Related papers: Structural evolution of protein-biofilms: Simulati…
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
The study of competitive and cooperative adsorption of functionalized molecules such as polymers, rheology modifiers and surfactant molecules on colloidal particles immersed in a solvent is undertaken using coarse grained, dissipative…
The formation of bacterial biofilms on solid surfaces within a fluid starts when bacteria attach to the substrate. Understanding environmental factors affecting the attachment and the early stages of the biofilm development as well as the…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Assessing the structural properties of large proteins is important to gain an understanding of their function in, e.g., biological systems or biomedical applications. We propose a method to examine the mechanical properties of proteins…
We have theoretically studied the uptake of a non-uniformly charged biomolecule, suitable to represent a globular protein or a drug, by a charged hydrogel carrier in the presence of a 1:1 electrolyte. Based on the analysis of a physical…
Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
Biofilms inhabit a range of environments, such as dental plaques or soil micropores, often characterized by intricate, non-even surfaces. However, the impact of surface irregularities on the population dynamics of biofilms remains elusive…
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprised of two…