Theme of this diploma thesis is the design of caravan meaning travel trailer. Concept is adapted to the technical and ergonomic requirements and the main goal of this concept is to provide original design with a view to the future. The complex concept meets the operational, technical and ergonomic demands of such trailers. The project is focused on the design concept of the implemented folding mechanism. Design of the travel trailer is due to todays modern technological methods and the construction ready for production and everyday operating usage.

The differences between refolding mechanisms of sperm whale apomyoglobin subsequent to three different unfolding conditions have been examined by atomistic level computer simulations. The three unfolding conditions used in this work are high-temperature, low temperature and low pH. The folding of this protein has been extensively studied experimentally, providing a large data base of folding parameters which can be probed using simulations. The crystal structure of sperm whale myoglobin was taken from Protein Data Bank, followed by the removal of the heme unit and a subsequent energy minimization was performed in order to generate the native apomyoblogin form. Thus, the native conformation of apomyoglobin utilized is the same in all the three different refolding simulations done in the present work. The differences are the way the initial unfolded conformations were obtained. The refolding trajectories were obtained at room temperature using the Stochastic Difference Equation in Length algorithm. The results reveal differences between the three refolding routes. In contrast to previous molecular simulations that modeled low pH denaturation, an extended intermediate with large helical content was not observed in the refolding simulations from the high-temperature unfolded state. Otherwise, a structural collapse occurs without formation of helices or native contacts. Once the protein structure is more compact (radius of gyration less than 18 angstroms) secondary and tertiary structures appear. The low pH simulations show some agreement with the low pH experimental data and previous molecular dynamics simulations, like formation of a conformation having radius of gyration around 20 angstroms and large helical content. And the refolding simulations after the low temperature unfolding present differences in the properties of apomyoglobin folding route, comparing to the other two previous conditions. The collapse of the protein during folding occurs later in the simulation when compared with high-temperature denaturing state, but earlier when compared to low pH simulations. These differences strongly suggest that a protein can follow different folding routes, depending on the nature and the structure of the unfolded state.

Dynamic Programming Algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms.

<div> The folding and unfolding processes of poly-protein has been tremendously studied recently. The poly-protein dynamics under an external force can play an important role in addressing the issue of the mechanics of muscle tissue. In this research, we use a single-molecule technique: magnetic tweezers to observe the dynamics of 8-mer poly-protein L under different loads applied and then in different Tris-buffered salines. Our result shows that more protein domains unfold as the force load becomes larger. At 6, 7 and 8 pN loads, the poly-protein is most likely to stay in state 1, 3 and 6 with 1, 3 and 6 domains unfolded, respectively according to the probability distribution. This can be well explained by our constructed free energy-related model. The fit results give protein L parameters of persistence length of 0.4 nm, contour length of 18.8 nm and the unfolding energy of 6.5 kT, all in reasonable ranges based on previously reported literature.</div><div> Besides, we also find the dependency of transition rate on force load and salt. The poly-protein has lower transition rate at high force than at low force due to the free energy tilting effect since high force extremely decreases the possibility of protein unfolding that results in a huge drop in the total number of folding and unfolding events. This inverse proportion effect can also be seen in different TRIS-buffered salines (TRIS-150mM NaCl, TRIS-1M NaCl, and TRIS-1M KCl,). We explore the effect of salt concentration, when the concentration of NaCl is increased, the transition rate increases while the probability distribution remains almost the same, indicating the protein unfolding barrier is lowered without altering the overall energy landscape. We attribute this to, first, the charge shielding effect that more interactions between ions and water molecules occur, causing fewer water molecules available to interact with the charged part of protein than before, and, second, more direct interactions of ions with protein that might affect the electrostatic-related transition rate. Considering the effect of salt type, the two 1M alkali metal-chloride salines are compared. We conclude that ions with larger size have less effect on transition rate because ions with smaller size (Na+) can create stronger bonds with water that increase the interference on the protein interaction with water and can easier penetrate into protein to directly interact with the protein.</div>

No description available.

Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods: The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. Results: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.

