of solvents and reagents are consumed in the course of the verification of appropriate configurations of polymerization reagents. Implementation of molecular modeling in the MIP sorbent development process appears to provide a solution to this...
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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Accurate modeling of quasi-resonant inverter fed IM drive
PublicationIn this paper wide-band modeling methodology of a parallel quasi-resonant dc link inverter (PQRDCLI) fed induction machine (IM) is presented. The modeling objective is early-design stage prediction of conductive electromagnetic interference (EMI) emissions of the considered converter fed IM drive system. Operation principles of the selected topology of PQRDCLI feeding IM drive are given. Modeling of the converter drive system is...
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Modeling SPMD Application Execution Time
PublicationParallel applications in a Single Process Multiple Data paradigm assume splitting huge amounts of data to multiple processors working in parallel at small data packets. As the individual data packets are not independent, the processors must interact with each other to exchange results of the calculations with their adjacent partners and take these results into account in their own computations. An example of SPMD is geometric parallelism...
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Modeling the application of steel slag in stabilizing expansive soil
PublicationThe objective of this study was to evaluate the suitability of steel slag as an additive to the engineering properties of weak clay soil. Different geotechnical laboratory tests were conducted on both stabilized and natural soils. Steel slag (SS) was added at a rate of 0, 5, 10, 15, 20, and 25% to the soil. Specific gravity, grain size analysis, Atterberg limit test, compaction test, free swell, California bearing ratio (CBR),...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Use of structural equation modeling in quantitative research in the field of management and economics: A bibliometric analysis in the systematic literature review
PublicationPURPOSE: This paper aims to provide a comprehensive review of scholarly research focusing on using quantitative methods and particularly structural equation modeling (SEM) in management and economics studies, as well as provide a bibliometric agenda including the time horizon of individual publications, the highest citation rate, geographic and industry areas, methodological context, and keywords. METHODOLOGY: A systematic literature...
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Turbulence Flow Modeling of One-Sharp-Groyne Field
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Numerical modeling of wave-seabed-structure interaction.
PublicationPraca doktorska przedstawia propozycję nowoczesnego rozwiązania obciążeń hydraulicznych przy uwzględnieniu nieliniowych oddziaływań pomiędzy falą wodną, przepuszczalnym dnem i porowatą konstrukcją morską. Nabrzeże pionowe, falochron podwodny i falochron kompozytowy były obiektem eksperymentów numerycznych, których wyniki były weryfikowane przy użyciu wyników laboratoryjnych (niszczących i nieniszczących). Krótki przegląd bieżącej...