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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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FEM approach to modeling of an irregular trabecular structure
PublicationThe aim of the study is elaboration of a method for creating irregular scaffolds that can be used to model the behaviour of trabecular bone placed in the proximal epiphysis of the femur. The scope of the study encompasses creating six numerical models of irregular scaffolds (two solid irregular scaffolds, two shell irregular scaffolds and two shell irregular scaffolds with fortification) and performing numerical analysis of the...
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Molecular modeling and evaluation of novel dibenzopyrrole derivatives as telomerase inhibitors and potential drug for cancer therapy
PublicationDuring previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central...
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Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublicationIn this paper we present the methodology for assessing the ionic liquids' viscosity at six temperature points (25, 35, 45, 50, 60 and 70 [C]), which utilizes only the in silico approach. The main idea of such assessment is based on the "correction equation" describing the correlation between experimentally measured viscosity and theoretically derived density (calculated with use of molecular mechanics), given at 6 different temperature...
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Modeling energy consumption of parallel applications
PublicationThe paper presents modeling and simulation of energy consumption of two types of parallel applications: geometric Single Program Multiple Data (SPMD) and divide-and-conquer (DAC). Simulation is performed in a new MERPSYS environment. Model of an application uses the Java language with extension representing message exchange between processes working in parallel. Simulation is performed by running threads representing distinct process...
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Structure and Molecular Dynamics in Renewable Polyamides from Dideoxy-Diamino Isohexide
PublicationThe chemical structure, the conformation, andthe flexibility of the polymer chain fragments present in thepolyamides synthesized from 2,5-diamino-2,5-dideoxy-1,4;3,6-dianhydrosorbitol, 1,4-diaminobutane, and either sebacic orbrassylic acid have been studied by liquid-state 2D NMRspectroscopy viz. correlation spectra (COSY) and heteronuclearmultiple-bond correlation spectra (gHMBC), by 13Ccross-polarization/magic-angle spinning...
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Modeling an Industrial Revolution: How to Manage Large-Scale, Complex IoT Ecosystems?
PublicationAdvancements around the modern digital industry gave birth to a number of closely interrelated concepts: in the age of the Internet of Things (IoT), System of Systems (SoS), Cyber-Physical Systems (CPS), Digital Twins and the fourth industrial revolution, everything revolves around the issue of designing well-understood, sound and secure complex systems while providing maximum flexibility, autonomy and dynamics. The aim of the...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Reliability Modeling for SPMD and DAC Applications in MERPSYS
PublicationIn this chapter we shall see a method for modeling of reliability of application execution in the MERPSYS system, and the results of reliability simulation of the same SPMD and DAC application which we have previously presented in this book. Unlike energy usage modeling and modeling of execution efficiency we could not compare the reliability model and simulation results to real experiment just because the experiment would last too...
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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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TIME-AND-SPACE STRUCTURE OF FORCE-DRIVEN RIGID SPHEREWAVEFIELD
PublicationThis paper introduces a time-domain, causality-inspired description of a vector-source acoustic wavefield of arbitrary time evolution, where a sphere is a practical realisation of quasi-point contact surface without which a point force would not be able to exert an impact onto non-viscous fluid. At every space location, the resulting acoustic field is described by a pair of physical variables characterising the time evolution of...
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Modeling BIM Objects From Point Clouds. Examples
PublicationThe article presents several ways to obtain BIM (Building Information Modeling) models from point clouds using standard commands in Revit 2018. In Revit geometric forms are possible to obtain in project, family or conceptual environments. Efficient modeling requires knowledge of methods of creating families and components in these environments and ways to combine them. Modeling methods with system and loadable families are presented,...
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Inverse surrogate modeling for low-cost geometry scaling of microwave and antenna structures
PublicationPurpose–The purpose of this paper is to investigate strategies for expedited dimension scaling ofelectromagnetic (EM)-simulated microwave and antenna structures, exploiting the concept of variable-fidelity inverse surrogate modeling.Design/methodology/approach–A fast inverse surrogate modeling technique is described fordimension scaling of microwave and antenna structures. The model is established using referencedesigns obtained...
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Accurate simulation-driven modeling and design optimization of compact microwave structures
PublicationCost efficient design optimization of microwave structures requires availability of fast yet reliable replacement models so that multiple evaluations of the structure at hand can be executed in reasonable timeframe. Direct utilization of full-wave electromagnetic (EM) simulations is often prohibitive. On the other hand, accurate data-driven modeling normally requires a very large number of training points and it is virtually infeasible...
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High-resolution microscopy assisted mechanical modeling of ultrafine electrospun network
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Modeling of free vibrations and resonant frequencies of simply-supported submerged horizontal plate
PublicationA theoretical approach was applied to study the vibration of simple-supported submerged horizontal plate. The derived analytical solution was used to determine natural frequencies for a horizontal plate vibrating in fluid. The investigations were conducted for a very wide range of material density and elasticity modulus covering all materials used in engineering practice. Analysis shows that plate vibration frequency decreases...
