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Two-dimensional (2D) particulate aggregates formed due to competing interactions exhibit a range of non-equilibrium steady state morphologies from finite-size compact crystalline structures to non-compact string-like conformations. We…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
This paper summarizes previous work linking protein aggregation to the heterozygosity of organisms. It also cites the literature showing a correlation between species' morphological complexity and the lengths of their proteins. These two…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein…
Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…
Biomolecular phase separation is typically attributed to the polymer physics of long, disordered chains. However, the underlying chemical grammar, i.e. the specific interactions between protein and RNA building blocks, remains poorly…
Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two…
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…
Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
We used Langevin dynamics simulations of short associative polymers with two stickers placed symmetrically along their contour to study the effect of the primary sequence of these polymers on their organization inside condensed droplets. We…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
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…
Proteins and nucleic acids form non-Newtonian liquids with complex rheological properties that contribute to their function in vivo. Here we investigate the rheology of the transcription factor NANOG, a key protein in sustaining embryonic…
A significant part of the proteome is composed of intrinsically-disordered proteins (IDPs). These proteins do not fold into a well-defined structure and behave like ordinary polymers. In this work we consider IDPs which have the tendency to…
Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined…
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…
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,…