Related papers: Mesoscopic helical models for DNA
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
Our previous molecular dynamic simulation studies of simple two-dimensional (2D) systems \cite{matt_big} suggested that both geometrical defects (localized, large-amplitude deviations from hexagonal ordering) and topological defects…
A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The…
We employ two different atomistic methods to investigate solute-defect interactions in nanosized palladium-hydrogen (Pd-H) systems across multiple time scales. The first method, referred to as Diffusive Molecular Dynamics (DMD), focuses on…
The time-dependent fields obtained by solving partial differential equations in two and more dimensions quickly overwhelm the analytical capabilities of the human brain. A meaningful insight into the temporal behaviour can be obtained by…
To obtain the probability distribution of 2D crack patterns in mesoscopic regions of a disordered solid, the formalism of Paper I requires that a functional form associating the crack patterns (or states) to their formation energy be…
The dynamics of a degree of freedom associated to an axial vector in contact with a heat bath is decribed by means of a probability distribution function obeying a Fokker-Planck equation. The equation is derived by using mesoscopic…
We address the physics of nematic liquid crystalline elastomers randomly crosslinked in the isotropic state. To do this, we construct a phenomenological effective replica Hamiltonian in terms of two order-parameter fields: one for the…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
The Hodge decomposition provides a very powerful mathematical method for the analysis of 2D and 3D vector fields. It states roughly that any vector field can be $L^2$-orthogonally decomposed into a curl-free, divergence-free, and a harmonic…
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…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
We present a self-consistent dynamical holographic QCD model to investigate the mass spectra and melting behavior of heavy and exotic mesons at finite temperature and finite density. Our approach is based on the Einstein-Maxwell-Dilaton…