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The structure of rarefied and densified PbSiO3 glass: a molecular dynamics study.
PublicationArtykuł przedstawia wyniki symulacji dynamiczno-molekularnychstruktury rozrzedzonego i zagęszczonego szkła PbSiO3 (w zakresie gęstości od 3000 kg/m3 do 8000 kg/m3). Otrzymane wyniki dokładnie przedyskutowano pod kątem blisko- i średnio-zasięgowego uporządkowania atomów i porównano ze strukturą szkła PbSiO3 o normalnej gęstości (5970kg/m3) oraz ze strukturą rozrzedzonych i zagęszczonych szkieł PbGeO3.
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library.
PublicationIn this work, we present the construction of a metagenomic library in Escherichia coli using pUC19 vector and environmental DNA directly isolated from Antarctic topsoil and screened for lipolytic enzymes. The screening on agar supplemented with olive oil and rhodamine B revealed one clone with lipolytic activity (Lip1) out of 11,000 E. coli clones. This clone harbored a plasmid, pLip1, which has an insert of 4722 bp that has been...
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Improving performance of large thrust bearings through modeling and experimentation
PublicationLarge thrust bearings are highly loaded machine elements and their failures cause serious losses. Start ups and stoppages of the bearing under load are specially critical regimes of operation. Load carrying capacity depends on the profile of the oil gap. In transient states this profile is also changing. In the design of large thrust bearings minimizing thermo-elastic deformations is an important goal, which can be accomplished...
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Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations
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Performance Modeling and Prediction of Real Application Workload in a Volunteer-based System
PublicationThe goal of this paper is to present a model that predicts the real workload placed on a volunteer based system by an application, with incorporation of not only performance but also availability of volunteers. The application consists of multiple data packets that need to be processed. Knowing the computational workload demand of a single data packet we show how to estimate the application workload in a volunteer based system. Furthermore,...
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Monte-Carlo Modeling of Optical Sensors for Postoperative Free Flap Monitoring
PublicationThis work aims to develop a numerical tissue model and implement software to simulate photon propagation using the Monte Carlo method to determine design guidelines for a physical measurement system. C++ was used for the simulation program, and Python as a programming environment to create an interface that allows the user to customize individual simulation elements, allowing for increased accuracy and flexibility when simulating...
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Monte-Carlo Modeling of Optical Sensors for Postoperative Free Flap Monitoring
PublicationThis work aims to develop a numerical tissue model and implement software to simulate photon propagation using the Monte Carlo method to determine design guidelines for a physical measurement system. C++ was used for the simulation program, and Python as a programming environment to create an interface that allows the user to customize individual simulation elements, allowing for increased accuracy and flexibility when simulating...
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Accidental wow evaluation based on sinusoidal modeling and neural nets prediction
PublicationReferat przedstawia opis algorytmu do określenia charakterystyki zniekształcenia kołysania dźwięku. Prezentowane podejście wykorzystuje sinusoidalną analizę dźwięku bazującą zarówno na amplitudowym jak i fazowym widmie sygnału fonicznego. Trajektorie poszczególnych składowych tonalnych, obrazujące zniekształcenie kołysania, określane są na podstawie analizy ich chwilowych amplitud, częstotliwości i faz. Dodatkowo referat przedstawia...
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Molecular Modeling of Interaction of the Vasopressin Analogs with Vasopressin and Oxytocin Receptors
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New approach to railway noise modeling employing Genetic Algorithms
PublicationMain goal of this paper was to describe an innovative method of noise prediction based on Genetic Algorithms. First part of the paper addresses the problem of growing noise, mainly in the context of a unified method for measuring noise. Further, Genetic Algorithms are described with regards to their fundamental features. Further a description is provided as to how Genetic Algorithms were used in the area of noise modeling. Next...
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Software Modeling from the Perspective of Intuitive Information Processing
PublicationThere is psychological evidence that humans process information not only consciously but also intuitively. Intuitive information processing is present also during the activities related to software modeling. The goal of this paper is to analyze software modeling from the perspective of theories which describe intuitive (nonconscious, implicit) information processing. The paper includes presentation of relevant psychological theories,...
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Dynamics of Field Line Mappings in Magnetic Flux Tubes
PublicationWe study the topological constraints on the dynamics of magnetic field lines in flux tubes. Our approach is based on the application of the topological invariant: fixed point index. We consider periodic flux tubes and find various restrictions on the field lines that come from the sequence of fixed point indices of iterations. We also analyze the case of a tube with a cylindrical obstacle, deducing some special dynamical properties...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Modeling of Electrified Transportation Systems Featuring Multiple Vehicles and Complex Power Supply Layout
PublicationThe paper proposes a novel approach to modeling electrified transportation systems. The proposed solution reflects the mechanical dynamics of vehicles as well as the distribution and losses of electric supply. Moreover, energy conversion losses between the mechanical and electrical subsystems and their bilateral influences are included. Such a complete model makes it possible to replicate, e.g., the impact of voltage drops on vehicle...
