Related papers: Numerical modeling of inhomogeneous DNA replicatio…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
The possible role of quantum effects in transfer of genetic information is studied. It's argued that the nucleotides selection during DNA replication is performed by means of proton tunneling between nucleotide and DNA-polimerase bound by…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
In material science, models are derived to predict emergent material properties (e.g. elasticity, strength, conductivity) and their relations to processing conditions. A major drawback is the calibration of model parameters that depend on…
Photo-induced processes are fundamental in nature, but accurate simulations are seriously limited by the cost of the underlying quantum chemical calculations, hampering their application for long time scales. Here we introduce a method…
Computer models are used to model complex processes in various disciplines. Often, a key source of uncertainty in the behavior of complex computer models is uncertainty due to unknown model input parameters. Statistical computer model…
Imperfect molecular detection in single-cell experiments introduces technical noise that obscures the true stochastic dynamics of gene regulatory networks. While binomial models of molecular capture provide a principled description of…
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…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
This paper addresses the numerical simulation of self-piercing rivetting processes to join fibre reinforced polymers and sheet metals. Special emphasis is placed on the modelling of the deformation and failure behaviour of the composite…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
Morphogenesis is a tightly regulated process that has been studied for decades. We are developing data-based and image-basd mechanistic models for a range of developmental processes with a view to integrate the available knowledge and to…
Recent advances in computer vision and robotics enabled automated large-scale biological image analysis. Various machine learning approaches have been successfully applied to phenotypic profiling. However, it remains unclear how they…
The cost of deriving actionable knowledge from large datasets has been decreasing thanks to a convergence of positive factors: low cost data generation, inexpensively scalable storage and processing infrastructure (cloud), software…
Metamorphosis is a method for diffeomorphic matching of shapes, with many potential applications for anatomical shape comparison in medical imagery, a problem which is central to the field of computational anatomy. An important tool for the…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Genetic algorithms have been used in recent decades to solve a broad variety of search problems. These algorithms simulate natural selection to explore a parameter space in search of solutions for a broad variety of problems. In this paper,…
Model merging is an effective strategy to merge multiple models for enhancing model performances, and more efficient than ensemble learning as it will not introduce extra computation into inference. However, limited research explores if the…