Related papers: A general, efficient and robust method to calculat…
We apply well-established concepts of Langevin sampling to derive a new class of algorithms for the efficient computation of free energy differences of fluctuating particles embedded in a 'fast' membrane, i.e., a membrane that…
We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks…
We introduce polynomial couplings, a generalization of probabilistic couplings, to develop an algorithm for the computation of equivalence relations which can be interpreted as a lifting of probabilistic bisimulation to polynomial…
Fast and accurate evaluation of free energy has broad applications from drug design to material engineering. Computing the absolute free energy is of particular interest since it allows the assessment of the relative stability between…
The Jarzynski equality allows the calculation of free-energy differences using values of work measured from nonequilibrium trajectories. The number of trajectories required to accurately estimate free-energy differences in this way grows…
Microscopic machines utilize free energy to create and maintain out-of-equilibrium organization in virtually all living things. Often this takes the form of converting the free energy stored in nonequilibrium chemical potential differences…
Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…
The purpose of this paper is to explore the applications of quantum computing to energy systems optimization problems and discuss some of the challenges faced by quantum computers with techniques to overcome them. The basic concepts…
Derivatives play a critical role in computational statistics, examples being Bayesian inference using Hamiltonian Monte Carlo sampling and the training of neural networks. Automatic differentiation is a powerful tool to automate the…
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be…
Recent progress in simulation methodologies and in computer power allow first principle simulations of condensed systems with Born-Oppenheimer electronic energies obtained by Quantum Monte Carlo methods. Computing free energies and…
The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…
Gradients in free energies are the driving forces of physical and biochemical systems. To predict free energy differences with high accuracy, Molecular Dynamics (MD) and other methods based on atomistic Hamiltonians conduct sampling…
We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passage rate for such systems. More specifically, the procedure…
The microscopic approach to calculating the free energy of a three-dimensional Ising-like system in a homogeneous external field is developed in the higher non-Gaussian approximation (the $\rho^6$ model) at temperatures above the critical…
We develop a systematic procedure to approximate generalized free energy in out of equilibrium stochastic systems. The procedure only requires knowledge of the averages of macroscopic observables and uses quasi-equilibrium distribution to…
The cost of information processing in physical systems calls for a trade-off between performance and energetic expenditure. Here we formulate and study a computation-dissipation bottleneck in mesoscopic systems used as input-output devices.…
In this work, we propose two models of coupled harmonic oscillators under Brownian motion to computationally study the applications of fluctuation theorems. This paper also illustrates how to analytically calculate free energy differences…
While the treatment of chemically relevant systems containing hundreds or even thousands of electrons remains beyond the reach of quantum devices, the development of quantum-classical hybrid algorithms to resolve electronic correlation…
A large collaboration carefully benchmarks 20 first principles many-body electronic structure methods on a test set of 7 transition metal atoms, and their ions and monoxides. Good agreement is attained between the 3 systematically converged…