optical modeling
Dotaz
Zobrazit nápovědu
The transition dipole coupling model allows to vary systematically many parameters, such as chromophore geometries and transition dipoles. We used it to explore conditions favorable to chirality enhancement observed in many experiments on protein amyloidal precipitates. Stacking of β-sheet planes has been identified as a particularly powerful mechanism of the enhancement.
- Klíčová slova
- Raman optical activity, circular dichroism, enhancement of optical activity, protein spectra, transition dipole coupling,
- MeSH
- molekulární modely MeSH
- multiproteinové komplexy chemie MeSH
- optická otáčivost * MeSH
- stereoizomerie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- multiproteinové komplexy MeSH
Design and development of scale-down approaches, such as microbioreactor (μBR) technologies with integrated sensors, are an adequate solution for rapid, high-throughput and cost-effective screening of valuable reactions and/or production strains, with considerably reduced use of reagents and generation of waste. A significant challenge in the successful and widespread application of μBRs in biotechnology remains the lack of appropriate software and automated data interpretation of μBR experiments. Here, it is demonstrated how mathematical models can be usedas helpful tools, not only to exploit the capabilities of microfluidic platforms, but also to reveal the critical experimental conditions when monitoring cascade enzymatic reactions. A simplified mechanistic model was developed to describe the enzymatic reaction of glucose oxidase and glucose in the presence of catalase inside a commercial microfluidic platform with integrated oxygen sensor spots. The proposed model allowed an easy and rapid identification of the reaction mechanism, kinetics and limiting factors. The effect of fluid flow and enzyme adsorption inside the microfluidic chip on the optical sensor response and overall monitoring capabilities of the presented platform was evaluated via computational fluid dynamics (CFD) simulations. Remarkably, the model predictions were independently confirmed for μL- and mL- scale experiments. It is expected that the mechanistic models will significantly contribute to the further promotion of μBRs in biocatalysis research and that the overall study will create a framework for screening and evaluation of critical system parameters, including sensor response, operating conditions, experimental and microbioreactor designs.
- Klíčová slova
- Bioprocess modeling, Computational fluid dynamics, Enzymatic biocatalysis, Mechanistic modeling, Microbioreactor, Oxygen monitoring,
- MeSH
- biokatalýza MeSH
- biologické modely * MeSH
- bioreaktory * MeSH
- glukosaoxidasa metabolismus MeSH
- katalasa metabolismus MeSH
- mikrofluidní analytické techniky * MeSH
- optická vlákna * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- glukosaoxidasa MeSH
- katalasa MeSH
Optical trapping of particles has become a powerful non-mechanical and non-destructive technique for precise particle positioning. The manipulation of particles in the evanescent field of a channel waveguide potentially allows for sorting and trapping of several particles and cells simultaneously. Channel waveguide designs can be further optimized to increase evanescent field prior to the fabrication process. This is crucial in order to make sure that the surface intensity is sufficient for optical trapping. Simulation configurations are explained in detail with specific simulation flow. Discussion on parameters optimization; physical geometry, optical polarization and wavelength is included in this paper. The effect of physical, optical parameters and beam spot size on evanescent field has been thoroughly discussed. These studies will continue toward the development of a novel copper ion-exchanged waveguide as a method of particle sorting, with biological cell propulsion studies presently underway.
