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Search results for: QM/MM FREE ENERGY SIMULATIONS
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Marek Czachor prof. dr hab.
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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The ONETEP linear-scaling density functional theory program
PublicationWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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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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Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution
PublicationFo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay...
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Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
Open Research DataThis data presents potential energy surfaces of Li atom interacting with LiCs dimer for the ground and first excited state. They were calculated using effective core potentials and MRCI method and include relativistic effects. The interatomic distance in the dimer is kept constant and equal to experimental value of 6.931704423 bohrs (3.6681 A). Energy...
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Vitamin B9 as a new eco-friendly corrosion inhibitor for copper in 3.5% NaCl solution
PublicationFolic acid salt (sodium folate) was studied as an eco-friendly and non-toxic copper corrosion inhibitor in 3.5% NaCl solution. Electrochemical impedance spectroscopy, polarization resistance and weight-loss measurements show that the inhibitor efficiency increases with concentration (the highest value- approx. 96% was reported for the solution containing 16 mM sodium folate after 24 h). EIS data and Tafel plots indicate that sodium...
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Carboxylic acids as efficient corrosion inhibitors of aluminium alloys in alkaline media
PublicationThe efficiency of AA5754 aluminium alloy corrosion inhibition achieved with maleic, malic, succinic, tartaric, citric, tricarballylic acids and serine in alkaline environment (pH 11) was examined. Selected corrosion inhibitors are characterized by different numbers and distribution of carbonyl and hydroxyl groups within their molecules. We have proposed and verified a novel approach for determining the adsorption isotherms based...
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Estimation of structural stiffness with the use of Particle Swarm Optimization
PublicationThe paper presents the theoretical background and four applications examples of the new method for the estimation of support stiffness coefficients of complex structures modelled discretely (e.g. with the use of the Finite Element Model (FEM) method based on the modified Particle Swarm Optimization (PSO) algorithm. In real-life cases, exact values of the supports’ stiffness coefficients may change for various reasons...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Window frame integrable air recuperation minichannel/minigap heat exchanger
PublicationThis article describes an evaluation of mini heat exchangers operation as a decentralized mechanical ventilation system with recuperative heat recovery that can be integrated into the window frame. The relatively small yet efficient air recuperation system allows for retrofitting existing buildings by reducing the overall energy consumption and thus the CO2 emissions. The proposed design, unlike existing systems, is easy to scale...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Strength parameters of masonry walls in modelling historic constructions
PublicationThe paper presents the determination of the basic material properties of a historic brickwork. Experimental studies were used to identify the basic material properties of bricks. The mechanical properties of the masonry, as an orthotropic homogenized material, were calculated. Then, numerical simulations using the Finite Element Method (FEM) were performed to verify the experimental outcomes. Macromodels with element sizes of 40,...
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Comprehensive dimension scaling of multi-band antennas for operating frequencies and substrate parameters
PublicationIn this paper, low-cost and comprehensive redesign of multi-band antennas with respect to the operating frequencies and material parameters of the substrate is presented. Our approach exploits an inverse surrogate model identified based on a set of reference designs optimized at the level of coarse-discretization EM simulations of the antenna at hand. An iterative correction procedure is also implemented to account for the initial...
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Numerical analysis of chip removing system operation in circular sawing machine using CFD software
PublicationPaper presents the analysis of the results of numerical simulations of the air flow process of wood chips removing system in the circular sawing machine. The attention is focused on the upper cover and bottom shelter of the chip removing system. Within the framework of the work a systematic numerical modeling of the air flow distribution in the cover and shelter during operation of the selected rotational speed of saw blade with...
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Electrochemistry from first-principles in the grand canonical ensemble
PublicationProgress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by first-principles quantum mechanical simulations with Density Functional Theory (DFT). However, such simulations are...
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Experimental Investigations on the Influence of Coil Arrangement on Melting/Solidification Processes
PublicationThe latent heat thermal energy storage units are very popular because of their high energy density and almost close to constant temperature during the charging/discharging. In the present study has been proposed new shell-and-coil geometry with a shifted coil position to enhance the performance of phase change thermal magazine. The experimental investigations have been performed both for the melting and solidification process of...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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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...
