Browsing by Author "Ivanova N."
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Item Characteristics of a Folate Receptor-α Anchored into a Multilipid Bilayer Obtained from Atomistic Molecular Dynamics Simulations(2020-01-14) Gocheva G.; Ivanova N.; Iliev S.; Petrova J.; Madjarova G.; Ivanova A.Thorough computational description of the properties of membrane-anchored protein receptors, which are important for example in the context of active targeting drug delivery, may be achieved by models representing as close as possible the immediate environment of these macromolecules. An all-atom bilayer, including 35 different lipid types asymmetrically distributed among the two monolayers, is suggested as a model neoplastic cell membrane. One molecule of folate receptor-α (FRα) is anchored into its outer leaflet, and the behavior of the system is explored by atomistic molecular dynamics simulations. The total number of atoms in the model is â¼185â»000. Three 1-μs-long simulations are carried out, where physiological conditions (310 K and 1 bar) are maintained with three different pressure scaling schemes. To evaluate the structure and the phase state of the membrane, the density profiles of the system, the average area per lipid, and the deuterium order parameter of the lipid tails are calculated. The bilayer is in liquid ordered state, and the specific arrangement varies between the three trajectories. The changes in the structure of FRα are investigated and are found time- A nd ensemble-dependent. The volume of the ligand binding pocket fluctuates with time, but this variation remains independent of the more global structural alterations. The latter are mostly ``waving`` motions of the protein, which periodically approaches and retreats from the membrane. The semi-isotropic pressure scaling perturbs the receptor most significantly, while the isotropic algorithm induces rather slow changes. Maintaining constant nonzero surface tension leads to behavior closest to the experimentally observed one.Item COMPOSITES OF WASTE RUBBER VULCANIZATES AND MODIFIED ADHESIVE SOLUTIONS TO CREATE CONTINUOUS COATINGS(2021-01-01) Dishovsky N.; Delchev N.; Ivanova N.; Malinova P.; Lachev A.Composites of waste rubber vulcanizates and polyurethane-based adhesive solutions have been developed, containing a waste sunflower oil as a modifying additive, intended for use as seamless floorings. The floorings are made in two versions: in laboratory conditions and in real conditions. The floorings of both variants are characterized by a number of important performance parameters: mechanical properties - in terms of tension and pressure, glass transition temperature, shock absorption according to head injury criterion (HIC) and criterion for maximum value of dynamic impact of free fall acceleration (G), potential elastic energy and energy density. It was found that the most important factors for the formation of the characteristics of the composites are the size, the specific surface of the rubber crumbs, respectively, the chemical nature of the adhesive used, the amount of the adhesive solution and the amount of the modifying additive. Based on the HIC and the G criteria, it is concluded that the created seamless coating has a safe fall height of 1 meter and can be used to cover playgrounds and sports facilities.Item Influence of the dimensionality of the periodic boundary conditions on the transport of a drug–peptide complex across model cell membranes(2022-01-01) Ivanova N.; Ivanova A.Many research efforts are devoted to improving the efficiency of chemotherapy. One of the aspects is to facilitate the transport of drugs across the cell membranes by attaching the therapeutics to a carrier molecule. The current study focuses on computational investigation of such a system with doxorubicin as the model drug, which is covalently bound to a cell-penetrating peptide. The correct description of its membrane translocation at the molecular level requires proper choice of the model membrane and of the simulation parameters. For the purpose, two phospholipid bilayers are built, one containing solely DPPC and another with mixed lipid content mimicking the composition of a human erythrocyte membrane. Atomistic molecular dynamics simulations are carried out in two types of periodic boundary conditions (2D and 3D PBC), in order to assess the effect of the periodicity dimensionality on the intermolecular interactions. The evolution of some basic characteristics of the bilayers and of the drug–peptide complex is tracked: mass density profiles, electrostatic potentials, lateral diffusion coefficients and areas per lipid, lipid-complex radial distribution functions, secondary structure of the peptide and orientation of the drug relative to the membrane. Thus, the influence of the periodic boundary conditions is quantified and it shows that the mixed system in 3D PBC is the most suitable for analysis of the translocation of the transporting moiety across cell membranes.Item PERFORMANCE AND TECHNOLOGICAL MODEL FOR PRODUCTION OF SOUND- AND SHOCK-ABSORBING COMPOSITES ON THE BASIS OF WASTE ELATOMERIC MATERIALS(2020-01-01) Dishovsky N.; Delchev N.; Ivanova N.; Mihaylov M.; Malinova P.; Lachev A.The aim of the present work is to investigate the possibilities of using waste sunflower oil as a modifying additive in order to eliminate some disadvantages of polyurethane adhesives used in the production and performance of insulating composites from ground waste rubber vulcanizates. A composition and a technological model for the production of sound- and shock-absorbing composite material have been developed as a result of the present study. A positive effect of the modifying additive on the technological process and the properties of the composite materials has been established. It is attributed to the composition of the waste sunflower oil comprising different types of fatty acids. The conducted tests and the obtained results give grounds to believe that the composite material developed can find applications as a sealing element in railways of rail and tram transport, in construction for sound insulation of buildings, as well as for covering children‘s and sports grounds.Item Physical properties of phospholipids at low temperatures through Slipid force field(2023-01-01) Ivanova N.; Chamati H.Slipid (Stockholm lipids) force field is suitable for the description of the physical properties of biological membranes composed of phospholipids at room temperature. So far, its accuracy to reproduce the behavior of the thermodynamic and structural quantities of