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Search results for: PROTEIN STRUCTURE PREDICTION, MULTISCALE MODELING, UNRES FORCE FIELD, FREE AND BIOINFORMATICS-ASSISTED MODELING, REPLICA-EXCHANGE MOLECULAR DYNAMICS
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ADAPTIVE PREDICTIONS OF THE EURO/ZŁOTY CURRENCY EXCHANGE RATE USING STATE SPACE WAVELET NETWORKS AND FORECAST COMBINATIONS
PublicationThe paper considers the forecasting of the euro/Polish złoty (EUR/PLN) spot exchange rate by applying state space wavelet network and econometric forecast combination models. Both prediction methods are applied to produce one-trading-day- ahead forecasts of the EUR/PLN exchange rate. The paper presents the general state space wavelet network and forecast combination models as well as their underlying principles. The state space...
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Structural Insights into σ1 Receptor Interactions with Opioid Ligands by Molecular Dynamics Simulations
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Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides
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Molecular Dynamics of Complexes of Atosiban with Neurohypophyseal Receptors in the Fully Hydrated Phospholipid Bilayer
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Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations
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Solvation of N-methylformamide by ethanol: a comparison of molecular dynamics calculations with the experimental data
PublicationWykonano obliczenia metodami dynamiki molekularnej dla tytułowego układu. Rezultaty porównano z uzyskanymi wcześniej wynikami pomiarów termodynamicznych oraz wnioskami z nich wyciągniętymi.
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Comparative molecular dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels
PublicationBadania polegały na przeprowadzeniu porównawczej dynamiki molekularnej dla dwóch typów kanałów amfoterycyny B. Obie symulacje różniły się rodzajem sterolu (cholesterol lub ergosterol). Na podstawie wyników przeprowadzonych prac ustalono jakie elementy strukturalne badanych kanałów mogą być odpowiedzialne za selektywne działanie amfoterycyny B.
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Molecular Dynamics study of short and medium range order in modified BGO glasses.
PublicationArtykuł przedstawia wyniki symulacji dynamiczno-molekularnychniemodyfikowanych i modyfikowanych szkieł BGO o różnych stechiometriach. Otrzymane wyniki dokładnie przedyskutowano pod kątem blisko- i średnio-zasięgowego uporządkowania atomów i porównano z innymi dostępnymi danymi literaturowymi.
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Modeling and optimizing the removal of cadmium by Sinapis alba L. from contaminated soil via Response Surface Methodology and Artificial Neural Networks during assisted phytoremediation with sewage sludge
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On Computationally-Efficient Reference Design Acquisition for Reduced-Cost Constrained Modeling and Re-Design of Compact Microwave Passives
PublicationFull-wave electromagnetic (EM) analysis has been playing a major role in the design of microwave components for the last few decades. In particular, EM tools allow for accurate evaluation of electrical performance of miniaturized structures where strong cross-coupling effects cannot be adequately quantified using equivalent network models. However, EM-based design procedures (parametric optimization, statistical analysis) generate...
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Modeling and simulation of blood flow under the influence of radioactive materials having slip with MHD and nonlinear mixed convection
PublicationRadioactive materials are widely in industry, nuclear plants and medical treatments. Scientists and workers in these fields are mostly exposed to such materials, and adverse effects on blood and temperature profiles are observed. In this regard, objective of the current study is to model and simulate blood based nanofluid with three very important radioactive materials, named as Uranium dioxide (UO2), Thorium dioxide (ThO2) and...
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Exploiting the S4–S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis
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Modeling Earth Systems and Environment
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Time-of-flight electron scattering from molecular hydrogen: Benchmark cross sections for excitation of the X1Σ+g→b3Σ+u transition
PublicationThe electron impact X1Σ+g to b3Σ+u transition in molecular hydrogen is one of the most important dissociation pathways to forming atomic hydrogen atoms, and is of great importance in modeling astrophysical and industrial plasmas where molecular hydrogen is a substantial constituent. Recently it has been found that the convergent close-coupling (CCC) cross sections of Zammit et al. [Phys. Rev. A 95, 022708 (2017)] are up to a factor...
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Performance of electrochemical immunoassays for clinical diagnostics of SARS-CoV-2 based on selective nucleocapsid N protein detection: Boron-doped diamond, gold and glassy carbon evaluation
PublicationThe 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later cause a global pandemic, which paralyzes the world since then. We have designed novel...
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Materials science. Quantum particle approach. 2022.
e-Learning Coursesquantum methods for materials and molecular modeling.
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Material Science Quantum Particle Approach 2021
e-Learning Coursesquantum methods for materials and molecular modeling.
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Measurements of Subnanometer Molecular Layers
PublicationSelected methods of formation and detection of nanometer and subnanometer molecular layers were shown. Additionally, a new method of detection and measurement with subnanometer resolution of layers adsorbed or bonded to the gate dielectric of the ion selective field effect transistor (ISFET) was presented.
