Search
Filters
total: 14169
filtered: 10561
-
Catalog
- Publications 10561 available results
- Journals 426 available results
- Conferences 19 available results
- People 277 available results
- Projects 10 available results
- Laboratories 1 available results
- e-Learning Courses 158 available results
- Events 9 available results
- Open Research Data 2708 available results
Chosen catalog filters
displaying 1000 best results Help
Search results for: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
-
Finite element modeling of shear localization in granular bodies in hypoplasticity with enhancements
PublicationW pracy omówiono wyniki numeryczne lokalizacji okształceń stycznych w materiałach granulowanych. Obliczenia wykonano stosując prawo hipoplastyczne z rozszerzeniami w ramach mechaniki ośrodka gradientowego, nielokalnego i mikropolarnego. Obliczenia przeprowadzono dla różnych problemów brzegowych z uwzględnieniem lokalizacji. Wyniki analiz porównano z doświadczeniami.
-
Modeling of wood frame structures with different insulation materials under damaging dynamic loading
PublicationWood frame buildings are very popular in regions that are exposed to different dynamic excitations, such as damaging earthquakes. Their seismic resistance is really important in order to prevent structural damages and human losses. This paper presents the results of advanced numerical investigation carried out using the FEM. Based on the models of wall panels, the numerical model of real structure of the wood frame building has...
-
Combining tight-binding and molecular dynamics methods to model the behaviour of metals in the plastic regime
PublicationOpisujemy zastosowanie metody dwuskalowej (kwantowo-klasycznej) w zastosowaniu do metali. Region energetycznie najważniejszy jest traktowany kwantowo, podczas gdy reszta układu jest traktowana klasycznie. Wprowadzamy własną implementację metody oraz przedstawiamy uzyskane wyniki dla metali.
-
Triticale extrudates – Changes of macrostructure, mechanical properties and molecular water dynamics during hydration
Publication -
MEL zeolite nanosheet membranes for water purification: insights from molecular dynamics simulations
Publication -
Crystal and molecular structure of bis(O,O'-diethyldithiophosphato-S,S')nickel(II): A redetermination
PublicationDoniesienie przedstawia ponownie wyznaczoną strukturę tytułowego, centrosymetrycznego kompleksu, [Ni{S2P(OC2H5)2}2]. Centralny rdzeń (S2P)2 jest płaski, co potwierdza wcześniejsze wyniki uzyskane przez McConnell'a i Kastalsky'ego, przy czym odchylenia standardowe są około siedmiokrotnie mniejsze oraz wyznaczono wszystkie pozycje atomów wodoru. W strukturze krystalicznej zaobserwowano róznież parę krótkich kontaktów HH (2.33 Å).
-
Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublicationAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
-
Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublicationWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
-
MutL protein as a constituent of vsp, ner and mmr repair systems
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
-
The anion [Mg6Cl8Cp*5]-: a final intermediate on the way to the molecular donor-free Grignard compound MgClCp*?
PublicationOtrzymano i scharakteryzowano strukturalnie rzadki przypadek związku Grignarda pozbawionego donora. Struktura krystaliczna [Mg6Cl8Cp*5][AlCp*2] C6H6 zawiera zarówno metallocen (Cp*AlCp*) jak i odwrócony metallocen (MgCp*Mg).
-
Enhancement of the Magnetic Coupling in Exfoliated CrCl 3 Crystals Observed by Low‐Temperature Magnetic Force Microscopy and X‐ray Magnetic Circular Dichroism
PublicationMagnetic crystals formed by 2D layers interacting by weak van der Waals forces are currently a hot research topic. When these crystals are thinned to nanometric size, they can manifest strikingly different magnetic behavior compared to the bulk form. This can be the result of, for example, quantum electronic confinement effects, the presence of defects, or pinning of the crystallographic structure in metastable phases induced by...
-
Effect of the template-assisted electrodeposition parameters on the structure and magnetic properties of Co nanowire arrays
Publication -
Collision-Free Network Exploration
PublicationA set of mobile agents is placed at different nodes of a n-node network. The agents synchronously move along the network edges in a collision-free way, i.e., in no round may two agents occupy the same node. In each round, an agent may choose to stay at its currently occupied node or to move to one of its neighbors. An agent has no knowledge of the number and initial positions of other agents. We are looking for the shortest possible...
