Related papers: Efficient sampling in complex materials at finite …
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling…
With the progress of nano-technology, thermodynamics also has to be scaled down, calling for specific protocols to extract and measure work. Usually, such protocols involve the action of an external, classical field (the battery) of…
Multispectral transmission imaging provides strong benefits for early breast cancer screening. The frame accumulation method addresses the challenge of low grayscale and signal-to-noise ratio resulting from the strong absorption and…
Simulated tempering (ST) has attracted a great deal of attention in the last years, due to its capability to allow systems with complex dynamics to escape from regions separated by large entropic barriers. However its performance is…
Algorithms for simulating complex physical systems or solving difficult optimization problems often resort to an annealing process. Rather than simulating the system at the temperature of interest, an annealing algorithm starts at a…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Thermodynamics is traditionally concerned with systems comprised of a large number of particles. Here we present a framework for extending thermodynamics to individual quantum systems, including explicitly a thermal bath and work-storage…
Temperature-accelerated sliced sampling (TASS) is a well-established enhanced sampling method that facilitates exhaustive exploration of high-dimensional collective variable (CV) space through directed sampling employing a combination of…
Structural mechanisms in disordered materials like amorphous semi-conductors and glasses can be explored with the activation-relaxation technique (ART). The application of a sequence of such mechanisms allows for the generation of…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
We extend the nested sampling algorithm to simulate materials under periodic boundary and constant pressure conditions, and show how it can be used to determine the complete equilibrium phase diagram, for a given potential energy function,…
Thermalization processes degrade the states of any working medium, turning any initial state into a passive state from which no work can be extracted. Recently, it has been shown that this degradation can be avoided if two identical…
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sampling method can readily sample multiple channels. In a…
We perform molecular dynamics simulations of repulsive athermal systems sheared at fixed normal load to study the effective temperature $T_L$ defined from time-dependent fluctuation-dissipation relations for density. We show that these…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
Optimal (reversible) processes in thermodynamics can be modelled as step-by-step processes, where the system is successively thermalized with respect to different Hamiltonians by an external thermal bath. However, in practice interactions…
A computational approach is presented to obtain energy-minimized structures in glassy materials. This approach, the activation-relaxation technique (ART), achieves its efficiency by focusing on significant changes in the microscopic…
The experimental investigation of matter under extreme densities and temperatures as they occur for example in astrophysical objects and nuclear fusion applications constitutes one of the most active frontiers at the interface of material…
The dynamics of amorphous silicon at low temperatures can be characterized by a sequence of discrete activated events, through which the topological network is locally reorganized. Using the activation-relaxation technique, we create more…