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The effect of chitosan concentration and molecular weight on endotoxin content
Open Research DataThe dataset includes results to determine the effect of chitosan concentration and molecular weight on endotoxin content as well as the effect of purification methods. The endotoxin concentration was determined using the PyroGene Recombinant Factor C Endpoint Fluorescent Assay. Chitosan 0.6% in 0.1M glycolic acid from Chemat LMW, MMW, and HMW were used...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Molecular dynamics studies of polyurethane nanocomposite hydrogels
PublicationPolyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...
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FPGA Based Real Time Simulations of the Face Milling Process
PublicationThe article presents a successful implementation of the milling process simulation at the Field-Programmable Gate Array (FPGA). By using FPGA, very rigorous Real-Time (RT) simulation requirements can be met. The response time of the FPGA simulations is significantly reduced, and the time synchronization is better than in a typical RT system implemented in software. The FPGA-based approach is characterized by enormous flexibility...
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Simulations of flows in the coastal zone of the Baltic Sea
Open Research DataThe study area is located in the Southern Baltic, within Polish Marine Areas, adjacent to the coastline in the vicinity of Lubiatowo village, where The Coastal Research Station (CRS) – a field laboratory of the Institute of Hydro-Engineering of the Polish Academy of Sciences (IBW PAN) –is situated. The numerical reconstruction of the coastal flow was...
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Optimization of Hydrogen - Evolving Photochemical Molecular Devices
PublicationA molecular photocatalyst consisting of a RuII photocenter, a tetrapyridophenazine bridging ligand, and a PtX2 (X=Cl or I) moiety as the catalytic center functions as a stable system for light-driven hydrogen production. The catalytic activity of this photochemical molecular device (PMD) is significantly enhanced by exchanging the terminal chlorides at the Pt center for iodide ligands. Ultrafast transient absorption spectroscopy...
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Constant vs. Variable Efficiency of Electric Drive in Train Run Simulations
PublicationTrain run simulations, which focus on various power- and energy-oriented aspects, should reflect the losses in the electric powertrain. In general, the powertrain efficiency varies with respect to load and speed. Including this relation in simulation requires knowledge about detailed drivetrain parameters, which are often unavailable. This paper verifies the possibility to approximate the drivetrain efficiency in train run simulations...
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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Novel steroid sulfatase inhibitors based on N ‐thiophosphorylated 3‐(4‐aminophenyl)‐coumarin‐7‐O‐sulfamates
PublicationIn the present work, we described convenient methods for the synthesis ofN-thiophosphorylated 3-(4-aminophenyl)-coumarin-7-O-sulfamates as steroid sulfatase(STS) inhibitors. To design the structures of the potential STS inhibitors, molecularmodeling techniques were used. A computational docking method was used to deter-mine the binding modes of the synthesized inhibitors as well as to identify potentialinteractions between specified...
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Numerical simulations of novel GFRP sandwich footbridge
PublicationIn the following paper some aspects of numerical analysis and designing stages of a footbridge made of composite materials are elucidated. Because of the used materials the design process in this case is not ordinary and requires the development of concepts, material selections, identification of material properties, numerical simulations, strength calculations, serviceability and durability analyses. This contribution presents...
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Molecular Targets for Anticandidal Chemotherapy
PublicationA relatively small number of anticandidal chemotherapeutics used in clinical practice is at least in part consequence of a limited number of their molecular targets: ergosterol in the membrane, lanosterol demethylase, b(1!3) glucan synthase, and DNA/RNA biosynthesis. Much more potential novel targets have been revealed by the comparative genomic studies identifying essential genes unique for Candida albicans or resulted from recognition...
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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The surface photoconductivity in molecular layers
PublicationW pracy przedstawiono rezultaty analizy fotoprądów powierzchniowych w cienkich warstwach tetracenu i pentacenu. W szczególności badano wpływ obecności defektów strukturalnych w warstwach na charakterystyki fotoprądów i transport nośników ładunku.
