Molecular self-assembly is a ubiquitous phenomenon in which individual atoms or molecules set up an ordered structure. It is of high interest for understanding the biology and a variety of diseases ...at the molecular level. In this work, we studied the self-assembly of tyrosine molecules
via
extensive molecular dynamics simulations. The formation of structures by self-assembly was systematically studied at various concentrations, from very low to very high. The temperature was kept constant, at which, in our former studies, we have already observed well-formed self-assembled structures. Depending on the concentration, the system displays a wide range of different structures, ranging from freely scattered monomers to very well formed four-fold structures. Different regimes of concentration dependence are observed. The results are proved by calculating the moments of inertia of the structures and the number of hydrogen bonds formed. Free energy landscapes calculated for the number of hydrogen bonds
versus
the number of contacts within a criterion provide insights into the structures observed.
Self-assembly responses of tyrosine molecules to concentration changes.
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•RTPF and RCA have been used for clay reinforcement/stabilization.•The strength of clay-fiber-RCA composites is significantly higher than clay.•Porosity/volume relations have been ...explored for clay-fiber-RCA composites.•Composites with 0.5%RTPF and 10%RCA are suited as subbase of flexible pavements.
The application of recycled materials for soil improvement is advantageous from the viewpoint of lowering construction costs, preventing depletion of natural resources, and reducing environmental pollutions. This experimental study investigates the application of recycled concrete aggregates to enhance the strength properties of clay soil reinforced with recycled tire polymer fibers and glass fibers. Unconfined compression and indirect tensile tests were performed on composite soils comprising clay reinforced with 0.5 % fibers and stabilized with 5 %, 10 % and 15 % recycled concrete aggregates. Laboratory findings elaborated that the increase in the RCA content and curing time would significantly improve the unconfined compressive and tensile strengths as compared to the clay. Moreover, the approximate ratio of tensile to compressive strength is a constant value for the composite soils, irrespective of fiber type, RCA amount and curing duration. Concerning the practical implications, the clay reinforced with 0.5 % fibers and stabilized with 10 % recycled concrete aggregates is strong enough after 28 days of curing to fulfill the strength requirements of subbase layers in both flexible and rigid pavements.
It is well known that all biological systems which undergo oxidative metabolism or oxidative stress generate a small amount of light. Since the origin of excited states producing this light is ...generally accepted to come from chemical reactions, the term endogenous biological chemiluminescence is appropriate. Apart from biomedicine, this phenomenon has potential applications also in plant biology and agriculture like monitoring the germination rate of seeds. While chemiluminescence capability to monitor germination has been measured on multiple agriculturally relevant plants, the standard model plant Arabidopsis thaliana has not been analyzed for this process so far. To fill in this gap, we demonstrate here on A. thaliana that the intensity of endogenous chemiluminescence increases during the germination stage. We showed that the chemiluminescence intensity increases since the second day of germination, but reaches a plateau on the third day, in contrast to other plants germinating from larger seeds studied so far. We also showed that intensity increases after topical application of hydrogen peroxide in a dose-dependent manner. Further, we demonstrated that the entropy of the chemiluminescence time series is similar to random Poisson signals. Our results support a notion that metabolism and oxidative reactions are underlying processes which generate endogenous biological chemiluminescence. Our findings contribute to novel methods for non-invasive and label-free sensing of oxidative processes in plant biology and agriculture.
A model is presented to study the random growth of the number of tumor cells. It contains deterministic growth and therapy terms, as well as a random term. The model is formulated as a Langevin ...equation and its corresponding Fokker–Planck equation is studied. Three forms for the time-dependence of the therapy are used and the results are compared to each other. Specifically, the ratio of the probability that the number of tumor cells be large to the probability that the number of tumor cells be small is investigated. The large time behavior of this ratio is considered as a figure of merit. Better therapies correspond to smaller values for this figure of merit. The behavior of this figure of merit in terms of various parameters of the therapy is investigated. It is seen that decreasing the amplitude or the period, decreases this figure of merit, hence improves the therapy.
With Casimir and electrostatic forces playing a crucial role for the performance and stability of microelectromechanical systems (MEMS), the presence of chaotic behavior, which is often unavoidable, ...leads to device malfunction due to stiction. Therefore, we investigate here how the optical properties of different materials influence the chaotic behavior of electrostatic torsional MEMS due to changes in magnitude of the Casimir forces and torques. We consider the materials Au, which is a good conductor, AIST, which is a phase change material being close to metal in the crystalline state, and finally doped SiC as a very poor conductor. For the conservative systems, there is no chaotic behavior and the analysis of phase portraits and bifurcation diagrams reveal the strong sensitivity of stable actuation dynamics on the material optical properties, while applied electrostatic potentials lead faster to instability and stiction for higher conductivity materials. For the driven systems, the Melnikov method is used to study the chaotic behavior. The results from this method are supported by the study of the contours of the transient time to stiction in the phase plane, which reveal a substantially increased chaotic behavior for higher conductivity materials, associated with stronger Casimir torques and applied electrostatic potentials.
