Related papers: Genus Distributions For Extended Matrix Models Of …
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
We train a neural network to predict distributional responses in gene expression following genetic perturbations. This is an essential task in early-stage drug discovery, where such responses can offer insights into gene function and inform…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
In a recent work [arXiv:1307.1382] it was pointed out that the link-weight distribution of microRNA (miRNA) co-target network of a wide class of species are universal up to scaling. The number cell types, widely accepted as a measure of…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…
In this paper we analyze the length-spectrum of blocks in $\gamma$-structures. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time RNA folding. A $\gamma$-structure is…
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…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
We obtain the topological expansion of the hermitian matrix model using its representation as a CFT on a hyperelliptic Riemann surface. To each branch point of the Riemann surface we associate an operator which represents a twist field…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
We discuss building models for nucleon generalized parton distributions (GPDs) H and E that are based on the formalism of double distributions (DDs). We found that the usual "DD+D-term" construction should be amended by an extra term, \xi…
Single-molecule force-extension experiments have allowed quantitative measurements of the mechanical responses of biomolecules to applied forces explaining their roles in key biological functions. Electrophoretic stretching of charged…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…