Multi-scale study of the dynamics of self-organizing molecular systems

Many research groups are studying self-assembly structures via using computational techniques to understand their behavior from a theoretical point of view. Taking different length scales into consideration becomes more important day by day. In this thesis, calculations are performed at the different length scales of meso-scale, quantum scale, and nano-scale. First of all, meso-scale calculations are performed by using the Dissipative Particle Dynamics simulation methodology to obtain the three dimensional morphologies and the corresponding equilibrium structures. These structures are obtained as a collection of beads each of which consists of several atoms. Hence, morphologies varying from spherical and cylindrical micellar to lamellar are obtained. Then, in order to understand origins of interactions between beads forming meso-scale morphologies, quantum mechanical calculations are carried out at the nanoscale by using chemical reactivities and Atoms-In-Molecules theory. The interactions that occur on the interatomic scale are found to control the meso-scale. In addition to meso-scale calculations to obtain morphology, micelles are investigated in terms of their surface-to-volume ratios to the micro-phase separation behavior. Consequently, phase change from spherical to cylindrical micellar and micellar to lamellar phase is observed in surface-to-volume versus concentration plot. Finally, molecular dynamics simulations on the atomic scale are performed to study the dynamics of self-assembled synthetic structures. A reverse mapping algorithm is developed to back fit atomistic detail to morphologies obtained from meso-scale calculations. The detailed structure is soaked into water to study the dynamics of interfacial water since the target structure is superhydrophobic

Modeling surface segregation of smart PU coatings at hydrophilic and hydrophobic interfaces via coarse-grained molecular dynamics and mesoscopic simulations

Developing adaptive coatings having desired functionalities at targeted interfaces is one of the major efforts in the coatings science area. The adaptation of the surface functionality to the changing surface conditions can be maintained by introducing dangling chains with different properties to the cross-linked polymer coatings. In this work, we strive to investigate the change in interfacial morphology of PU coatings as exposed to hydrophilic (HPI) and hydrophobic (HPB) interfaces by employing molecular simulations at the coarse-grained and mesoscopic levels. The molecular structure and surface segregation dynamics are studied for PU coatings having pure HPI, mixture of HPI and HPB, and amphiphilic dangling chains. The dual-scale simulations, Dissipative Particle Dynamics (DPD) and MARTINI model, yield results about the dangling chain structures at the interface in terms of their end-to-end distances, where HPI chains adopt a more extended conformation in water in comparison to oil interfaces. The reverse is observed to be valid for the HPB chains. Regarding the dangling chain dynamics, a swift migration towards the interfaces is noticed at about 10 ns for both of the simulation methods. The structures of the dangling chains and their interaction with the interfaces are also characterized by computing the radial distribution function (RDF) profiles. Preferential interactions between the HPI/water and HPB/oil are clearly noted. The switchability of the surfaces is also studied by simulating the system in cycles, such that the interface is changed from water to oil and back to water. The migration of HPI groups in the dangling chains towards water and vice versa in each cycle is clearly shown by the simulations. In all, the inherent structure and dynamics of the dangling chains is obtained at the molecular level by the dual-scale molecular simulations. Our findings reveal a significant level of understanding about interfacial morphology of thermoset coatings modified by dangling chains, where the results can be extended to find applications in guiding the experimental studies

Parametrizing hydrogen bond interactions in dissipative particle dynamics simulations: the case of water, methanol and their binary mixtures