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Mesoscopic simulations of crack propagation in concrete using cohesive elements
PublicationThe paper presents results of two-and three-dimensional meso-scale simulations of fracture in notched concrete beams subjected to three-point bending test. Concrete was assumed as a 3-phase material composed of aggregate grains placed in the cement matrix with Interfacial Transitional Zones (ITZs) between then. In 2D simulations macro-voids were also taken into account. The particle distribution was taken from real concrete beams...
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Some Optimization Methods for Simulations in Volunteer and Grid Systems
PublicationIn this chapter, some optimization methods have been presented for improving performance of simulations in the volunteer and grid computing system called Comcute. Some issues related to the cloud computing can be solved by presented approaches as well as the Comcute platform can be used to simulate execution of expensive and energy consuming long-term tasks in the cloud environment. In particular, evolutionary algorithms as well...
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Molecular Design Using Selected Concentration Effects in Optically Activated Fluorescent Matrices
PublicationMolecular physics plays a pivotal role in various fields, including medicine, pharmaceuticals, and broader industrial applications. This study aims to enhance the methods for producing specific optically active materials with distinct spectroscopic properties at the molecular level, which are crucial for these sectors, while prioritizing human safety in both production and application. Forensic science, a significant socio-economic...
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Molecular Physics Reports
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Discussing daylight simulations in a proposal for online daylighting education.
PublicationThere is increasing interest concerning daylighting in the building sector. However, such knowledge is difficult to penetrate the curricula of architects and designers as existing educational programmes often do not provide sufficient training on BPS. This also leads to superficial use of daylight simulations. This paper presents a proposal for a needs-based education package on daylighting design, that mixes modular eLearning...
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Introduction in to tyre simulations
PublicationW artykule przedstawiono wyniki symulacji komputerowej zachowania się opony w czasie badania jej oporów toczenia w oparciu o program LMS Virtual Lab. Przedstawiono także wnioski wynikające z przeprowadzonej symulacji.
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Acceleration of Electromagnetic Simulations on Reconfigurable FPGA Card
PublicationIn this contribution, the hardware acceleration of electromagnetic simulations on the reconfigurable field-programmable-gate-array (FPGA) card is presented. In the developed implementation of scientific computations, the matrix-assembly phase of the method of moments (MoM) is accelerated on the Xilinx Alveo U200 card. The computational method involves discretization of the frequency-domain mixed potential integral equation using...
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Searching for Critical Conditions During Lifeboat Launching – Simulations
PublicationThe article describes numerical simulations of the process of lifeboat launching at the ship’s side. The research is aimed at finding the values of ship motion parameters which appear to be most dangerous for people in the lowered lifeboat due to the generated accelerations. The simplified model of ship hull motion adopted at this research stage bases on a superposition of harmonic motions with given amplitudes and periods in six...
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International Review on Modelling and Simulations (IREMOS)
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Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublicationThe hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results,...
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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Molecular properties with dual basis set methods
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MOLECULAR PHARMACEUTICS
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Positron binding to alkali-metal hydrides: The role of molecular vibrations
PublicationThe bound vibrational levels for J=0 have been computed for the series of alkali-metal hydride molecules from LiH to RbH, including NaH and KH. For all four molecules the corresponding potential-energy curves have been obtained for each isolated species and for its positron-bound complex (e+XH). It is found that the calculated positron affinity values strongly depend on the molecular vibrational state for which they are obtained...
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Short-range order structure and free volume distribution in liquid bismuth: X-ray diffraction and computer simulations studies
PublicationThe structure of liquid bismuth was studied by X-ray diffraction and computer simulation methods. The contraction of the atomic structure within the first coordination sphere in the temperature interval of 575- 1225 K is reported. The temperature dependencies of the coordination numbers and of the free volume are analysed. On the basis of the temperature dependencies of the free volume, the temperature dependencies of viscosity...
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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublicationMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Improvement of ships seakeeping performance by application of the full-scale cfd simulations
PublicationThe ship’s fuel economy is increasingly important. The paper presents the effect of redesigning a case study ship for increasing seakeeping performance. Selected wave parameters reflect very difficult operational conditions existing on the North Sea and the Baltic Sea. The analyzed variants of a case study ship represent the latest developments of modern hull forms. The concepts similar to V-shaped bulbous bow, X-bow, X-aft, B-bow...
