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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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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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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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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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Dependence Modeling
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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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TIME SERIES MODELING 2023/2024
e-Learning Coursesprowadzący: assoc. prof. Ján Dvorský, PhD
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Network Modeling and Analysis in Health Informatics and Bioinformatics
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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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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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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...
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Multidiscipline Modeling in Materials and Structures
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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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Modeling the Networks - ed. 2021/2022
e-Learning CoursesThe goal of this course is to present optimization problems for road networks, where the road network is a set of n distinct lines, or n distinct (open or closed) line segments, in the plane, such that their union is a connected region.
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Modeling Methodologies for Environment 22/23
e-Learning CoursesZrozumienie procesów które mają wpływ na migrację i przemiany zanieczyszczeń w środowisku (ze szczególnym uwzględnieniem wód powierzchniowych). Zajęcia dotyczą podstaw i zasad budowy modeli jakości wody oraz służą pokazaniu jak te modele mogą być wykorzystywane do rozwiązywania problemów w inżynierii środowiska.
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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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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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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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Sylwester Kaczmarek dr hab. inż.
PeopleSylwester Kaczmarek received his M.Sc in electronics engineering, Ph.D. and D.Sc. in switching and teletraffic science from the Gdansk University of Technology, Gdansk, Poland, in 1972, 1981 and 1994, respectively. His research interests include: IP QoS and GMPLS and SDN networks, switching, QoS routing, teletraffic, multimedia services and quality of services. Currently, his research is focused on developing and applicability...
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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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Rengel Cane Sia Doctoral Candidate
PeopleI’m Rengel, born and raised in the Philippines. As an undergraduate I did kinetic modeling on Copper-catalyzed atom transfer radical addition (ATRA). Then I was inspired to do both theoretical and experimental studies, which led me to propose my master’s thesis on Synthesis, Computational, Electrochemical, and Photoconductivity Studies on Naphthalene and its derivatives. This led to a master’s degree in Chemistry in the Mindanao...
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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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Determining the optimal filling of the surface with a linker with Universal Force Field and Reax Force Field
Open Research DataThe DataSet contains the atomic slabs of diamond surfaces with ATP molecules in water. The calculated data includes different sized surfaces from 90 Angstrom^2 to 691 Angstrom^2. Structures were relaxed using the Reax Force Field method with the Limited Memory Broyden–Fletcher–Goldfarb–Shanno algorithm. Structures were calculated with a convergence...