Simulating water has always been a challenge. Due to the intrinsic hydrogen bond interactions, water exhibits structural properties, such as a tetrahedral coordination resulting in a specific Radial Distribution Function (RDF), which are not trivial to predict computationally. In this paper, we attempt to use coarse-grained Dissipative Particle Dynamics (DPD) simulations to parameterize the hydrogen bond interactions without violating the classical DPD framework. We model the hydrogen bond interactions by incorporating a Morse potential, where the parameters are computed by taking the experimental enthalpy of evaporation and hydrogen bond distances as reference. We show that with the proposed procedure the RDF, the coordination number, the isothermal compressibility, and the three-body angular distributions (to demonstrate the tetrahedral structure) of pure water are predicted in great extent compatible with the experiments. To test the applicability of the procedure to mixtures, we simulated pure methanol and methanol/water mixtures at different molar fractions. The predicted RDF profiles for methanol-methanol, methanol-water and water-water represent the characteristic experimental RDF behavior. Moreover, the calculated negative excess volumes as a function of mole fraction compare quite well with the experimentally observed excess volumes. Our findings motivate the further development and use of DPD simulations in modeling hydrogen bond interactions, which are crucial not only in water (or alcohols), but in more complex systems such as biomolecules, proteins or biopolymers

Computing dissipative particle dynamics interactions to render molecular structure and temperature-dependent properties of simple liquids

Simulating structural and thermodynamical properties of liquids has always been a challenge. Typical examples of liquids that demonstrate particular structure and properties are water and the low molecular weight alcohols, for which hydrogen bond interactions lead to their distinctive properties, such as cage-like structures and temperature-dependent properties. Modeling these materials at the coarse-grained level is even a bigger challenge due to the loss of atomistic-level interactions. Nevertheless, one is interested in mimicking these typical properties at the coarse-grained level due to the relevance of these systems in complex environments, for which fully atomistic simulations still remain a challenge. In this paper, we introduce a mesoscopic level parameterization of DPD interactions to study the particular structural and thermodynamic properties of liquid water, methanol, ethanol and 1-propanol. The conservative repulsive DPD interactions are explicitly computed by a bottom-up parameterization, in which experimental thermodynamics data are used. A previously developed statistical mechanics approach is used to compute the hydrogen bond strength. The transport properties, such as viscosity, and thermodynamical properties, such as isothermal compressibility, are found to agree reasonably well with experimental data. Moreover, the structure as characterized by the radial distribution function and angular distributions of three neighboring molecules are in line with the atomistic simulations performed in this work. Furthermore, the temperature-dependency of the repulsive DPD interactions is modeled by incorporating the experimental isothermal compressibilities at different temperatures. The effect of the temperature on the hydrogen bond strengths is considered as well and the structural properties are predicted via the DPD simulations. In general, our work can be viewed as an attempt to model systems by the DPD simulations, where hydrogen bonds play a crucial role. The computed parameterization of DPD interactions is believed to pave the way towards extending the current applicability of DPD method to more complex systems

Correction to “Structure of a Thermoset Polymer near an Alumina Substrate as Studied by Dissipative Particle Dynamics”

No abstract

Immunohistochemical evaluation of CD20 expression in patients with multiple myeloma

Objective: CD20 expression was reported at different rates in patients with multiple myeloma. The importance of this B-cell antigen for plasma cells is still unknown. This study aimed to investigate CD20 expression of myeloma cells in bone marrow, and any relationship between the stage of disease, isotype and clinical features. Methods: Sixty-one patients who were admitted to the hematology clinic of the Adnan Menderes Medical School with the diagnosis of multiple myeloma according to the criteria of the "International Myeloma Working Group" were enrolled in this study. Age, gender, Durie-Salmon stage, history of autologous hematopoietic stem cell transplantation, and the distribution pattern and positivity of CD20 expression on multiple myeloma cells in bone marrow were evaluated. The Mann-Whitney U and chi-square tests were used for statistical analysis with a p-value < 0.05 being accepted as statistically significant. Results: Thirty patients (48.9%) had positive scores for CD20 with the distribution pattern being most likely interstitial in 55.6% of the cases. There was no statistically significant difference between immunohistochemical positivity for CD20 expression on multiple myeloma cells, immunoglobulin type, and the stage of disease. Conclusion: The combination of immunohistochemical studies with flow cytometry may reveal the importance of CD20 positivity in patients with multiple myeloma more clearly

