Related papers: Self-assembling multiblock amphiphiles: Molecular …
Cells make use of semi-flexible biopolymers such as actin or intermediate filaments to control their local viscoelastic response by dynamically adjusting the concentration and type of cross-linker molecules. The microstructure of the…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
Magnetic nanoparticles in a colloidal solution self-assemble in various aligned structures, which has a profound influence on the flow behavior. However, the precise role of the microstructure in the development of the rheological response…
The packing geometry of macromolecules in complex mesophases is of key importance to self-organization in synthetic and biological soft materials. While approximate or heuristic models rely on often-untested assumptions about how flexible…
We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of $N$ distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical…
Discrete mesoscale network models, in which explicitly modeled polymer chains are replaced by implicit pairwise potentials, are capable of predicting the macroscale mechanical response of polymeric materials such as elastomers and gels,…
Planar brushes formed by end-grafted semiflexible polyampholyte chains, each chain containing equal number of positively and negatively charged monomers is studied using molecular dynamics simulations. Keeping the length of the chains…
Complex colloidal cluster morphologies are desirable for the fabrication of advanced materials, such as photonic crystals and meta-materials, and can be formed through evaporation-driven packing. By coupling lattice Boltzmann and discrete…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
Bilayer membranes self-assembled from simple amphiphiles in solution always have a planar ground-state shape. This is a consequence of several internal relaxation mechanisms of the membrane and prevents the straightforward control of…
The pursuit of green methodologies for fabricating optoelectronic devices necessitates the adoption of self-assembly-based strategies to engineer efficient and sustainable platforms. Microbubble lithography (MBL) stands out as a directed…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…
Meso-scale simulation of structure formation for AB-dimers in solution W monomers was performed by dissipative particle dynamics (DPD) algorithm. As a simulation model, modified Jury Model was adopted Jury, S. et al. "Simulation of…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
We present a generic model to describe the fractal self-assembly of proteins in terms of electrostatic and hydrophobic interactions. The predictions of the model were correlated with the simulated fractals obtained using patchy…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Swimmers and self-propelled particles are physical models for the collective behaviour and motility of a wide variety of living systems, such as bacteria colonies, bird flocks and fish schools. Such artificial active materials are amenable…