Related papers: Kinetics of seeded protein aggregation: theory and…

Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…

We address the problem of learning on sets of features, motivated by the need of performing pooling operations in long biological sequences of varying sizes, with long-range dependencies, and possibly few labeled data. To address this…

In established theories of grain coarsening, grains disappear either by shrinking or by rotating as a rigid object to coalesce with an adjacent grain. Here we report a third mechanism for grain coarsening, in which a grain splits apart into…

Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…

Information processing and decision making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years however, both experimentalists and theorists have begun to…

We propose an exactly solvable simplified statistical mechanical model for the thermodynamics of beta-amyloid aggregation, generalizing a well-studied model for protein folding. The monomer concentration is explicitly taken into account as…

Mixing describes the process by which solutes evolve from an initial heterogeneous state to uniformity under the stirring action of a fluid flow. Fluid stretching forms thin scalar lamellae which coalesce due to molecular diffusion. Owing…

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…

Superpixel algorithms aim to over-segment the image by grouping pixels that belong to the same object. Many state-of-the-art superpixel algorithms rely on minimizing objective functions to enforce color ho- mogeneity. The optimization is…

Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…

Seeded PageRank is an important network analysis tool for identifying and studying regions nearby a given set of nodes, which are called seeds. The seeded PageRank vector is the stationary distribution of a random walk that randomly resets…

Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…

In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in…

Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…

Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…

Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…

We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…

Ample experimental evidence has been accumulated demonstrating that the formation of monodispersed colloids proceeds through a more complex mechanism, than the generally excepted diffusional "burst nucleation" process. Instead, the…

A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…

Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…