-
In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublicationDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
-
Density Functional Theory Studies on Ir Spectra of the Triphenylene Derivatives. A Scaled Quantum Mechanical Force Field Approach
Publication -
Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
Publication -
Image-based numerical modeling of the tensile deformation behavior and mechanical properties of additive manufactured Ti–6Al–4V diamond lattice structures
PublicationThis work concerns the numerical modeling of the deformation process and mechanical properties of structures obtained by the additive method laser power bed fusion (LPBF). The investigation uses diamond structures of Ti–6Al–4V titanium implantation alloy with various relative densities. To model the process of tensile deformation of the materials, geometric models were used, mapping the realistic shape of the examined structures....
-
Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
-
Analysis of molecular structure of starch citrate obtained by a well-stablished method
Publication -
Spin probe dynamics in relation to free volume in crystalline organics from ESR and PALS: N-tridecane
Publication -
Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
-
Collision-free network exploration
PublicationMobile agents start at different nodes of an n-node network. The agents synchronously move along the network edges in a collision-free way, i.e., in no round two agents may occupy the same node. An agent has no knowledge of the number and initial positions of other agents. We are looking for the shortest time required to reach a configuration in which each agent has visited all nodes and returned to its starting location. In...
-
The Boltzmann sequence-structure channel
PublicationWe rigorously study a channel that maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein statistics. This channel, which we also call the Boltzmann sequence-structure channel, is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. In our previous work, we verified experimentally that the channel capacity has a phase transition for...
-
The Metal-Free Regioselective Deuteration of 2-Methylquinolin-8-ol and 2,5-Dimethylquinolin-8-ol, Spectroscopic and Computational Studies
PublicationAbstract: Aim and Background: Introducing deuterium to a molecule is of interest to a wide variety of research, including investigation of reaction mechanisms or kinetics, analysis of drug metabolism, structural elucidation of molecules, and syntheses of isotopically labeled materials used for NMR spectroscopy and medicinal research. Objective: The transition-metal-free regioselective deuteration of 2-methylquinolin-8-ol...
-
Sustainable Investing. Socio-Economic Impacts of Exchange-Traded Funds
PublicationSustainable Investing: Socio-Economic Impacts of Exchange-Traded Funds examines the social and economic effects of sustainable investing ETFs and their impacts on the global financial system. The book presents the key issues with regard to sustainable investing, discussing exchange-traded funds mechanisms and categories in comparison to competing investment funds. The book outlines the theoretical determinants of ETF markets development...
-
CORPORATE BANKRUPTCY PREDICTION IN POLAND AGAINST THE BACKGROUND OF FOREIGN EXPERIENCE
PublicationIn highly developed countries, research in the field of bankruptcy risk prediction has been conducted for many years. For example, in the United States, which can be considered a pioneering country, the first publications appeared in the early twentieth century. In Poland, due to political and economic reasons, the interest in this issue dates back to the early 1990s. For this reason, this publication attempts to answer the following...
-
CORPORATE BANKRUPTCY PREDICTION IN POLAND AGAINST THE BACKGROUND OF FOREIGN EXPERIENCE
PublicationIn highly developed countries, research in the field of bankruptcy risk prediction has been conducted for many years. For example, in the United States, which can be considered a pioneering country, the first publications appeared in the early twentieth century. In Poland, due to political and economic reasons, the interest in this issue dates back to the early 1990s. For this reason, this publication attempts to answer the following...
-
A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublicationRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
-
Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
-
Theoretical Design of the Molecular Structure of Bent-Core Mesogens with Large Second-Order Nonlinear Optical Properties
PublicationABSTRACT: The first hyperpolarizability of two series of moleculeswith bent-shaped structures has been calculated at the ab initio level.The two series consist of carboxyl derivatives for which somemolecules are known to exhibit banana phases and of their sulfinatehomologues that have not been synthesized yet. The final purpose isto reveal the relevance or not in synthesizing these latter molecules.The strategy is based on reporting...
-
New insights into modeling two-step nitrification in activated sludge systems – The effects of initial biomass concentrations, comammox and heterotrophic activities
PublicationIn this study, the conventional two-step nitrification model was extended with complete ammonia oxidation (comammox) and heterotrophic denitrification on soluble microbial products. The data for model calibration/validation were collected at four long-term washout experiments when the solid retention time (SRT) and hydraulic retention time (HRT) were progressively reduced from 4 d to 1 d, with mixed liquor suspended solids (MLSS)...
