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Search results for: Universal Force Field
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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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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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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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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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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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A Simple Neural Network for Collision Detection of Collaborative Robots
PublicationDue to the epidemic threat, more and more companies decide to automate their production lines. Given the lack of adequate security or space, in most cases, such companies cannot use classic production robots. The solution to this problem is the use of collaborative robots (cobots). However, the required equipment (force sensors) or alternative methods of detecting a threat to humans are usually quite expensive. The article presents...
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Współczynniki strat energetycznych w elementach napędu hydrostatycznego
PublicationW każdym układzie napędowym należy zastąpić obraz przepływu mocy opisany dotychczas powszechnie stosowanym wykresem Sankey’a spadku mocy zgodnego z kierunkiem przepływu mocy proponowanym przez autora wykresem wzrostu mocy w układzie przeciwnego do kierunku przepływu mocy. Należy więc opisywać straty i sprawność energetyczną a także pole pracy każdego silnika i układu napędowego jako zależne od wielkości fizycznych niezależnych...
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Experiments with the Universal Constructor in the DigiHive Environment
PublicationThe paper discusses the performance and limitations of the universal constructor embedded in the DigiHive environment and presents the result of two simulation experiments showing the possibility of workaround the limitations.
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Information transfer during the universal gravitational decoherence
PublicationRecently Pikovski et al. (Nat Phys 11:668, 2015) have proposed in an intriguing universal decoherence mechanism, suggesting that gravitation may play a conceptually important role in the quantum-to-classical transition, albeit vanishingly small in everyday situations. Here we analyze information transfer induced by this mechanism. We show that generically on short time-scales, gravitational decoherence leads to a redundant information...
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Grzebowiska dla zwierząt w Polsce
PublicationW niniejszym artykule podjęto tematykę miejsc pochówku zwierząt. Problem został omówiony w odniesieniu do terenu Polski na tle przykładów z zagranicy. Współczesne grzebowiska dla zwierząt powstają w naszym kraju od niedawna i mimo że cmentarze dla zwierząt są u nas stosunkowo nowym zjawiskiem, to już teraz można dostrzec ich typowe cechy przestrzenne. Autorka, na co dzień zajmująca się zagadnieniami z dziedziny architektury, starała...
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Method for universal detection of two-photon polarization entanglement
PublicationDetecting and quantifying quantum entanglement of a given unknown state poses problems that are fundamentally important for quantum information processing. Surprisingly, no direct (i.e., without quantum tomography) universal experimental implementation of a necessary and sufficient test of entanglement has been designed even for a general two-qubit state. Here we propose an experimental method for detecting a collective universal...
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Zestaw STEVAL PCC009V1 i biblioteki Universal Dongle
PublicationW artykule przedstawiono zestaw STEVAL PCC009V1 i dołączone do niego biblioteki programistyczne Universal Dongle. Sposób ich wykorzystania pokazano na przykładzie komunikacji z akcelerometrem ST LIS35DE.
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Constructing a map of an anonymous graph: applications of universal sequences
PublicationWe study the problem of mapping an unknown environmentrepresented as an unlabelled undirected graph. A robot (or automaton)starting at a single vertex of the graph G has to traverse the graph and return to its starting point building a map of the graph in the process. We are interested in the cost of achieving this task (whenever possible) in terms of the number of edge traversal made by the robot. Another optimization criteria...
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Towards Universal Visualisation of Emotional States for Information Systems
PublicationThe paper concerns affective information systems that represent and visualize human emotional states. The goal of the study was to find typical representations of discrete and dimensional emotion models in terms of color, size, speed, shape, and animation type. A total of 419 participants were asked about their preferences for emotion visualization. We found that color, speed, and size correlated with selected discrete emotion...