National Repository of Grey Literature 37 records found  1 - 10nextend  jump to record: Search took 0.01 seconds. 
Work and heat at the mesoscale
Pajger, Šimon ; Ryabov, Artem (advisor) ; Kolář, Michal (referee)
Title: Work and heat at the mesoscale Author: Bc. Šimon Pajger Department: Department of Macromolecular Physics Supervisor: RNDr. Artem Ryabov, Ph.D., KMF MFF UK Abstract: Understanding the conversion between heat and work by heat engines led to the discoveries of entropy and to the formulation of the Second law of clas- sical macroscopic thermodynamics. At the microscale and mesoscale, quantum coherences are a potential resource for various quantum processes. Quantum coherences can be used to enhance the performance of various devices beyond the limits demanded by classical physics. Recently many models have been es- tablished clarifying how coherences affect the speed and irreversibility of ther- modynamic processes and raising the question of what experimentally relevant consequences various generalizations of the formalism of classical thermodynam- ics to the microscopic level may have. Here we study a few of these models in great detail. Specifically, we discuss fluctuations of coherence-enhanced heat currents, propose a model of a heat engine that does work while being in a steady state, and derive a condition on the rate of decoherence that specifies, when coherence-enhanced currents provide a significant advantage over the case without any coherence. Then we discuss coherence-inducing heat bath...
Normalisation algorithms for spatially resolved transcriptomic data
Nádvorníková, Bára ; Kolář, Michal (advisor) ; Abaffy, Pavel (referee)
Spatially resolved transcriptomics is a novel method that enables the study of gene expression in tissue samples without loss of spatial context. It can be used to map the distribution of mRNA to individual cells as well as subcellular locations. Data obtained using this method provide important insights into various aspects of biology, including embryology, oncology, or immunology. The functioning and mutual interaction of individual cells cannot be fully explained without knowledge of their exact location in the tissue. Due to the novelty of the method, reconciling the obtained information on gene expression and spatial arrangement of cells is currently a major challenge and bioinformatics approaches are still being established. The aim of this work is to map the current algorithms for the normalisation of spatially resolved transcriptomics data and to compare these algorithms based on available data sets. Eventually, selected algorithms will be implemented and integrated into the workflow used at IMG CAS. The work includes i. survey of available solutions, ii. selection of a suitable solution or design of a new one, iii. implementation of the solution and its testing on available data.
Transcriptional changes associated with melanoma resistance to small inhibitor treatment
Dorčáková, Terézia ; Kolář, Michal (advisor) ; Modrák, Martin (referee)
Malignant melanoma is an aggressive skin tumour with increasing incidence and, in advanced stages, limited therapeutic results. The major oncogenic alteration in melanoma is mutational activation of the B-Raf protein, with the predominant mutation V600E, which occurs in 60% of cases and hyperactivates the ERK signaling pathway. This cascade of Raf, MEK and ERK protein kinases is an integral part of an evolu- tionarily conserved signaling network that allows eukaryotic cells to sense a variety of extracellular signals. These protein kinases sequentially activate each other and translate extracellular signals into cellular responses such as proliferation, di↵erentiation, cell cycle changes, apoptosis or cell migration. The central role of the ERK pathway in oncogen- esis has made it one of the targets for therapeutic intervention, and inhibitors targeting mutant Raf, such as vemurafenib or dabrafenib, have been approved for the treatment of melanoma. These molecules specifically target B-Raf(V600E) and have led to a revo- lution in melanoma treatment. Unfortunately, such targeted therapy is complicated by the ability of cancer cells to acquire resistance. The aim of this work is to study at the transcriptional level the emergence of this resistance in patients who respond well to treatment and in...
Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design
Kříž, Kristian ; Řezáč, Jan (advisor) ; Klimeš, Jiří (referee) ; Kolář, Michal (referee)
Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design Doctoral thesis Kristian Kříž The subject of this thesis is the optimization of semiempirical quantum mechanical methods (SQM) for their use in in silico drug design. The thesis covers two topics - COSMO2 solvation model optimization part and PLF547, PLA15 dataset development part. The first part is devoted to the optimization of COSMO solvation model by addition of a nonpolar term and reparametrization of the model for SQM methods PM6 and PM7. We have shown that the accuracy of the resulting "COSMO2" optimized model improved on all the tested datasets and we have compared it to other selected SQM solvation models. The method has also been tested on the protein ligand complexes as a part of a scoring function, where it provides better preditction of binding affinity of drug candidates for their target protein. The second part of the thesis describes the construction of datasets for noncovalent interactions aimed speicificly to represent an environment of an enyzme active site complexed with a ligand with reliable benchmark values of interaction energies in vacuum and solvent (water). The developed PLF547 and PLA15 datasets are suitable for testing and development of methods for the use in drug design. We have...
