Related papers: Template-directed growth of copolymers
We describe a class of growth algorithms for finding low energy states of heteropolymers. These polymers form toy models for proteins, and the hope is that similar methods will ultimately be useful for finding native states of real proteins…
Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with…
The theoretical understanding of pattern formation in active systems remains a central problem of interest. Heterogeneous flocks made up of multiple species can exhibit a remarkable diversity of collective states that cannot be obtained…
An approach to modeling the oligomer composition distribution function in the irreversible step growth homopolymerization process based on a mixture of oligomers of arbitrary composition is developed. The approach is based on consideration…
Temporal point process is an expressive tool for modeling event sequences over time. In this paper, we take a reinforcement learning view whereby the observed sequences are assumed to be generated from a mixture of latent policies. The…
For an interacting spatio-temporal lattice system we introduce a formal way of expressing multi-time correlation functions of local observables located at the same spatial point with a time state, i.e. a statistical distribution of…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
In this work we used dissipative particle dynamics simulations to study the copolymerization process in the presence of spatial heterogeneities caused by incompatibility between polymerizing monomers. The polymer sequence details as well as…
Copulas are a powerful tool for modeling multivariate distributions as they allow to separately estimate the univariate marginal distributions and the joint dependency structure. However, known parametric copulas offer limited flexibility…
We study a chemotaxis-growth system with nonlinear local and nonlocal reactions and gradient-dependent damping. Under suitable conditions on the system parameters and spatial dimension, we prove that solutions exist globally in time and…
This paper considers random graph approach to simulate irreversible step-growth polymerization. We study generalization of approach developed by Kryven~I. by introducing different types of bonds each with its own weight representing…
Pattern forming systems allow for a wealth of states, where wavelengths and orientation of patterns varies and defects disrupt patches of monocrystalline regions. Growth of patterns has long been recognized as a strong selection mechanism.…
We consider the micellization of block copolymers in solution, employing self consistent field theory with an additional constraint that permits the examination of intermediate structures. From the information for an isolated micelle…
We report a theoretical study of stochastic processes modeling the growth of first-order Markov copolymers, as well as the reversed reaction of depolymerization. These processes are ruled by kinetic equations describing both the attachment…
Confirming Turing's theory of morphogens in developmental processes is challenging, and synthetic biology has opened new avenues for testing Turing's predictions. Synthetic mammalian pattern formation has been recently achieved through a…
We show that in a particular model of catalytic reaction systems, known as the binary polymer model, there is a mathematical invariance between two versions of the model: (1) random catalysis and (2) template-based catalysis. In particular,…
A computational framework that leverages data from self-consistent field theory simulations with deep learning to accelerate the exploration of parameter space for block copolymers is presented. This is a substantial two-dimensional…
Emergence and maintenance of polymers with complex sequences is a major question in the study of origins of life. To answer this, we studied a model polymerization reaction, where polymers are synthesized by stepwise ligation from two types…
By analytically solving some simple models of phase-ordering kinetics, we suggest a mechanism for the onset of non-equilibrium behaviour in colloid-polymer mixtures. These mixtures can function as models of atomic systems; their physics…