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Polymer composites are ubiquitous in biology and industry alike, owing to their emergent desirable mechanical properties not attainable in single-species systems. At the same time, polymer topology has been shown to play a key role in…
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…
We consider a two-dimensional system of elongated particles driven over a random quenched disorder landscape. For varied pinning site density, external drive magnitude, and particle elongation, we find a wide variety of dynamic phases,…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
DNA cloning methods are fundamental tools in molecular biology, synthetic biology, and genetic engineering that enable precise DNA manipulation for various scientific and biotechnological applications. This review systematically summarizes…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
Motivated by genome-wide association studies, we consider a standard linear model with one additional random effect in situations where many predictors have been collected on the same subjects and each predictor is analyzed separately.…
We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…
We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
The photophysical properties of deoxyribonucleic acid (DNA) are fundamental to life sciences and biophotonics. While previous studies have generally been restricted to fluorescence, attributing it to pi-pi* transitions and charge transfer…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
When multivalent salts are added to dilute DNA solution, the DNA chains condense into bundles of a well-defined size. We explore two physical problems motivated by this phenomenon: the origin of the attractive interactions between the…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Taking advantage of the base-pairing specificity and tunability of DNA interactions, we investigate the spontaneous formation of hyperbranched clusters starting from purposely designed DNA tetravalent nanostar monomers, encoding in their…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…