Mechanical Engineering / Makina Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/4129
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Article Citation - WoS: 21Citation - Scopus: 22Daily Application of Low Magnitude Mechanical Stimulus Inhibits the Growth of Mda-Mb Breast Cancer Cells in Vitro(BioMed Central Ltd., 2014) Ölçüm, Melis; Özçivici, EnginIntroduction: Mechanical loads can regulate cell proliferation and differentiation at various stages of development and homeostasis. However, the extension of this regulatory effect of mechanical loads on cancer cells is largely unknown. Increased physical compliance is one of the key features of cancer cells, which may hamper the transmission of mechanical loads to these cells within tumor microenvironment. Here we tested whether brief daily application of an external low magnitude mechanical stimulus (LMMS), would impede the growth of MDA-MB-231 aggressive type breast cancer cells in vitro for 3 wks of growth. Methods: The signal was applied in oscillatory form at 90 Hz and 0.15 g, a regimen that would induce mechanical loads on MDA-MB-231 cells via inertial properties of cells rather than matrix deformations. Experimental cells were exposed to LMMS 15 min/day, 5 days/week in ambient conditions while control cells were sham loaded. Cell proliferation, viability, cycle, apoptosis, morphology and migration were tested via Trypan Blue dye exclusion, MTT, PI, Annexin V, Calcein-AM and phalloidin stains and scratch wound assays. Results: Compared to sham controls, daily application of LMMS reduced the number and viability of cancerous MDA-MB-231 cells significantly after first week in the culture, while non-cancerous MCF10A cells were found to be unaffected. Flow cytomety analyses suggested that the observed decrease for the cancer cells in the LMMS group was due to a cell cycle arrest rather than apoptosis. LMMS further reduced cancer cell circularity and increased cytoskeletal actin in MDA-MB-231 cells. Conclusion: Combined, results suggest that direct application of mechanical loads negatively regulate the proliferation of aggressive type cancer cells. If confirmed, this non-invasive approach may be integrated to the efforts for the prevention and/or treatment of cancer.Article Citation - WoS: 26Citation - Scopus: 27Internal Surface Electric Charge Characterization of Mesoporous Silica(Nature Publishing Group, 2019) Şen, Tümcan; Barışık, MuratMesoporous silica is an emerging technology to solve problems of existing and to support projected revolutionary applications ranging from targeted drug delivery to artificial kidney. However, one of the major driving mechanisms, electric charging of internal mesoporous surfaces, has not been characterized yet. In the nanoscale confinements of mesoporous structures made of pore throats and pore voids, surface charges diverge from existing theoretical calculations and show local variation due to two occurrences. First, when the size of pore throat becomes comparable with the thickness of ionic layering forming on throats' surfaces, ionic layers from opposite surfaces overlap so that ionic concentration on the surface becomes different than Boltzmann distribution predicts, and there will no longer be an equilibrium of zero electric potential at pore throat centers. Second, when this non zero potential inside throats becomes different than the potential of pore voids, ionic diffusion from void to throat creates axial ionic variation on surfaces. For such a case, we performed a pore level analysis on mesoporous internal surface charge at various porosities and ionic conditions. Pore parameters strongly affected the average internal charge which we characterized as a function of overlap ratio and porosity, first time in literature. Using this, a phenomenological model was developed as an extension of the existing theory to include nano-effects, to predict the average mesoporous internal surface charge as a function of EDL thickness, pore size and porosity.Article Citation - WoS: 26Citation - Scopus: 27Electric Charge of Nanopatterned Silica Surfaces(Royal Society of Chemistry, 2019) Özçelik, H. Gökberk; Barışık, MuratThe most recent technologies employ nanoscale surface patterning or roughening in order to engineer desired properties on a surface. Electrokinetic properties at the interface of such surfaces and ionic liquids show different behavior to the well-known theoretical descriptions. Basically, the ionic distribution on the surface differs due to electrical double layer overlap effects in the pits and curvature effects at the tips of surface structures. Generally, the charge density of a surface is assumed to be a material property and surface roughness effects are overlooked in most of the literature. In contrast, we properly calculated the local surface charges based on surface chemistry at the corresponding local ionic concentration (charge regulation) for various surface roughness and solution conditions. The results showed that the surface charge density of silica decreased at the pits but increased at the tips of surface patterns. Even for the simplest case of self-repeating surface structures, the average of local surface charges becomes lower than the theoretical predictions. Based on numerical calculations, a phenomenological model was developed as an extension to the existing flat surface theory, which can successfully predict the average surface charge on a nano patterned surface as a function of the surface pattern size, ionic concentration and pH.Article Citation - WoS: 14Citation - Scopus: 14Size Dependent Surface Charge Properties of Silica Nano-Channels: Double Layer Overlap and Inlet/Outlet Effects(Royal Society of Chemistry, 2018) Şen, Tümcan; Barışık, MuratTransport inside nano-channels and tubes is highly dependent on their surface charge properties. While previous studies assume that the charge density of a surface is a material property and independent of confinement size, this study properly characterized the surface charge of a nanochannel as a function of channel height and length under various solution conditions. By calculating the local surface