Related papers: Model for Folding and Aggregation in RNA Secondary…
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
We investigate aggregation and fragmentation dynamics of tracers and inertial aggregates in random flows leading to steady state size distributions. Our objective is to elucidate the impact of changes in aggregation rates, due to…
This article focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid-liquid…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
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 structure and mechanical properties of a simple two-dimensional model of a cohesive powder are investigated by molecular dynamics simulations. Micromechanical ingredients involve elasticity, friction, a short range attraction and,…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which is…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
We present theoretical analyses and numerical simulations for the adhesion-induced phase separation of multi-component membranes with two types of ligand-receptor complexes (junctions). We show that after integrating all possible…
Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…