Related papers: Kinetics of seeded protein aggregation: theory and…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
We consider through simulations the behavior of elongated grains on a vibrating ratchet-shaped base. We observe differences in layer velocity profile and in net grain velocity for grains that are composed of one, two, or three colinear…
Given two graphs, the graph matching problem is to align the two vertex sets so as to minimize the number of adjacency disagreements between the two graphs. The seeded graph matching problem is the graph matching problem when we are first…
Rate of grain growth, which aides in achieving desired properties in polycrystalline materials, is conventionally estimated by measuring the size of grains and tracking its change in micrographs reflecting the temporal evolution. Techniques…
The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the `critical nucleaus size', ${n_c}$. The implicit assumption, that amyloids nucleate in the same way, has…
We study the segregation of granular mixtures in two-dimensional silos using a set of coupled equations for surface flows of grains. We study the thick flow regime, where the grains are segregated in the rolling phase. We incorporate this…
Preliminary results are presented for the kinetics of phase separation in three distinct models of protein aggregation. The first is a model of the formation of spherical microcrystals of insulin via an initial formation of fractal clusters…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the…
Protein amyloid fibrils are a form of linear protein aggregates that are implicated in many neurodegenerative diseases. Here, we study the dynamics of amyloid fibril elongation by performing Langevin dynamic simulations on a coarse-grained…
Motivated by the biologically important and complex phenomena of A\beta\ peptide aggregation in Alzheimer's disease, we introduce a model and simulation methodology for studying protein aggregation that includes extra-cellular aggregation,…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on…
This study proposes a new analytical model for grain boundary pinning by second phase particles in two-dimensional polycrystals. This approach not only considers how particles impede grain growth, but also elucidates their role in…
The importance of understanding the mechanism of protein aggregation into insoluble amyloid fibrils relies not only on its medical consequences, but also on its more basic properties of self--organization. The discovery that a large number…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…
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…