charge based on local ionic concentrations, the surface charge of a nano-channel was studied by considering the effects of both overlapping electrical double layers (EDLs) and inlet/outlet regions. First, the surface charge of silica decreased with the increase in EDL overlap, which is characterized by the ratio of EDL thickness to channel height. Second, the local surface charge showed variation at the inlet/outlet regions where the channel’s electrokinetics was in development. We defined a general entrance length as a function of EDL thickness for the electrokinetically developing part of different cases, after which the surface charge reached its equilibrium value and remained constant. Based on such length scales, we extended the existing theory to include nano-effects. A phenomenological model was developed, which can predict the average nano-channel surface charge as a function of EDL thickness, pH, channel length and channel height.Article Citation - WoS: 2Citation - Scopus: 2Staphylococcus Epidermidis Adhesion on Surface-Treated Open-Cell Ti6al4v Foams(Walter de Gruyter GmbH, 2016) Türkan, Uğur; Güden, Mustafa; Sudağıdan, MertThe effect of alkali and nitric acid surface treatments on the adhesion of Staphylococcus epidermidis to the surface of 60% porous open-cell Ti6Al4V foam was investigated. The resultant surface roughness of foam particles was determined from the ground flat surfaces of thin foam specimens. Alkali treatment formed a porous, rough Na2Ti5O11 surface layer on Ti6Al4V particles, while nitric acid treatment increased the number of undulations on foam flat and particle surfaces, leading to the development of finer surface topographical features. Both surface treatments increased the nanometric-scale surface roughness of particles and the number of bacteria adhering to the surface, while the adhesion was found to be significantly higher in alkali-treated foam sample. The significant increase in the number of bacterial attachment on the alkali-treated sample was attributed to the formation of a highly porous and nanorough Na2Ti5O11 surface layer.Article Citation - WoS: 44Citation - Scopus: 47Electric Field Controlled Transport of Water in Graphene Nano-Channels(American Institute of Physics, 2017) Çelebi, Alper Tunga; Barışık, Murat; Beşkök, AliMotivated by electrowetting-based flow control in nano-systems, water transport in graphene nano-channels is investigated as a function of the applied electric field. Molecular dynamics simulations are performed for deionized water confined in graphene nano-channels subjected to opposing surface charges, creating an electric field across the channel. Water molecules respond to the electric field by reorientation of their dipoles. Oxygen and hydrogen atoms in water face the anode and cathode, respectively, and hydrogen atoms get closer to the cathode compared to the oxygen atoms near the anode. These effects create asymmetric density distributions that increase with the applied electric field. Force-driven water flows under electric fields exhibit asymmetric velocity profiles and unequal slip lengths. Apparent viscosity of water increases and the slip length decreases with increased electric field, reducing the flow rate. Increasing the electric field above a threshold value freezes water at room temperature.Article Citation - WoS: 6Citation - Scopus: 7An Entropy-Based Analysis of Lane Changing Behavior: An Interactive Approach(Taylor and Francis Ltd., 2017) Koşun, Çağlar; Özdemir, SerhanObjectives: As a novelty, this article proposes the nonadditive entropy framework for the description of driver behaviors during lane changing. The authors also state that this entropy framework governs the lane changing behavior in traffic flow in accordance with the long-range vehicular interactions and traffic safety. Methods: The nonadditive entropy framework is the new generalized theory of thermostatistical mechanics. Vehicular interactions during lane changing are considered within this framework. The interactive approach for the lane changing behavior of the drivers is presented in the traffic flow scenarios presented in the article. According to the traffic flow scenarios, 4 categories of traffic flow and driver behaviors are obtained. Through the scenarios, comparative analyses of nonadditive and additive entropy domains are also provided. Results: Two quadrants of the categories belong to the nonadditive entropy; the rest are involved in the additive entropy domain. Driving behaviors are extracted and the scenarios depict that nonadditivity matches safe driving well, whereas additivity corresponds to unsafe driving. Furthermore, the cooperative traffic system is considered in nonadditivity where the long-range interactions are present. However, the uncooperative traffic system falls into the additivity domain. The analyses also state that there would be possible traffic flow transitions among the quadrants. This article shows that lane changing behavior could be generalized as nonadditive, with additivity as a special case, based on the given traffic conditions. Conclusions: The nearest and close neighbor models are well within the conventional additive entropy framework. In this article, both the long-range vehicular interactions and safe driving behavior in traffic are handled in the nonadditive entropy domain. It is also inferred that the Tsallis entropy region would correspond to mandatory lane changing behavior, whereas additive and either the extensive or nonextensive entropy region would match discretionary lane changing behavior. This article states that driver behaviors would be in the nonadditive entropy domain to provide a safe traffic stream and hence with vehicle accident prevention in mind.Article Citation - WoS: 24Citation - Scopus: 28Atomic Density Effects on Temperature Characteristics and Thermal Transport at Grain Boundaries Through a Proper Bin Size Selection(American Institute of Physics, 2016) Vo, Truongquoc; Barışık, Murat; Kim, BohungThis study focuses on the proper characterization of temperature profiles across grain boundaries (GBs) in order to calculate the correct interfacial thermal