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Wyniki wyszukiwania dla: 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
Dane BadawczeThe 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
Publikacjahas 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
PublikacjaThe 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
PublikacjaThe 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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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
PublikacjaWe 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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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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Density Functional Theory Studies on Ir Spectra of the Triphenylene Derivatives. A Scaled Quantum Mechanical Force Field Approach
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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
Dane BadawczeThe 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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Imaging of ferroelectric properties of sinter by means of Piezoresponse Force Microscopy
Dane BadawczeFerroelectricity is a property of certain materials [1], characterized by a spontaneous electrical polarization that can be reversed by applying an external electric field. Ferroelectric properties can be used to make capacitors with adjustable capacity. The permeability of ferroelectrics is not only regulated, but usually also very high, especially...
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Anna Wałek dr
OsobyDr Anna Wałek, Prezydent International Association of University Libraries (IATUL), dyrektor Biblioteki Politechniki Gdańskiej, ekspert w zakresie otwartego dostępu do zasobów naukowych (Open Science, Open Access, Open Research Data) oraz organizacji i zarządzania biblioteką naukową. Od lutego 2023 r. ekspert i Koordynator Hubu Wschodniego (East Hub) w ramach projektu Focusing on Open, Collaboration and Useful Science (EOSC Focus)...
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Raw data for the paper "Mutually polarizable QM/MM model with in situ optimized localized basis functions"
Dane BadawczeThis dataset contains raw data used to generate plots in the paper Mutually polarizable QM/MM model with in situ optimized localized basis functions. The paper is devoted to a second generation of the TINKTEP model -- an QM/MM approach combining linear-scaling DFT (ONETEP) and a polarizable force field (AMOEBA).
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Tensile strength test of PE foils modified with zinc oxide and zinc salts
Dane BadawczeThis 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
Dane BadawczeThe 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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Electronic conductivity in the SiO2-PbO-Fe2O3 glass containing magnetic nanostructures
PublikacjaThe 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
PublikacjaThis 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
Dane BadawczeThe 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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Imaging of graphene surface by means of tapping mode AFM
Dane BadawczeGraphene [1] is a material consisting of carbon planes with a hexagonal structure. One of the facts of interest from a purely scientific point of view is the very high mobility of electrons in the described material, allowing the study of relativistic effects inside a solid sample. Other features, such as bactericidal activity, make graphene an interesting...
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Wave propagation signals in concrete beams under 3-point bending
Dane BadawczeThe 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...