Related papers: RNA thermodynamic structural entropy
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Here we derive and experimentally test a free energy functional that captures the adhesion of DNA-coated emulsion droplets. Generalizing previous approaches, the theory combines important energetic and entropic effects of microscopic DNA…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate…
Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design.…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
Test time adaptation (TTA) equips deep learning models to handle unseen test data that deviates from the training distribution, even when source data is inaccessible. While traditional TTA methods often rely on entropy as a confidence…
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…
Effective feature interaction modeling is critical for enhancing the accuracy of click-through rate (CTR) prediction in industrial recommender systems. Most of the current deep CTR models resort to building complex network architectures to…
Entropy rate of sequential data-streams naturally quantifies the complexity of the generative process. Thus entropy rate fluctuations could be used as a tool to recognize dynamical perturbations in signal sources, and could potentially be…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
Entropy production plays an important role in the regulation and stability of active matter systems, and its rate quantifies the nonequilibrium nature of these systems. However, entropy production is hard to be experimentally estimated even…
We derive the expressions of photon energy and particle currents inside an open nanosystem interacting with light using non-equilibrium Green's functions. The model allows different temperatures for the electron reservoirs, which basically…