Related papers: Harnessing the Peripheral Surface Information Entr…
The recent introduction of geometric partition entropy brought a new viewpoint to non-parametric entropy quantification that incorporated the impacts of informative outliers, but its original formulation was limited to the context of a…
To harness the true potential of topological insulators as quantum materials for information processing, it is imperative to maximise topological surface state conduction, while simulateneously improving their quantum coherence. However,…
Building upon [2308.02636], we investigate the constraining power of persistent homology on cosmological parameters and primordial non-Gaussianity in a likelihood-free inference pipeline utilizing machine learning. We evaluate the ability…
Free-energy landscapes for short peptides -- specifically for variants of the pH Low Insertion Peptide (pHLIP) -- in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant…
Topological insulators (TIs) present a neoteric class of materials, which support delocalised, conducting surface states despite an insulating bulk. Due to their intriguing electronic properties, their optical properties have received…
Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
Deep learning approaches achieved significant progress in predicting protein structures. These methods are often applied to protein-protein interactions (PPIs) yet require Multiple Sequence Alignment (MSA) which is unavailable for various…
We put forth a unifying formalism for the description of the thermodynamics of continuously monitored systems, where measurements are only performed on the environment connected to a system. We show, in particular, that the conditional and…
The article proposes an algorithm to model the collision between arbitrary ellipsoids in viscous fluid. It is composed of several steps, each improving upon the standard procedure employed in the current literature. First, an efficient…
Physics-informed neural network architectures have emerged as a powerful tool for developing flexible PDE solvers which easily assimilate data, but face challenges related to the PDE discretization underpinning them. By instead adapting a…
Protein adsorption/desorption upon nanoparticle surfaces is an important process to understand for developing new nanotechnology involving biomaterials, while atomistic picture of the process and its coupling with protein conformational…
Entropy is a central concept in physics, but can be challenging to calculate even for systems that are easily simulated. This is exacerbated out of equilibrium, where generally little is known about the distribution characterizing simulated…
Driven non-equilibrium lattice models have wide-ranging applications in contexts such as mass transport, traffic flow, and transport in biological systems. In this work, we investigate the steady-state properties of a one-dimensional…
We extend thresholding methods for numerical realization of mean curvature flow on obstacles to the anisotropic setting where interfacial energy depends on the orientation of the interface. This type of schemes treats the interface…
Protein interaction networks (PINs) are often used to "learn" new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP) could improve the learning accuracy. LP uses…
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…
There is a growing interest in the study of coupled plasma-liquid systems because of their applications to biomedicine, biological and chemical disinfection, agriculture, and other areas. Without an understanding of the near-surface gas…
Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…