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Now showing items 11-13 of 13
Dissertation
Protein Folding Simulations: Confinement, External Fields and Sequence Design
(2010-04-08)
The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied:
1) the effect of confining potential barriers,
2) the effect of a static external field and
3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum).
Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet ...
Dissertation
Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets
(2016-03-16)
In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First, we independently consider ...
Dissertation
Relativistic LCAO with Minimax Principle and New Balanced Basis Sets
(2011-01-13)
Relativistic density functional theory is widely applied in molecular calculations with heavy atoms, where relativistic and correlation effects are on the same footing. Variational stability of the Dirac Hamiltonian is a very important field of research from the beginning of relativistic molecular calculations on, among efforts for accuracy, efficiency, and density functional formulation, etc. Approximations of one- or two-component methods and searching for suitable basis sets are two major means for good projection ...