Related papers: Entropy involved in fidelity of DNA replication
Permutation entropy quantifies the diversity of possible orderings of the values a random or deterministic system can take, as Shannon entropy quantifies the diversity of values. We show that the metric and permutation entropy…
Phase-space versions of quantum mechanics -- from Wigner's original distribution to modern discrete-qudit constructions -- represent some states with negative quasi-probabilities. Conventional Shannon and R\'enyi entropies become…
We prove the full equivalence between Assembly Theory (AT) and Shannon Entropy via a method based upon the principles of statistical compression renamed `assembly index' that belongs to the LZ family of popular compression algorithms (ZIP,…
Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the…
The body morphology plays an important role in the way information is perceived and processed by an agent. We address an information theory (IT) account on how the precision of sensors, the accuracy of motors, their placement, the body…
Many partially-successful attempts have been made to find the most natural discrete-variable version of Shannon's entropy power inequality (EPI). We develop an axiomatic framework from which we deduce the natural form of a discrete-variable…
Entropy rate of sequential data-streams naturally quantifies the complexity of the generative process. Thus entropy rate fluctuations could be used as a tool to recognize dynamical perturbations in signal sources, and could potentially be…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
Thermodynamic entropy, as defined by Clausius, characterizes macroscopic observations of a system based on phenomenological quantities such as temperature and heat. In contrast, information-theoretic entropy, introduced by Shannon, is a…
We observe an infinite sequence of independent identically distributed random variables $X_1,X_2,\ldots$ drawn from an unknown distribution $p$ over $[n]$, and our goal is to estimate the entropy $H(p)=-\mathbb{E}[\log p(X)]$ within an…
A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
Maximum entropy estimation is of broad interest for inferring properties of systems across many different disciplines. In this work, we significantly extend a technique we previously introduced for estimating the maximum entropy of a set of…
We investigate the memory properties of discrete sequences built upon a finite number of states. We find that the block entropy can reliably determine the memory for systems modeled as Markov chains of arbitrary finite order. Further, we…
We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
I consider the effect of a finite sample size on the entropy of a sample of independent events. I propose formula for entropy which satisfies Shannon's axioms, and which reduces to Shannon's entropy when sample size is infinite. I discuss…
Living systems produce copies of information-carrying molecules such as DNA by assembling monomer units into finite-length oligomer (short polymer) copies. We explore the role of initiation and termination of the copy process in the…
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…