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The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Molecular dynamics calculations were preformed on organic crystals 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium tosylate (DAST) and 4-N,N-dimethylamino-4'-N'-methylstilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS). Vibrational modes of…
The protein-ligand residence time, tau, influences molecular function in biological networks and has been recognized as an important determinant of drug efficacy. To predict tau, computational methods must overcome the problem that tau…
The magnetisation relaxations of three different types of geometrically frustrated magnetic systems have been studied with the same experimental procedures as previously used in spin glasses. The materials investigated are Y$_2$Mo$_2$O$_7$…
Using Langevin molecular dynamics simulations we study relaxation processes of interacting skyrmion systems with and without quenched disorder. Using the typical diffusion length as the time-dependent length characterizing the relaxation…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Hypothesis: Aging in colloidal suspensions manifests as a reduction in kinetic freedom of the colloids. In aqueous suspensions of charged colloids, the role of inter-particle electrostatics interactions on the aging dynamics is well…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic…
Hypoxia and acidity act as environmental stressors promoting selection for cancer cells with a more aggressive phenotype. As a result, a deeper theoretical understanding of the spatio-temporal processes that drive the adaptation of tumour…
Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the…
We report a computer simulation study of a model gel-former obtained by modifying the three-body interactions of the Stillinger-Weber potential for silicon. This modification reduces the average coordination number and consequently shifts…
Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters. During the review period, a wide range of enhanced sampling…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
The effect of structural constriction on molecular mobility is investigated by broadband dielectric spectroscopy (BDS) within three types of molecular arrangements: monomers, oligomers and self-assembled monolayers (SAMs). While disordered…
Water diffusion MRI is a very powerful tool for probing tissue microstructure, but disentangling the contribution of compartment-specific structural disorder from cellular restriction and inter-compartment exchange remains an open…
The overall goal of this thesis is to investigate the connection between the dynamics and structure of molecular glass formers, by testing different scaling laws for both. The inspiration for this work is the Isomorph theory because it…
We study the relaxation process in a two-dimensional lattice gas model, where the interactions come from the excluded volume. In this model particles have three arms with an asymmetrical shape, which results in geometrical frustration that…