Related papers: The entropic lock and key of the histone code
The main difficulty when modelling gene networks is the identification of the parameters that govern their dynamics. It is particularly difficult for models in which time is continuous: parameters have real values which cannot be…
Understanding strongly correlated quantum many-body states is one of the most difficult challenges in modern physics. For example, there remain fundamental open questions on the phase diagram of the Hubbard model, which describes strongly…
Polydomain liquid crystalline (nematic) elastomers have highly unusual mechanical properties, dominated by the dramatically non-linear stress-strain response that reflects stress-induced evolution of domain patterns. Here, we study the…
Digital stiffness programmability is fulfilled with a heterogeneous mechanical metamaterial. The prototype consists of an elastomer matrix containing tessellations of diamond shaped cavities selectively confined with semi-rigid plastic beam…
Multideterminant calculations have been performed on model systems to emphasize the role of many-body effects in the general description of charge quantization experiments. We show numerically and derive analytically that a closed-shell…
Chirality manifests across multiple scales, yielding unique phenomena that break mirror symmetry. In chiral materials, unexpectedly large spin-filtering or photogalvanic effects have been observed even in materials composed of light…
The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…
The recent years have witnessed an emergence of the field of all-spin-based devices without any flow of charge. An ultimate goal of this scientific direction is the realization of full spectrum of spin-based networks like in modern…
Molecular testing of tumor samples for targetable biomarkers is restricted by a lack of standardization, turnaround-time, cost, and tissue availability across cancer types. Additionally, targetable alterations of low prevalence may not be…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
Nanoscale chromatin domains, variously termed nucleosome clutches, nanodomains, or packing domains, have emerged as fundamental architectural units of the mammalian genome during interphase and mitosis. Unlike cohesin-dependent loops or…
Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature…
The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid…
We consider a monitoring application where sensors periodically report data to a common receiver in a time division multiplex fashion. The sensors are constrained by the limited and unpredictable energy availability provided by Energy…
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation…
Molecular crystals possess a highly complex crystallographic landscape which in many cases results in the experimental observation of multiple crystal structures for the same compound. Accurate results can often be obtained for such systems…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
A morphogenic protein known as Dorsal patterns the embryonic dorsoventral body axis of Drosophila by binding to transcriptional enhancers across the genome. Each such enhancer activates a neighboring gene at a unique threshold concentration…