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Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
A generic method to estimate the relative feasibility of formation of high entropy compounds in a single phase, directly from first principles, is developed. As a first step, the relative formation abilities of 56 multi-component, AO,…
Modeling strongly correlated atoms demonstrates the possibility to prepare quantum superpositions that are robust against experimental imperfections and temperature. Such superpositions of vortex states are formed by adiabatic manipulation…
We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling [Skilling J. (2004) In AIP Conference Proceedings, vol. 735, p. 395.; Skilling…
Although self-consistent multi-configuration methods have been used for decades to address the description of atomic and molecular many-body systems, only a few trials have been made in the context of nuclear structure. This work aims at…
The local arrangement of atoms is one of the most important predictors of mechanical and functional properties of materials. However, algorithms for identifying the geometrical arrangements of atoms in complex materials systems are lacking.…
A reliable description of surfaces structures in a reactive environment is crucial to understand materials functions. We present a first-principles theory of replica-exchange grand-canonical-ensemble molecular dynamics (REGC-MD) and apply…
Understanding the mechanism of nucleation of the stable phase inside the metastable parent phase during a first order phase transition has been a subject of outstanding interest in natural science. The problem becomes even more challenging…
Cytoskeletal filaments are capable of self-assembly in the absence of externally supplied chemical energy, but the rapid turnover rates essential for their biological function require a constant flux of ATP or GTP hydrolysis. The same is…
A one-dimensional Ising model with nearest neighbour interactions is applied to study compaction processes in granular media. An equivalent particle-hole picture is introduced, with the holes being associated to the domain walls of the…
Many-mode interacting Bose gases (1D,2D,3D) are simulated from first principles. The model uses a second-quantized Hamiltonian with two-particle interactions (possibly ranged), external potential, and interactions with an environment, with…
It is analyzed whether the potential energy landscape of a glass-forming system can be effectively mapped on a random model which is described in statistical terms. For this purpose we generalize the simple trap model of Bouchaud and…
We propose an unsupervised learning methodology with descriptors based on Topological Data Analysis (TDA) concepts to describe the local structural properties of materials at the atomic scale. Based only on atomic positions and without a…
We present a systematical approach to developing arbitrarily high order, unconditionally energy stable numerical schemes for thermodynamically consistent gradient flow models that satisfy energy dissipation laws. Utilizing the energy…
Predicting phase stabilities of crystal polymorphs is central to computational materials science and chemistry. Such predictions are challenging because they first require searching for potential energy minima and then performing arduous…
We describe our efforts of the past few years to create a large set of more than 500 highly-accurate vertical excitation energies of various natures ($\pi \to \pi^*$, $n \to \pi^*$, double excitation, Rydberg, singlet, doublet, triplet,…
The total energies and the spin states for atoms and their first ions with Z = 1-86 are calculated within the the local spin-density approximation (LSDA) and the generalized-gradient approximation (GGA) to the exchange-correlation (xc)…
This paper presents the first thermodynamic assessment of binary and pseudo-binary phase diagrams in the Ba--La--S and Ga--La--S systems by means of the CALPHAD method. Experimental phase diagram equilibrium data and thermodynamic…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…