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Tuning Ferulic Acid Solubility in Choline-Chloride- and Betaine-Based Deep Eutectic Solvents: Experimental Determination and Machine Learning Modeling
PublicationDeep eutectic solvents (DES) represent a promising class of green solvents, offering particular utility in the extraction and development of new formulations of natural compounds such as ferulic acid (FA). The experimental phase of the study undertook a systematic investigation of the solubility of FA in DES, comprising choline chloride or betaine as hydrogen bond acceptors and six different polyols as hydrogen bond donors....
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Katarzyna Merkel dr hab.
PeopleOver the past 15 years, my work has mainly been related to the study of liquid crystal compounds with a diverse structure (discotic, dendrimeric, banana, bimedogenic, uniaxial and biaxial nematics and smectics) as well as polymeric materials (biopolymers, nano-composites) and biological materials. My work concerned mainly the issues of organization, observation of orientation effects, studying the dynamics of molecular processes...
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Efficient Surrogate Modeling and Design Optimization of Compact Integrated On-Chip Inductors Based on Multi-Fidelity EM Simulation Models
PublicationHigh-performance and small-size on-chip inductors play a critical role in contemporary radio-frequency integrated circuits. This work presents a reliable surrogate modeling technique combining low-fidelity EM simulation models, response surface approximations based on kriging interpolation, and space mapping technology. The reported method is useful for the development of broadband and highly accurate data-driven models of integrated...
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Utilizing pulse dynamics for non-invasive Raman spectroscopy of blood analytes
PublicationNon-invasive measurement methods offer great benefits in the field of medical diagnostics with molecular-specific techniques such as Raman spectroscopy which is increasingly being used for quantitative measurements of tissue biochemistry in vivo. However, some important challenges still remain for label-free optical spectroscopy to be incorporated into the clinical laboratory for routine testing. In particular, non-analyte-specific...
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Modeling of TEC Variations Based on Signals from Near Zenith GNSS Satellite Observed by Dense Regional Network
PublicationCurrently the substantial successes in high-resolution ionospheric mapping is declared in many publications. Nevertheless, up to now there are no examples of dynamic visualization of TEC disturbances on regional scale with as high resolution as tropospheric models. Over the years, ionosphere has been modeling basing on the simple assumption, that it is a thin layer, which surrounds the Earth at some arbitrary height. However, the...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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Numerical Simulations and Tracer Studies as a Tool to Support Water Circulation Modeling in Breeding Reservoirs
PublicationThe article presents a proposal of a method for computer-aided design and analysis of breeding reservoirs in zoos and aquariums. The method applied involves the use of computer simulations of water circulation in breeding pools. A mathematical model of a pool was developed, and a tracer study was carried out. A simplified model of two-dimensional flow in the form of a biharmonic equation for the stream function (converted into...
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Dynamics of Chains as a Tool to Study Thermomechanical Properties of Proteins.
PublicationPolymer dynamics can be formulated on different levels of detail. One approach eliminates microscopic degrees of freedom and a polymer molecule is represented by a simplified structure—a chain. In the simplest case monomers of ideal chain have fixed length, and their orientation is independent of the orientations and positions of neighbouring monomers. This is reason that two monomers can co-exist at the same place. Ideal chain...
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Electric field-assisted dissociation of singlet excitons in tris-(8-hydro-xyquinolinato)aluminium (III)
PublicationW pracy podano szczegółowemu badaniu kompleks organo-metaliczny 8-hydroksy-chinoliny i aluminium (ALq3) metodą pomiaru fotopądów i elektromodulacji luminescencji. Stwierdzono, że w obszarze wysokich pól elektrycznych (F>105 V/cm) ładunek wytwarzany jest w procesie dysocjacji wzbudzonych stanów single-towych. Wyjaśnienie przebiegów prądowych w zakresie niskich pól elektrycznych (F<105 V/cm) wymagało włączenia zjawiska rekombinacji...
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The evaluation of COD fractionation and modeling as a key factor for appropriate optimization and monitoring of modern cost-effective activated sludge systems
PublicationA study was conducted to characterize the raw wastewater entering a modern cost effective municipal WWTP in Poland using two approaches; 1) a combination of modeling and carbonaceous oxygen demand (COD) fractionation using respirometric test coupled with model estimation (RTME) and 2) flocculation/filtration COD fractionation method combined with BOD measurements (FF-BOD). It was observed that the particulate fractions of COD obtained...
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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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International Journal of Computational Bioinformatics and In Silico Modeling
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Multicomponent ionic liquid CMC prediction
PublicationWe created a model to predict CMC of ILs based on 704 experimental values published in 43 publications since 2000. Our model was able to predict CMC of variety of ILs in binary or ternary system in a presence of salt or alcohol. The molecular volume of IL (Vm), solvent-accessible surface (Sˆ), solvation enthalpy (DsolvGN), concentration of salt (Cs) or alcohol (Ca) and their molecular volumes (Vms and Vma, respectively) were chosen...
