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Search results for: epigenetic remodelling
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ACM/IEEE International Conference on Modelling, Analysis and Simulation of Wireless and Mobile Systems
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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Efficient parallel implementation of crowd simulation using a hybrid CPU+GPU high performance computing system
PublicationIn the paper we present a modern efficient parallel OpenMP+CUDA implementation of crowd simulation for hybrid CPU+GPU systems and demonstrate its higher performance over CPU-only and GPU-only implementations for several problem sizes including 10 000, 50 000, 100 000, 500 000 and 1 000 000 agents. We show how performance varies for various tile sizes and what CPU–GPU load balancing settings shall be preferred for various domain...
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Atmospheric degradation mechanism of anthracene initiated by OH•: A DFT prediction
PublicationDensity functional theory (DFT) calculations at the M06-2X/def2-TZVP level have been employed to investigate the atmospheric oxidation mechanism of anthracene (ANT) initiated by HO•. Direct hydrogen atom abstraction from the ANT using HO• takes place hardly at ambient conditions while the addition of HO• to the C1, C2, and C4 sites are thermodynamically and kinetically more advantageous. The addition reactions are controlled by...
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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublicationIn this paper we present a new environment called MERPSYS that allows simulation of parallel application execution time on cluster-based systems. The environment offers a modeling application using the Java language extended with methods representing message passing type communication routines. It also offers a graphical interface for building a system model that incorporates various hardware components such as CPUs, GPUs, interconnects...
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Ships Shore Service Optimization Using the Queueing Theory
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Seeking genetic signature of radiosensitivity - a novel method for data analysis in case of small sample sizes
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
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Molecular dynamics-based model of VEGF-A and its heparin interactions
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Invariant measures for interval translations and some other piecewise continuous maps
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Ensemble fits of restrained peptides’ conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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Simplified AutoDock force field for hydrated binding sites
Publicationhas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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Visualizing spatially decomposed intermolecular correlations in the infrared spectra of aprotic liquids
PublicationInfrared (IR) spectroscopy is commonly used to study intermolecular interactions in the liquid phase, including solvation phenomena. On the other hand, ab initio molecular dynamics (AIMD) simulations offer the possibility to obtain IR spectra from first principles. Surpassing the experiment, AIMD simulations can deliver additional information on the spatial intermolecular correlations underlying the IR spectrum of the liquid. Although...
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Robust design in delta domain for SISO plants: PI and PID controllers
PublicationW pracy przedstawiono zunifikowaną metodę numerycznie odpornej syntezy sterowników (regulatorów) działających w dyskretnym czasie w układach sterowania skalarnymi obiektami czasu ciągłego. Wykorzystano dyskretnoczasowe modele takich obiektów, oparte na tak zwanym operatorze delta, charakteryzującym się korzystnymi odpornościowymi cechami w przypadku stosowania dostatecznie małych wartości okresu próbkowania przetwarzanych sygnałów....
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Conceptual system development in a concurrent environment
PublicationW artykule omówiono możliwości wspomagania jednego z najważniejszych obszarów projektowania, a mianowicie projektowania koncepcyjnego. Rozważania te odniesiono do otoczenia inżynierii wspozadaniowej, co dodatkowo skomplikowano problemy decyzyjne podejmowane na tym etapie projektowania. Zaproponowano szereg elementów wspomagania projektowania koncepcyjnego ze szczególnym uwzględnieniem możliwości praktycznej implementacji takiego...
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The methods of design reliable distributed networks
PublicationOpisano dwie metody projektowania niezawodnych sieci rozległych. W pierwszej metodzie przyjęto, że koszt konstrukcji każdego połączenia jest jednakowy, w drugiej koszty opisuje zadana macierz kosztów. Jako parametr niezawodnościowy przyjęto liczbę niezależnych dróg pomiędzy węzłami sieci. Pierwsza z metod jest metodą dokładną, druga heurystyczną. Zdefiniowano i oceniono błąd metody heurystycznej. Opublikowano wyniki otrzymane...
