相关论文: Effect of Sequence-Dependent Rigidity on Plectonem…
DNA supercoiling plays an important role on a biological point of view. One of its consequences at the supra-molecular level is the formation of DNA superhelices named plectonemes. Normally separated by a distance on the order of 10 nm, the…
We develop a statistical mechanical framework, based on a variational approximation, to describe closed loop plectonemes. This framework incorporates weak helix structure dependent forces into the determination of the free energy and…
In a Monte Carlo study the conductivity of two-dimensional random stick systems is investigated from the percolation threshold up to ten times the percolation threshold density. We propose a model explicitly depending on the stick density…
We employed the VicCA model to investigate the influence of step-edge potential on nucleation and pattern formation, aiming to gain deeper insights into island formation and growth. Our study explores fractal structures governed by general…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
The effect of different Monte Carlo move sets on the the folding kinetics of lattice polymer chains is studied from the geometry of the conformation-network. The networks have the characteristics of small- world. The Monte Carlo move, rigid…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
Directed Percolation (DP) is a classic model for nonequilibrium phase transitions into a single absorbing state (fixation). It has been extensively studied by analytical and numerical techniques in diverse contexts. Recently, DP has…
Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for…
Understanding the rolling and adhesion behavior of a cell on the vascular surface under viscous shear flow is important to better understand many biological processes. One of the important examples is the adhesion of the leukocytes onto…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
The effect of silicon-oxide interface roughness on the weak-localization magnetoconductance of a silicon MOSFET in a magnetic field, tilted with respect to the interface, is studied. It is shown that an electron picks up a random Berry's…
SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and…
The huge amount of available data nowadays is a challenge for kernel-based machine learning algorithms like SVMs with respect to runtime and storage capacities. Local approaches might help to relieve these issues and to improve statistical…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…