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Influence of aminoacid side-chain ionization on protein structure
Tomanová, Ema ; Nová, Lucie (advisor) ; Muzdalo, Anja (referee)
Protein folding is governed by many different types of interactions. Aside from the formation of hydrophobic cores and hydrogen bonding, Coulombic forces are believed to play an important role in this process. Their importance arises mainly in partially unfolded states and pH sensitive regions where ionization of amino acid side chains may trigger conformational changes. Better understanding of the role of ionizable residues in folding thereby provides us with new opportunities in protein design and property-enhancing protein modifications.
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Molecular Simulation of Electrospinning.
Jirsák, Jan ; Moučka, F. ; Nezbeda, Ivo
Our recent attempts to apply standard molecular simulation techniques to the process of electrospinning are presented. We employ a molecular dynamics simulation to study phenomena involved in the electrospinning of polymer solutions, with particular attention to the formation of the Taylor cone and the development of a liquid jet. A molecular-based approach allows us to reveal the molecular structure and dynamics, which are inaccessible to continuum methods.
Fulltext: content.csg -  PDF
Plný tet: SKMBT_22317031713170 - PDF
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Pokroky v popisu termodynamických vlastností soustav obsahujících alkanoly
Aim, Karel ; Nezbeda, Ivo
Two lines of research dealing with the applications of the so called primitive models (of association) to describe the thermodynamic properties of alkanolic systems will be outlined, namely (i) molecular simulations for the water and methanol mixtures, and (ii) equation of state developments for the alkanol and carbon dioxide systems. Molecular simulations on water–methanol mixtures were performed by using primitive models that descend from realistic models of molecular interaction for both compounds. The results for both the excess mixing and partial molar properties of the system over the entire concentration range were compared with the molecular simulation results for the commonly accepted complex realistic models (effective pair-wise potentials) and with experimental data.
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Simulace reaktivních systémů na molekulární úrovni
Lísal, Martin ; Smith, W. R. ; Brennan, J. K.
We rewiew the reaction ensemble method for the computer simulation of chemically-reacting systems in bulk and confinement. We show applications of the method to reactive distillation and plasmas, and reactions in carbon slits and carbon nanotubes. We further present direct simulation methods for reacting and noncreating systems at fixed total internal energy or enthalpy, and we discussed their applications to calculations of adiabatic reaction temperature for industrially important ammonia synthesis reaction and to Joule-Thomson processes. Finally, we present combination of the reaction ensemble method with molecular dynamics to model reactions and adsorptions in nanochemical devices.
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