resistance (ITR) and reveal the influence of GB geometries onto thermal transport. The solid-solid interfaces resulting from the orientation difference between the (001), (011), and (111) copper surfaces were investigated. Temperature discontinuities were observed at the boundary of grains due to the phonon mismatch, phonon backscattering, and atomic forces between dissimilar structures at the GBs. We observed that the temperature decreases gradually in the GB area rather than a sharp drop at the interface. As a result, three distinct temperature gradients developed at the GB which were different than the one observed in the bulk solid. This behavior extends a couple molecular diameters into both sides of the interface where we defined a thickness at GB based on the measured temperature profiles for characterization. Results showed dependence on the selection of the bin size used to average the temperature data from the molecular dynamics system. The bin size on the order of the crystal layer spacing was found to present an accurate temperature profile through the GB. We further calculated the GB thickness of various cases by using potential energy (PE) distributions which showed agreement with direct measurements from the temperature profile and validated the proper binning. The variation of grain crystal orientation developed different molecular densities which were characterized by the average atomic surface density (ASD) definition. Our results revealed that the ASD is the primary factor affecting the structural disorders and heat transfer at the solid-solid interfaces. Using a system in which the planes are highly close-packed can enhance the probability of interactions and the degree of overlap between vibrational density of states (VDOS) of atoms forming at interfaces, leading to a reduced ITR. Thus, an accurate understanding of thermal characteristics at the GB can be formulated by selecting a proper bin size.Article Citation - WoS: 76Citation - Scopus: 79Near-Surface Viscosity Effects on Capillary Rise of Water in Nanotubes(American Physical Society, 2015) Vo, Truong Quoc; Barışık, Murat; Kim, BoHungIn this paper, we present an approach for predicting nanoscale capillary imbibitions using the Lucas-Washburn (LW) theory. Molecular dynamics (MD) simulations were employed to investigate the effects of surface forces on the viscosity of liquid water. This provides an update to the modified LW equation that considered only a nanoscale slip length. An initial water nanodroplet study was performed to properly elucidate the wetting behavior of copper and gold surfaces. Intermolecular interaction strengths between water and corresponding solid surfaces were determined by matching the contact angle values obtained by experimental measurements. The migration of liquid water into copper and gold capillaries was measured by MD simulations and was found to differ from the modified LW equation. We found that the liquid layering in the vicinity of the solid surface induces a higher density and viscosity, leading to a slower MD uptake of fluid into the capillaries than was theoretically predicted. The near-surface viscosity for the nanoscale-confined water was defined and calculated for the thin film of water that was sheared between the two solid surfaces, as the ratio of water shear stress to the applied shear rate. Considering the effects of both the interface viscosity and slip length of the fluid, we successfully predicted the MD-measured fluid rise in the nanotubes.Article Citation - WoS: 25Citation - Scopus: 27Trabecular Bone Recovers From Mechanical Unloading Primarily by Restoring Its Mechanical Function Rather Than Its Morphology(Elsevier Ltd., 2014) Özçivici, Engin; Judex, StefanUpon returning to normal ambulatory activities, the recovery of trabecular bone lost during unloading is limited. Here, using a mouse population that displayed a large range of skeletal susceptibility to unloading and reambulation, we tested the impact of changes in trabecular bone morphology during unloading and reambulation on its simulated mechanical properties. Female adult mice from a double cross of BALB/cByJ and C3H/HeJ strains (n = 352) underwent 3. wk of hindlimb unloading followed by 3. wk of reambulation. Normally ambulating mice served as controls (n = 30). As quantified longitudinally by in vivo μCT, unloading led to an average loss of 43% of trabecular bone volume fraction (BV/TV) in the distal femur. Finite element models of the μCT tomographies showed that deterioration of the trabecular structure raised trabecular peak Von-Mises (PVM) stresses on average by 27%, indicating a significant increase in the risk of mechanical failure compared to baseline. Further, skewness of the Von-Mises stress distributions (SVM) increased by 104% with unloading, indicating that the trabecular structure became inefficient in resisting the applied load. During reambulation, bone of experimental mice recovered on average only 10% of its lost BV/TV. Even though the addition of trabecular tissue was small during reambulation, PVM and SVM as indicators of risk of mechanical failure decreased by 56% and 57%, respectively. Large individual differences in the response of trabecular bone, together with a large sample size, facilitated stratification of experimental mice based on the level of recovery. As a fraction of all mice, 66% of the population showed some degree of recovery in BV/TV while in 89% and 87% of all mice, PVM and SVM decreased during reambulation, respectively. At the end of the reambulation phase, only 8% of the population recovered half of the unloading induced losses in BV/TV while 50% and 49% of the population recovered half of the unloading induced deterioration in PVM and SVM, respectively. The association between morphological and mechanical variables was strong at baseline but progressively decreased during the unloading and reambulation cycles. The preferential recovery of trabecular micromechanical properties over bone volume fraction emphasizes that mechanical demand during reambulation does not, at least initially, seek to restore bone's morphology but its mechanical integrity.