Related papers: Harnessing the Peripheral Surface Information Entr…
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly…
Surface topography governs tribological performance, yet conventional parameters describe either amplitude statistics or spectral content in isolation. We introduce a scale-dependent framework that represents surface height and directional…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
Interacting particle system (IPS) models have proven to be highly successful for describing the spatial movement of organisms. However, it has proven challenging to infer the interaction rules directly from data. In the field of equation…
We develop a weak-form sparse identification method for interacting particle systems (IPS) with the primary goals of reducing computational complexity for large particle number $N$ and offering robustness to either intrinsic or extrinsic…
The s=1/2 Ising chain with uniform nearest-neighbor and next-nearest-neighbor coupling is used to construct a system of floating particles characterized by motifs of up to six consecutive local spins. The spin couplings cause the assembly…
Superconducting-proximity topological insulators (STIs) have garnered significant research attention over the past two decades. In this Letter, we demonstrate that a low-dimensional STI in the topological-nontrivial phase (TP) exhibits an…
We present results of testing of the ability of eleven popular scoring functions to predict native docked positions using a recently developed method [1] for estimation the entropy contributions of relative motions to protein-ligand binding…
Protein surface fingerprint encodes chemical and geometric features that govern protein-protein interactions and can be used to predict changes in binding affinity between two protein complexes. Current state-of-the-art models for…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
Information theory is a powerful tool to express principles to drive autonomous systems because it is domain invariant and allows for an intuitive interpretation. This paper studies the use of the predictive information (PI), also called…
During a spontaneous change, a macroscopic physical system will evolve towards a macro-state with more realizations. This observation is at the basis of the Statistical Mechanical version of the Second Law of Thermodynamics, and it provides…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
The Shannon based conditional entropy that underlies five-dimensional Einstein-Hilbert gravity coupled to a dilaton field is investigated in the context of dynamical holographic AdS/QCD models. Considering the UV and IR dominance limits of…
Despite an explosion in the number of experimentally determined, atomically detailed structures of biomolecules, many critical tasks in structural biology remain data-limited. Whether performance in such tasks can be improved by using large…
A new particle-based sampling and approximate inference method, based on electrostatics and Newton mechanics principles, is introduced with theoretical ground, algorithm design and experimental validation. This method simulates an…
The Boltzmann-Gibbs celebrated entropy $S_{BG}=-k\sum_ip_i \ln p_i$ is {\it concave} (with regard to all probability distributions $\{p_i\}$) and {\it stable} (under arbitrarily small deformations of any given probability distribution). It…
The ion-sputtering induced intermixing is studied by molecular dynamics (MD) simulations and by Auger electron spectroscopy depth profiling (AES-DP) analysis in Pt/Ti/Si substrate (Pt/Ti) and Ta/Ti/Pt/Si substrate (Ti/Pt) multilayers.…
Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the…