Related papers: Self-Templated Nucleation in Peptide and Protein a…
Amyloid fibers are aggregates of proteins. They are built out of a peptide called $\beta$--amyloid (A$\beta$) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the…
Each living species carries a complex DNA sequence that determines their unique features and functionalities. It is generally assumed that life started from a random pool of oligonucleotides sequences, generated by a prebiotic…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Based on experimental observations it is known that various biological cells exhibit a persistent random walk during migration on flat substrates. The persistent random walk is characterized by `stop-and-go' movements : unidirectional…
Alzheimer's disease causes severe neurodegeneration in the brain that leads to a certain death. The defining factor is the formation of extracellular senile amyloid plaques in the brain. However, therapeutic approaches to remove them have…
Calcification and mineralization are fundamental physiological processes, yet the mechanisms of calcification, in trabecular bone and in calcified lesions in atherosclerotic calcification, are unclear. Recently, it was shown in in vitro…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
The fluid phase diagram of trimer particles composed of one central attractive bead and two repulsive beads was determined as a function of simple geometric parameters using flat-histogram Monte Carlo methods. A variety of self-assembled…
Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical and cosmetic applications. Increasing…
We analyze linear independence of rank one tensors produced by tensor powers of randomly perturbed vectors. This enables efficient decomposition of sums of high-order tensors. Our analysis builds upon [BCMV14] but allows for a wider range…
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of…
Experimental evidence suggests that the folding and aggregation of the amyloid $\beta$-protein (A$\beta$) into oligomers is a key pathogenetic event in Alzheimer's disease (AD). Inhibiting the pathologic folding and oligomerization of…
Alzheimer's disease is characterised by the spreading of misfolded proteins and progressive structural changes in the brain. Despite significant clinical research, understanding how microscopic protein dynamics translate into macroscopic…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
We present several ordering mechanisms in diblock copolymers. For temperatures above the order-disorder temperature and in the weak segregation regime, a linear response theory is presented which gives the polymer density in the vicinity of…
Alzheimer's disease (AD) is driven by the accumulation of amyloid-beta (Abeta) proteins in the brain, leading to memory loss and cognitive decline. While monoclonal antibodies targeting Abetahave been approved, optimizing their use to…
Macroscopic properties of suspensions, such as those composed of globular particles (e.g., colloidal or macromolecular), can be tuned by controlling the equilibrium aggregation of the particles. We examine how aggregation -- and, hence,…