Related papers: Simulating Mono-and Multi-Protein Phosphorylation …
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Confluent cell monolayers and epithelia tissues show remarkable patterns and correlations in structural arrangements and actively-driven collective flows. We simulate these properties using multiphase field models. The models are based on…
To explain the effect of electron density saturation at high phosphorus concentrations the model of negatively charged phosphorus clusters was compared with the experimental data. A number of negatively charged clusters incorporating a…
Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the…
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…
The utilization of multiple phosphorylation sites in regulating a biological response is ubiquitous in cell signaling. If each site contributes an additional, equivalent binding site, then one consequence of an increase in the number of…
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital…
In recent experiments involving PNIPAM copolymers it has been observed that stable spherical nanoparticles are being formed by association of several chains in poor aqueous solution instead of aggregation. This type of mesoscopic structures…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Positively charged cluster ions of phosphorus were formed upon electron ionization of doped helium nanodroplets. The vapors of red phosphorus and a phosphate sample were picked up into neutral and charged helium nanodroplets. Independent on…
We address the crystallization of monodisperse hard spheres in terms of the properties of finite- size crystalline clusters. By means of large scale event-driven Molecular Dynamics simulations, we study systems at different packing…
We apply tools from real algebraic geometry to the problem of multistationarity of chemical reaction networks. A particular focus is on the case of reaction networks whose steady states admit a monomial parametrization. For such systems we…
We present a novel approach for finding and evaluating structural models of small metallic nanoparticles. Rather than fitting a single model with many degrees of freedom, the approach algorithmically builds libraries of nanoparticle…
Fluids under nanoscale confinement differ -- and often dramatically -- from their bulk counterparts. A notorious feature of nanoconfined fluids is their inhomogeneous density profile along the confining dimension, which plays a key role in…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…