S. A Beccara | Searcharxiv

arXiv2017

Self Consistent Path Sampling: Making Accurate All-Atom Protein Folding Simulations Possible on Small Computer Clusters

We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble of reactive pathways, exponentially reducing the cost of simulating thermally activated transitions. The algorithm also yields a rigorous stochastic estimate of the reaction coordinate. After illustrating this approach on a simple toy model, we successfully validate it against the results of ultra-long plain MD protein folding simulations for a fast folding protein (Fip35), which were performed on the Anton supercomputer. Using our algorithm, computing a folding trajectory for this protein requires only 1000 core hours, a computational load which could be even carried out on a desktop workstation.

physics.bio-ph↗

arXiv2016

Quantum Propagation of Electronic Excitations in Macromolecules: A Computationally Efficient Multi-Scale Approach

We introduce a theoretical approach to study the quantum-dissipative dynamics of electronic excitations in macromolecules, which enables to perform calculations in large systems and cover long time intervals. All the parameters of the underlying microscopic Hamiltonian are obtained from \emph{ab-initio} electronic structure calculations, ensuring chemical detail. In the short-time regime, the theory is solvable using a diagrammatic perturbation theory, enabling analytic insight. To compute the time evolution of the density matrix at intermediate times, typically $\lesssim$~ps, we develop a Monte Carlo algorithm free from any sign or phase problem, hence computationally efficient. Finally, the dynamics in the long-time and large-distance limit can be studied combining the microscopic calculations with renormalization group techniques to define a rigorous low-resolution effective theory. We benchmark our Monte Carlo algorithm against the results obtained in perturbation theory and using a semi-classical non-perturbative scheme. Then we apply it to compute the intra-chain charge mobility in a realistic conjugate polymer.

cond-mat.mes-hall↗