Related papers: Local Interactions and Protein Folding: A Model St…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
An important open problem in materials science is whether a direct connection exists between single-particle elastic properties and the macroscopic bulk behavior. Here we address this question by focusing on the archetype of soft colloids:…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
In this work we characterize the configurational space of a short chain of colloidal particles as function of the range of directional and heterogeneous isotropic interactions. The individual particles forming the chain are colloids…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…
We investigate the structural and thermodynamic properties of a model of particles with $2$ patches of type $A$ and $10$ patches of type $B$. Particles are placed on the sites of a face centered cubic lattice with the patches oriented along…
This paper focuses on characterizing the energy profile along pathways connecting different regions of configuration space in the context of a prototypical glass model, the pure spherical $p$-spin model with $p=3$. The study investigates…
We model and study the patterns created through the interaction of collectively moving self-propelled particles (SPPs) and elastically tethered obstacles. Simulations of an individual-based model reveal at least three distinct large-scale…
We consider the low energy spectrum of spin-1/2 two-dimensional triangular lattice models subject to a ferromagnetic Heisenberg interaction and a three spin chiral interaction of variable strength. Initially, we consider quasi-one…
Conformational properties of intrinsically disordered proteins (IDPs) are governed by a sequence-ensemble relationship. To differentiate the impact of sequence-local versus sequence-nonlocal features of an IDP's charge pattern on its…
This work examines a discrete elastic energy system with local interactions described by a discrete second-order functional in the symmetric gradient and additional non-local random long-range interactions. We analyze the asymptotic…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
Simple coarse-grained hydrophobic-polar models for heteropolymers as the lattice HP and the off-lattice AB model allow a general classification of characteristic behaviors for hydrophobic-core based tertiary folding. The strongly reduced…
We enumerate all minimal energy packings (MEPs) for small single linear and ring polymers composed of spherical monomers with contact attractions and hard-core repulsions, and compare them to corresponding results for monomer packings. We…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…
We give an example of a relation between local and effective properties for elastic structures, up to geometric constants. The model considered is a periodic structure with isotropic and homogeneous local elasticity tensor in planar linear…
Geometrical arrangements of minimum energy of a system of identical repelling particles in two dimensions are studied for different forms of the interaction potential. Stability conditions for the triangular structure are derived, and some…
We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer…
A key starting assumption in many classical interatomic potential models for materials is a site energy decomposition of the potential energy surface into contributions that only depend on a small neighbourhood. Under a natural stability…