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Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the…
Dispersed colloidal particles within a suspension can aggregate and spontaneously self-organize into a robust, percolating structure known as a gel. These network-like structures are prevalent in nature and play a critical role in many…
Many experiments show that protein condensates formed by liquid-liquid phase separation exhibit aging rheological properties. Quantitatively, recent experiments by Jawerth et al. (Science 370, 1317, 2020) show that protein condensates…
Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
We develop a general theory for three states of equilibrium of amyloid peptides: the monomer, oligomer, and fibril. We assume that the oligomeric state is a disordered micelle-like collection of a few peptide chains held together loosely by…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
One of the challenges of self-assembling finite-sized colloidal aggregates with a sought morphology is the necessity of precisely sorting the position of the colloids at the microscopic scale to avoid the formation of off-target structures.…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…
We investigate the self-assembly of amphiphilic nanocubes under rest and shear using molecular dynamics (MD) simulations and kinetic Monte Carlo (KMC) calculations. These particles combine both interaction and shape anisotropy, making them…
Liquid cellular compartments spatially segregate from the cytoplasm and can regulate aberrant protein aggregation, a process linked to several medical conditions, including Alzheimer's and Parkinson's diseases. Yet the mechanisms by which…
Amorphous materials driven away from equilibrium display a diverse repertoire of complex, history-dependent behaviors. One striking feature is a failure to return to equilibrium after an abrupt change in otherwise static external…
By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones…
Peptides are recognized for their varied self-assembly behaviors, forming a wide array of structures and geometries, such as spheres, fibers, and hydrogels, each presenting a unique set of material properties. The functionalities of these…
The problem of ring formation in solutions of cylindrical micelles is reinvestigated theoretically, taking into account a finite bending rigidity of the self-assembled linear objects. Transitions between three regimes are found when the…
Similarly-charged polymers in solution, known as polyelectrolytes, are known to form aggregated structures in the presence of oppositely charged counterions. Understanding the dependence of the equilibrium phases and the dynamics of the…
The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…