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Search results for: POTENTIAL OF MEAN FORCE
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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size
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Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit
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Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods
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CENTRAL-FORCE DECOMPOSITION OF THE TERSOFF POTENTIAL
PublicationCentral forces play important role in the analysis of results obtained with particle simulation methods, since they allow evaluating stress fields. In this work we derive expressions for a central-force decompositon of the Tersoff potential, which is often used to describe interatomic interactions in covalently bonded materials. We simplify the obtained expressions and discuss their properties.
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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains
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Effect of mean grain diameter on vortices, force chains and local volume changes in granular shear zones
PublicationW artykule pokazano rozwój różnych zjawisk mikrostrukturalnych na poziomie ziarna materiału granulowanego podczas parcia pasywnego piasku na sztywną ściankę przemieszczającą się poziomo. Obliczenia wykonano stosując metodę DEM. Wyniki na poziomie globalnym porównano z wynikami MES. Szczególna uwagę zwrócono na rozwój wirów i łańcuchów sił miedzy ziarnami.
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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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Central-force decomposition of spline-based modified embedded atom method potential
PublicationCentral-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in...
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Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water
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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains
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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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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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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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Towards hand grip force assessment by using EMG estimators
PublicationThe purpose of this study was to propose a method to assess individual regression (calibration) curves to establish a relationship between an isometric grip force and surface electromyography (EMG) estimator. In this study 18 healthy volunteers (12 male (23.0 ± 2.0 years) and 6 female (23.2 ± 0.7 years)) had been examined. Ten EMG estimators (mean absolute value, root mean square, entropy, energy, turns per second, mean of zero...
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Lamb wave-based monitoring of shear failure of an adhesive lap joint
PublicationThe paper presents a study on the elastic wave propagation in adhesive joints of steel plates subjected to tensile loading. A single lap joint was chosen for analysis because of its simplicity and plurality of applications. Experimental investigations consisted of the uniaxial extension of prepared specimens. Force and displacement values were recorded by a testing machine. Simultaneously, guided Lamb waves were excited and signals...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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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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Study of Nanohydroxyapatite Coatings Prepared by the Electrophoretic Deposition Method at Various Voltage and Time Parameters
PublicationThe aim of the work is to compare the properties of nanohydroxyapatite coatings obtained using the electrophoretic deposition method (EDP) at 10 V, 20 V, and 30 V, and with deposit times of 2 and 5 min. The primary sedimentation was used to minimize the risk of the formation of particle agglomerates on the sample surface. Evaluation of the coating was performed by using a Scanning Electron Microscope (SEM), Energy-Dispersive Spectroscopy...
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Torque Transmitted by Multi-plate Wet Clutches in Relation to Number of Friction Plates and Their Dimensions
PublicationIn the paper results of experimental tests on multi-plate wet clutch torque capacity for various diameters and numbers of friction plates are presented. Construction of an apparatus for laboratory tests of wet clutch engagement, drag torque and maximum torque is shown. Methodology of maximum torque capacity experiment and hydraulic circuit diagram, which supplies a motor and an actuator for the experiment are described. Analytically...
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Application of magnetic nanoparticles for magnetic solid-phase extraction in preparing biological, environmental and food samples
PublicationThe need to obtain meaningful results as the basis for determining the content of trace amounts of analytes has become the driving force behind the development of modern analytical techniques, including sample-preparation techniques, such as solid-phase extraction (SPE). Recently, great interest was aroused in the use of magnetic nanoparticles (MNPs) in SPE. These materials exhibit high selectivity, and, in small amounts, can provide...
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Wykorzystanie kamery termowizyjnej nowej generacji do oceny wpływu sił ortodontycznych na dziąsło = The application of a new-generation thermal imaging camera for the assessment of hemodynamic changes in gingiva during orthodontic treatment
PublicationIntroduction. One ot the most interesting modern methods of assessing microcirculation is thermovisiual examination. Thermovision cameras are commonly used in general medicine. As the periodontium is one of the most vascularized tissues in the human body, the application of high-sensitivity thermovision cameras may allow tor noninvasive asses- sment and early detection ot pathological changes in the gingiva by giving a complete...
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The Concept of Accuracy Analysis of the Vertical Displacements Gained from the Hydrostatic Levelling Systems’ Measurements
PublicationAbstract: Nowadays, hydrostatic levelling is a widely used method for the vertical displacements’ determinations of objects such as bridges, viaducts, wharfs, tunnels, high buildings, historical buildings, special engineering objects (e.g., synchrotron), sports and entertainment halls. The measurements’ sensors implemented in the hydrostatic levelling systems (HLSs) consist of the reference sensor (RS) and sensors located on the...
