相关论文: Experimental Free Energy Surface Reconstruction Fr…
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the…
The energy of fluctuating electromagnetic field is investigated for the thermal Casimir force acting between parallel plates made of real metal. It is proved that for nondissipative media with temperature independent dielectric permittivity…
The discrete energy-eigenvalues of two nucleons interacting with a finite-range nuclear force and confined to a harmonic potential are used to numerically reconstruct the free-space scattering phase shifts. The extracted phase shifts are…
Symmetry energy, temperature and density at the time of the intermediate mass fragment formation are determined in a self-consistent manner, using the experimentally reconstructed primary hot isotope yields and anti-symmetrized molecular…
In the setting of continuum elasticity, phase transformations involving martensitic variants are modeled by a free energy density function that is non-convex in strain space. Here, we adopt an existing mathematical model in which we…
Phase retrieval is a prevalent problem in digital signal processing and experimental physics that consists of estimating a complex signal from magnitude measurements. This paper expands the classical phase retrieval framework to electric…
We explore the possibility for the reconstruction of the generative physical models describing interactions between atomic units in solids from observational electron microscopy data. Here, scanning transmission electron microscopy (STEM)…
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,…
Protein rotational kinetics are essential for understanding macromolecular behavior in crowded environments, yet measuring these dynamics at solid-liquid interfaces remains a significant challenge due to low signal strengths. Here, we…
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule…
Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature, it has the potential to provide…
The Jarzynski relation is a recently discovered result relating the average exponential of the work done under nonequilibrium conditions to an equilibrium free energy difference. We illustrate this remarkable relation by considering the…
We consider the elastic energy of a hanging drape -- a thin elastic sheet, pulled down by the force of gravity, with fine-scale folding at the top that achieves approximately uniform confinement. This example of energy-driven pattern…
We present a new approach to the Helmholtz spectrum for arbitrarily shaped boundaries and general boundary conditions. We derive the boundary induced change of the density of states in terms of the free Green's function from which we obtain…
We show that the Comment [arXiv:0808.1224] by Horowitz and Jarzynski obtains as a main result a general free energy change for a harmonic system that in the macroscopic limit does not recover the textbook expression for the energy change of…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
We propose a novel periodicity-free unfolding method of the electronic energy spectra. Our new method solves a serious problem that calculated electronic band structure strongly depends on the choice of the simulation cell, i.e.,…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…