Related papers: Entropic contributions to the splicing process
We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
Encouraging exploration is a critical issue in deep reinforcement learning. We investigate the effect of initial entropy that significantly influences the exploration, especially at the earlier stage. Our main observations are as follows:…
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…
Alternative cassette exons are known to originate from two processes exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
Above a certain density threshold, suspensions of rod-like colloidal particles form system-spanning networks. Using Monte Carlo simulations, we investigate how the depletion forces caused by spherical particles affect these networks in…
Entropic forces in colloidal suspensions and in polymer-colloid systems are of long-standing and continuing interest. Experiments show how entropic forces can be used to control the self-assembly of colloidal particles. Significant advances…
Enzymatic ligation is essential for the synthesis of long DNA. However, the number of ligated products exponentially decays as the DNA synthesis proceeds in a random manner. The controlling of ligation randomness is of importance to…
Transcription is one of the essential processes for cells to read genetic information encoded in genes, which is initiated by the binding of RNA polymerase to related promoter. Experiments have found that the nucleotide sequence of promoter…
Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have…
Adhesive cell-substrate interactions are crucial for cell motility and are responsible for the necessary traction that propels cells. These interactions can also change the shape of the cell, analogous to liquid droplet wetting on adhesive…
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…
Large language models achieve strong reasoning performance, yet existing decoding strategies either explore blindly (random sampling) or redundantly (independent multi-sampling). We propose Entropy-Tree, a tree-based decoding method that…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…
The dynamical properties and mechanical functions of amorphous materials are governed by their microscopic structures, particularly the elasticity of the interaction networks, which is generally complicated by structural heterogeneity. This…
We discuss an evaporation-induced wetting transition on superhydrophobic stripes, and show that depending on the elastic energy of the deformed contact line, which determines the value of an instantaneous effective contact angle, two…