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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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A newly-developed model for predicting cutting power during wood sawing with circular saw blades
PublicationIn the classical approach, cutting forces and cutting power in sawing processes of orthotropic materials such as wood are generally calculated on the basis of the specific cutting resistance kc (cutting force per unit area of cut). For every type of sawing kinematics (frame saws, band saws and circular sawing machines) different empirical values of specific cutting resistance kc have to be applied. It should be emphasised that...
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Theoretical consideration of free convective heat transfer from a round isothermal plate slightly inclined from the vertical
PublicationA semi-analytical solution of simplified Navier-Stokes and Fourier-Kirchhoff equations describing free convective heat transfer from a round isothermal surface slightly inclined from the vertical is presented. The solution is based on the assumption, typical for natural convection, that the velocity component normal to the surface is negligibly small in comparison to the tangential one. Next we neglect the nonlinear inertia force...
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Sensitivity analysis based on non-intrusive regression-based polynomial chaos expansion for surgical mesh modelling
PublicationThe modelling of a system containing implants used in ventral hernia repair and human tissue suffers from many uncertainties. Thus, a probabilistic approach is needed. The goal of this study is to define an efficient numerical method to solve non-linear biomechanical models supporting the surgeon in decisions about ventral hernia repair. The model parameters are subject to substantial variability owing to, e.g., abdominal wall...
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INFLUENCE OF CERAMIC COATING ON MECHANICAL PROPERTIES OF STAINLESS STEEL
PublicationCrystal structure and phase composition of stainless steel substrates (AISI 304 type) was studied and it was found that they adopted the cubic symmetry. The calculated elementary cell parameter for the mayor Fe-Ni phase (weight fraction 99%) was a = 3.593 Å, whereas the mean grain size was = 2932 Å. Morphology of the stainless steel substrate surface was studied with profilometry. Mechanical properties of the stainless steel...
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Visual method for detecting critical damage in railway contact strips
PublicationEnsuring an uninterrupted supply of power in the electric traction is vital for the safety of this important transport system. For this purpose, monitoring and diagnostics of the technical condition of the vehicle's power supply elements are becoming increasingly common. This paper presents a new visual method for detecting contact strip damage, based on measurement and analysis of the movement of the overhead contact line (OCL)...
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Development and test of fex, a fingers extending exoskeleton for rehabilitation and regaining mobility
PublicationThis paper presents the design process of an exoskeleton for executing human fingers' extension movement for the rehabilitation procedures and as an active orthosis purposes, together with its first clinical usability tests of a robotic exoskeleton. Furthermore, the Fingers Extending eXoskeleton (FEX) is a serial, under-actuated mechanism capable of executing fingers' extension. FEX is based on the state-of-art FingerSpine serial...
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Drill holes decrease cancellous bone strength: A comparative study of 33 paired osteoporotic human and 9 paired artificial bone samples
PublicationThis study was designed to compare compressive strength of cancellous bone retrieved from the femoral head in a specimen with and without guide wire hole, with comparison to synthetic bone samples. Femoral heads retrieved from 33 patients who sustained femoral neck fractures and underwent hip arthroplasty were cut into cuboids leaving two matching samples from the same femoral head. Similar samples were prepared from synthetic femurs....
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Hydrogen production from wood waste by mean of dark fermentation
PublicationThe utilization of wood wastes in clean and green chemistry method like by mean of dark fermentation, is a highly desired solution of waste management. In the article model for the estimation hydrogen potential of wood waste is given. The model has been used to calculate the potential theoretical hydrogen mass that can be produced from wood wastes in Pomerania and Silesia: pine, spruce, fir, beech and oak. In the introduction,...
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Experimental and numerical study on deformed steel columns subjected to impact load during earthquakes
PublicationThe soft-storey failure is one of the most typical types of damage observed in buildings during earthquakes. The failure of an upper soft storey of a structure results in large impact load acting on the lower floors and if the resistance of the structural members of the lower storeys is not sufficient it may further lead to progressive collapse of the whole building. The aim of the present paper is to investigate the dynamic behaviour...
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Homoclinics for singular strong force Lagrangian systems
PublicationWe study the existence of homoclinic solutions for a class of generalized Lagrangian systems in the plane, with a C1-smooth potential with a single well of infinite depth at a point ξ and a unique strict global maximum 0 at the origin.Under a strong force condition around the singular point ξ, via minimization of an action integral, we will prove the existence of at least two geometrically distinct homoclinic solutions.
