Related papers: Universal Free Energy Landscape Produces Efficient…
Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005…
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…
Electron energy loss spectroscopy is consolidating as a powerful tool to explore electronic (as well as vibrational) excitations of matter, including molecules. Performed in a scanning transmission electron microscope, this technique is…
We exploit free-space interactions between electron beams and tailored light fields to imprint on-demand phase profiles on the electron wave functions. Through rigorous semiclassical theory involving a quantum description of the electrons,…
Describing the complex landscape of infinite-dimensional free energy is generally a challenging problem. This difficulty arises from the existence of numerous minimizers and, consequently, a vast number of saddle points. These factors make…
The advantages of convergent beam electron diffraction for symmetry determination at the scale of a few nm are well known. In practice, the approach is often limited due to the restriction on the angular range of the electron beam imposed…
An oft-used concept in modeling macromolecules is the free energy landscape, obtained by coarse-graining a vast number of microstates into a low-dimensional mesh of mesostates. If the landscape contains two or more local minima…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity…
Free-electron radiation results from the interaction between swift electrons and the local electromagnetic environment. Recent advances in material technologies provide powerful tools to control light emission from free electrons and may…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
Electrochemistry is the underlying mechanism in a variety of energy conversion and storage systems, and it is well known that the composition, structure, and properties of electrochemical materials near active interfaces often deviates…
It is shown theoretically that the strong coupling of electrons to a high-frequency electromagnetic field results in the nulling of electron backscattering within the Born approximation. The conditions of the effect depend only on field…
We address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually simple yet effective algorithm for estimating the parameters…
In this paper we show how The Free Energy Principle (FEP) can provide an explanation for why real-world networks deviate from scale-free behaviour, and how these characteristic deviations can emerge from constraints on information…
This paper develops high-order well-balanced (WB) energy stable (ES) finite difference schemes for multi-layer (the number of layers $M\geqslant 2$) shallow water equations (SWEs) on both fixed and adaptive moving meshes, extending our…
In materials science and particularly electron microscopy, Electron Back-scatter Diffraction (EBSD) is a common and powerful mapping technique for collecting local crystallographic data at the sub-micron scale. The quality of the…