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Qualitative and quantitative mechanisms in managing IT projects in concur-rent engineering environment
PublicationW artykule przedstawiono wprowadzenie do twardych i miękkich moetod modelowania. Nastepnie wprowadzono czytelnika do obszaru inżynierii równoległej (współzadaniowej). Całość zaproponowano jakośrodowisko wspomagania decyzji w procesach zarządzania złożonymi międzynarodowymi projektami badawczymi w obszaru Information Technology.
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I-lossless factorisations for robust H-inf-control in delta-domain
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Non-regular, incomplete and singular dynamical systems: impasse points indynamical systems
PublicationRozważono nieregularne, niezupełne i osobliwe różniczkowe systemy dynamicznez zastosowaniem metod geometrii różniczkowej.
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Robust pole placement in delta domain for SISO plans
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Vehicle Suspension Design, W, TiL II st., sem. 03, letni 23/24 (PG_00062882)
e-Learning CoursesRole of the suspension. Suspension kinematics and compliances theoretical background and practical measuring schemes. Suspension design an overview of suspension design properties and review of current design philosophy. Review of typical designs. Current design trends. Practical implications. Case studies introduction to modelling and simulation software and discussion of practical case studies.
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Vehicle Suspension Design, W, MiBM II st., sem. 03, letni 23/24 (PG_00062882)
e-Learning CoursesRole of the suspension. Suspension kinematics and compliances theoretical background and practical measuring schemes. Suspension design an overview of suspension design properties and review of current design philosophy. Review of typical designs. Current design trends. Practical implications. Case studies introduction to modelling and simulation software and discussion of practical case studies.
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Role patterns in IT projects teams - design of a selection module using fuzzy logic techniques
PublicationPresented paper introduces an approach based on usage of role patterns and modelling by the use of fuzzy logic tool for selection process with limitation to the area of IT projects environment. The article shows a concept of role patterns structures and their further usage in process of forming a fuzzy model dedicated to candidate assessment process support
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Wrażliwość probabilistyczna stanów granicznych konstrukcji - metoda Monte Carlo
PublicationPraca ukazuje zastosowanie metody symulacyjnej Monte Carlo w analizie losowej konstrukcji inżynierskich. Systematyka metod losowych obejmuje ich trzy poziomy, z zaznaczeniem poziomu trzeciego, o dowolnych typach zmiennych losowych – zmiennych podstawowych problemu. Ukazano przykład modelowana losowego obciążenia wiatrem na podstawie 10-letnich pomiarów prędkości wiatru, wykazując zgodność zbioru danych z rozkładem ekstremów Gumbela....
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Fractional Order Circuit Elements Derived from Electromagnetism
PublicationIn this paper, derivations of fractional-order (FO) circuit-element equations from electromagnetism are presented. Whilst many papers are devoted to FO modelling of electrical circuits, there are no strong foundations for such an approach. Therefore, we investigate relations between the FO electromagnetism and the FO circuit theory. Our derivations start from quasi-static (QS) approximations of Maxwell's equations in media with...
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Selected aspects of customization of cognitive dimensions for evaluation of visual modeling languages.
PublicationFor the successful application of diagrams in software engineering, high quality visual modelling languages (VML) are required. There is a need for new effective methodologies of VML evaluation. This paper discusses selected aspects of applying cognitive dimensions as a basis of the evaluation. Then, it briefly presents CD-VML methodology which integrates the cognitive dimensions with a theory of visual modelling languages. Finally,...
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Tomasz Goluch mgr inż.
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On Non-holonomic Boundary Conditions within the Nonlinear Cosserat Continuum
PublicationWithin the framework of the nonlinear micropolar elastic continuum we discuss non-holonomic kinematic boundary conditions. By non-holonomic boundary conditions we mean linear relations between virtual displacements and virtual rotations given on the boundary. Such boundary conditions can be used for modelling of complex material interactions in the vicinity of the boundaries and interfaces.
