Related papers: Native state of natural proteins optimises local e…
We show that it is possible to learn protocols that effect fast and efficient state-to-state transformations in simulation models of active particles. By encoding the protocol in the form of a neural network we use evolutionary methods to…
In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and…
Several physical mechanisms have been proposed to explain allostery in proteins. They differ by the number of internal states that they assume a protein to occupy, leaving open the question of what controls the emergence of these distinct…
We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
The global steady state of a system in thermal equilibrium exponentially favors configurations with lesser energy. This principle is a powerful explanation of self-organization because energy is a local property of a configuration. For…
Several studies demonstrate that there are critical differences between real wireless networks and simulation models. This finding has permitted to extract spatial and temporal properties for links and to provide efficient methods as biased…
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
Limited resources motivate decomposing large-scale problems into smaller,``local" subsystems and stitching together the so-found solutions. We explore the physics underlying this approach and discuss the concept of ``local hardness", i.e.,…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
Many modern datasets don't fit neatly into $n \times p$ matrices, but most techniques for measuring statistical stability expect rectangular data. We study methods for stability assessment on non-rectangular data, using statistical learning…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determine characteristic temperatures that relate to the…
We introduce a simple theoretical approach for an equilibrium study of proteins with known native state structures. We test our approach with results on well-studied globular proteins, Chymotrypsin Inhibitor (2ci2), Barnase and the alpha…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
A physical system is in local equilibrium if it cannot be distinguished from a global equilibrium by ``infinitesimally localized measurements''. This should be a natural characterization of local equilibrium, but the problem is to give a…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
We use a combination of unsupervised clustering and sparsity-promoting inference algorithms to learn locally dominant force balances that explain macroscopic pattern formation in self-organized active particle systems. The self-organized…
Topological entanglement entropy is a topological invariant which can detect topological order of quantum many-body ground state. We assume an existence of such order parameter at finite temperature which is invariant under smooth…