Vývoj a aplikace molekulové dynamiky pro molekulovou spektroskopii

This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...Katedra fyzikální a makromol. chemieDepartment of Physical and Macromolecular ChemistryFaculty of SciencePřírodovědecká fakult

Circular Dichroism is Sensitive to Monovalent Cation Binding in Monensin Complexes

We present a lock-free version of the light-weight userlevel task management library called Wool, in an aim to show that even extremely well tuned, in terms of synchronization,applications can benefit from lock-free programming.Explicit multi-threading is an efficient way to exploit the offered parallelism of multi-core and multi-processor based systems. However, it can sometimes be hard to expressthe inherited parallelism in programs using a limited number of long lived threads. Often it can be more straightforwardto dynamically create a large number of small tasks that in turn automatically execute on the available threads.Wool is a promising and efficient library and framework that allows the programmer to create user tasks in C with a very low overhead. The library automatically executestasks and balances the load evenly on a given number of threads by utilizing work stealing techniques. However, thesynchronization for stealing tasks is based on mutual exclusion which is known to limit parallelism and efficiency. We have designed and implemented a new lock-free algorithmfor synchronization of stealing tasks in Wool. Experiments show similar or significantly improved performance on a setof benchmarks executed on a multi-core platform

Comparison of the Accuracy of Bibliographical References Generated for Medical Citation Styles by EndNote, Mendeley, RefWorks and Zotero

Bibliographical references to online and printed articles, books, contributions to edited books and web resources generated by EndNote, Mendeley, RefWorks and Zotero were compared with manually written references according to the citation instructions in 15 biomedical journals and the NLM citation style. The fewest mistakes were detected in references generated by Zotero for 11 journals and the NLM style, while the second fewest number of mistakes was found in Mendeley. The largest number of mistakes for 9 journals was found in references generated by EndNote and in the other 4 journals the largest number of mistakes was detected in RefWorks references. With regard to the individual types of resources, the lowest number of mistakes was shown by Zotero, while RefWorks had the greatest number of mistakes. All programs had problems especially with generating the URL and the date of access in the reference to online documents. It was also found that several mistakes were caused by technical limitations of the reference managers, while other mistakes originated due to incorrect setting of the citation styles. A comparison showed that Zotero and Mendeley are the most suitable managers

Development and applications of molecular dynamics for chiral systems

The Thesis deals with MD simulations of solutions of chiral solutes in chiral solvents. These solutions consist of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol and 1-phenyl- ethanamine.The differences in NMR properties between different combnations of solvent and solute absolute configuration were modeled. Indeed, differences in radial distribution functions and conformer abundances of solute calculated by the WHAM method were found. These results correlated with experimental differences in NMR shifts. Additionally, a method of cluster preselection was developed. It significantly decreased the amount of clusters needed for computations of NMR shieldings and hence the computer time. Keywords: chirality, molecular dynamic, nuclear magnetic resonanc

Development and applications of molecular dynamics for molecular spectroscopy

This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce..

Development and applications of molecular dynamics for molecular spectroscopy

This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce..

Structure of supramolecular astaxanthin aggregates revealed by molecular dynamics and electronic circular dichroism spectroscopy

We report the molecular dynamics and electronic circular dichroism computations of astaxanthin aggregates, to find a link between the aggregate structure and spectral shapes, and the environment.</p