Related papers: Energy landscape theory for cotranslational protei…
Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…
Powering radio access networks using renewables, such as wind and solar power, promises dramatic reduction in the network operation cost and the network carbon footprints. However, the spatial variation of the energy field can lead to…
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding of a tube-like representation of a polypeptide chain gives rise to free energy landscapes that exhibit a small number of metastable minima…
We propose a principled method for autoencoding with random forests. Our strategy builds on foundational results from nonparametric statistics and spectral graph theory to learn a low-dimensional embedding of the model that optimally…
Established theoretical studies of diffusion in rugged (or rough) potential surfaces have largely focused on quenched energy landscapes. Here we study diffusion on a rugged energy landscape in the presence of dynamic disorder, a situation…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
We study rough high-dimensional landscapes in which an increasingly stronger preference for a given configuration emerges. Such energy landscapes arise in glass physics and inference. In particular we focus on random Gaussian functions, and…
Energy landscape analysis is a data-driven method to analyze multidimensional time series, including functional magnetic resonance imaging (fMRI) data. It has been shown to be a useful characterization of fMRI data in health and disease. It…
Energy landscapes are high-dimensional surfaces representing the dependence of system energy on variable configurations, which determine crucially the system's emergent behavior but are difficult to be analyzed due to their high-dimensional…
Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally,…
Random walks on multidimensional nonlinear landscapes are of interest in many areas of science and engineering. In particular, properties of adaptive trajectories on fitness landscapes determine population fates and thus play a central role…
We study transition paths in energy landscapes over multi-categorical Potts configurations using the mean-field approach introduced by Mauri et al., {\em Phys Rev Lett 130, 158402 (2023)}. Paths interpolate between two fixed configurations…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
In experiments and in simulations, the free energy of a state of a system can be determined from the probability that the state is occupied. However, it is often necessary to impose a biasing potential on the system so that high energy…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…