Related papers: Dummy Atom Based Thermodynamic Integration Accurat…
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI calculations are computationally expensive and typically…
We demonstrate an efficient and accurate, general-purpose first-principles blueprint for calculating anharmonic vibrational free energy and predicting structural phase transition temperatures of solids. Thermodynamic integration is…
Using normalizing flows and reweighting, Boltzmann Generators enable equilibrium sampling from a Boltzmann distribution, defined by an energy function and thermodynamic state. In this work, we introduce Thermodynamic Interpolation (TI),…
Thermodynamic Integration (TI) is the state-of-the-art computational technique for accurate Gibbs free energy predictions of solids. Conventional TI schemes start from an NVT harmonic reference and require three successive corrections to…
A theory for thermodynamic induction (TI) under isothermal conditions is presented. This includes a treatment of the Helmholtz free energy budget available for a gate variable to utilize towards aiding another variable's approach towards…
The process of deriving an interatomic potentials represents an attempt to integrate out the electronic degrees of freedom from the full quantum description of a condensed matter system. In practice it is the derivatives of the interatomic…
Two machine learning-aided thermodynamic integration schemes to compute the chemical potentials of atoms and molecules have been developed and compared. One is the particle insertion method, and the other combines particle insertion with…
We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible…
Precise prediction of phase diagrams in molecular dynamics (MD) simulations is challenging due to the simultaneous need for long time scales, large length scales and accurate interatomic potentials. We show that thermodynamic integration…
We develop a method to fit high-temperature Gibbs free energy data for the development of interatomic potentials for atomic systems. The approach is based on Hamiltonian thermodynamic integration, enabling the identification of suitable…
Experimental realizations of a variety of atomic binary Bose-Fermi mixtures have brought opportunities for studying composite quantum systems with different spin-statistics. The binary atomic mixtures can exhibit a structural transition…
Cold-start drug-target interaction (DTI) prediction focuses on interaction between novel drugs and proteins. Previous methods typically learn transferable interaction patterns between structures of drug and proteins to tackle it. However,…
A novel thermodynamic integration (TI) scheme is presented that allows computing the free energy of grain boundaries (GBs) in crystals from atomistic computer simulation. Unlike previous approaches, the method can be applied at arbitrary…
Standard harmonic-to-anharmonic thermodynamic integration (TI) is known to develop a near singularity in the integrand for solids exhibiting diffusive degrees of freedom, such as rotating functional groups or migrating defects. This…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favour the progressive establishment of native interactions. At variance with traditional…
Successful doping of single-layer transition metal dichalcogenides (TMDs) remains a formidable barrier to their incorporation into a range of technologies. We use density functional theory to study doping of molybdenum and tungsten…
The thermoelectric performance of materials exhibits complex nonlinear dependencies on both elemental types and their proportions, rendering traditional trial-and-error approaches inefficient and time-consuming for material discovery. In…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…