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Toward Mechanosynthesis of diamondoid structures: III. Quantum-chemical study of silylene molecule and silicon atom transfer mechanism from caped SWCNT tip to the reaction center on a hydrogenated Si(111) surface
PublicationOpublikowana wcześniej (Modelling Simul. Mater. Sci. Eng., Vol. 7, 1999, pp. 43-58) strategia mechanosyntezy struktur krzemu na uwodornionej płaszczyźnie Si(111) została poszerzona poprzez uwzględnienie ostrza w postaci zamkniętej SWCNT jako urządzenia kontrolującego położenie cząsteczki sililenu oraz atomu krzemu.
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Computational algorithm for the analysis of mechatronic systems with distributed parameter elements
PublicationThe paper presents a systematic computational package for analysis of complex systems composed of multiple lumped and distributed parameter subsystems. The algorithm is based on the transfer function method (DTFM). With this algorithm, a bond graph technique for the modelling is developed to simplify computations. Analysis of different systems requires only changing the inputs data in the form of the bond graph diagram
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Secure access control and information protection mechanisms in radio system for monitoring and acquisition of data from traffic enforcement cameras
PublicationThe study presents the architecture of the Radio System for Monitoring and Acquisition of Data from Traffic Enforcement Cameras (in short: RSMAD), particularly concerning access control and protection of confidential data. RSMAD security structure will be discussed in relation to network security issues. Additionally, the paper presents the results of the work associated with the modelling of potential threats to system security.
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The particle method for simulation of self-organization phenomena
PublicationThe aim of the work was to design, implement, and use, in a number of experiments, an abstract software environment (an artificial world)suitable for modelling systems consisting of many moving and interactingobjects distributed in space. The environment, named DigiHive, is directed towards modeling of complex systems manifested by processes of self-organization, self-reproduction and self modifications. The environment is mainly...
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The new investing effectiveness evaluation multi-criteria method in modern supply systems
PublicationThe important problem in the processes of modelling and programming the development of sustainable energy sector is the multi-criteria manner of assessing the effectiveness of investments. The goal of this paper is to show how to take into account the impact of investments in multidimensional modelling decision-making processes. This goal can be achieved through the development, presentation, and use of a new multi-criteria method...
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Coupled Urban Areas Inundation Model with Interaction Between Storm Water System and Surface Flow - Case Study of Sea Level Impact on Seaside Areas Flooding
PublicationInundations are becoming more frequent than ever. What is connected with increasing area of impervious surface in cities. This makes predicting urban flooding and its scale especially important. At the seaside we observe additional conditions such as sea level that makes accurate numerical modelling of issue even harder. With complex approach to the matter which is simultaneous calculation of storm water conduit flow and overland...
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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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Influence of Added Water Mass on Ship Structure Vibration Parameters in Virtual and Real Conditions
PublicationModelling of ship structures in a virtual environment is now standard practice. Unfortunately, many engineers forget to consideri the influence of added water on the frequency values and the amplitude of natural vibrations. The article presents the effect of water damping on the frequency values of the individual natural vibration modes. The tests were carried out in two stages. First, the mentioned values were determined using...
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Experimental and computational study on mechanical behaviour of carpentry corner log joints
PublicationThis work concerns experimental and numerical research on carpentry joints used in historic wooden buildings in southeastern Poland and western Ukraine. These structures are mainly sacred buildings, and the types of corner log joints characteristic of this region are primarily saddle-notch and dovetail joints; thus, these two types of joints were analysed in this study. The modelling of historic timber structures is a complex...
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Kacper Wereszko mgr inż.
PeopleKacper Wereszko received the M.Sc. in 2016 (field of study: computer science, specialization: Internet technologies and algorithms). Since 2017 he is a Ph.D. student in the field of computer science. He works as assistant in Department of Algorithms and System Modelling. His research interests focus on security properties of graphs, domination problems in graphs and their practical applications.
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Long-term hindcast simulation of water temperature and salinity in the Baltic Sea
Open Research DataThe dataset contains the results of numerical modelling of water temperature and salinity over a period of 50 years (1958-2007) in the Baltic Sea. A long-term hindcast simulation was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997). The hydrodynamic...
