Related papers: Mesoscopic helical models for DNA
A major challenge in biology is to understand how molecular processes determine phenotypic features. We address this fundamental problem in a class of model systems by developing a general mathematical framework that allows the calculation…
A simulation model is presented, comprising elastic spheres with a short range attraction. Besides conservative forces, radial- and shear friction, and radial noise are added. The model can be used to simulate colloids, granular solids and…
Short, partially complementary, single-stranded (ss)DNA strands can form nanostructures with a wide variety of shapes and mechanical properties. It is well known that semiflexible, linear dsDNA can undergo an isotropic to nematic (IN) phase…
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length of ~50 nm, driven by its elegant double helical structure. While double and multiple helix structures appear widely in nature, only rarely are these found in…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
The study of vesicles in suspension is important to understand the complicated dynamics exhibited by cells in vivo and in vitro. We developed a computer simulation based on the boundary-integral method to model the three dimensional…
We derive and validate a partition function for low-dimensional systems interacting with a heat bath, addressing the general issue of thermodynamic modeling of nanoscale systems. In contrast to bulk systems in the canonical (NVT) ensemble…
We consider a one-dimensional optical lattice of three-dimensional Harmonic Oscillators which are loaded with neutral fermionic atoms trapped into two hyperfine states. By means of a standard variational coherent-state procedure, we derive…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
Molecular-scale materials with bistable behavior and tunable properties are increasingly relevant for next-generation nanoscale electronic devices. Helical foldamers are promising candidates, but their structural and mechanical properties…
Rheological responses are the most relevant features to describe soft matter. So far, such constitutive relations are still not well understood in terms of small scale properties, although this knowledge would help the design of synthetic…
We perform atomistic computer simulations to study the mechanism of homogeneous dislocation nucleation in two dimensional (2D) hexagonal crystalline films during indentation with a circular nanoindenter. The nucleation process is governed…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account.…