Related papers: RNA thermodynamic structural entropy
We compute the entanglement entropy in a two dimensional conformal field theory at finite size and finite temperature in the large central charge limit via the replica trick. We first generalize the known monodromy method for the…
We analyze the nature of the structural order established in liquid TIP4P water in the framework provided by the multi-particle correlation expansion of the statistical entropy. Different regimes are mapped onto the phase diagram of the…
We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…
Recently, some of us developed a novel model glass-forming liquid with k extra interactions with pseudo neighbours to each liquid particle over and above the regular interactions with its neighbours. Analysis of the structure and dynamics…
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,…
Machine Learning methods and, in particular, Artificial Neural Networks (ANNs) have demonstrated promising capabilities in material constitutive modeling. One of the main drawbacks of such approaches is the lack of a rigorous frame based on…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
The field of RNA secondary structure prediction has made significant progress with the adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep learning model using axial attention and recycling in the…
We analyze the thermodynamic costs of the three main approaches to generating random numbers via the recently introduced Information Processing Second Law. Given access to a specified source of randomness, a random number generator (RNG)…
Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA sequence undergoes a finite temperature glass transition. We…
We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…
Estimating entropy production from real observation data can be difficult due to finite resolution in both space and time and finite measurement statistics. We characterize the statistical error introduced by finite sample size and compare…
Based on the Tool-Narayanaswami formalism for structural relaxation we propose an experiment which independent of the relaxation time distribution determines the structural relaxation rate by subtracting relaxations following two different…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
We develop information-theoretic measures of spatial structure and pattern in more than one dimension. As is well known, the entropy density of a two-dimensional configuration can be efficiently and accurately estimated via a converging…
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…
The configurational entropy is among the key observables to characterize experimentally the formation of a glass. Physically, it quantifies the multiplicity of metastable states in which an amorphous material can be found at a given…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…