Related papers: Free energy reconstruction from steered dynamics w…
We introduce a massively parallel replica-exchange grand-canonical sampling algorithm to simulate materials at realistic conditions, in particular surfaces and clusters in reactive atmospheres. Its purpose is to determine in an automated…
Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
We propose two metadynamics (MetaD)-based methodologies for efficiently mapping free energy surfaces (FESs) of multiple interacting carriers diffusing in crystalline solids. Our approaches circumvent the challenges of high-dimensional…
The multiple range random walk algorithm recently proposed by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)] is adapted to the computation of free energy profiles for molecular systems along reaction coordinates. More generally, we show…
Energy landscapes play a crucial role in shaping dynamics of many real-world complex systems. System evolution is often modeled as particles moving on a landscape under the combined effect of energy-driven drift and noise-induced diffusion,…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
Describing the complex dependence structure of extreme phenomena is particularly challenging. To tackle this issue we develop a novel statistical algorithm that describes extremal dependence taking advantage of the inherent hierarchical…
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…
In adaptive-bias enhanced sampling methods, a bias potential is added to the system to drive transitions between metastable states. The bias potential is a function of a few collective variables and is gradually modified according to the…
When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities,…
We investigate the dynamics of a gas of non-interacting particle-like soliton waves, demonstrating that phase transitions originate from their collective behavior. This is predicted by solving exactly the nonlinear equations and by…
Properties of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form are investigated numerically. A considerable number of glassy local…
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch…
Inspired by the recent development on calculating the free energy change via a relaxation process [Nat. Phys. 14, 842 (2018)], we investigate the role of heat released in an irreversible relaxation following a large perturbation. Utilizing…
The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
A Potts model and the Replica Exchange Wang-Landau algorithm are used to construct an energy landscape for a crystalline solid containing surfaces and grain boundaries. The energy landscape is applied to an equation of motion from the…