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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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Data recorded for the purpose of the 3D sound intensity visualization around the organ pipe (des sound)
Open Research DataThe set contains data recorded using the Cartesian robot and multichannel acoustic vector sensor (from Microflown) for the purpose of the 3D sound intensity visualization of radiated acoustic energy around the organ pipe.
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Gold nanocubic structures functionalization with organic layers
Open Research DataThis dataset contains the XPS spectra obtained for gold nanocubes (AuNC), which were deposited at the gold electrode surface and dried. The AuNC's were first functionalized with either cysteamine in EtOH or mercaptopropionic acid in EtOH. The concentration of these compounds was 20 mM. The interaction of the functionalized with the AuNC surface was...
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Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function
PublicationAmphotericin B (AmB), one of the most powerful but also toxic drugs used to treat systemic mycoses, is believed to selectively permeabilize fungal cell membranes to ions in a sterol-dependent manner. Unfortunately, the structure of the biologically active AmB channels has long eluded researchers, obstructing the design of safer alternatives. Here, we investigate the structural and thermodynamic aspects of channel formation, stability,...
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Variable-fidelity shape optimization of dual-rotor wind turbines
PublicationPurpose Dual-rotor wind turbines (DRWTs) are a novel type of wind turbines that can capture more power than their single-rotor counterparts. Because their surrounding flow fields are complex, evaluating a DRWT design requires accurate predictive simulations, which incur high computational costs. Currently, there does not exist a design optimization framework for DRWTs. Since the design optimization of DRWTs requires numerous model...
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Wind resource assessment and energy yield prediction for the small wind turbine on the Szubieniczne Hill
PublicationThe goal of this study is to preliminary assess the wind resources on the Szubieniczne Hill in order to predict the annual energy production for planned small wind turbine. The analyzed site is located close to the Gdańsk University of Technology campus, in complex urban environment additionally surrendered by forested hills. The assessment is based on Computational Fluid Dynamics simulations which allow to evaluate the wind energy potential...
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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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Towards Carbon Neutral Settlements. The Importance of Early-Stage Urban and Energetic Optimizations
PublicationThe aim of the research was to verify the essence of interdisciplinary energy optimizations in earlystage urban design process. A further aim was to the find most optimal design variant and scenario in terms of urban energy efficiency for the future development in Nowy Port, located in Gdansk, Poland - a place requiring complex revitalization. The research combined qualitative and quantitative approaches; an urban design layer...
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A Concept for Safe and Less Expensive Acceleration of a Marine Steam Turbine Start-up
PublicationThis paper analyses the issue of accelerated start-up of a marine steam turbine, which is an important problem because the start-up of a steam machine involves the combustion of fuel that is not transformed into useful energy. To find novel technologies that offer improvements in this aspect is essential due to restrictions on reducing ship emissions. Thus, the shorter the start-up time, the better for the environment and economy....
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Prediction of consumer electricity needs based on Internet weather forecasts
PublicationElectrical energy is considered both as an important driver for producing and transporting goods in companies, as well as a good in itself which requires planning and management for generating and delivering it to consumers in proper time and amounts. Weather information can be considered to convey part of the data on energy delivery needs of consumers. Free meteorological data sources on the Web do not offer consistent data to...
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Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
PublicationCoarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...
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Influence of the annealing condictions on the chemical structure of LaBaGdCo ceramics
Open Research DataCeramic samples based on Barium, Lanthanum, Gadolinium and Cobaltium were produced by solid state reaction. After sintring in a furnance, samples were annealed at 300 Celsius degree in wet and dry atmosphere. Annealing takes 72h or 2h. Results of annealing were observed by X-Ray photoemission spectroscopy (XPS), OmicronNanotechnology. XPS analysis...
