Related papers: Protein Folding Simulations in a Deformed Energy L…
The best techniques for the constrained maximum-entropy sampling problem, a discrete-optimization problem arising in the design of experiments, are via a variety of concave continuous relaxations of the objective function. A standard…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
The assisted tunneling of a metastable state between barriers is investigated analytically by means of a simplified one dimensional model. A time dependent perturbation changes the pole spectrum of the wave function introducing a larger…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
We develop a new simulation technique based on path-integral molecular dynamics for calculating ground-state tunneling splitting patterns from ratios of symmetrized partition functions. In particular, molecular systems are rigorously…
The low-temperature quasi-universal behavior of amorphous solids has been attributed to the existence of spatially-localized tunneling defects found in the low-energy regions of the potential energy landscape. Computational models of…
We introduce a differentiable clustering method based on stochastic perturbations of minimum-weight spanning forests. This allows us to include clustering in end-to-end trainable pipelines, with efficient gradients. We show that our method…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions,…
Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial…
We present a variation on classic beam thresholding techniques that is up to an order of magnitude faster than the traditional method, at the same performance level. We also present a new thresholding technique, global thresholding, which,…
Environmental noise can enhance transport, an effect known as environmental noise-assisted quantum transport. Most theoretical studies focus on optimizing system parameters under spatially uniform system-environment coupling. Here, instead,…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…