National Repository of Grey Literature 26 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Development and testing of computer models of phospholipid membranes
Nencini, Ricky ; Jungwirth, Pavel (advisor) ; Předota, Milan (referee)
Molecular dynamics simulations are an important tool for the study of biological systems, such as biomembranes. The missing electronic polarization in classical non- polarizable force fields, however, produces significant inaccuracies in the interactions of membranes with charged particles, such as ions. In this work, we implement the missing electronic polarization effects into CHARMM36 force field for phospatidylcholine lipids. This implementation is done in the mean field way by using electronic continuum correction (ECC) model. We will validate the strength of ion-membrane interactions using the electrometer concept. This concept connects the response of choline order parameters of lipid molecules with the amount of charge present in the surface of the membrane. Keywords: phosphatydylcholine, calcium ions, sodium ions, electronic continuum cor- rection, electrometer concept 1
Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor) ; Otyepka, Michal (referee) ; Tarek, Mounir (referee)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
Pairing of biologically relevant ions in aqueous solutions
Baxová, Katarína ; Jungwirth, Pavel (advisor) ; Předota, Milan (referee)
Not accounting for the electronic polarizability due to divalent ions such as Ca2+ introduces a significant artifacts to force field-based molecular dynamic simulations of biological systems. Two newly developed parameter refinements were used to compute the free energy profile of the Ca2+ -Cl- ion dissociation in aqueous solutions, to be compared with a free energy profile obtained from ab-intio molecular dynamics and to data from neutron scattering. Next, the computational evidence for the existence of a local free energy min- imum representing a guanidinium-guanidinium contact ion pair in aqueous solu- tions is provided suggesting a global preference for a contact ion pair. Finally, the passive membrane penetration mechanism of oligoarginines was investigated on a cell membrane model systems - lipid vesicles - by fluorescent spectroscopy. In this study, a mechanistic link between membrane penetration and vesicle aggregation and fusion was found. 1
Modeling interactions of proteins with ions and membranes
Kadlec, Jan ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee)
The protein recoverin, localized in the eye in the rod outer segment of the retina, is a neuronal calcium sensor involved in vision adaptation. Recoverin reversibly associates with cellular membranes via its calcium-activated myristoyl switch. This reversible interaction is vastly dependent on the concentration of calcium ions in the cytosol and on conformation of recoverin. By using methods of molecular dynamics simulations and free energy calculations this work presents a detailed analysis of the energetics of myristoyl insertion into a lipid bilayer and interactions of non-myristoylated recoverin with the membrane. These results are in a perfect agreement with experimental data. The thesis provides a piece of puzzle to the so far unexplored mechanism of myristamide insertion into the membrane and also to recoverin conformational change. It gives an important insight into binding of recoverin to a membrane, which has a significant biological role.
Theoretical study of ions at phase interfaces
Vrbka, Luboš ; Jungwirth, Pavel (advisor) ; Hof, Martin (referee) ; Ettrich, Rüdiger (referee)
1 ABSTRACT IN ENGIISři Abstract in English The present thesis consists of ten publicationsl-10 in international peer-reviewed journals with an extended introduction and a detailed discussion of the content of these papers. The work can be divided into three different topics, with ion behavior at interfaces being the common denominator. Namely, we focused on the following three issues: o lons at the ďr/water interface \\'e discuss the fact that certain inorganic ions can (contrary to the textbook knowl- edge) exhibit a propensity for the air/water interface. This is particularly true for large poiarizable anions, such as heavier halides, azide, or thiocyanate. Cations with aliphatic chains also show affinity to the surface, however, due to different reason - their hydrophobicity. The interplay between hydration and polarization forces in complex ionic mixtures is discussed in detail in this part of the thesis. o Ions at the ice/water interface Brine rejection from freezing salt solutions (e.g., sea water) is a very important natural phenomenon influencing the global climate. Molecular details of this process are established using molecular dynamics simulations. o lons at the protein/water interface We studied specific ion-protein interactions. First, we discuss the possible reasons behind the salt induced...
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...
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 modeling of the inner ear
Perlácová, Tereza ; Jungwirth, Pavel (advisor) ; Vejchodský, Tomáš (referee)
Do mechanického modelu kochley zavádzame implicitné numerické metódy. Tes- tujeme konkrétne štyri metódy: implicitný Euler, Crank-Nicolson, BDF druhého a tretieho rádu na lineárnej a nelineárnej verzii modelu. Nelineárny model obsahuje funkciu so saturujúcou vlastnosťou. Aplikácia implicitných metód na nelineárny model vedie na sústavu nelineárnych rovníc. Predstavujeme dva spôsoby, ako túto sústavu numericky riešiť. Prvý z nich zahrňuje nelinearitu do pravej strany novovzniknutej lineárnej sústavy. Druhý robí linearizáciu nelineárnej funkcie. V práci porovnávame oba spôsoby z hľadiska efektivity a sledujeme ich konvergenciu k referenčnému riešeniu. Pre hodnotu tolerancie, ktorú používame na určenie numerickej konvergencie, je prvý spôsob efektívnejší. V úplne nelineárnom režime druhý spôsob zlyháva, pretože nekon- verguje k referenčnému riešeniu. Výsledkom porovnania implicitných metód je, že Crank-Nicolsonova metóda s prvým spôsobom riešenia nelineárnej sústavy je pre účely nášho modelu najlepšia. Použitie tejto metódy v mechanickom modeli nám umožňuje vytvoriť ľubovoľne presné prepojenie medzi mechanickým a elektrickým modelom kochley, rešpektujúc fyziológiu človeka. 1
Computer modelling of biomolecules - potential chemoterapeutics
Maláč, Kamil ; Jungwirth, Pavel (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.
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...

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