Related papers: Multiple scales and phases in discrete chains with…
This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
The order-disorder transition of a sphere-forming block copolymer thin film was numerically studied through a Cahn-Hilliard model. Simulations show that the fundamental mechanisms of pattern formation are spinodal decomposition and…
We study a Cahn-Hilliard model for phase separation in composite materials with multiple periodic microstructures. These are modeled by considering a highly oscillating potential. The focus of this paper is in the case where the scales of…
Using transfer operator and fundamental measure theories, we examine the structural and thermodynamic properties of hard rectangles confined between two parallel hard walls. The side lengths of the rectangle ($L$ and $D$, $L>D$) and the…
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
Histogram-reweighting grand canonical Monte Carlo simulations are used to obtain the critical properties of lattice chains composed of solvophilic and solvophobic monomers. The model is a modification of one proposed by Larson \emph{et al.}…
We explore the phase structure of a chiral model of constituent quarks and gluons implementing scale symmetry breaking at finite temperature and chemical potential. In this model the chiral dynamics is intimately linked to the trace anomaly…
I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
The world of two-dimensional crystals is of great significance for the design and study of structural and functional materials with novel properties. The world of two-dimensional crystals is of great significance for the design and study of…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
The complexity of condensed matter arises from emergent behaviors that cannot be understood by analyzing individual constituents in isolation. While traditional condensed-matter approaches-developed primarily for ideal crystalline…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…