Related papers: Unfolding designable structures
Studying shape changing thick surfaces induced by differential growth helps us understand morphogenesis in biology and offers opportunities for device design. While ideal 2D differential growth maps have been well studied for both isotropic…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
Inspired by natural cellular materials such as trabecular bone, lattice structures have been developed as a new type of lightweight material. In this paper we present a novel method to design lattice structures that conform with both the…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…
Pattern forming systems allow for a wealth of states, where wavelengths and orientation of patterns varies and defects disrupt patches of monocrystalline regions. Growth of patterns has long been recognized as a strong selection mechanism.…
The main goal of the article is testing a new classification algorithm. To this end we apply it to a relevant problem of describing the integrable cases of a subclass of two-dimensional lattices. By imposing the cut-off conditions…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
We describe a class of "bare bones" models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the…
In a non-compact setting, the notion of hyperbolicity, and the associated structure of stable and unstable manifolds (for unbounded orbits), is highly dependent on the choice of metric used to define it. We consider the simplest version of…
In this paper we introduce a novel method of deriving a pairwise potential for protein folding. The potential is obtained by optimization procedure, which simultaneously maximizes the energy gap for {\it all} proteins in the database. To…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
In this paper we construct nonlinear partial differential equations in more than 3 independent variables, possessing a manifold of analytic solutions with high, but not full, dimensionality. For this reason we call them ``partially…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
We construct algorithms and topological invariants that allow us to distinguish the topological type of a surface, as well as functions and vector fields for their topological equivalence. In the first part (arXiv:2501.15657), we discused…
The design of desired behaviors in mechanical metamaterials has produced remarkable advances but has generally neglected two aspects - the inevitable presence of undesired behaviors and the role of dynamics in avoiding such behaviors.…