In the present study we are performing simulation of simple model of two patch colloidal particles undergoing irreversible diffusion limited cluster aggregation using patchy Brownian cluster dynamics. In addition to the irreversible aggregation of patches, the spheres are coupled with isotropic reversible aggregation through the Kern-Frenkel potential. Due to the presence of anisotropic and isotropic potential we have also defined 3 different kinds of clusters formed due to anisotropic potential and isotropic potential only as well as both the potentials together. We have investigated the effect of patch size on self-assembly under different solvent qualities for various volume fractions. We will show that at low volume fractions during aggregation process, we end up in a chain conformation for smaller patch size while in a globular conformation for bigger patch size. We also observed a chain to bundle transformation depending on the attractive interaction strength between the chains or in other words depending on the quality of the solvent. We will also show that bundling process is very similar to nucleation and growth phenomena observed in colloidal system with short range attraction. We have 1 arXiv:1710.09255v1 [cond-mat.soft] 27 Sep 2017 also studied the bond angle distribution for this system, where for small patches only 2 angles are more probable indicating chain formation, while for bundling at very low volume fraction a tail is developed in the distribution. While for the case of higher patch angle this distribution is broad compared to the case of low patch angles showing we have a more globular conformation. We are also proposing a model for the formation of bundles which are similar to amyloid fibers using two patch colloidal particles.
Aggregation of protein into bundles is responsible for many neurodegenerative diseases. In this work, we show how two-patch colloidal particles self assemble into chains and a sudden transition to bundles takes place by tuning the patch size and solvent condition. We study the kinetics of formation of chains, bundles and network like structures using Patchy Brownian cluster dynamics. We also analyse the ways to inhibit and accelerate the formation of these bundles. We show that in presence of inert immobile obstacles, the kinetics of formation of bundles slows down. Whereas, in presence of mobile aggregating particles which exhibit inter-particle attraction and intra-particle repulsion, the kinetics of bundle formation accelerates slightly. We also show that if we introduce mobile obstacles which exhibit intra-particle attraction and inter-particle hard sphere repulsion, the kinetics of formation of bundles is inhibited. This is similar to the inhibitory effect of peptide P4 on the formation of insulin fibres. We are providing a model of mobile obstacles undergoing directional interactions to inhibit the formation of bundles.
Nuclear molecules control the functional properties of the chromatin fiber by shaping its morphological properties. The biophysical mechanisms controlling how bridging molecules compactify the chromatin are a matter of debate. On the one side, bridging molecules could cross-link faraway sites and fold the fiber through the formation of loops. Interacting bridging molecules could also mediate long-range attractions by first tagging different locations of the fiber and then undergoing microphase separation. Using a coarse-grained model and Monte Carlo simulations, we study the conditions leading to compact configurations both for interacting and non-interacting bridging molecules. In the second case, we report on an unfolding transition at high densities of the bridging molecules. We clarify how this transition, which disappears for interacting bridging molecules, is universal and controlled by entropic terms. In general, chains are more compact in the case of interacting bridging molecules since, in this case, interactions are not valence-limited. However, this result is conditional on the ability of our simulation methodology to relax the system towards its ground state. In particular, we clarify how, unless using reaction dynamics that change the length of a loop in a single step, the system is prone to remain trapped in metastable, compact configurations featuring long loops.
Patchy particles are considered to be a good model for protein aggregation. We calculate the equilibrium phase diagram of two-patch colloidal particles undergoing aggregation along with isotropic potential. This investigation demonstrates the coexistence of different phases like disordered clusters, chains, crystals and bundles depending on the relative strength of isotropic and anisotropic potential, which are also reported for glucose isomerase proteins. We also show that the formation of network of bundles is metastable against the formation of thermodynamically favored finite sized bundles which are also metastable along with crystals. These bundles appear to be helical in structure similar to that observed in sickle cell hemoglobin.
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