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Non-destructive inspection of ground anchors using guided wave propagation
PublicationThis paper deals with numerical and experimental investigations of specific problems of guided wave propagation in ground anchors. The research focuses on recognizing the phenomenon of the energy transfer between anchor components. Particular attention is paid to characteristic features of guided waves propagating in free and embedded parts of the tendon, at the interface between the tendon and the surrounding anchor body as well...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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On the use of uniaxial one-parameter damage laws for estimating fatigue life under multiaxial loading
PublicationThe goal of this paper is to evaluate the capabilities of different one-parameter fatigue laws to estimate crack initiation in notched components under multiaxial loading. Fatigue damage is accounted for through stress-based, strain-based, and energy-based approaches while the cyclic plasticity at the notch-controlled process zone is estimated using linear-elastic simulations. The results show that energy-based formulations established...
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Anti-plane waves in an elastic thin strip with surface energy
PublicationWe consider anti-plane motions of an elastic plate taking into account surface energy within the linear Gurtin–Murdoch surface elasticity. Two boundary-value problems are considered that describe complete shear dynamics of a plate with free faces or with free and clamped faces, respectively. These problems correspond to anti-plane dynamics of an elastic film perfectly or non-perfectly attached to a rigid substrate. Detailed analysis...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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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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Valence state of Manganium in a MnCoO ceramics
Open Research DataManganium -cobalt based ceramics materials were produced by solid state reaction and sintred in a furnance in air atmosphere for 20h. Annealing temperature was 600 Celsius degree. For investigations a series of samples, with a various composition was chosen: MnCoO, Mn, Co2O and Mn2CoO. In order to determine valence states of the Mn, X-Ray photoemission...
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Lanthanum investigations in ceramics annealed in a dry and wet atmosphere
Open Research DataCeramics based on Barium, Lanthanum, Gadolinium and Cobaltium were produced by standard solid state reaction from oxides and carbonate powders. After sintring, samples were annealed for 2 hours or 72 hours at 300 Celsius degree in a both: wet and dry atmosphere. Results of annealing on a chemical composition and valence state of lanthanum were observed...
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Electrochemically directed biofunctionalization of a lossy-mode resonance optical fiber sensor
PublicationIn this work, we present a direct electrochemical biofunctionalization of an indium-tin-oxide-coated lossy-mode resonance optical fiber sensor. The functionalization using a biotin derivative was performed by cyclic voltammetry in a 10 mM biotin hydrazide solution. All stages of the experiment were simultaneously verified with optical and electrochemical techniques. Performed measurements indicate the presence of a poly-biotin...
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Balancing Energy Inputs/Outputs and GHG Emissions for Sustainable Wastewater Treatment – a Case Study
PublicationThe aim of the study is a model-based evaluation of the selected operating modes and technological upgrades on the energy balance and greenhouse gas (GHG) emissions in a large wastewater treatment plant in the city of Slupsk (northern Poland). The considered scenarios focus on energy savings for aeration, increasing energy recovery via biogas cogeneration and reduction of the CO2 equivalent emission from both direct processes (related...
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Numerical Estimation of Hull Hydrodynamic Derivatives in Ship Maneuvering Prediction
PublicationPrediction of the maneuvering characteristics of the ship at the design stage can be done by means of model tests, computational simulations or a combination of both. The model tests can be realized as direct simulation of the standard maneuvers with the free running model, which gives the most accurate results, but is also the least affordable as it requires very large tank or natural lake, as well as complex equipment of the...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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ENERGY EFFICIENT SMALL INLAND PASSENGER SHUTTLE FERRY WITH HYBRID PROPULSION - CONCEPT DESIGN, CALCULATIONS AND MODEL TESTS
PublicationIn recent years, there has been a significant development in “green” and energy efficient propulsion systems, which fits into the general trend of environmentally friendly “green shipping”. The pursued goal is to construct a safe passenger ship that is low in energy demand and equipped with a highly energy efficient, emission-free propulsion system. The paper presents main problems encountered by designers of a small, hybrid-powered...
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Role of cholesterol in substrate recognition by -secretase
Publication-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Numerical Study of the Impinging Jets Formed by an Injector with Different Nozzle Diameters
Open Research DataThe data set contains the simulation files related to the research paper “Numerical Study of the Impinging Jets Formed by an Injector with Different Nozzle Diameters”, https://doi.org/10.4271/2022-01-1080.