Related papers: An ab initio approach to free-energy reconstructio…
For orbital-free {\it ab initio} molecular dynamics, especially on systems in extreme thermodynamic conditions, we provide the first pseudo-potential-adapted generalized gradient approximation (GGA) functional for the non-interacting free…
We present a theoretical first-principles method to calculate the free energy of a magnetic system in its high-temperature paramagnetic phase, including vibrational, electronic, and magnetic contributions. The method for calculating free…
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid…
A theoretical framework is proposed for an energy decomposition scheme along the reaction coordinate, in which the ensemble average of the potential energy weighted with reactive flux intensity is decomposed into energy components at the…
The calculation of free energies from first principles in materials is a formidable task which enables the prediction of phase stability with high accuracy; these calculations are complicated in magnetic materials by the interplay of…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
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…
An analytical approximation of a nonlinear force-free magnetic field (NLFFF) solution was developed in Paper I, while a numerical code that performs fast forward-fitting of this NLFFF approximation to a line-of-sight magnetogram and coronal…
We introduce an efficient and robust method to compute alchemical free energy differences, resulting from the application of multiple walker Adaptive Biasing Force (ABF) in conjunction with strongly damped Langevin $\lambda$-dynamics.…
Quantum-chemical processes in liquid environments impact broad areas of science, from molecular biology to geology to electrochemistry. While density-functional theory (DFT) has enabled efficient quantum-mechanical calculations which…
At present there are two vastly different ab initio approaches to the description of the the many-body dynamics: the Density Functional Theory (DFT) and the functional integral (path integral) approaches. On one hand, if implemented…
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,…
Classical density functional theory (cDFT) and dynamical density functional theory (DDFT) are modern statistical mechanical theories for modeling many-body colloidal systems at the one-body density level. The theories hinge on knowing the…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
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…
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is…
Recently \1, we presented a general theory for calculat- ing the strength and properties of colloidal interactions mediated by ligand-receptor bonds (such as those that bind DNA-coated colloids). In this communication, we derive a…
To go beyond Gaussian approximation to the Hohenberg-Kohn free energy playing the key role in the density functional theory (DFT), the density functional \textit{integral} representation would be relevant, because field theoretical approach…
A density functional theory (DFT) framework is presented that links functional derivatives of free-energy functionals to non-linear static density response functions in quantum many-body systems. Within this framework, explicit expressions…
Predicting interfacial thermodynamics across molecular and continuum scales remains a central challenge in computational science. Classical density functional theory (cDFT) provides a first-principles route to connect microscopic…