Related papers: Entropy-driven phase behaviour of all-DNA associat…
Living and engineered systems rely on the stable coexistence of two interspersed liquid phases. Yet surface tension drives their complete separation. Here we show that stable droplets of uniform and tuneable size can be produced through…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
Within self-consistent field theory we study the phase behavior of a symmetrical binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
The dynamical properties and mechanical functions of amorphous materials are governed by their microscopic structures, particularly the elasticity of the interaction networks, which is generally complicated by structural heterogeneity. This…
Recent theoretical studies found that mixtures of active and passive colloidal particles phase separate but only at very high activity ratio. The high value poses serious obstacles for experimental exploration of this phenomenon. Here we…
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecule due to the intricate interplay between their activity and topological constraints. This study focuses on…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
We calculate the entanglement entropy of strongly correlated low-dimensional fermions in metallic, superfluid and antiferromagnetic insulating phases. The entanglement entropy reflects the degrees of freedom available in each phase for…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
Elastic MicroPhase Separation (EMPS) provides a simple route to create soft materials with homogeneous microstructures by leveraging the supersaturation of crosslinked polymer networks with liquids. At low supersaturation, network…
The entanglement spectrum serves as a powerful tool for probing the structure and dynamics of quantum many-body systems, revealing key information about symmetry, topology, and excitations. While the entanglement entropy (EE) of ground…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
Vibrational entropy plays a central role in determining phase stability and temperature dependent behavior in materials, yet its calculation from first-principles phonon methods remains computationally demanding. In this work, we combine…