Related papers: Simulating topological domains in human chromosome…
Topological constraints can affect both equilibrium and dynamic properties of polymer systems, and can play a role in the organization of chromosomes. Despite many theoretical studies, the effects of topological constraints on the…
The elastic properties of the double-stranded DNA handles used in optical tweezers experiments on biomolecules are customarily modeled by an extensible worm-like chain model. Fitting such model to experimental data however is no trivial…
Molecular graphs generally contain subgraphs (known as groups) that are identifiable and significant in composition, functionality, geometry, etc. Flat latent representations (node embeddings or graph embeddings) fail to represent, and…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Topological constraints (TCs) between polymers determine the behaviour of complex fluids such as creams, oils and plastics. Most of the polymer solutions used every day life employ linear chains; their behaviour is accurately captured by…
Topological materials exhibit protected edge modes that have been proposed for applications in for example spintronics and quantum computation. While a number of such systems exist, it would be desirable to be able to test theoretical…
Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
The mechanical properties of cells, which influence the properties of the tissue they belong to, are controlled by various mechanisms. Bi et al. theoretically demonstrated that density-independent rigidity transition occurs in…
We introduce a new computational methodology for the identification and characterization of free volume within/around atomistic configurations. This scheme employs a three-stage workflow, by which spheres are iteratively grown inside of…
Spectroscopy is one of the most accurate probes of the molecular world. However, predicting molecular spectra accurately is computationally difficult because of the presence of entanglement between electronic and nuclear degrees of freedom.…
Strongly correlated analogues of topological insulators have been explored in systems with purely on-site symmetries, such as time-reversal or charge conservation. Here, we use recently developed tensor network tools to study a quantum…
The phase behavior of symmetric diblock copolymers under three-dimensional (3D) soft confinement is investigated using the self-consistent field theory. The soft confinement is realized in binary blends composed AB diblock copolymers and C…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure,…
The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence.…
Persistent homology (PH) is a popular tool for topological data analysis that has found applications across diverse areas of research. It provides a rigorous method to compute robust topological features in discrete experimental…
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…
Ribbons are topological objects of biological and technological importance. Here, we study the folding of thick ribbons with hydrophobic surfaces in a bad solvent in regimes in which either the ribbon's thickness or the solvent molecule…
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide…