Related papers: Bubbles, clusters and denaturation in genomic DNA:…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
We propose a phonon-assisted tunnelling model for explanation of conductivity dependence on temperature and temperature-dependent I-V characteristics in deoxyribonucleic acid (DNA) molecules. The capability of this model for explanation of…
The thermodynamic binding networks (TBN) model is a tool for studying engineered molecular systems. The TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition,…
Neural Network Potentials (NNPs) have emerged as a powerful tool for modelling atomic interactions with high accuracy and computational efficiency. Recently, denoising diffusion models have shown promise in NNPs by training networks to…
Brownian motion provides access to hydrodynamic properties of nanoscale objects independent of their optical resolvability. Here, we present a diffusion-based approach to infer effective particle size distributions of DNA-functionalized…
An in-house numerical model has been developed to study the temperature destratification induced by bubble plumes in reservoirs. The mean flow of the mixed fluid phase is solved using the Reynolds-Averaged Navier-Stokes Equations, while the…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
We present a theoretical model for the evolution of mixture concentrations in a micro-pervaporation device, similar to those recently presented experimentally. The described device makes use of the pervaporation of water through a thin PDMS…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We…
This work discusses the numerical aspects of representing the diffusional (condensational) growth in particulate systems such as atmospheric clouds. It focuses on the Eulerian modeling approach, in which the evolution of the particle size…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
We propose a new binary classification model called Phase Separation Binary Classifier (PSBC). It consists of a discretization of a nonlinear reaction-diffusion equation coupled with an Ordinary Differential Equation, and is inspired by…
The photophysical properties of deoxyribonucleic acid (DNA) are fundamental to life sciences and biophotonics. While previous studies have generally been restricted to fluorescence, attributing it to pi-pi* transitions and charge transfer…
The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…
Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on…