Related papers: Parallel DNA Synthesis : Two PCR product from one …
We propose a compartmental lateral inhibition system that generates contrasting patterns of gene expression between neighboring compartments. The system consists of a set of compartments interconnected by channels. Each compartment contains…
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…
Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is widely used for gene delivery. It is considered here in terms of discrete charges of DNA. We concentrate on the worst scenario case when in the…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
Retrosynthesis planning remains a central challenge in molecular discovery due to the vast and complex chemical reaction space. While traditional template-based methods offer tractability, they suffer from poor scalability and limited…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
Leading neutron production on protons is known to be subject to strong absorptive corrections, which have been under debate for a long time. On nuclear targets these corrections are significantly enhanced and push the partial cross sections…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
Several technological limitations of traditional silicon based computing are leading towards the paradigm shift, from silicon to carbon, in computational world. Among the unconventional modes of computing evolved in past several decades,…
Retrosynthesis is a procedure where a target molecule is transformed into potential reactants and thus the synthesis routes can be identified. Recently, computational approaches have been developed to accelerate the design of synthesis…
Electroporation is a physical method to induce the uptake of therapeutic drugs and DNA, by eukaryotic cells and tissues. The phenomena behind electro-mediated membrane permeabilization to plasmid DNA have been shown to be significantly more…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
Multi-contrast MRI protocols increase the level of morphological information available for diagnosis. Yet, the number and quality of contrasts is limited in practice by various factors including scan time and patient motion. Synthesis of…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
The synthesis of antenna arrays in presence of mutual coupling using generalized scattering matrices in terms of characteristic modes is proposed. For the synthesis, the array is built of synthetic elements that are described by their modal…
Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence-dependence of the local unzipping of double-stranded DNA, the first step…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…