Related papers: Optimality in self-organized molecular sorting
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
We use molecular dynamics to study the ordering of a nematic liquid crystal around a spherical particle or droplet. Homeotropic boundary conditions and strong anchoring create a hedgehog director configuration on the particle surface and in…
The behavior of particles driven through a narrow constriction is investigated in experiment and simulation. The system of particles adapts to the confining potentials and the interaction energies by a self-consistent arrangement of the…
Ample experimental evidence has been accumulated demonstrating that the formation of monodispersed colloids proceeds through a more complex mechanism, than the generally excepted diffusional "burst nucleation" process. Instead, the…
A theoretical model is presented for early evolutionary cell sorting within cellular aggregates. The model involves an energy-saving mechanism and principles of collective self-organization analogous to those observed in bicycle pelotons…
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…
Sorting and separation of microparticles is a challenging problem of interdisciplinary nature. Existing technologies can differentiate microparticles by their bulk properties, such as size, density, electric polarizability, etc. The next…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
The question how complex systems become more organized and efficient with time is open. Examples are, the formation of elementary particles from pure energy, the formation of atoms from particles, the formation of stars and galaxies, the…
Organic molecular crystals are appealing for next-generation optoelectronic applications, most notably due to their multiexciton generation process that can increase the efficiency of photovoltaic devices. However, a general understanding…
We review theoretical explanation of mechanisms of control of uniformity in growth of nanosize particles and colloids. The nanoparticles are synthesized as nanocrystals, by burst nucleation from solution. The colloids are self-assembled by…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
We study a model of cell motility where the condition of optimal trade-off between performance and metabolic cost can be made precise. In this model a steadily crawling fragment is represented by a layer of active gel placed on a frictional…
Self-organized monolayers of highly flexible \Frechet dendrons were deposited on graphite surfaces by solution casting. Scanning tunneling microscopy (STM) reveals an unprecedented variety of patterns with up to seven stable hierarchical…
Dataset distillation provides an effective approach to reduce memory and computational costs by optimizing a compact dataset that achieves performance comparable to the full original. However, for large-scale datasets and complex deep…
A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing…
Conventional gas-liquid phase transitions feature a coexistence line that has a monotonic and positive slope in line with our intuition that cooling always leads to condensation. Here we study the inverse phenomenon, condensation of…