08 Fakultät Mathematik und Physik
Permanent URI for this collectionhttps://elib.uni-stuttgart.de/handle/11682/9
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Item Open Access Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures(2021) Xin, Ling; Duan, Xiaoyang; Liu, NaIn living organisms, proteins are organized prevalently through a self-association mechanism to form dimers and oligomers, which often confer new functions at the intermolecular interfaces. Despite the progress on DNA-assembled artificial systems, endeavors have been largely paid to achieve monomeric nanostructures that mimic motor proteins for a single type of motion. Here, we demonstrate a DNA-assembled building block with rotary and walking modules, which can introduce new motion through dimerization and oligomerization. The building block is a chiral system, comprising two interacting gold nanorods to perform rotation and walking, respectively. Through dimerization, two building blocks can form a dimer to yield coordinated sliding. Further oligomerization leads to higher-order structures, containing alternating rotation and sliding dimer interfaces to impose structural twisting. Our hierarchical assembly scheme offers a design blueprint to construct DNA-assembled advanced architectures with high degrees of freedom to tailor the optical responses and regulate multi-motion on the nanoscale.Item Open Access Optimizing NV magnetometry for magnetoneurography and magnetomyography applications(2023) Zhang, Chen; Zhang, Jixing; Widmann, Matthias; Benke, Magnus; Kübler, Michael; Dasari, Durga; Klotz, Thomas; Gizzi, Leonardo; Röhrle, Oliver; Brenner, Philipp; Wrachtrup, JörgMagnetometers based on color centers in diamond are setting new frontiers for sensing capabilities due to their combined extraordinary performances in sensitivity, bandwidth, dynamic range, and spatial resolution, with stable operability in a wide range of conditions ranging from room to low temperatures. This has allowed for its wide range of applications, from biology and chemical studies to industrial applications. Among the many, sensing of bio-magnetic fields from muscular and neurophysiology has been one of the most attractive applications for NV magnetometry due to its compact and proximal sensing capability. Although SQUID magnetometers and optically pumped magnetometers (OPM) have made huge progress in Magnetomyography (MMG) and Magnetoneurography (MNG), exploring the same with NV magnetometry is scant at best. Given the room temperature operability and gradiometric applications of the NV magnetometer, it could be highly sensitive in the pT/Hz-range even without magnetic shielding, bringing it close to industrial applications. The presented work here elaborates on the performance metrics of these magnetometers to the state-of-the-art techniques by analyzing the sensitivity, dynamic range, and bandwidth, and discusses the potential benefits of using NV magnetometers for MMG and MNG applications.Item Open Access Solubilization of inclusion bodies : insights from explainable machine learning approaches(2023) Walther, Cornelia; Martinetz, Michael C.; Friedrich, Anja; Tscheließnig, Anne-Luise; Voigtmann, Martin; Jung, Alexander; Brocard, Cécile; Bluhmki, Erich; Smiatek, JensWe present explainable machine learning approaches for gaining deeper insights into the solubilization processes of inclusion bodies. The machine learning model with the highest prediction accuracy for the protein yield is further evaluated with regard to Shapley additive explanation (SHAP) values in terms of feature importance studies. Our results highlight an inverse fractional relationship between the protein yield and total protein concentration. Further correlations can also be observed for the dominant influences of the urea concentration and the underlying pH values. All findings are used to develop an analytical expression that is in reasonable agreement with experimental data. The resulting master curve highlights the benefits of explainable machine learning approaches for the detailed understanding of certain biopharmaceutical manufacturing steps.Item Open Access Molecular dynamics simulations for the study of interaction between non-canonical DNA structures and biochemically relevant co-solutes(2023) Oprzeska-Zingrebe, Ewa Anna; Smiatek, Jens (Priv.-Doz. Dr.)Non-canonical nucleic acid structures, such as DNA G-quadruplexes and i-Motifs, have been proved to play an important role in key biological processes, including gene expression, replication, regulation or telomere maintenance. The presence of G-quadruplexes in promoter regions of certain oncogenes turn them into a potential target for cancer therapies. Besides their biological implications, non-canonical DNA structures are present in genomes of various organisms, who adopt certain levels of co-solutes to protect their internal structures against the harsh environment. This study presents the research on the selected non-canonical DNA structures of particular biological relevance: G-quadruplex with only two tetrads, small DNA hairpin and ssDNA strand as well as canonical double helix. The atomistic molecular dynamics (MD) simulations have been applied to elucidate the structural, configuration and solvation properties of the analyzed structures in the presence of assorted co-solutes, composing the native cellular environment in nature: urea, ectoine and trimethylamine-N-oxide (TMAO). With the application of molecular theory of solutions, one determines and exemplifies the thermodynamic properties of investigated structures in various environments close