With the increasing demand of compact and lightweight wireless devices, there is a significant need to miniaturize the antennas, which are one of the largest radiofrequency components. The radiation performance of antennas degrades as their physical size becomes smaller in terms of operating wavelength [1]. The key challenge in antenna design, therefore, lies in the compromise between size and radiation performance. This challenge becomes critical for low frequency antennas such as for the RFID band. The Antenna-in-Package (AiP) concept, where the antenna is realized as part of the package along with the driving electronics, provides some console in terms of size as the antenna does not need any additional space. In this approach, the package becomes a functional module along with its primary job of protecting the components from the environment. This work aims to investigate various miniaturization techniques for a UHF RFID tag on package. Firstly, a dipole is given a 3D shape by carefully folding it over a package, in a manner that the currents on different segments add constructively. Secondly, the package material (which acts as the substrate for the antenna) is chosen to have a dielectric constant of 5.3 which further helps in size reduction. Finally, loading of slow-wave structures, comprising of inductors and capacitors, is used to achieve further miniaturization. The Artificial Transmission Line approach is utilized to determine the required values of the lumped components, and its location is optimized by analyzing the current distribution of the antenna to maintain a good efficiency. The RFID chip with a large capacitive impedance is conjugately matched to the antenna without an external matching network. This is done by carefully selecting the values of the lumped components as well as by adjusting the trace width of the antenna. The package has been realized through a low-loss filament (𝑡𝑎𝑛(𝛿) = 0.004) with the Raise3D Pro2 printer, and the conductor has been realized by copper tape using laser patterning technology with the laser platform PLS6MW. At an operational frequency of 866 MHz, a 𝑘𝑎 of 0.26, a read-range of 2.7 𝑚, and a radiation efficiency of approximately 32% is achieved.

Protein aggregation is deleterious to human health and detrimental to therapeutic shelf-life. The physical processes that induce aggregation are the same processes that drive productive folding reactions. As such, protein aggregation is a non-productive form of protein folding. To gain insight into the steps that serve as a partition between the folding and aggregation reactions, the folding mechanisms of several β-rich proteins with links to human disease or medicine were examined. In the ALS-linked protein, SOD1, a subpopulation of the unfolded ensemble is found to be a common source of both nonnative structure and frustrated folding. These behaviors are only observed upon the reduction of the intrinsic disulfide bond, indicating that this covalent interaction wards against aggregation. The nonnative structure presents an attractive target for the development of new therapeutic agents. In VH domains from therapeutic mAbs, the intramolecular disulfide bond protects against aggregation. However, it can also introduce complexity to the folding mechanism. This complexity is linked to the formation of a strained orientation of the disulfide bond. This strained orientation of the disulfide in certain VH domains is energetically unfavorable enough to disrupt the formation of the disulfide in the full length mAbs. The novel relationship observed between disulfide orientation, folding complexity, and incomplete oxidation warrants further examination in other Ig domains. Overall, these results demonstrate that mapping the folding free energy landscape for proteins with roles in human disease or therapeutics can provide valuable insights for developing and improving treatment options.

(βα)8 TIM barrel proteins are one of the most common structural motifs found in biology. They have a complex folding free energy landscape that includes an initial off-pathway intermediate as well as two on-pathway intermediates. The formation of these intermediates is hypothesized to be driven by large clusters of the branched chain amino acids, isoleucine, leucine, and valine (ILV). All-atom MD simulations and circular dichroism experiments on polar mutants of the hydrophobic clusters of α-Trp synthase, a TIM barrel protein, revealed the importance of dehydrating the clusters on intermediate states. Custom, single-piece microfluidic chips were interfaced with small angle x-ray scattering and time resolved FRET experiments to monitor the role of a large ILV cluster on the microsecond timescale in a second TIM barrel protein, sIGPS. Dimensional analysis of the initial misfolded intermediate showed an ILV cluster was responsible for the initiation of structure in the intermediate. Early structure formation in the ILV cluster was confirmed by coarse grained simulations. Native state hydrogen exchange experiments were used to probe the higher energy species that are in equilibrium with the native state. Results from the NMR experiment complement the kinetic studies as the core of stability found by NMR mapped back to the same region of the ILV cluster that was found to initiate folding. When taken together, the results show the importance of hydrophobic clusters on the entire free energy surface of TIM barrel proteins.

Early events in folding can determine if a protein is going to fold, misfold, or aggregate. Understanding these deterministic events is paramount for de novo protein engineering, the enhancement of biopharmaceutical stabilities, and understanding neurodegenerative diseases including amyotrophic lateral sclerosis and Alzheimer's disease. However, the physicochemical and structural biases within high energy states of protein biopolymers are poorly understood. A combined experimental and computational study was conducted on the small β/α-repeat protein CheY to determine the structural basis of its submillisecond misfolding reaction to an off-pathway intermediate. Using permutations, we were able to discriminate between the roles of two proposed mechanisms of folding; a nucleation condensation model, and a hydrophobic collapse model driven by the formation of clusters of isoleucine, leucine, and valine (ILV) residues. We found that by altering the ILV cluster connectivity we could bias the early folding events to either favor on or off-pathway intermediates. Structural biases were also experimentally observed in the unfolded state of a de novo designed synthetic β/α-repeat protein, Di-III_14. Although thermodynamically and kinetically 2-state, Di-III_14 has a well structured unfolded state that is only observable under native-favoring conditions. This unfolded state appears to retain native-like structure, consisting of a hydrophobic 7 core (69% ILV) stabilized by solvent exposed polar groups and long range electrostatic interactions. Together, these results suggest that early folding events are largely deterministic in these two systems. Generally, low contact order ILV clusters favor local compaction and, in specific cases, long range electrostatic interactions may have stabilizing effects in higher energy states.