Related papers: Multi-Layer Free Energy Perturbation
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system…
Targeted free energy perturbation uses an invertible mapping to promote configuration space overlap and the convergence of free energy estimates. However, developing suitable mappings can be challenging. Wirnsberger et al. (2020)…
A generalization of the free energy perturbation identity is derived, and a computational strategy based on this result is presented. A simple example illustrates the efficiency gains that can be achieved with this method.
In Federated Learning (FL), a global statistical model is developed by encouraging mobile users to perform the model training on their local data and aggregating the output local model parameters in an iterative manner. However, due to…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Influence of pulsed electric field (PEF) simultaneous to pressure treatment on moisture expression from fine-cut cellular raw material has been investigated. Dependencies of specific conductivity $\sigma$, liquid yield $Y$, instantaneous…
Chaotic free surface flows are challenging problems to simulate numerically, mainly due to the significant changes in geometry and frequent topological changes. Methods that track the evolution of the fluid in a Lagrangian formulation are a…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
It is difficult to relate the properties of liquids and glasses directly to their structure because of complexity in the structure which defies precise definition. The potential energy landscape (PEL) approach is a very insightful way to…
Dynamical energy analysis was recently introduced as a new method for determining the distribution of mechanical and acoustic wave energy in complex built up structures. The technique interpolates between standard statistical energy…
The free energy principle (FEP) in the neurosciences stipulates that all viable agents induce and minimize informational free energy in the brain to fit their environmental niche. In this study, we continue our effort to make the FEP a more…
The free energy principle (FEP), along with the associated constructs of Markov blankets and ontological potentials, have recently been presented as the core components of a generalized modeling method capable of mathematically describing…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
The urgency of the energy transition requires improving the performance and longevity of hydrogen technologies. AlphaPEM is a dynamic one-dimensional (1D) physics-based PEM fuel cell system simulator, programmed in Python and experimentally…
Laser manipulation plays a critical role in precisely tailoring relativistic electron beams through energy modulation, enabling the generation of coherent, intense, and ultrashort radiation in accelerator-based light sources such as…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
A novel finite element formulation for gradient-regularized damage models is presented which allows for the robust, efficient, and mesh-independent simulation of damage phenomena in engineering and biological materials. The paper presents a…
The photon flux resulting from high-energy electron beam interactions with high field systems, such as in the upcoming FACET-II experiments at SLAC National Accelerator Laboratory, may give deep insight into the electron beam's underlying…