Related papers: Optimal reconstruction of the folding landscape us…

Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of 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…

In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…

The Free Energy Principle (FEP) states that self-organizing systems must minimize variational free energy to persist, but the path from principle to implementable algorithm has remained unclear. We present a constructive proof that the FEP…

In light of the evidence for dynamical dark energy (DE) found from the most recent Dark Energy Spectroscopic Instrument (DESI) baryon acoustic oscillation (BAO) measurements, we perform a non-parametric, model-independent reconstruction of…

We present a fast and transparent multi-variate event classification technique, called PDE-RS, which is based on sampling the signal and background densities in a multi-dimensional phase space using range-searching. The employed algorithm…

Directed energy deposition (DED) produces complex thermo-mechanical responses that can lead to distortion and reduced dimensional accuracy of a manufactured part. Thermo-mechanical finite element simulations are widely used to estimate…

This paper proposes an integrative approach to feature (input and output) selection in Data Envelopment Analysis (DEA). The DEA model is enriched with zero-one decision variables modelling the selection of features, yielding a Mixed Integer…

We propose a method to decompose the total energy of a supercell containing defects into contributions of individual atoms, using the energy density formalism within density functional theory. The spatial energy density is unique up to a…

A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…

We present cosmological constraints from the Dark Energy Camera All Data Everywhere (DECADE) cosmic shear analysis. This work uses shape measurements for 107 million galaxies measured through Dark Energy Camera (DECam) imaging of $5,\!412$…

Variational algorithms are promising candidates to be implemented on near-term quantum computers. The variational quantum eigensolver (VQE) is a prominent example, where a parametrized trial state of the quantum mechanical wave function is…

We present a comprehensive description of vector chromatography that includes deterministic and stochastic transport in 1D-periodic free-energy landscapes, with both energetic and entropic contributions, and highlights the parameters…

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…

The nature of dark energy (DE) remains elusive, even though it constitutes the dominant energy-density component of the Universe and drives the late-time acceleration of cosmic expansion. By combining measurements of the expansion history…

We have developed a new simulation method to estimate the distance between the native state and the first transition state, and the distance between the intermediate state and the second transition state of a protein which mechanically…

The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative models of fundamental…

We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching…

Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…

The first and second year results of DESI provide consistent evidence that dark energy may not be quantum vacuum energy ($\Lambda$). If true, this would be an extraordinary development in the 25-year quest to understand cosmic acceleration.…