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Simulations of air and water flow in a model dike during overflow experiments
PublicationFlow in flood dikes, earth dams, and embankments occurs in variably saturated conditions, with pores of the earth material filled partly with water and partly with air. In routine engineering analysis, the influence of pore air is neglected and the air pressure is assumed equal to atmospheric. In some circumstances, for example, during overtopping of the dike by water, the effect of pore air on water flow and stability of the structure...
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Membrane model of human abdominal wall. Simulations vs. in vivo measurements
PublicationThe study presents a methodology of defining a numerical model of human abdominal wall based on the experimentally registered data of the abdomen geometry due to variations of the intraabdominal pressure. The abdominal wall is modelled here as a simple homogeneous membrane structure made of linear orthotropic material The displacements registered during the increase of pressure are compared with the re-sults of the model static...
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Simulations of Shear Zones and Cracks in Engineering Materials Using eXtended Finite Element Method
PublicationNumerical simulations of cracks and shear zones in quasi-brittle materials are presented. Extended Finite Element Method is used to describe both cracks and shear zones. In a description of tensile cracks, a Rankine criterion is assumed. A discrete Mohr-Coulomb law is adopted for simulations of shear zones. Results of simple numerical tests: unixial tension, bending and biaxial compression are demonstrated.
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Molecular structures of two E-azobenzocrown ethers
PublicationRentgenowska analiza strukturalna monokryształów posłużyła do scharakteryzowania struktury izomerów E dwóch azobenzokoron: 13- i 16-członowej. Oba związki krystalizują w układzie jednoskośnym. W komórce elementarnej, w każdym przypadku znajdują się dwie niezależne cząsteczki, różniące się konformacją, szczególnie łańcucha eterowego. Porównując konformacje ''wolnych'' makrocykli z konformacjami ich kompleksów z jonami metali wskazano,...
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Experimental investigations and simulations of the microturbine unit with permanent magnet generator
PublicationIn dispersed power generation, low power devices are used for local combined generating of heat end electric power. There are developing concepts of micropower plants with electric generators driven by steam or gas microturbines. The paper presents the results of an experimental investigations of the microturbine set consists of the turbine with partial admission, permanent magnet generator and three phase AC-to-DC rectifier. The...
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Systematic Management of Simulation State for Multi-Branch Simulations in Simulink
PublicationSystematic simulation is a technique related and motivated by the formal analysis of hybrid dynamic systems. It combines the exhaustive and conservative nature of traditional model checking with numerical simulation for providing efficient algorithms to manage simulations. Multi-branch simulation is the concept advancing simulation efficiency by reducing the number of state transitions. This paper introduces an approach to implement...
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Fatty acids as molecular carriers in cleavable antifungal conjugates
PublicationConjugates composed of C2-18 fatty acid (FA) residues as a molecular carrier and 5-fluorocytosine (5-FC) as an active agent, released upon the action of intracellular esterases on the ester bond between FA and “trimethyl lock” intramolecular linker, demonstrate good in vitro activity against human pathogenic yeasts of Candida spp. The minimal inhibitory concentrations (MIC) values for the most active conjugates containing caprylic...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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Antenna Modeling Using Variable-Fidelity EM Simulations and Constrained Co-Kriging
PublicationUtilization of fast surrogate models has become a viable alternative to direct handling of fullwave electromagnetic (EM) simulations in EM-driven design. Their purpose is to alleviate the difficulties related to high computational cost of multiple simulations required by the common numerical procedures such as parametric optimization or uncertainty quantification. Yet, conventional data-driven (or approximation) modeling techniques...
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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Open Research DataThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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Towards an efficient multi-stage Riemann solver for nuclear physics simulations
PublicationRelativistic numerical hydrodynamics is an important tool in high energy nuclear science. However, such simulations are extremely demanding in terms of computing power. This paper focuses on improving the speed of solving the Riemann problem with the MUSTA-FORCE algorithm by employing the CUDA parallel programming model. We also propose a new approach to 3D finite difference algorithms, which employ a GPU that uses surface memory....