Related papers: An Efficient Algorithm for Topological Characteris…
The concept of a `persistent worm' is introduced, representing the smallest possible length of a wormlike micelle, and modelled by a bead-spring chain with sticky beads at the ends. Persistent worms are allowed to combine with each other at…
Cellular manufacturing (CM) is an approach that includes both flexibility of job shops and high production rate of flow lines. Although CM provides many benefits in reducing throughput times, setup times, work-in-process inventories but the…
We survey the linear viscoelasticity of a new type of transient network: bridged wormlike micelles, whose structure has been characterized recently [Ramos and Ligoure, (2007)]. This composite material is obtained by adding telechelic…
We present a machine learning approach that leverages persistent homology to classify bacterial flagellar motors into two functional states: rotated and stalled. By embedding protein structural data into a topological framework, we extract…
Amphiphilic block copolymer solutions form various micellar structures including micelles and vesicles. We applied the density functional theory for block copolymers which we have proposed to amphiphilic block copolymer systems. The 3…
State-of-the-art cosmological hydrodynamical simulations have star particles with typical mass between $\sim 10^8$ and $\sim 10^3$ M$_{\odot}$ according to resolution, and treat them as simple stellar populations. On the other hand,…
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interations deform vesicle membrane is a fundamental question in biophysics. In this article we developed a fast algorithm to…
We compare the ability of a simulated annealing program and an evolutionary algorithm to find molecules with large molecular average hyperpolarizabilities. This property is an important component of nonlinear optical materials. Both…
Surfactants are amphiphilic molecules that spontaneously self-assemble in aqueous solution into various ordered and disordered phases. Under certain conditions, one-dimensional structures in the form of long, flexible wormlike micelles can…
Weak form Scientific Machine Learning (WSciML) is a recently developed framework for data-driven modeling and scientific discovery. It leverages the weak form of equation error residuals to provide enhanced noise robustness in system…
We provide a comprehensive overview of the current theoretical understanding of the dynamic structure factor of stiff polymers in semidilute solution based on the wormlike chain (WLC) model. We extend previous work by computing exact…
We carry out numerical simulations of vesicle formation based on the density functional theory for block copolymer solutions. It is shown by solving the time evolution equations for concentrations that a polymer vesicle is spontaneously…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
We construct algorithms and topological invariants that allow us to distinguish the topological type of a surface, as well as functions and vector fields for their topological equivalence. In the first part (arXiv:2501.15657), we discused…
The formation of self assembled structures such as micelles has been intensively studied and is well understood. The ability of a solution of amphiphilic molecules to develop micelles is depending on the concentration and characterized by…
Owing to the advances in computational techniques and the increase in computational power, atomistic simulations of materials can simulate large systems with higher accuracy. Complex phenomena can be observed in such state-of-the-art…
Determination of the nature of the dynamical state of a system as a function of its parameters is an important problem in the study of dynamical systems. This problem becomes harder in experimental systems where the obtained data is…
Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural…
A novel, particle based, probabilistic approach for the simulation of cloud microphysics is proposed, which is named the Super-Droplet Method (SDM). This method enables accurate simulation of cloud microphysics with less demanding cost in…
In simulations of crystals, unlike liquids or gases, it may happen that the properties of the studied system depend not only on the volume of the simulation cell but also on its shape. For such cases it is desirable to change the shape of…