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Search results for: Universal Force Field
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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...
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A Maximum-Likelihood Approach to Force-Field Calibration
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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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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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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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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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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field
PublicationSecondary structure is a solid scaffold on which the three-dimensional structure of a protein is built. Therefore, care must be taken to reproduce the secondary structure as accurately as possible in the simulations of protein systems. In this chapter, we summarize the physics-based energy terms that govern secondary-structure formation, the auxiliary restraints on secondary structure derived from bioinformatics and from the experimental...
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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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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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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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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Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
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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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Density Functional Theory Studies on Ir Spectra of the Triphenylene Derivatives. A Scaled Quantum Mechanical Force Field Approach
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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
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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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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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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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Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods
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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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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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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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Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
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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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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins
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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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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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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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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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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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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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Determination of mechanical properties of Ti13Nb13Zr cubes made with STL technology subjected to uniaxial compression
Open Research DataThe aim of the study was to determine the mechanical properties of Ti13Nb13Zr cubes made with STL technology (3D printing). The experiments were carried out on the Hung Ta universal test machine HT-2402. Cubes with the initial dimensions of 10x10x10 mm were subjected to compression by increasing force to over 80 kN. In various experiments, the angle...
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Anna Wałek dr
PeopleDr Anna Wałek, President of IATUL – International Association of University Libraries, director of the Gdańsk University of Technology Library. An experienced library manager, an expert in the field of Open Science, and organization and management of a scientific library. She conducts scientific research in data management in various scientific disciplines, metadata for research data, and data management support services - incl....
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Tensile strength test of PE foils modified with zinc oxide and zinc salts
Open Research DataThis dataset contains the results of PE foils mechanical tests, in which the material was evaluated for strength and extensibility at the moment of breaking and based on the same tests preceded by material fatigue in 50 stretching cycles. The principle of the method is to stretch the test sample placed in the clamps of the stretching apparatus at a...
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Compression test results of fused filamend fabricated polylactyde and polylactyde with carbon fiber filler
Open Research DataThe DataSet contains the results of the mechanical behaviour of cube specimens with dimensions 30 x 30 x 30 cm3. The specimens were additively manufactured with the fused filament fabrication (FFF) method. They used two different materials polylactide (PURE PLA) and polylactide with carbon fibre filler (PLA+CF). The specimens were segregated into three...
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Kazimierz Darowicki prof. dr hab. inż.
PeopleStudia wyższe ukończyłem w czerwcu 1981 roku po zdaniu egzaminu dyplomowego i obronie pracy magisterskiej. Opiekunem pracy magisterskiej był dr hab. inż. Tadeusz Szauer. W roku 1991, 27 listopada uzyskałem stopień naukowy broniąc pracę doktorską zatytułowaną „Symulacyjna i korelacyjna analiza widm immitancyjnych inhibitowanej reakcji elektrodowej”. Promotorem pracy był prof. dr hab. inż. Józef Kubicki (Wydział Chemiczny...
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Electronic conductivity in the SiO2-PbO-Fe2O3 glass containing magnetic nanostructures
PublicationThe linear impedance spectra of iron–silicate–lead glass samples were measured in the frequency range from 1 MHz to 1 MHz and in the temperature range from 153 K to 423 K. The structure was investigated by means of XRD and atomic force microscopy. Local electrical and magnetic properties of the samples were tested with the aid of electrostatic force microscopy (EFM) and magnetic force microscopy (MFM). The obtained results show...
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Experimental ultimate strength assessment of stiffened plates subjected to marine immersed corrosion
PublicationThis study experimentally analyses the impact of marine immersed corrosion degradation on the compressive strength of the stiffened plates where the lower degradation levels were considered. The corrosion degradation test was accelerated by controlling the natural corrosion environmental factors, avoiding applying an electric current. Different groups of corrosion degradation levels and initial plate thicknesses were investigated....
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Tensile test results of fused filamend fabricated polylactyde and polylactyde with carbon fiber filler
Open Research DataThe Dataset contains the results of the mechanical behaviour of dog-bone shaped specimens. The specimens were additively manufactured with the fused filament fabrication (FFF) method. They used two different materials polylactide (PURE PLA) and polylactide with carbon fibre filler (PLA+CF). The specimens were segregated into three groups - unsterilized,...
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Medially positioned plate in first metatarsophalangeal joint arthrodesis
PublicationObjective The purpose of this study was to biomechanically compare the stability of first metatarsophalangeal (MTP1) joint arthrodesis with dorsally and medially positioned plates. Methods A physical model of the MTP1 joint consists of printed synthetic bones, a titanium locking plate and screws. In the experiments, samples with dorsally and medially positioned plates were subjected to loading of ground load character in a universal...
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Wave propagation signals in concrete beams under 3-point bending
Open Research DataThe DataSet contains the results of the mechanical behaviour of a concrete beams with dimensions 40 x 40 x 160 cm3under the 3-point bending. The beams were made of concrete with the following ingredients: CEM I 42.5R (450 kg/m3), water (177 kg/m3), sand 0-2 (675 kg/m3) and gravel 2-8 (675 kg/m3). The bending test was performed using a Zwick/Roell Z10...