相关论文: Selection of prebiotic oligonucleotides by cyclic …

Spontaneous stratification of granular mixtures has been reported by Makse et al. [Nature 386, 379 (1997)] when a mixture of grains differing in size and shape is poured in a quasi-two-dimensional heap. We study this phenomenon using two…

Neural Networks sequentially build high-level features through their successive layers. We propose here a new neural network model where each layer is associated with a set of candidate mappings. When an input is processed, at each layer,…

In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…

We introduce a filtration-based framework for studying when and why adding taxa improves phylodynamic inference, by constructing a natural ordering of observed tips and applying sequential Bayesian analysis to the resulting filtration. We…

Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…

Cell cortex contraction is essential for shaping cells, enabling movement, ensuring proper division, maintaining tissue integrity, guiding development, and responding to mechanical signals - all critical for the life and health of…

In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…

The reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions.…

To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…

We study the self-assembly of branching-chain networks and crystals in a binary colloidal system with tunable interactions. The particle positions are extracted from microscope images and order parameters are extracted by image processing…

Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…

We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…

A novel mechanism for sympatric speciation that takes into account complex bio-processes within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated…

We present a theoretical model for predicting the phase behavior of polymer solutions in which phase separation competes with oligomerization. Specifically, we consider scenarios in which the assembly of polymer chains into stoichiometric…

Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…

Phylogenetic methods, traditionally used in biology to trace the evolutionary relationships among species, are emerging as a powerful framework to reconstruct evolutionary processes in galaxies from chemical information. We apply galactic…

Switching on high activity in a relatively dense system of active Janus colloids, we observe fast clustering, followed by cluster aggregation towards full phase separation. The phase separation process is however interrupted when large…

We study the genealogy of a solvable population model with $N$ particles on the real line which evolves according to a discrete-time branching process with selection. At each time step, every particle gives birth to children around $a$…

A symmetric phase field model is used to study wavelength selection in two dimensions. We study the problem in a finite system using a two-pronged approach. First we construct an action and, minimizing this, we obtain the most probable…

A machine learning approach is presented to accelerate the computation of block polymer morphology evolution for large domains over long timescales. The strategy exploits the separation of characteristic times between coarse-grained…