Related papers: Entropic contributions to the splicing process
Dislocation nucleation is essential to our understanding of plastic deformation, ductility and mechanical strength of crystalline materials. Molecular dynamics simulation has played an important role in uncovering the fundamental mechanisms…
We study the elasto-plastic behavior of dense attractive emulsions under mechanical perturbation. The attraction is introduced through non-specific depletion interactions between the droplets and is controlled by changing the concentration…
The depletion interaction mediated by non-adsorbing polymers promotes condensation and assembly of repulsive colloidal particles into diverse higher-order structures and materials. One example, with particularly rich emergent behaviors, is…
In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also…
A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers.…
We are interested in the comparison of transcript boundaries from cells which originated in different environments. The goal is to assess whether this phenomenon, called differential splicing, is used to modify the transcription of the…
Membrane wrapping underlies nanoparticle uptake during endocytosis, whereas the reverse process of membrane unwrapping accompanies particle expulsion and membrane fusion events. Existing theoretical descriptions typically focus on adhesion…
Deleterious genetic variants can be evaluated as quantitative traits using information theory-based sequence analysis of recognition sites. To assess the effect of such variants, fitness and genetic load of SNPs which alter binding site…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
The efficiency of Monte Carlo samplers is dictated not only by energetic effects, such as large barriers, but also by entropic effects that are due to the sheer volume that is sampled. The latter effects appear in the form of an entropic…
Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or…
We consider the von Neumann and R\'enyi entropies of the one dimensional quarter-filled Hubbard model. We observe that for periodic boundary conditions the entropies exhibit an unexpected dependence on system size: for L=4 mod 8 the results…
Bioinformatics encompass storing, analyzing and interpreting the biological data. Most of the challenges for Machine Learning methods like Cellular Automata is to furnish the functional information with the corresponding biological…
Inclusions in mobile brushes experience apparent (depletion) attraction, which arises from a tendency to minimize the volume of depletion zones around the inclusions, thereby to maximize the entropy of the surrounding polymers. Here, we…
Cellular uptake through the lipid membranes plays an important role in adsorbing nutrients and fighting infection and can be used for drug delivery and nanomedicine developments. Endocytosis is one of the known pathways of the cellular…
Quantitative predictions are presented of a depletion-induced torque and force acting on a single colloidal hard rod immersed in a solvent of hard spheres close to a planar hard wall. This torque and force, which are entirely of entropic…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…