E-commerce Design
Kolář, Michal ; Dyk, Tomáš (referee) ; Luhan, Jan (advisor)
Bachelor’s thesis deals with a creation of design and implementation of e-commerce for the newly formed company, focused primarily on Apple devices service. The work focuses on the analysis of the company, requirements and implementation of e-commerce with innovatice elements.
Úloha Londonových disperzních sil ve stabilitě struktury DNA: in silico experiment
Kolář, Michal
Author: Michal Kolář The Role of London Dispersion Forces in DNA structure stability: in silico experiment By means of computer simulations the role of the dispersion forces was elucidated. The free energy calculations obtained from the biased molecular dynamics and the simulations of the Dickerson's dodecamer of DNA suggested that the dispersion forces are important for the structure determination. While the overall aggregation of the DNA strands is attributed to the hydrophobic effect of the surrounding water, the particular conformation of the DNA, i.e. double helix, is claimed to be stabilised by London dispersion forces. These conclusions are with agreement with the previous theories. Keywords: dispersion force, DNA, molecular dynamics, hydrophobic effect, free energy Author: Michal Kolář Úloha Londonových disperzních sil ve stabilitě struktury DNA: in silico exper- iment Pomocí metod výpočetní chemie byla vyšetřována úloha disperzních sil ve stabilitě struk- tury DNA. Za účelem určení volné energie asociace bazí nukleových kyselin ve vodném prostředí byly provedeny molekulově dynamické simulace na pozměněné potenciálové hy- perploše a tyto výsledky byly porovnány se simulacemi Dickersonova dodecameru. Dis- perzní energie byla shledána jako důležitá komponenta...
Blocky accumulation mapping from RPAS LiDAR and image data
Kolář, Michal ; Potůčková, Markéta (advisor) ; Dušánek, Petr (referee)
With merit of constant development in measuring technology it is possible to obtain data of high resolution and accuracy describing Earth's surface. During the project "Vegetation and Krkonoše tundra change detection method development by analyzing data from multispectral, hyperspectral and LiDAR UAV sensors" high quality data were acquired, with point density reaching up to 800 points/m2 and orthophoto of GSD 0.02 m. Data are capturing cryoplanation terraces in NE parth of Luční hora in three time periods: June, July and August 2019. The aim of this work is to devise a methodology of blocky accumulation mapping and evaluating detail of data. Key words: blocky accumulation, laser scanning, UAV, point cloud, orthophoto, segmentation
Technological analysis of the usability of new thermosetting materials for the construction of headlamps
Rašner, Martin ; Kolář, Michal (referee) ; Píška, Miroslav (advisor)
The diploma thesis presents the usability of a new thermosetting material BMC for the construction of a car headlight. In the theoretical part there are described headlights, basic characteristics and properties of plastics focussing on polymer composite materials and material testing. The practical part deals with the processing of test samples for mechanical testing by compression moulding and also with the production of real samples of reflectors and carrier frames by injection moulding. The evaluation is based on comparison of the results of the performed tests of alternative material and the currently used BMC TETRADUR TD 492/2 in HELLA Autotechnik Nova s.r.o. Basic physical-mechanical properties such as strength, stiffness, toughness and hardness are tested and monitored. The reflectors and carrier frames are assembled into the headlight and then tested according to legal and customers´ requirements for climate and vibration resistance and photometry.
Limitations of variant consequence predictors
Břicháčková, Kateřina ; Daněček, Petr (advisor) ; Kolář, Michal (referee)
Thanks to numerous large-scale sequencing projects, the number of discovered genomic variants is increasing. The key step in analyzing the variant data is the functional annotation, since it helps researchers and clinicians to categorize, filter and prioritize the variants for further research. This thesis discusses five commonly-used variant consequence predictors, offers advice on how to use them and briefly goes through the algorithms they employ. Moreover, various data formats as well as the human reference genome and different genome annotations are described in the thesis. The correctness of the reference is of great importance as all the predictors rely on it. This thesis highlights some situations in which the results given by different predictors can vary. All the tests were made using the Ensembl gene annotation (release 92) and the GRCh38 reference assembly.

National Repository of Grey Literature : 37 records found   1 - 10nextend  jump to record:
See also: similar author names
18 KOLÁŘ, Martin
32 KOLÁŘ, Michal
10 KOLÁŘ, Miroslav
1 Kolář, M.
18 Kolář, Martin
1 Kolář, Matěj
2 Kolář, Michael
10 Kolář, Milan
10 Kolář, Miroslav
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