We discuss the use of a Langevin equation with a colored (correlated) noise to perform constanttemperature molecular dynamics simulations. Since the equations of motion are linear in nature, it is easy to predict the response of a Hamiltonian system to such a thermostat and to tune at will the relaxation time of modes of different frequency. This allows one to optimize the time needed to therma...

Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental da...

We describe a general purpose parallel molecular dynamics code, for simulations of arbitrary mixtures of exible molecules in solution. The program allows us to simulate molecular systems described by standard force elds like AMBER, GROMOS or CHARMM, containing terms for short-range interactions of the Lennard-Jones type, electrostatic interactions, covalent bonds, covalent angles and torsional ...

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Three chitosan (CS), polyethylene glycol (PEG) and polylactic acid (PLA) nanocomposite systems containing SiO2 nanoparticles and water molecules were designed by molecular dynamics (MD) simulations to deliver pipobromane (PIP) anticancer drug in order to discover the most appropriate drug delivery system (DDS) in aqueous medium which was analogous to the human body. The density for the CS matri...

In this contribution, molecular dynamics (MD) simulations in combination with continuum mechanical (CM) approaches are performed to investigate particle movements under uniaxial deformations of an amorphous polymer at resolution. A coarse-grained (CG) model atactic polystyrene is used as exemplary system. We propose a hybrid dynamics-continuum (MD-CM) approach simulate the deformation behavior ...

studying the interaction of pharmaceutical ionic liquids with human serum albumin (hsa) can help investigating whether or not ionic liquid formation can enhance pharmacological profile of the discrete ingredients. in this respect, in the present work, the interactions of benzalkonium ibuprofenate, as a well-known active pharmaceutical ionic liquid, benzalkonium chloride, and also sodium ibuprof...