The effects of nitrofurantoin on rat urinary bladder contraction

Nitrofurantoin is a drug used in the antibacterial treatment of urinary tract infections (UTIs) for over 60 years. The aim of our study was to investigate the possible effects of nitrofurantoin, which is commonly used as a urinary tract antiseptic, on bladder contractions in male rats. Bladder tissues obtained from male Sprague-Dawley rats were used in the study (n=24). After decapitation, bladder tissues were suspended in an isolated organ bath of 5 ml containing a Krebs-Ringer bicarbonate solution by applying a tension of 1.5 grams. Nitrofurantoin was administered to three groups at doses of 50, 500 and 1000 &#956;M, respectively. The area, peak-to-peak (p-p) and frequency values of bladder contractions were analyzed before and after administration of nitrofurantoin. The data obtained from the analysis were evaluated using the Paired T-Test in the IBM SPSS Statistics Software. Nitrofurantoin was observed to have an inhibitory effect on bladder contractions at all doses. The decrease in the area and peak-to-peak values was statistically significant at all doses (P [Med-Science 2019; 8(1.000): 192-6

Mesoscopic structure and swelling properties of crosslinked polyethylene glycol in water

In this paper, we present our efforts in modeling and simulation of polyethylene glycol crosslinked with an isocyanate tHDI. The polymer, by its nature, is hydrophilic and has strong hydrogen bond interactions with water. The simulations are performed at coarse-grained scale by using a dissipative particle dynamics (DPD) simulation method. The effect of hydrogen bond between water and polymer beads on the structure of the crosslinked hydrophilic polymer structure is studied. The polymer is observed to phase separate with water in the absence of hydrogen bonds in DPD simulations. In the reverse case, where hydrogen bonds are explicitly included in DPD simulations, polymer mixes with water. This behavior is investigated by plotting the density profiles. Moreover, the volumetric swelling behavior in mixtures with different water contents is estimated from simulations and extrapolated by a polynomial fit to compare with experiments. It is observed that the predicted swelling ratio is in good agreement with the experimental measurements

Pupillometry measurement and its relationship to retinal structural changes in children with attention deficit hyperactivity disorder

Aslan, Mehmet Gokhan/0000-0002-3250-1606; Okutucu, Murat/0000-0002-3104-8838; Findik, Huseyin/0000-0001-7343-8757; KACAR, MURAT/0000-0002-8887-2991WOS: 000522698600002PubMed: 32236704Purpose This study aims to assess the pupillometry measurements of the attention deficit hyperactivity disorder (ADHD) patients and to investigate their correlations with macular and RNFL thickness parameters by comparing the values with a healthy control group. Methods Newly diagnosed ADHD patients in a child and adolescent clinic of a tertiary hospital were consulted in an ophthalmology clinic. All participants had undergone a standard ophthalmological examination including refractometry, best corrected visual acuity, color vision, anterior segment biomicroscopy, fundoscopy, pupillometry, and OCT. All results were compared with a healthy control group at the same age. Results the study group consisted of 32 patients and there were 43 children in the control group. Mean pupillary velocities of ADHD patients and control group were 0.60 +/- 0.11 mm/s and 0.63 +/- 0.11 mm/s, and 0.49 +/- 0.12 mm/s and 0.50 +/- 0.10 mm/s, for right and left eyes, respectively. the difference was statistically significant for both eyes (p < 0.05). Mean RNFL thickness measurements of the study group were 90.69 +/- 8.58 mu m and 89.63 +/- 8.14 mu m for right and left eyes, respectively and those were 87.35 +/- 7.67 mu m and 88.77 +/- 7.44 mu m, respectively in the healthy group. Correlation between right pupillary velocity and RNFL thickness was statistically significant (r = 0.339, p = 0.003). Conclusion Higher pupillary velocity values were observed in both eyes of children with ADHD and that was positively correlated with RNFL measurements of their right eyes