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Search results for: RIVER ICE DYNAMICS
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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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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Area-Averaged Surface Moisture Flux over Fragmented Sea Ice: Floe Size Distribution Effects and the Associated Convection Structure within the Atmospheric Boundary Layer
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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EARTHQUAKE ENGINEERING & STRUCTURAL DYNAMICS
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CLIMATE DYNAMICS
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Transcriptome Dynamics Underlying Planticine®-Induced Defense Responses of Tomato (Solanum lycopersicum L.) to Biotic Stresses
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Ammonium sorption from aqueous solutions by the natural zeolite Transcarpathian clinoptilolite studied under dynamics conditons
PublicationPrzeprowadzone badania z wykorzystaniem wodnych roztworów modelowych amoniaku mogą stanowić podstawę do następujących wniosków:- maksymalna pojemność sorpcyjna klinoptylolitu w stosunku do jonów NH4+ w warunkach dynamicznych jest zdecydowanie wyższa niż w warunkach statycznych,- proces usuwania jonów amonowych podlega intensyfikacji w przypadku zastosowania frakcji zeolitu o mniejszej średnicy ziaren,- istotną rolę w procesie sorpcji...
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New possibilities of the passive layer cracking dynamics detection using a new Dynamic Electrochemical Impedance Spectroscopy.
PublicationNowa metoda Dynamicznej Elektrochemicznej Spektroskopii Impedancyjnej opracowana w Katedrze Elektrochemii, Korozji i Inżynierii Materiałowej Politechniki Gdańskiej daje możliwości określania charakterystyki impedancyjnej w dziedzinie czasu podczas procesu pękania ochronnej warstwy pasywnej. Fakt ten jest związany z procedurą analizującą wspomnianej techniki, która umożliwia selektywną analizę czasowo-częstotliwościową uzyskanych...
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Modelling of a medium-term dynamics in a shallow tidal sea, based on combined physical and neural network methods
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Impact of climate and humans on the range dynamics of the woolly mammoth (Mammuthus primigenius) in Europe during MIS 2
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Low-energy positron scattering from gas-phase pyrimidine: A quantum treatment of the dynamics and a comparison with experiments
PublicationWe are reporting detailed quantum scattering calculations that describe the diffusion of a beam of low-energy positrons interacting with the pyrimidine target as a gas-phase partner. The calculations have employed an essentially ab initio model for the short-range correlation interaction and for the electrostatic interaction of an impinging positron and the electron+nuclear structure of the target molecule at its equilibrium geometry.
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Conformation analysis and semiclassical dynamics study of charge exchange process induced by collision of C2+ ions with tetrahydrofuran
PublicationWe present the results of recent investigations of charge transfer processes in the collisions of C²⁺ ions with heterocyclic molecules of tetrahydrofuran.
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Regional effects of amphetamine, cocaine, nomifensine and GBR 12909 on the dynamics of dopamine release and metabolism in the rat brain
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Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
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Independent dynamics of slow, intermediate, and fast intracranial EEG spectral activities during human memory formation
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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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Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
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Spin probe dynamics in relation to free volume in crystalline organics from ESR and PALS: N-tridecane
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Gluten-Free Bread with Cricket Powder—Mechanical Properties and Molecular Water Dynamics in Dough and Ready Product
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Effect of the Relative Position of the Face Milling Tool towards the Workpiece on Machined Surface Roughness and Milling Dynamics
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Measurement Of The Dynamics Of The Sheave Block Of Shipyard Crane With 1000 T Lifting Capacity For Verification Of The Laboratory Stand
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Orientational order and dynamics of the dendritic liquid crystal organo-siloxane tetrapodes determined using dielectric spectroscopy
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Increasing Energy Efficiency and Productivity of the Comminution Process in Tumbling Mills by Indirect Measurements of Internal Dynamics—An Overview
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Investigation on the effect of anti-pitch fins for reducing the motion and acceleration of ships using computational fluid dynamics
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Chip suction system in circular sawing machine: empirical research and computational fluid dynamics numerical simulations
PublicationThe experimental analysis of the wood chip removing system during its redesigning in the existing sliding table circular saw and computational fluid dynamic (CFD) numerical simulations of the air flow process is presented in the paper. The attention was focused on the extraction hood and the bottom shelter of the actual existing system. The main aim was to perform experimental research on the pressure distribution inside the...
