National Repository of Grey Literature 40 records found  1 - 10nextend  jump to record: Search took 0.01 seconds. 
Developing biomolecular interactions models for molecular simulations: Critical evaluation of force field parametrizations
Tempra, Carmelo ; Jungwirth, Pavel (advisor) ; Vácha, Robert (referee) ; Vega de las Heras, Carlos (referee)
Force field molecular dynamics methods are nowadays commonly used to study molecular interactions in many scientific fields. The accuracy of force fields has been improving over the years, allowing for a meaningful physical description of molecular phenomena. However, force fields have limitations. In this dissertation, I explored some of these limitations resulting from the parametrization strategy of force fields and the extent to which non-classical behavior, such as nuclear quantum effects, can be incorporated into classical force field molecular dynamics. In the first part, I investigated to what extent nuclear quantum effects can be accounted for within a classical force field for water. This allowed us to model the differences between bulk light vs. heavy water. The developed model was then used to describe solvent isotope effects on biomolecules, such as amino acids, proteins, and biomembranes, and to seek an explanation why heavy water (unlike light water) tastes sweet. In the second part, I pointed out the drawbacks of using certain training datasets in comparison to others when optimizing a force field, using aqueous calcium chloride as an example. In the third part, I demonstrated the importance of using an accurate water model during the optimization of force fields for phospholipids to adequately capture...
Investigation of monomolecular organic layers and their interaction with atmospheric oxidants and pollutants
Habartová, Alena ; Jungwirth, Pavel (advisor) ; Jedlovszky, Pal (referee) ; Klán, Petr (referee)
Title: Investigation of monomolecular organic layers and their interaction with atmospheric oxidants and polutants Author: Mgr. Alena Habartová Institute: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Advisor: prof. Mgr. Pavel Jungwirth, DSc. Abstract: Using classical molecular dynamics simulations, we studied interac- tions between Langmuir monolayers of palmitic acid (PA) and haloalkanes as serious atmospheric pollutants, to model naturally occurring and atmospherical- ly relevant complex surfaces of extended water bodies and aqueous aerosols. We investigated partitioning, orientation, solvation, as well as structure and morphol- ogy of the individual components and their mixture at water/vapor interfaces at different temperatures in order to validate our computational model and com- plement experimental data with molecular-level details. First, we have shown that halocarbon molecules adsorbed on amorphous ice nanoparticles at 100 K remain mostly isolated and do not form aggregates, in contrast to their cluste- ring on cryogenic argon nanoparticles. Next, we report that chloro-, bromo-, and iodoalkanes with short alkyl chains (up to C5) exhibit high preference for the outermost region of the water/vapor interface. Their average residence times of several...
Structure and dynamics of electronic defects in liquid water
Maršálek, Ondřej ; Jungwirth, Pavel (advisor) ; Horáček, Jiří (referee) ; Pittner, Jiří (referee)
Title: Structure and dynamics of electronic defects in liquid water Author: Ondřej Maršálek Institute: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Supervisor: prof. Mgr. Pavel Jungwirth, DSc. Supervisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: In this thesis we present ab inito molecular dynamics simulations of two different electronic defects in water. Photoionization of liquid water produces a cationic hole, which undergoes ultrafast dynamics and forms the hydrated proton and the hydroxyl radical as its products. We study both the dynamics and spectroscopy of this process. The hydrated electron is a key intermediate in radiation chemistry of aqueous systems. We simulate its equilibrium properties in anionic water clusters as well as the dynamics of vertical electron attachment to cold and warm clusters. The hydrated electron reacts with a hydrated proton to form a hydrogen atom. We examine this reaction at a finite temperature in a larger cluster as well as in more detail in a smaller cluster. Because both of the electronic defects studied here are challenging open-shell species, we put emphasis on benchmarking and testing our computational setup. Six published articles are attached to the thesis. Keywords: density functional theory,...
Molecules in Cell Membranes
Timr, Štěpán ; Jungwirth, Pavel (advisor) ; Böckman, Rainer (referee) ; Ettrich, Rüdiger (referee)
Biological membranes are actively involved in a multitude of processes in living cells; therefore, a detailed characterization of their structure, dynamics, and function is essential for an understanding of living organisms at the molecular level. In this work, we made use of the high spatial and temporal resolution offered by computer simulations to investigate the behavior of several molecular species which associate with cellular membranes. Using a combination of classical molecular dynamics simulations and ab initio electronic structure calculations, we were able to characterize nonlinear optical properties of membrane- embedded fluorescent probes and thus contribute to establishing two-photon polarization microscopy as a tool of structural biology. Moreover, our molecular dynamics simulations provided an atomistic picture of the reversible membrane binding of recoverin, a neuronal calcium-sensing protein involved in vision adaptation, and they also yielded an important insight into the mechanism of its calcium-induced myristoyl switch. In addition, we examined the biological role of cholesterol oxidation and compared two methods of representing transmembrane voltage in molecular dynamics simulations.