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Long-term hindcast simulation of currents in the Baltic Sea
Open Research DataThe dataset contains the results of numerical modelling of currents over a period of 50 years (1958-2007) in the Baltic Sea . A long-term hindcast simulation was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997). The hydrodynamic model was coupled...
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On a Method of Efficiency Increasing in Kaplan Turbine
PublicationThis paper presents a method of increasing efficiency in Kaplan-type turbine. The method is based on blade profile optimisation together with modelling the interaction between rotor and stator blades. Loss coefficient was chosen as the optimisation criterion, which is related directly to efficiency. Global optimum was found by means of Genetic Algorithms, and Artificial Neural Networks were utilised for approximations to reduce...
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Planning optimised multi-tasking operations under the capability for parallel machining
PublicationThe advent of advanced multi-tasking machines (MTMs) in the metalworking industry has provided the opportunity for more efficient parallel machining as compared to traditional sequential processing. It entailed the need for developing appropriate reasoning schemes for efficient process planning to take advantage of machining capabilities inherent in these machines. This paper addresses an adequate methodical approach for a non-linear...
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How to model ROC curves - a credit scoring perspective
PublicationROC curves, which derive from signal detection theory, are widely used to assess binary classifiers in various domains. The AUROC (area under the ROC curve) ratio or its transformations (the Gini coefficient) belong to the most widely used synthetic measures of the separation power of classification models, such as medical diagnostic tests or credit scoring. Frequently a need arises to model an ROC curve. In the biostatistical...
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Laser scanning point clouds of a 32-meter radiotelescope located in the radioastronomical observatory in Piwnice (Poland)
Open Research DataThis dataset contains laser scanning point clouds of a 32-meter RT4 radiotelescope located in the radioastronomical observatory in Piwnice in Poland. Measurements were performed on 18th May 2018 using two laser scanners: Leica P40 (shared by Leica Geosystems Poland) and Riegl VZ400 (shared by Geotronics Dystrybucja Sp. z o.o.). The cloud points from...
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Direct injection liquid chromatography-mass spectrometry (DI-LC-MS) analysis for rapid lipidomic profiling of extracellular vesicles
PublicationExtracellular vesicles (EVs) are small, spherical particles produced by eukaryotic and prokaryotic cells, surrounded by a bilayer membrane and carrying various bioactive molecules, such as proteins, surface receptors, membrane and soluble proteins, lipids, and nucleic acids. EVs are of substantial interest because of their important roles in cell communication, epigenetic regulation and possible application in disease diagnosis...
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Nonlocal Models of Plates and Shells with Applications in Micro- and Nanomechanics
PublicationNowadays, the use of small-scale structures in micro/nanomachines has become more and more widespread. The most important applications of such small-sized parts are in micro-electro-mechanical systems (MEMS) as well as nano-electro-mechanical systems (NEMS) as actuators, sensors, energy harvesters. For example, nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and...
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G2DC-PL+: a gridded 2 km daily climate dataset for the union of the Polish territory and the Vistula and Odra basins
PublicationG2DC-PL+, a gridded 2 km daily climate dataset for the union of the Polish territory and the Vistula and Odra basins, is an update and extension of the CHASE-PL Forcing Data – Gridded Daily Precipitation and Temperature Dataset – 5 km (CPLFD-GDPT5). The latter was the first publicly available, high-resolution climate forcing dataset in Poland, used for a range of purposes including hydrological modelling and bias correction of...
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CPLFD-GDPT5: High-resolution gridded daily precipitation and temperature data set for two largest Polish river basins
PublicationThe CHASE-PL (Climate change impact assessment for selected sectors in Poland) Forcing Data–Gridded Daily Precipitation & Temperature Dataset–5 km (CPLFD-GDPT5) consists of 1951–2013 daily minimum and maximum air temperatures and precipitation totals interpolated onto a 5 km grid based on daily meteorological observations from the Institute of Meteorology and Water Management (IMGW-PIB; Polish stations), Deutscher Wetterdienst...