Related papers: Mesoscopic Properties of Molecular Folding and Agg…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…

We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…

Motivated by recent experimental findings in chemical synthesis of colloidal particles, we draw an analogy between self-assembly processes occurring in biological systems (e.g. protein folding) and a new exciting possibility in the field of…

Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…

We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…

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…

Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…

Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…

Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…

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…

Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…

The formation and proliferation of protein aggregates play a central role in a number of devastating neuro-degenerative diseases. Many experimental studies indicate that the ability of existing aggregates to replicate is a key property in…

The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…

A new model that describes adsorption and clustering of particles on a surface is introduced. A {\it clustering} transition is found which separates between a phase of weakly correlated particle distributions and a phase of strongly…

Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…

Formation of monodispersed colloidal particles is a complex process: nuclei, produced rapidly in a supersaturated solution, grow to nanosize primary particles, which then aggregate (coagulate) to form much larger final colloids. This paper…

Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of…