We theoretically calculate here how random roughness affects the contact current density and equivalently contact resistance by utilizing a perturbative expansion method. Then, By taking into ...consideration self-affine roughness on the surface of the solids, we find the contact current density. The obtained results illustrate the total contact current exhibits significant dependence on the properties of the self-affine rough surface such as root-mean-square of roughness and Hurst exponent. Assuming a lower value of root-mean-square roughness for a solid in a higher potential compared to another which is connected to a lower potential, results in a decrement of the total contact current compared to the current between solids without roughness. By considering similar rough parameters for both solids, the contribution of the perturbed contact current becomes zero. Moreover, repercussions by considering the conductivity contrast between components are explored.
•Roughening is an unavoidable factor during the fabrication of electronic devices.•Surface roughness affects the contact current density and contact resistance.•Contact current exhibits significant dependence on the properties of rough surfaces.
Titanium oxide (TiO2) has been widely utilized for application in environmental pollution due to its unique properties. However, large bandgap (3.2 eV) and low surface area of bulk TiO2 are the main ...properties that limit its photocatalytic applications. In this work, a thin layer of TiO2 (<200 nm) nanoparticles (NPs) on mechanically roughened glass substrates is deposited by a simple sol-gel method followed by a dip-coating process along with fast heating and sintering. The effect of substrate surface roughness on the morphology, hydrophilicity, and optical properties which results in a more electron-hole generation and consequently improved photocatalytic activity was investigated by different characterization techniques. The TiO2 layer on the roughest substrate (RMS = 76.90 nm) showed the smallest average NP size (3 nm) with the highest surface roughness (RMS = 121.00 nm) and hydrophilicity (74.5%) as well as strong optical absorption. This sample photodegraded the pollutant with an efficiency of 85% at a rate of 0.0054 min−1 under the illumination of the vis-light emitting diode (LED)-based source (440 and 590 nm). Therefore, an enhanced photocatalytic activity accompanied by recyclability was achieved by modifying the substrate surface roughness and thermal treatment in the process of synthesis. Conclusively, intrinsic defects and grain boundaries appear which behave as active areas for charge transfer in the photocatalytic process under visible irradiation. This research may provide an insight into the fabrication of highly efficient photocatalysts based on commonly used wide band gap materials to work in the absence of UV light.
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•Application of a simple process for deposition of visible photoactive TiO2 nanoparticles (NPs) on mechanically roughened glass substrates.•Investigating the effect of substrate roughness on the operating parameters in the visible photocatalytic activity.•Highest photo-degradation of pollutant with an efficiency of 85% at a rate of 0.0054 min−1 under the illumination of the vis-LED for the TiO2 NPs on the substrate with RMS roughness of 76.90 nm.•Explaining the corresponding mechanism for enhancing the visible photo-degradation of TiO2 NPs with roughness.
Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and ...domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region.
Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 A resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs.
The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics.
The temperature correction to the Casimir torque and the lateral Casimir force between two plates is calculated. The plates are assumed to be rough, homogeneous, isotropic, and correlated to each ...other. It is seen that the force and torque tend to constant values for small temperatures, and are linear in temperature for large temperatures. Temperature corrections for both small and large temperatures are also calculated.
•The dynamics of a capacitor with a moving plate is investigated.•The effect of conductor being real, and the effect of roughness are studied.•The stationary and nonstationary behaviors of the ...system, and especially the emergence of chaotic behavior, are investigated.
The static and dynamic behavior of a fixed-fixed beam under the effect of Casimir force is studied. Two different corrections are studied: the effect of real conductor (in contrast to the ideal conductor) on the Casimir force, and the effect of electrode roughness on the electric and Casimir forces. The bifurcation diagrams and the phase portraits are presented and compared. The chaotic behavior of the system is studied for the case a harmonic voltage is added to the dc voltage, and there is a damping force. It is shown that for autonomous systems (no ac voltage and no damping), the stable region is enlarged when real conductor corrections are applied, applying both the real conductor and roughness corrections shrinks the stable region (compared to applying only the real conductor corrections). Finally, the appearance of chaotic behavior is investigated and the threshold values of the control parameters are found, in the perturbative limit (small values of the harmonic and damping forces). The chaotic regions are compared for the flat ideal, flat real, and rough real cases.
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