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Proceedings of the 9th International Conference on Structural Dynamics, EURODYN 2014
PublicationSince offshore wind turbine supporting structures are subjected to dynamic environments with time-varying loading conditions, it is important to model their dynamic behavior and validate these models by means of vibrational experiments. In this paper assessment of dynamical state of the structure is investigated by means of both: numerical modeling, and experimental modal analysis. In experimental modal analysis, capturing the...
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The Opening of Central and Eastern European Countries to Free Trade: A Critical Assessment
PublicationThree decades after the fall of the Berlin wall and one and a half decades after the Big Bang enlargement of the European Union (2004-2007), we revisit contrasting narratives about the benefit of both free trade and the EU enlargement for Central and Eastern European (CEE) countries. We distinguish old, pre-2004 EU countries from CEE countries that joined the EU in 2004-2007, as well as from the CEE countries that have not become...
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Experimental Comparison of Straight Lines and Polynomial Interpolation Modeling Methods in Ship Evolutionary Trajectory Planning Problem
PublicationPaper presents the application of evolutionary algorithms and polynomial interpolation in ship evolutionary trajectory planning method and its comparison to classic approach, where trajectory is modeled by straight lines. Evolutionary algorithms are group of methods that allows\ to find a collision free trajectory in real time, while polynomial interpolation allows to model smooth trajectory, which keeps continuity of velocity...
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Massively parallel linear-scaling Hartree–Fock exchange and hybrid exchange–correlation functionals with plane wave basis set accuracy
PublicationWe extend our linear-scaling approach for the calculation of Hartree–Fock exchange energy using localized in situ optimized orbitals [Dziedzic et al., J. Chem. Phys. 139, 214103 (2013)] to leverage massive parallelism. Our approach has been implemented in the ONETEP (Order-N Electronic Total Energy Package) density functional theory framework, which employs a basis of non-orthogonal generalized Wannier functions (NGWFs) to achieve...
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Molecular Umbrella as A Nanocarrier for Antifungals
PublicationA molecular umbrella composed of two O‐sulfated cholic acid residues was applied for the construction of conjugates with cispentacin, containing a “trimethyl lock” (TML) or o‐dithiobenzylcarbamoyl moiety as a cleavable linker. Three out of five conjugates demonstrated antifungal in vitro activity against C. albicans and C. glabrata but not against C. krusei, with MIC90 values in the 0.22–0.99 mM range and were not hemolytic. Antifungal...
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Effects of Coulomb interaction on the electronic structure and lattice dynamics of the Mott insulatorFe2SiO4spinel
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Elements of Bioinformatics 2021/22
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Elements of Bioinformatics 2022/23
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Elements of Bioinformatics 2023/24
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Geometry Modeling and Processing
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Molecular geometry of hexachlorobenzene
Open Research DataPresented data shows molecular geometry of the ground singlet state of hexachlorobenzene and hexachlorobenzene with potassium atom in 10 angstrom distance. The geometry was obtained via MP2 and CCSD calculations using balanced polarized triple-zeta def2-TZVP basis set. Geometry is provided in the XYZ file format.
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Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology
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Variable‐fidelity modeling of antenna input characteristics using domain confinement and two‐stage Gaussian process regression surrogates
PublicationThe major bottleneck of electromagnetic (EM)-driven antenna design is the high CPU cost of massive simulations required by parametric optimization, uncertainty quantification, or robust design procedures. Fast surrogate models may be employed to mitigate this issue to a certain extent. Unfortunately, the curse of dimensionality is a serious limiting factor, hindering the construction of conventional data-driven models valid over...
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Estimation of groundwater recharge in a shallow sandy aquifer using unsaturated zone modeling and water table fluctuation method
PublicationQuantification of groundwater recharge is one of the most important issues in hydrogeology, especially in view of the ongoing changes in climate and land use. In this study, we use numerical models of 1D vertical flow in the vadose zone and the water table fluctuation (WTF) analysis to investigate local-scale recharge of a shallow sandy aquifer in the Brda outwash plain in northern Poland. We show that these two methods can be...
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Piezoresponse force microscopy and dielectric spectroscopy study of Ba0.6Sr0.4TiO3 thin films
PublicationResearch on synthesis, characterization and determination of processing – structure – property relationships of commercially important ferroelectric thin films has been performed. The sol-gel-type solution deposition technique was applied to produce good quality thin films of Ba0.6Sr0.4TiO3 (BST60/40) chemical composition on the stainless steel substrates. The thin films were characterized in terms of their microstructure, crystal...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Determination of viscosity changes of protein hydrolyzate solutions depending on shear rate
Open Research DataRheological characteristics of connective tissue protein solutions were made on the basis of viscosity measurement using a Brookfield viscometer using LV SC4 - 27 spindles and shear rate of 85 s-1 (Fig. 1). Solutions of protein hydrolysates with a concentration of 2% in 0.5M acetic acid were prepared.
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H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage
PublicationRadiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This...
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ACM Transactions on Modeling and Performance Evaluation of Computing Systems
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