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Highly antifouling polymer-nanoparticle-nanoparticle/polymer hybrid membranes
PublicationWe introduce highly antifouling Polymer-Nanoparticle-Nanoparticle/Polymer (PNNP) hybrid membranes as multi-functional materials for versatile purification of wastewater. Nitrogen-rich polyethylenimine (PEI)-functionalized halloysite nanotube (HNT-SiO2-PEI) nanoparticles were developed and embedded in polyvinyl chloride (PVC) membranes for protein and dye filtration. Bulk and surface characteristics of the resulting HNT-SiO2-PEI...
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Dedicated scheduling of tasks to minimize mean flow time
PublicationThis paper investigates the complexity of scheduling biprocessor tasks on dedicated processors to minimize mean flow time. Since the general problem is strongly NP-hard, we assume some restrictions on task lengths and the structure of associated scheduling graphs. Of particular interest are acyclic graphs. In this way we identify a borderline between NP-hard and polynomially solvable special cases.
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Enhancing capabilities of Atomic Force Microscopy by tip motion harmonics analysis
PublicationMotion of a tip used in an atomic force microscope can be described by the Lennard-Jones potential, approximated by the van der Waals force in a long-range interaction. Here we present a general framework of approximation of the tip motion by adding three terms of Taylor series what results in non-zero harmonics in an output signal. We have worked out a measurement system which allows recording of an excitation tip signal and its...
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Mean Crossover in evolutionary path planning method for maritime collision avoidance
PublicationAbstract: This paper presents the use of mean crossover genetic operator for path planning using evolutionary algorithm for collision avoidance on sea. Mean crossover ensures widening of the possible solutions' set that can be achieved in comparison to exchange crossover variant. The research shown, that the mean crossover allows to achieve results independent from the initial generation and quicker transition of thealgorithm from...
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On the Usefulness of the Generalised Additive Model for Mean Path Loss Estimation in Body Area Networks
PublicationIn this article, the usefulness of the Generalised Additive Model for mean path loss estimation in Body Area Networks is investigated. The research concerns a narrow-band indoor off-body network operating at 2.45 GHz, being based on measurements performed with four different users. The mean path loss is modelled as a sum of four components that depend on path length, antenna orientation angle, absolute difference between transmitting...
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MEAN SHIFT BASED SEGMENTATION FOR BLEEDING REGIONS IN ENDOSCOPIC VIDEOS
PublicationWith a set of 38 manually marked bleeding regions form endoscopic videos, the authors attempted to find an optimal image segmentation method for reproducing doctor’s markup. Mean shift segmentation combined with HSV histogram segmentation were used as a segmentation method, which was then optimized by tuning the parameters of the method using global optimization algorithm. A target function for measuring the quality of segmentation was...
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A space-efficient algorithm for computing the minimum cycle mean in a directed graph
PublicationAn algorithm is introduced for computing the minimum cycle mean in a strongly connected directed graph with n vertices and m arcs that requires O(n) working space. This is a considerable improvement for sparse graphs in comparison to the classical algorithms that require O(n^2) working space. The time complexity of the algorithm is still O(nm). An implementation in C++ is made publicly available at http://www.pawelpilarczyk.com/cymealg/.
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Two families of infinitely many homoclinics for singular strong force Hamiltonian systems
PublicationWe are concerned with a planar autonomous Hamiltonian system with a potential possessing a single well of infinite depth at a point X and a unique strict global maximum 0 at a point A. Under a strong force condition around the singularity X, via minimization of an action integral and using a shadowing chain lemma together with simple geometrical arguments, we prove the existence of infinitely many geometrically distinct homoclinic...
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Perceptual and Motor Effects of Muscle Co-activation in a Force Production Task
PublicationWe tested several predictions of the theory of motor control with spatial referent coordinates related to effects of muscle coactivation on force production and perception. In particular, we predicted that subjects would produce unintentional force increase by finger flexors and be unaware of this force increase. Healthy subjects performed steady force production task in isometric conditions with visual feedback on the force level....
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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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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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An Approach to Mean Path Loss Model Estimation for Off-Body Channels
PublicationThis paper presents an approach to estimation of the mean path loss model parameters in off-body Body Area Networks channels. In this approach, the path loss exponent is constrained to a value obtained for the line-of-sight (LoS) propagation in the co-polarised channel, considering a generalised static scenario. The comparison of the goodness of fit between the proposed approach and other approaches, for a set of measurements obtained...
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Problems in estimation of hand grip force based on EMG signal
PublicationThere has recently been a significant increase in the number of publications on and applications of bioelectric signals for diagnostic purposes. While the use of ECG (electrocardiography) is not surprising, the use of signals from registration of brain activity (EEG) and muscles activity (EMG) still finds new applications in various fields. The authors focus on the use of EMG signals for estimating hand grip force. Currently,...
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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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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...