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Dynamics of Asymmetric Conflict: Pathways toward Terrorism and Genocide
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SAE International Journal of Vehicle Dynamics Stability and NVH
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Dynamics of Continuous, Discrete and Impulsive Systems Series A: Mathematical Analysis
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Expansion and population dynamics of a non-native invasive species: the 40-year history of American mink colonisation of Poland
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Diagnostics of UV Nanosecond Laser Generated Plasma Plume Dynamics in Ambient Air Using Time-Resolved Imaging
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Dynamics of cutting power during sawing with circular saw blades as an effect of wood properties changes in the cross section
PublicationIn the paper the effect of the method calculation upon the cutting power is presented. In computations were used models in which fracture toughness was incorporated. The comparison concerned models as follows: FM-CM – classic model in which the sum of all uncut chip thicknesses of the simultaneously teeth engaged represented the mean uncut chip thickness, FM-FDM – full dynamical model in which besides variable uncut chip thickness...
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Investigating the Ischaemic Phase of Skin NADH Fluorescence Dynamics in Recently Diagnosed Primary Hypertension: A Time Series Analysis
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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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Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies
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LF NMR spectroscopy analysis of water dynamics and texture of Gluten-Free bread with cricket powder during storage
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Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations
PublicationCalculations are reported for electron and positron scattering from isolated cytosine and thymine, where the two pyrimidinic single-ring DNA bases, in the gas-phase at energies near the elastic threshold, they reveal the special features of the dipole-driven scattering states. All molecules examined exhibit, in fact, supercritical (>1.67 D) permanent dipoles which can therefore also support, below threshold, excited bound compound...
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
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Hydrophobic and hydrophilic properties of pollutants as a factor influencing their redistribution during snowpack melt
PublicationGlaciers accumulate organic pollutants delivered by snow. However, our understanding of the exact dynamics of organic pollutants in the snowpack relies primarily on laboratory experiments and mathematical models. To fill the gap related to the detailed field data, we have conducted observations of melting snow profiles in two locations and three different stages of melting on one High Arctic glacier, as well as in superimposed...
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Optical method supported by machine learning for dynamics of C‐reactive protein concentrations changes detection in biological matrix samples
PublicationIn this article we present the novel spectroscopy method supported with machine learning for real-time detection of infectious agents in wastewater. In the case of infectious diseases, wastewater monitoring can be used to detect the presence of inflammation biomarkers, such as the proposed C-reactive protein, for monitoring inflammatory conditions and mass screening during epidemics for early detection in communities of concern,...
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Three-dimensional modeling and automatic analysis of the human nasal cavity and paranasal sinuses using the computational fluid dynamics method
PublicationPurpose The goal of this study was to develop a complete workflow allowing for conducting computational fluid dynam- ics (CFD) simulation of airflow through the upper airways based on computed tomography (CT) and cone-beam computed tomography (CBCT) studies of individual adult patients. Methods This study is based on CT images of 16 patients. Image processing and model generation of the human nasal cavity and paranasal sinuses...
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Metric entropy and digital image correlation in deformation dynamics analysis of fibre glass reinforced composite under uniaxial tension
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Historic bridge modelling using laser scanning, ground penetrating radar and finite element methods in the context of structural dynamics
PublicationPraca dotyczy modelowania MES zabytkowej konstrukcji mostowej przy użyciu danych geometrycznych pochodzących ze skanowania laserowego oraz georadaru. Z uwagi na brak badań materiału budujcego most, przeprowadza się analize wrażliwości konstrukcji na zmiany modułu sprężystości granitu.
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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