Related papers: Estimating configurational entropy and energy of m…
We introduce discontinuous spectral-element methods of arbitrary order that are well balanced, conservative of mass, and conservative or dissipative of total energy (i.e., a mathematical entropy function) for a covariant flux formulation of…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
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…
It is shown that the fraction f of imaginary frequency instantaneous normal modes (INM) may be defined and calculated in a random energy model(REM) of liquids. The configurational entropy S and the averaged hopping rate among the states R…
We develop a systematic framework for computing symmetry-resolved entanglement entropies (SREE) in charged quantum systems based on an improved heat kernel approach. Although the conventional Sommerfeld formula proves effective for neutral…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
Although recent advances in simulating open quantum systems have lead to significant progress, the applicability of numerically exact methods is still restricted to rather small systems. Hence, more approximate methods remain relevant due…
For a first principles understanding of macromolecular processes, a quantitative understanding of the underlying free energy landscape and in particular its entropy contribution is crucial. The stability of biomolecules, such as proteins,…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
Computer simulations have been employed in recent years to evaluate the configurational entropy changes in model glass-forming liquids. We consider two methods, both of which involve the calculation of the `intra-basin' entropy as a means…
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…
We connect the configurational entropy of a liquid to the geometrical properties of its local energy landscape, using a high-temperature expansion. It is proposed that correlations between local structures arises from their overlap and,…
Image restoration, which aims to recover high-quality images from their corrupted counterparts, often faces the challenge of being an ill-posed problem that allows multiple solutions for a single input. However, most deep learning based…
We explore the sensitivity of several core-level spectroscopic methods to the underlying atomistic structure by using the water molecule as our test system. We first define a metric that measures the magnitude of spectral change as a…
Constructing approximations that can accurately mimic the behavior of complex models at reduced computational costs is an important aspect of uncertainty quantification. Despite their flexibility and efficiency, classical surrogate models…
Buildings rarely perform as designed/simulated and and there are numerous tangible benefits if this gap is reconciled. A new scientific yet pragmatic methodology - called Enhanced Parameter Estimation (EPE) - is proposed that allows…
We introduce a general, variational scheme applied to Kohn-Sham density functional theory that allows for partitioning of the ground-state density matrix into distinct spectral domains, each of which spanned by an independent diagonal…
By means of the concept of balanced estimation of diffusion entropy we evaluate reliable scale-invariance embedded in different sleep stages and stride records. Segments corresponding to Wake, light sleep, REM, and deep sleep stages are…
Recently, a new neutron spectroscopy for the dynamics in complex (bio-) systems has been proposed [A. Benedetto, and G. J. Kearley, Sci. Rep. 6, 34266, (2016)]. This spectroscopy is ideal where only the overall relaxation time in a…
Mixture proportion estimation (MPE) is the problem of estimating the weight of a component distribution in a mixture, given samples from the mixture and component. This problem constitutes a key part in many "weakly supervised learning"…