to the physiological conditions present in living cells. This study uncovers the versatile nature of DNA interaction with diverse co-solutes and water, as well as the cross-interactions between the inorganic components of the biomolecular solution. The cellular mechanisms of DNA structural stabilization and destabilization are hereby described in terms of preferential binding and preferential exclusion, with particular emphasis on the properties of solvent structure within individual solvation shells. In this regards, this work presents a comprehensive study on the intracellular interactions involving nucleic acids, thus shedding light into their microscopic properties and opening the path for further biomedical research.Item Open Access Item Open Access Predicting concentrations of mixed sugar solutions with a combination of resonant plasmon-enhanced SEIRA and principal component analysis(2022) Pfezer, Diana; Karst, Julian; Hentschel, Mario; Giessen, HaraldThe detection and quantification of glucose concentrations in human blood or in the ocular fluid gain importance due to the increasing number of diabetes patients. A reliable determination of these low concentrations is hindered by the complex aqueous environments in which various biomolecules are present. In this study, we push the detection limit as well as the discriminative power of plasmonic nanoantenna-based sensors towards the physiological limit. We utilize plasmonic surface-enhanced infrared absorption spectroscopy (SEIRA) to study aqueous solutions of mixtures of up to five different physiologically relevant saccharides, namely the monosaccharides glucose, fructose, and galactose, as well as the disaccharides maltose and lactose. Resonantly tuned plasmonic nanoantennas in a reflection flow cell geometry allow us to enhance the specific vibrational fingerprints of the mono- and disaccharides. The obtained spectra are analyzed via principal component analysis (PCA) using a machine learning algorithm. The high performance of the sensor together with the strength of PCA allows us to detect concentrations of aqueous mono- and disaccharides solutions down to the physiological levels of 1 g/L. Furthermore, we demonstrate the reliable discrimination of the saccharide concentrations, as well as compositions in mixed solutions, which contain all five mono- and disaccharides simultaneously. These results underline the excellent discriminative power of plasmonic SEIRA spectroscopy in combination with the PCA. This unique combination and the insights gained will improve the detection of biomolecules in different complex environments.Item Open Access Influence of bacterial swimming and hydrodynamics on attachment of phages(2024) Lohrmann, Christoph; Holm, Christian; Datta, Sujit S.Bacteriophages (“phages”) are viruses that infect bacteria. Since they do not actively self-propel, phages rely on thermal diffusion to find target cells - but can also be advected by fluid flows, such as those generated by motile bacteria themselves in bulk fluids. How does the flow field generated by a swimming bacterium influence how it encounters phages? Here, we address this question using coupled molecular dynamics and lattice Boltzmann simulations of flagellated bacteria swimming through a bulk fluid containing uniformly-dispersed phages. We find that while swimming increases the rate at which phages attach to both the cell body and flagellar propeller, hydrodynamic interactions strongly suppress this increase at the cell body, but conversely enhance this increase at the flagellar bundle. Our results highlight the pivotal influence of hydrodynamics on the interactions between bacteria and phages, as well as other diffusible species, in microbial environments.Item Open Access Functionalized nanogap for DNA read‐out : nucleotide rotation and current‐voltage curves(2020) Maier, Frank C.; Fyta, MariaFunctionalized nanogaps embedded in nanopores show a strong potential for enhancing the detection of biomolecules, their length, type, and sequence. This detection is strongly dependent on the features of the target biomolecules, as well as the characteristics of the sensing device. In this work, through quantum‐mechanical calculations, we elaborate on representative such aspects for the specific case of DNA detection and read‐out. These aspects include the influence of single DNA nucleotide rotation within the nanogap and the current‐voltage (I‐V) characteristics of the nanogap. The results unveil a distinct variation in the electronic current across the functionalized device for the four natural DNA nucleotides with the applied voltage. These also underline the asymmetric response of the rotating nucleotides on this applied voltage and the respective variation in the rectification ratio of the device. The electronic tunneling current across the nanogap can be further enhanced through the proper choice of an applied bias voltage. We were able to correlate the enhancement of this current to the nucleotide rotation dynamics and a shift of the electronic transmission peaks towards the Fermi level. This nucleotide specific shift further reveals the sensitivity of the device in reading‐out the identity of the DNA nucleotides for all different configurations in the nanogap. We underline the important information that can be obtained from both the I‐V curves and the rectification characteristics of the nanogap device in view of accurately reading‐out the DNA information. We show that tuning the applied bias can enhance this detection and discuss the implications in view of novel functionalized nanopore sequencers.