Computer modelling of biomolecules - potential chemoterapeutics
Maláč, Kamil ; Barvík, Ivan (advisor) ; Jungwirth, Pavel (referee) ; Ettrich, Rüdiger (referee)
Classical molecular dynamics simulations were applied on complexes of RNA-dependent RNA-polymerase, Ribonuclease H, Argonaute and Ribonuclease L with chemically modified nucleic acids, which are studied as potential chemotherapeutic agents. Powerful graphics processing units, through which these molecular dynamics simulations were performed, enabled to acquire trajectory length from hundreds of nanoseconds to one microsecond. Molecular dynamics simulations allowed capture differences in binding of various modified nucleic acids to the above mentioned enzymes. These identified differences fitted well with experimental results. It opens the door for rational design of the structure of potential chemotherapeutic agents based on chemically modified nucleic acids.
Structure, dynamics and reactivity of the hydrated electron
Uhlig, Frank ; Jungwirth, Pavel (advisor) ; Pittner, Jiří (referee) ; Sebastiani, Daniel (referee)
Structure, dynamics and reactivity of the hydrated electron Frank Uhlig In this work, one of the products of ionization of water, namely the hydrated electron, has been investigated. The hydrated electron is a key-intermediate in aqueous radiation chemistry. Although known to exist for over 50 years, its structure remained elusive and under discussion up to the present day. We show in this work, that we can obtain a faithful picture of the hydrated electron, its equilibrium structure, dynamics after attachment to water, and its reactivity, using ab initio methods. To this end, small cluster models and extended bulk and slab geometries of water including an excess electron have been investigated.
Molekulové simulace nukleace ledu
Pluhařová, Eva ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee)
Title: Molecular simulations of ice nucleation Author: Eva Pluhařová Department: Department of Physical and Macromolecular Chemistry Faculty of Science UK Advisor: doc. Mgr. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: By means of molecular dynamics simulations we have systematically investigated homogeneous ice nucleation in neat and surface contaminated water. As models of the adsorbates we have assumed pentanol and pentanoic acid. In neat water nucleation preferentially starts in the subsurface region, which accommodates better than the bulk the volume increase associated with freezing. Homogeneous ice nucleation is affected more by alcohol than by acid. Water slabs covered by a disordered layer of pentanol exhibit negligible preference for subsurface nucleation and longer nucleation times in comparison with neat water, while nucleation times are almost unaffected by the presence of pentanoic acid and the subsurface preference is only slightly decreased. We tried to rationalize the differences between the effects of different compounds by their ability to orient water molecules and to change their mobility. The fact that adsorbates differ in the influence on homogeneous ice nucleation has important implications for the microphysics of...
Molecular dynamics simulations of complexes consisting of proteins and nucleic acids
Zíma, Vlastimil ; Barvík, Ivan (advisor) ; Jungwirth, Pavel (referee)
At first, numerical integration algorithms was studied. Main objective was a study of active sites of HCV and HIV polymerases in complexes with a natural substrate and in complexes where an approaching nucleosidetriphosphate was replaced with inhibitors (S)-HMPMGpp and (S)-HMPMApp respectively. Further, an ABF method was used to obtain free energy profiles of water and methane molecules passing through a boundary between water and vacuum. Finally, the same method was used to obtain free energy profiles of water, methane and guanosine molecules passing through a lipid bilayer.
On a molecular theory of water
Jirsák, Jan ; Nezbeda, Ivo (advisor) ; Hrubý, Jan (referee) ; Kolafa, Jiří (referee) ; Jungwirth, Pavel (referee)
/ Summary Water is the most important liquid on Earth, but despite an errormous cffort put into research, it is not yet fully understood. A number of thermodyna- mic anomalies have been identified in water (e.g. the maximum of density at 4"C) and their occurrence intuitively linked to a strong intermolecular associ- ative force, i.e., hydrogen bonding. Nevertheiess, so far no rigorous molecular theory has been formulated. The present work attempts to propose and apply a rigorous statistical- -mechanical approach to water. The approach is based on recent findings that the structure of associating fluids is determined rnainly by the short-range forces (both repulsive ancl attractive). This fact enables us to apply the per- turbation theory taking a short-range model as a reference. The properties of the short-range reference model are then estimated by means of a simple, so-called primitive, model. Primitive models are anaiytically constructed to reproduce the structure of the short-range reference model keeping the in- teractions simple enough for theory. The contribution of the primitive model evaluated by Wertheim's TPT2 is used as a reference term in the perturbation expansion. The equation of state is then completed by adding dispersion and dipole-dipole correction terms. Main results of the work are as...

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