相关论文: Information-theoretic View of Sequence Organizatio…
A number of observations are made on Hofstadter's integer sequence defined by Q(n)= Q(n-Q(n-1))+Q(n-Q(n-2)), for n > 2, and Q(1)=Q(2)=1. On short scales the sequence looks chaotic. It turns out, however, that the Q(n) can be grouped into a…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…
An orientable sequence of order $n$ over an alphabet $\{0,1,\ldots, k{-}1\}$ is a cyclic sequence such that each length-$n$ substring appears at most once \emph{in either direction}. When $k= 2$, efficient algorithms are known to construct…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
A refinement of Shor's Algorithm for determining order is introduced, which determines a divisor of the order after any one run of a quantum computer with almost absolute certainty. The information garnered from each run is accumulated to…
We suggest that ensembles of self-replicating entities such as biological systems naturally evolve into a self-organized critical state in which fluctuations, as well as waiting-times between phase transitions are distributed according to a…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
Here we try and delienate the properties of the function that corresponds to fluctuations in the momentum distribution. The quantity denoted by $ N(k,k^{'}) $ is quite an interesting object. It satisfies various elegant sum rules and is…
It is well known that the mathematically accurate description of ordering and related symmetry breaking in statistical systems requires to consider the thermodynamic limit. But the order does not appear from nowhere, and yet before the…
Aging is a universal consequence of life, yet researchers have identified no universal theme. This manuscript considers aging from the perspective of entropy, wherein things fall apart. We first examine biological information change as a…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Mixed order transitions are those which show a discontinuity of the order parameter as well as a divergent correlation length. We show that the behaviour of the order parameter correlation function along the transition line of mixed order…
Many systems in nature, from ferromagnets to flocks of birds, exhibit ordering phenomena on the large scale. In physical systems order is statistically robust for large enough dimensions, with relative fluctuations due to noise vanishing…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
The concept of the order parameter is extremely useful in physics. Here, I discuss extensions of this concept to cases when the order parameter is no longer a constant but fluctuates or oscillates in space and time. This allows one to…