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Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
Rapid advances in computing technology over the past few decades have spurred two extraordinary phenomena in science: large-scale and high-throughput data collection coupled with the creation and implementation of complex statistical…
The nucleation rate derived in the classical theory contains at least one undetermined parameter, which may be expressed in terms of the Langer first-principles theory. But the uncertainties in the accounting for fluctuation modes, which…
Microarray data are often used to determine which genes are differentially expressed between groups, for example, between treatment and control groups. There are methods of determining which genes have a high probability of differential…
The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
Previously, it has been shown that maximum-entropy models of immune-repertoire sequence can be used to determine a person's vaccination status. However, this approach has the drawback of requiring a computationally intensive method to…
The counting statistics give insight into the properties of quantum states of light and other quantum states of matter such as ultracold atoms or electrons. The theoretical description of photon counting was derived in the 1960s and was…
In quantum many-body systems, measurements can induce qualitative new features, but their simulation is hindered by the exponential complexity involved in sampling the measurement results. We propose to use machine learning to assist the…
Nucleon-nucleon scattering observables are considered in the context of the large $N_c$ limit of QCD for initial states with moderately high momenta ($p \sim N_c$). The scattering is studied in the framework of the time-dependent mean-field…
Although the realization of useful quantum computers poses significant challenges, swift progress in emerging quantum technologies is making this goal realistically approachable. In this context, one of the essential resources is quantum…
Enzymatic ligation is essential for the synthesis of long DNA. However, the number of ligated products exponentially decays as the DNA synthesis proceeds in a random manner. The controlling of ligation randomness is of importance to…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
The problem of sequentially detecting an abrupt change in a sequence of independent and identically distributed (IID) random variables is addressed. Whereas previous approaches assume a known probability density function (PDF) at the start…
A random sequence having two segments being the homogeneous Markov processes is registered. Each segment has his own transition probability law and the length of the segment is unknown and random. The transition probabilities of each…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
In order to avoid unnecessary applications of Miller-Rabin algorithm to the number in question, we resort to trial division by a few initial prime numbers, since such a division take less time. How far we should go with such a division is…