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Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
We numerically investigate the morphology and disclination line dynamics of active nematic droplets in three dimensions. Although our model only incorporates the simplest possible form of achiral active stress, active nematic droplets…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
The competition of depletion attractions and longer-ranged repulsions between colloidal particles in colloid-polymer mixtures leads to the formation of heterogeneous gel-like structures. For instance, gel networks, i.e., states where the…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
Neurodegenerative diseases are driven by the accumulation of protein aggregates in the brain of affected individuals. The aggregation behaviour in vitro is well understood and driven by the equilibration of a super-saturated protein…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
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…
Microgels are elastic and deformable particles with a hybrid nature between that of polymers and colloids and unconventional behaviours with respect to hard colloids. We investigated the dynamics of a soft microgel made of interpenetrated…
Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins…
Evidence accumulated over the past decade provides support for liquid-liquid phase separation as the mechanism underlying the formation of biomolecular condensates, which include not only membraneless organelles such as nucleoli and RNA…
Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Molecular dynamics (MD) simulation has been employed to study the nonequilibrium structure formation of two types of particles in a colloidal suspension, driven by type-dependent forces. We examined the time evolution of structure formation…
Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular…