Related papers: Optimality in self-organized molecular sorting
Proteinaceous aggregation occurs through self-assembly-- a process not entirely understood. In a recent article [1], an analytical theory for amyloid fibril growth via secondary rather than primary nucleation was presented. Remarkably, with…
The size segregation of granular materials in a vibrating container is investigated using Molecular Dynamics. We find that the rising of larger particles is accompanied by the existence of convection cells even in the case of the lowest…
Diffusion of colloidal particles in a complex environment such as polymer networks or biological cells is a topic of high complexity with significant biological and medical relevance. In such situations, the interaction between the…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Motivated by recent experimental findings in chemical synthesis of colloidal particles, we draw an analogy between self-assembly processes occurring in biological systems (e.g. protein folding) and a new exciting possibility in the field of…
Evolutions of the trading landscape lead to the capability to exchange the same financial instrument on different venues. Because of liquidity issues, the trading firms split large orders across several trading destinations to optimize…
We introduce Adjoint Sampling, a highly scalable and efficient algorithm for learning diffusion processes that sample from unnormalized densities, or energy functions. It is the first on-policy approach that allows significantly more…
Cellular Potts models are broadly applied across developmental biology and cancer research. We overcome limitations of the traditional approach, which reinterprets a modified Metropolis sampling as ad hoc dynamics, by introducing a physical…
In recent years, diffusion models trained on equilibrium molecular distributions have proven effective for sampling biomolecules. Beyond direct sampling, the score of such a model can also be used to derive the forces that act on molecular…
We develop a coagulation-fragmentation model to study a system composed of a small number of stochastic objects moving in a confined domain, that can aggregate upon binding to form local clusters of arbitrary sizes. A cluster can also…
The problem of natural selection in dispersal-structured populations consisting of individuals characterized by different diffusion coefficients is studied. The competition between the organisms is taken into account through the assumption…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
We study dynamic self-organisation and order-disorder transitions in a two-dimensional system of self-propelled particles. Our model is a variation of the Vicsek model, where particles align the motion to their neighbours but repel each…
The role of particle shape in evaporation-induced auto-stratification in dispersed colloidal suspensions is explored with molecular dynamics simulations of mixtures of solid spheres, aspherical particles, and hollow spheres. A unified…
A fundamental issue discussed in evolutionary biology is the transition from unicellular to multicellular organisms. Here we develop non-robust models provided in [1] and attempt to get robust models investigated how differentiation of…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
A microscopic model of the effect of unbinding in diffusion limited aggregation based on a cellular automata approach is presented. The geometry resembles electrochemical deposition - ``ions'' diffuse at random from the top of a container…
We adapt Vertex models to understand the physical origin of the formation of long-range ordered structures in repulsive soft particles. The model incorporates contributions from the volume and surface area of each particle. Sampling using…