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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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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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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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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field
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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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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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JOURNAL OF MOLECULAR MODELING
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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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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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublicationUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
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Journal of Multiscale Modeling
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Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Induction machine behavioral modeling for prediction of EMI propagation.
PublicationThis paper presents the results of wideband behavioral modeling of an induction machine (IM). The proposed solution enables modeling the IM differential- and common-mode impedance for a frequency range from 1 kHz to 10 MHz. Methods of parameter extraction are derived from the measured IM impedances. The developed models of 1.5 kW and 7.5 kW induction machines are designed using the Saber Sketch scheme editor and simulated in the...
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JOURNAL OF MOLECULAR STRUCTURE
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Rough Set Based Modeling and Visualization of the Acoustic Field Around the Human Head
PublicationThe presented research aims at modeling acoustical wave propagation phenomena by applying rough set theory in a novel manner. In a typical listening environment sound intensity is determined by numerous factors: a distance from a sound source, signal levels and frequencies, obstacles’ locations and sizes. Contrarily, a free-field is characterized by direct, unimpeded propagation of the acoustical waves. The proposed approach is...
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Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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MULTISCALE MODELING & SIMULATION
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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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Introductory modeling for decision-making using AMPL
e-Learning CoursesIntroductory modeling for decision-making using AMPL
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Modeling projects for decision-making using AMPL
e-Learning CoursesModeling projects for decision-making using AMPL
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Numerical Modeling of Hydrosystems 2023/2024
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublicationMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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Ahmer Bin Hafeez
PeopleI have experience in Microbiology & Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. Currently, my interest lies in translatable omics studies and drug discovery against novel protein targets involved in cancer and infectious diseases and Host-Pathogen PPIs. My aim involves the use of computational methods for the identification of novel targets and to...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Nonlinear planar modeling of massive taut strings travelled by a force-driven point-mass
PublicationThe planar response of horizontal massive taut strings, travelled by a heavy point-mass, either driven by an assigned force, or moving with an assigned law, is studied. A kinematically exact model is derived for the free boundary problem via a variational approach, accounting for the singularity in the slope of the deflected string. Reactive forces exchanged between the point-mass and the string are taken into account via Lagrange...
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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublicationParylene C, poly(chloro-para-xylylene) is the most widely used member of the parylene family due to its excellent chemical and physical properties. In this work we analyzed the formation of the parylene C film using molecular mechanics and molecular dynamics methods. A five unit chain is necessary to create a stable hydrophobic cluster and to adhere to a covered surface. Two scenarios were deemed to take place. The obtained results...
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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Numerical Modeling of Hydrosystems 2022/2023 (summer)
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
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Numerical Modeling of Hydrosystems 2022/2023 (winter)
e-Learning CoursesKurs do przedmiotu NUMERICAL MODELING OF HYDROSYSTEMS Specjalność: Environmental Engineering (WILiŚ), II stopnia, stacjonarne dr hab. inż. Michał Szydłowski, prof. PG
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Computer modeling and design of materials 2022/2023
e-Learning CoursesComputer modeling and design of materials, kierunek: Nanotechnologia, specjalność: Mathematics for new materials design, II stopień, semestr 3
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Prediction of Overall In Vitro Microsomal Stability of Drug Candidates Based on Molecular Modeling and Support Vector Machines. Case Study of Novel Arylpiperazines Derivatives
PublicationOther than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach its therapeutic site of action. Despite many recent excellent achievements in the field of computational methods supporting drug metabolism studies, a well-recognized procedure to model...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublicationWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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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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Multiscale and Multidisciplinary Modeling, Experiments and Design
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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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Modeling in Machine Design
e-Learning CoursesThe course is meant to show the students how to build calculation models in machine design
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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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Dynamics of S-unimodal maps used in population modeling.
Open Research DataS-unimodal maps are maps of the interval with negative Schwarzian derivative and having only one turning point (such that the map is increasing to the left of the turning point and decreasing to the right of it). Theory of S-unimodal maps is now a well-developed branch of discrete dynamical systems, including famous Singer theorem which implies existence...
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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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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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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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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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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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Journal of Chemical Information and Modeling
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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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JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
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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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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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A Maximum-Likelihood Approach to Force-Field Calibration
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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...