- Klíčová slova
- Beam propagation method, Channel waveguide, Optical manipulation,
- MeSH
- analýza selhání vybavení MeSH
- design s pomocí počítače MeSH
- design vybavení MeSH
- ionty chemie MeSH
- měď chemie MeSH
- optická pinzeta * MeSH
- počítačová simulace MeSH
- povrchová plasmonová rezonance přístrojové vybavení MeSH
- radiační rozptyl MeSH
- světlo MeSH
- teoretické modely * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- ionty MeSH
- měď MeSH
BACKGROUND: Optical coherence tomography (OCT) is a well established imaging technique with different applications in preclinical research and clinical practice. The main potential for its application lies in the possibility of noninvasively performing "optical biopsy". Nevertheless, functional OCT imaging is also developing, in which perfusion imaging is an important approach in tissue function study. In spite of its great potential in preclinical research, advanced perfusion imaging using OCT has not been studied. Perfusion analysis is based on administration of a contrast agent (nanoparticles in the case of OCT) into the bloodstream, where during time it specifically changes the image contrast. Through analysing the concentration-intensity curves we are then able to find out further information about the examined tissue. METHODS: We have designed and manufactured a tissue mimicking phantom that provides the possibility of measuring dilution curves in OCT sequence with flow rates 200, 500, 1000 and 2000 μL/min. The methodology comprised of using bolus of 50 μL of gold nanorods as a contrast agent (with flow rate 5000 μL/min) and continuous imaging by an OCT system. After data acquisition, dilution curves were extracted from OCT intensity images and were subjected to a deconvolution method using an input-output system description. The aim of this was to obtain impulse response characteristics for our model phantom within the tissue mimicking environment. Four mathematical tissue models were used and compared: exponential, gamma, lagged and LDRW. RESULTS: We have shown that every model has a linearly dependent parameter on flow ([Formula: see text] values from 0.4914 to 0.9996). We have also shown that using different models can lead to a better understanding of the examined model or tissue. The lagged model surpassed other models in terms of the minimisation criterion and [Formula: see text] value. CONCLUSIONS: We used a tissue mimicking phantom in our study and showed that OCT can be used for advanced perfusion analysis using mathematical model and deconvolution approach. The lagged model with three parameters is the most appropriate model. Nevertheless, further research have to be performed, particularly with real tissue.
- Klíčová slova
- Deconvolution, Impulse response, Model, Optical coherence tomography, Perfusion analysis, Phantom,
- MeSH
- 3D tisk MeSH
- design vybavení MeSH
- fantomy radiodiagnostické * MeSH
- kontrastní látky chemie MeSH
- kovové nanočástice chemie MeSH
- nanotrubičky chemie MeSH
- optická koherentní tomografie metody MeSH
- počítačové zpracování obrazu MeSH
- teoretické modely * MeSH
- tkáňové podpůrné struktury chemie MeSH
- zlato chemie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kontrastní látky MeSH
- zlato MeSH
Bacterial cellulose nanopaper (BC) is a multifunctional material known for numerous desirable properties: sustainability, biocompatibility, biodegradability, optical transparency, thermal properties, flexibility, high mechanical strength, hydrophilicity, high porosity, broad chemical-modification capabilities and high surface area. Herein, we report various nanopaper-based optical sensing platforms and describe how they can be tuned, using nanomaterials, to exhibit plasmonic or photoluminescent properties that can be exploited for sensing applications. We also describe several nanopaper configurations, including cuvettes, plates and spots that we printed or punched on BC. The platforms include a colorimetric-based sensor based on nanopaper containing embedded silver and gold nanoparticles; a photoluminescent-based sensor, comprising CdSe@ZnS quantum dots conjugated to nanopaper; and a potential up-conversion sensing platform constructed from nanopaper functionalized with NaYF4:Yb(3+)@Er(3+)&SiO2 nanoparticles. We have explored modulation of the plasmonic or photoluminescent properties of these platforms using various model biologically relevant analytes. Moreover, we prove that BC is and advantageous preconcentration platform that facilitates the analysis of small volumes of optically active materials (∼4 μL). We are confident that these platforms will pave the way to optical (bio)sensors or theranostic devices that are simple, transparent, flexible, disposable, lightweight, miniaturized and perhaps wearable.