membranes at low temperatures has not yet been tested in sufficient details. In the present study, we compute some characteristic quantities of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) using GROMACS in conjunction with Slipid force field. The initial configuration of the SOPC system composed of 128 lipid molecules distributed equally in each monolayer and 5120 water molecules was generated with the aid of CHARMM-GUI. Atomistic molecular dynamic (MD) simulations were performed at several temperatures. By virtue of a statistical analysis of trajectories, we computed the main structural parameters of the lipid molecules and thermodynamic quantities characterizing the phase behavior of the bilayer. The results are compared to available experimental data, as well as theoretical predictions. The Slipid force field was found to describe fairly well the structural behavior of the lipids at low temperatures.Item Probing Slipids Force Field for Phase Transitions in SOPC Lipid Bilayers with Various Cholesterol Concentrations(2024-08-01) Ivanova N.; Chamati H.We explore the phase behavior of lipid bilayers containing SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with various molar concentrations (0 mol%, 10 mol% and 30 mol%) of cholesterol. To this end, we performed extensive atomistic molecular dynamics simulations in conjunction with the Slipids force field with optimized parameters for the headgroups of phospholipids. We computed thermodynamic and structural quantities describing the ordering of the tails, the mobility of the heads and the arrangement of the lipids in the bilayers. We analyzed the behavior of the named quantities over the temperature range between 271 K and 283 K, where the experimentally determined melting temperature, (Formula presented.) K, lies, as well as at 400 K, which is used as a reference temperature. The obtained results are compared to available experimental data along with the outcome from molecular dynamics simulations of similar phospholipids containing different amounts of cholesterol. In the temperature interval of interest, we found evidence of the occurrence of a thermal-driven phase transition (melting) in both the pure system and the one with the lower concentration of cholesterol, while in the remaining system, the higher amount of cholesterol in the bilayer smears out the transitional behavior. Thus, we demonstrate the ability of the Slipids force field to predict the phase behavior of bilayers of SOPC and SOPC mixed with cholesterol.Item Study of Ammonia Adsorption on Magnetite Surfaces with Molecular Dynamics Simulations(2024-07-01) Ivanova N.; Karastoyanov V.; Betova I.; Bojinov M.The present study proposes an atomistic molecular dynamics model system of a magnetite (Fe3O4) {111} surface. The effect of temperature on the adsorption process of ammonia (NH3) at low concentrations in the aqueous phase has been considered. The molecular dynamics simulations were carried out using the Clay force field (Clay FF) with a modification for the iron atoms in the NPT ensemble at a pressure of 90 bar. The considered system was heated in a temperature range from 293 to 473 K, and additional relaxations were performed at temperatures of interest. Within the scope of this study, the basic parameters of the magnetite surface were calculated and the distances between the ammonia molecules and the surface were determined. A general idea of the degree and rate of adsorption at specific temperatures was obtained. The calculation results were compared to the experimental data where possible and to other available simulations of adsorption processes on metal oxides.Item The Effect of Cholesterol in SOPC Lipid Bilayers at Low Temperatures(2023-03-01) Ivanova N.; Chamati H.We study the behavior of lipid bilayers composed of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with different concentrations of cholesterol, ranging from 10 mol% to 50 mol% at 273 K. To this end, we carry out extensive atomistic molecular dynamic simulations with the aid of the Slipid force field aiming at computing basic bilayer parameters, as well as thermodynamic properties and structural characteristics. The obtained results are compared to available relevant experimental data and the outcome of atomistic simulations performed on bilayers composed of analogous phospholipids. Our results show a good quantitative, as well as qualitative, agreement with the main trends associated with the concentration increase in cholesterol. Moreover, it comes out that a change in the behavior of the bilayer is brought about at a concentration of about 30 mol% cholesterol. At this very concentration, some of the bilayer properties are found to exhibit a saturation and a significant long-range ordering of the lipid molecules in the membrane shows up.Item THE INFLUENCE OF THE HYDRATION NUMBER IN A MIXED LIPID BILAYER WITH CHOLESTEROL(2024-01-01) Ivanova N.The main structural component of biological membranes are phospholipids. A large proportion of the constituent lipids have monounsaturated hydrophobic tails. The study of this type of system is adequate for the development of a number of pharmaceutical substances. Molecular dynamics (MD) is suitable for describing the structure of membranes at the molecular level. The degree of hydration of the molecules is of essential importance for the correct composition of the atomistic models of the lipid bilayers. For this reason, an atomistic MD model of a lipid bilayer composed of 128 SOPC molecules and 128 cholesterol molecules symmetrically placed in both monolayers at a temperature of 273K was constructed. The Slipids force field was used, showing good results in the simulation of lipid systems. Three degrees of hydration corresponding to a hydration number (Hn) of 25, 40 and 50 were studied with two different water models (TIP3P and TIP4P). The interaction between the lipids and the aqueous phase is described by radial distribution function (RDF) and the number of hydrogen bonds. The basic parameters of the lipid bilayer related to the mobility of the heads such as lateral diffusion coefficient were calculated. It was found that the 25 hydration number resulted in an unrealistic immersion of the lipid heads in the water molecules. The high degree of hydration (50 waters per lipid) gives a better description of water, but there is no significant difference in surface phenomena compared to hydration number 40. The model containing 40 waters per lipid in combination with water model TIP3P reproduces experimental data and is suitable for further consideration.