Related papers: The entropic lock and key of the histone code
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
The effect of bond randomness on the spin-gapped ground state of the spin-1 bond-alternating antiferromagnetic Heisenberg chain is discussed. By using the loop cluster quantum Monte Carlo method, we investigate the stability of topological…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
In continuation to earlier works where the problem of joint information embedding and lossless compression (of the composite signal) was studied in the absence \cite{MM03} and in the presence \cite{MM04} of attacks, here we consider the…
Gene regulation in higher eukaryotes involves a complex interplay between the gene proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive spatio-temporal expression. The experimental…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
Critical state problems which incorporate more than one component for the magnetization vector of hard superconductors are investigated. The theory is based on the minimization of a cost functional ${\cal C}[\vec{H}(\vec{x})]$ which weighs…
Development of resistance limits transferability of most anticancer therapies into curative treatment and understanding mechanisms beyond it remains a big challenge. Many high resolution experimental observations show enormous intratumor…
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
Token-level reweighting is a simple yet effective mechanism for controlling supervised fine-tuning, but common indicators are largely one-dimensional: the ground-truth probability reflects downstream alignment, while token entropy reflects…
A broad class of blocked or jammed configurations of particles on the one-dimensional lattice can be characterized in terms of local rules involving only the lengths of clusters of particles (occupied sites) and of holes (empty sites).…
We formulate the entropy of a quantized artificial neural network as a differentiable function that can be plugged as a regularization term into the cost function minimized by gradient descent. Our formulation scales efficiently beyond the…
The trapezoidal rule, which is a special case of the Newmark family of algorithms, is one of the most widely used methods for transient hyperbolic problems. In this work, we show that this rule conserves linear and angular momenta and…
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
The past decade has seen a revolution in genomic technologies that enable a flood of genome-wide profiling of chromatin marks. Recent literature tried to understand gene regulation by predicting gene expression from large-scale chromatin…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
Finite plasticity theories are still a subject of controversy and lively discussions. Among the approaches to finite elastoplasticity two became especially popular. The first, implemented in the commercial finite element codes, is based on…