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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublikacjaIn 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
PublikacjaExascale 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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Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst
PublikacjaTime-dependent density functional theory calcula- tions combinedwith the Marcus theory of electron transfer (ET) were app lied on the molecular photocatalys t [(tbbpy) 2 Ru(tpph z)PdC l 2 ] 2 + in order to elucidate thelight-in- duced relaxation pathways populated upon excitation in the longer wavelength range of its absorption spectrum. The computational resultsshow that after the initial excitation, metal (Ru) to ligand (tpphz)chargetransfer...
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Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublikacjaW pracy przedstawiono wyniki symulacji wczesnych etapów kondensacji z fazy gazowej w układzie xH2O (1-x)N2. Przeanalizowano całkowitą liczbę klastrów, średni rozmiar klastra i rozmiar klastra maksymalnego w funkcji czasu.
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublikacjaPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
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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
PublikacjaIn 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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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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Transcriptome Dynamics Underlying Planticine®-Induced Defense Responses of Tomato (Solanum lycopersicum L.) to Biotic Stresses
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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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Gluten-Free Bread with Cricket Powder—Mechanical Properties and Molecular Water Dynamics in Dough and Ready Product
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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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Spin probe dynamics in relation to free volume in crystalline organics from ESR and PALS: N-tridecane
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Dynamics of changes in the concentration levels of organic pollutants in the proglacial waters of the Scott River (Spitsbergen, SW Svalbard)
PublikacjaThe study area covered the NW part of the Wedel Jarlsberg Land. The present study concerns participation of organic pollutants inflow from glacier and seaside plane of Calypsostranda to proglacial waters of the Scott River due to occurrence of precipitation. Concentration ranges for phenols and formaldehyde in water samples are respectively:
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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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Low-energy positron scattering from gas-phase pyrimidine: A quantum treatment of the dynamics and a comparison with experiments
PublikacjaWe 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
PublikacjaWe 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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Effect of the Relative Position of the Face Milling Tool towards the Workpiece on Machined Surface Roughness and Milling Dynamics
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Chip suction system in circular sawing machine: empirical research and computational fluid dynamics numerical simulations
PublikacjaThe 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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New possibilities of the passive layer cracking dynamics detection using a new Dynamic Electrochemical Impedance Spectroscopy.
PublikacjaNowa 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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Ammonium sorption from aqueous solutions by the natural zeolite Transcarpathian clinoptilolite studied under dynamics conditons
PublikacjaPrzeprowadzone 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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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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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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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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LF NMR spectroscopy analysis of water dynamics and texture of Gluten-Free bread with cricket powder during storage
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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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Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations
PublikacjaCalculations 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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A systematic approach to understand hydrogeochemical dynamics in large river systems: Development and application to the River Ganges (Ganga) in India
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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
PublikacjaIn 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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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublikacjaThe 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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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublikacjaPraca 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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Hydrophobic and hydrophilic properties of pollutants as a factor influencing their redistribution during snowpack melt
PublikacjaGlaciers 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...