-
Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case
PublicationThis paper presents the impact of the choice of building representation techniques and hydrodynamic models on urban flood simulations using HEC-RAS 2-D for the Toce River physical model. To this end, eight numerical models based on previous laboratory experiments were prepared to simulate unsteady urban flooding on each side of building units. Two simplified building layouts (aligned and staggered) were examined, where models were...
-
Escherichia coli K-12 suppressor-free mutants lacking early glycosyltransferases and late acyltransferases. Minimal lipopolysaccharide structure and induction of envelope stress response.
PublicationTo elucidate the minimal lipopolysaccharide (LPS) structure needed for the viability of Escherichia coli, suppressor-free strains lacking either the 3-deoxy-d-manno-oct-2-ulosonic acid transferase waaA gene or derivatives of the heptosyltransferase I waaC deletion with lack of one or all late acyltransferases (lpxL/M/P) and/or various outer membrane biogenesis factors were constructed. Δ(waaC lpxL lpxM lpxP) and waaA mutants exhibited...
-
Application of reversed-phase thin layer chromatography and QSRR modelling for prediction of protein binding of selected β-blockers
Publication -
Evaluation of the prediction ability of air pollutants based on the electronic nose responses
PublicationElectronic noses are able to perform on-line measurements of the toxic volatile compounds in air. Due to their low cost and compact size they can be placed in the areas exposed to pollution, outside the laboratory. Those advantages, on the other side, force the need for development of the reliable sensors data analysis procedures. One of the most important issues connected with electronic noses is the lack of stability of the gas...
-
Noncentrosymmetric Triangular Magnet CaMnTeO6: Strong Quantum Fluctuations and Role of s0 versus s2 Electronic States in Competing Exchange Interactions
PublicationNoncentrosymmetric triangular magnets offer a unique platform for realizing strong quantum fluctuations. However, designing these quantum materials remains an open challenge attributable to a knowledge gap in the tunability of competing exchange interactions at the atomic level. Here, a new noncentrosymmetric triangular S = 3/2 magnet CaMnTeO6 is created based on careful chemical and physical considerations. The model material...
-
Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
PublicationThe increasing interest in polyurethane materials has raised the question of the environmental impact of these materials. For this reason, the scientists aim to find an extremely difficult balance between new material technologies and sustainable development. This work attempts to validate the possibility of replacing petrochemical polyols with previously synthesized bio-polyols and their impact on the structure and properties...
-
Dynamics of quantum entanglement
PublicationA model of discrete dynamics of entanglement of a bipartite quantum state is considered. It involves a global unitary dynamics of the system and periodic actions of local bistochastic or decaying channel. For initially pure states the decay of entanglement is accompanied by an increase of von Neumann entropy of the system. We observe and discuss revivals of entanglement due to unitary interaction of subsystems. For some mixed states...
-
Numerical modeling of exciton impact in two crystalographic phases of the organo-lead halide perovskite (CH3NH3PbI3) solar cell
PublicationTo improve the power conversion efficiency of solar cells based on organo–lead halide perovskites, a detailed understanding of the device physics is fundamental. Here, a computational analysis of excitons impact is reported for these types of photocell. Numerical calculations based on the model, which take into account electronic charge carriers (electrons and holes), excitons and ions, have been carried out. The role of excitons...
-
The Comparison of the Crypto- and Fiat Currencies’ Exchange Rate Volatility in The Years 2015–2017
PublicationThe article describes the issues related to exchange rate volatility of crypto- and fiat currencies. The first part presents the issue of exchange rate volatility as well as methods of its evaluation and criteria of the conducted research. In the next part the author presented the essence of currencies and the main currency i.e. fiat money in the global economy in terms of the volume of transactions on the FOREX market. Then the...
-
Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublicationNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
-
Dynamics of Ice Jam Formation and Release
PublicationThe numerical model DynaRICE and its application to ice jam formation and release is presented. The model is a two-dimensional coupled flow and ice dynamic model. The ice dynamic component, which includes both the internal ice resistance and boundary friction on ice motion, uses a Lagrangian SPH method. The hydrodynamic component of the model uses a streamline upwind finite element method, which is capable of simulating trans-critical...
-
Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
-
MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
-
Modelling gene expression of a self-regulating protein
PublicationWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
-
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....
-
Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation
PublicationIntroduction: Carbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule–CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics. Methods: Herein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession...
-
Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
-
General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
-
Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublicationW 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.