- Klíčová slova
- biosensing, composite, nanocellulose, optical sensors, photoluminescent devices, plasmonic devices,
- MeSH
- absorpce radiace MeSH
- biosenzitivní techniky přístrojové vybavení MeSH
- celulosa chemie MeSH
- kovové nanočástice chemie MeSH
- kvantové tečky chemie MeSH
- optické jevy MeSH
- optické prostředky * MeSH
- papír * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- celulosa MeSH
We report results of first-principles calculations of electronic and optical properties of pristine 1T-TiS(2) and 1T-TiS(2) intercalated with lithium. Calculations have been performed using the full-potential linearized augmented plane wave method based on density functional theory together with the local density approximation for the exchange correlation energy functional. We have calculated the band structure, density of states, and the linear optical properties. We compare our results of the intercalated 1T-LiTiS(2) with the host 1T-TiS(2) to ascertain the effect of Li intercalation on the electronic and optical properties. The Li-s and Li-p bands are very broad and do not contribute much to the density of states. Our calculations show that the electronic and optical properties are influenced significantly when TiS(2) is intercalated with lithium.
- MeSH
- chemické modely MeSH
- elektrony * MeSH
- lithium chemie MeSH
- optické jevy MeSH
- počítačová simulace MeSH
- povrchové vlastnosti MeSH
- titan chemie MeSH
- zdroje elektrické energie * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- lithium MeSH
- titan MeSH
- titanium sulfide MeSH Prohlížeč
Free-Space Optical (FSO) communications link performance is highly affected when propagating through the time-spatially variable turbulent environment. In order to improve signal reception, several mitigation techniques have been proposed and analytically investigated. This paper presents experimental results for the route diversity technique evaluations for a specific case when several diversity links intersects a common turbulent area and concurrently each passing regions with different turbulence flows.
Change of molecular properties with pressure is an attracting means to regulate molecular reactivity or biological activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of vibrational optical activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in vibrational circular dichroism and Raman optical activity spectra are predicted to be 2-3-times larger than for non-polarized IR and Raman techniques.
- Klíčová slova
- density functional theory, high pressure, molecular dynamics, spectra simulations, vibrational optical activity,
- MeSH
- dipeptidy chemie MeSH
- disacharidy chemie MeSH
- molekulární konformace MeSH
- nukleotidy chemie MeSH
- optické jevy * MeSH
- simulace molekulární dynamiky MeSH
- tlak * MeSH
- vibrace * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- dipeptidy MeSH
- disacharidy MeSH
- nukleotidy MeSH
Most organic compounds provide vibrational spectra within the CH stretching region, yet the signal is difficult to interpret because of multiple difficulties in experiment and modeling. To better understand various factors involved, the ability of several harmonic and anharmonic computational approaches to describe these vibrations was explored for α-pinene, fenchone, and camphor as test compounds. Raman, Raman optical activity (ROA), infrared absorption (IR), and vibrational circular dichroism (VCD) spectra were measured and compared to quantum chemical computations. Surprisingly, the harmonic vibrational approach reasonably well reproduced the measured spectral patterns, including the vibrational optical activity (VOA). The CH stretching, however, appeared to be more sensitive to the basis set and solvent variations than lower-frequency vibrations. For a higher accuracy in frequencies and spectral shapes, anharmonic corrections were necessary. Accurate harmonic and anharmonic force fields were obtained with the mPW2PLYP double-hybrid functional. A limited vibrational configuration interaction (LVCI) where the CH stretching motion was decoupled from other vibrations provided the best simulated spectra. A balanced harmonic oscillator basis set had to be used, containing also states indirectly interacting with fundamental vibrations. A simpler second-order perturbational approach (PT2) appeared less useful. The modeling provided unprecedented agreement with experimental vibrational frequencies; spectral shapes were reproduced less faithfully. The possibility of ab initio interpretation of the CH spectral region for relatively large molecules further broadens the application span of vibrational spectroscopy.
- Publikační typ
- časopisecké články MeSH
Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.
- Klíčová slova
- Raman optical activity, density functional theory, glutathione, molecular dynamics, spectra modeling,
- MeSH
- glutathion MeSH
- molekulární konformace MeSH
- optická otáčivost MeSH
- Ramanova spektroskopie * metody MeSH
- simulace molekulární dynamiky * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- glutathion MeSH