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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Reliable Microwave Modeling By Means of Variable-Fidelity Response Features
PublicationIn this work, methodologies for low-cost and reliable microwave modeling are presented using variable-fidelity response features. The two key components of our approach are: (i) a realization of the modeling process at the level of suitably selected feature points of the responses (e.g., S-parameters vs. frequency) of the structure at hand, and (ii) the exploitation of variable-fidelity EM simulation data, also for the response...
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Triangulation-based Constrained Surrogate Modeling of Antennas
PublicationDesign of contemporary antenna structures is heavily based on full-wave electromagnetic (EM) simulation tools. They provide accuracy but are CPU-intensive. Reduction of EM-driven design procedure cost can be achieved by using fast replacement models (surrogates). Unfortunately, standard modeling techniques are unable to ensure sufficient predictive power for real-world antenna structures (multiple parameters, wide parameter ranges,...
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Recent improvements in prediction of protein structure by global optimization of a potential energy function
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Ionosphere variability II: Advances in theory and modeling
PublicationThis paper aims to provide an overview on recent advances in ionospheric modeling capabilities, with the emphasis in the efforts relevant to electron density variability. The discussion spans a wide range of model formulations (e.g., from purely empirical to physics-based ones and data-driven approaches) seeking for advances or gaps with regard to present challenges. This discussion is further supported by consideration of the...
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Adaptive prediction of stock exchange indices by state space wavelet networks
PublicationThe paper considers the forecasting of the Warsaw Stock Exchange price index WIG20 by applying a state space wavelet network model of the index price. The approach can be applied to the development of tools for predicting changes of other economic indicators, especially stock exchange indices. The paper presents a general state space wavelet network model and the underlying principles. The model is applied to produce one session...
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Visual Dimensions of Modeling Languages in Interdisciplinary Perspective
PublicationUżyteczność języków modelowania wizualnego zależy od notacji. Notacja może być postrzegana jako zestaw wizualnych komponentów, które w określony sposób oddziałują na ludzkie oko i ludzki mózg. Referat przedstawia analizę interdyscyplinarną wykonaną w celu lepszego zrozumienia wizualnych wymiarów języków modelowania. Wizualne wymiary pochodzą z teorii opisujących percepcję wzrokową, wizualizację danych oraz reprezentacje poznawcze....
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Numerical modeling of sound intensity distributions around acoustic transducer
PublicationThe aim of this research study is to measure, simulate and compare sound intensity distribution generated by the acoustic transducers of the loudspeaker. The comparison of the gathered data allows for validating the numerical model of the acoustic radiation. An accurate model of a sound source is necessary in mathematical modeling of the sound field distribution near the scattering obstacles. An example of such obstacle is a human...
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Special Issue "Applications of Finite Element Modeling for Mechanical and Mechatronic Systems"
PublicationNumerical modeling is very important in today's engineering because, among other things, it reduces the costs associated with prototyping or predicting the occurrence of potentially dangerous situations during operation in certain defined conditions. Different methods have so far been used to implement the real structure into the numerical version. The most popular have been variations of the finite element method (FEM). The aim...
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Characterization of Defects Inside the Cable Dielectric With Partial Discharge Modeling
PublicationThe continuous monitoring of power system devices is an important step toward keeping such capital assets safe. Partial discharge (PD)-based measurement tools provide a reliable and accurate condition assessment of power system insulations. It is very common that voids or cavities exist in every solid dielectric insulation medium. In this article, different voids are modeled and analyzed using an advanced finite element (FE)-based...
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Semantic modeling of contextual augmented reality environments
PublicationDespite significant progress in the field of augmented reality (AR), regarding both hardware and software, there is still a lack of universal models and methods that would enable building ubiquitous AR systems that could be used anywhere and anytime, covering different application areas. This dissertation describes a new approach to building AR systems, called the Contextual Augmented Reality Environment (CARE). The CARE approach...
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Wideband Modeling of DC-DC Buck Converter with GaN Transistors
PublicationThe general wideband modeling method of the power converter is presented on the example of DC-DC buck converter with GaN High Electron Mobility Transistors (HEMT). The models of all basic and parasitic components are briefly described. The two methods of Printed Circuit Board (PCB) layout parameter extraction are presented. The results of simulation in Saber@Sketch simulation software and measurements are compared. Next, the model...
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ENTERPRISE ACTIVITIES MODELING BY BPMN NOTATION
PublicationDepending on the process behavior, available know-how and organizational goals, different techniques and tools can be used for business process modeling. We concentrate on e-commerce, and try to find the best marketing strategy for the sales process improvement. In the paper we present the multilayer approach to define enterprise scenarios. This allows us to collect the suitable knowledge necessary for enterprise analysis and improvement....