Related papers: Unfolding designable structures
Flexible mechanical metamaterials possess repeating structural motifs that imbue them with novel, exciting properties including programmability, anomalous elastic moduli and nonlinear and robust response. We address such structures via…
Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size $4\times3\times3$. We used two types of amino acids…
We address protein structure prediction in the 3D Hydrophobic-Polar lattice model through two novel deep learning architectures. For proteins under 36 residues, our hybrid reservoir-based model combines fixed random projections with…
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…
We investigate two and three-dimensional shell-structured-inflatable froths, which can be constructed by a recursion procedure adding successive layers of cells around a germ cell. We prove that any froth can be reduced into a system of…
From self-assembly and protein folding to combinatorial metamaterials, a key challenge in material design is finding the right combination of interacting building blocks that yield targeted properties. Such structures are fiendishly…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
Proteins are an example of heteropolymers able to self-assemble in specific target structures. The self-assembly of designed artificial heteropolymers is still, to the best of our knowledge, not possible with control over the single chain…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
We construct open sets of degenerate unfoldings of heterodimensional cycles of any co-index $c>0$ and homoclinic tangencies of arbitrary codimension $c>0$. These sets are known to be the support of unexpected phenomena in families of…
We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…
Three-dimensional shell-like structures can be obtained spontaneously at the microscale from the self-folding of 2D templates of rigid panels. At least for simple structures, the motion of each panel is consistent with a Brownian process…
Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in…
A large family of deployable filamentary structures can be built by connecting two elastic rods along their length. The resulting structure has interesting shapes that can be stabilized by tuning the material properties of each rod. To…
The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by…