Search for: All records

The characteristics of the interface between DNA and metallic carbon nanotube (CNT) in supramolecular assemblies are important to understand for electronic and sensing applications. We study the mechanical stability and electronic properties of these interfaces with amino and ester linkers using computational experiments. Our study demonstrates that both linkers significantly enhance the mechanical stability of DNA–CNT systems, with the DNA adopting a stable and lower energy perpendicular orientation relative to the CNT as opposed to a conventional parallel arrangement. This lower energy configuration is driven by nonbonded interactions between the DNA base and the CNT surface. Our calculations also reveal that interface resistance is primarily governed by DNA–CNT interactions with negligible contribution from the linkers. In the case of the amino linker, we predict a 100-fold transmission ratio between parallel and perpendicular configurations of DNA relative to CNT. This observation can be used to build an electromechanical switch with fast switching times (30 ns). The ester linker, on the contrary, enables a better electronic coupling between the DNA and CNT even when strained. 

Force fields were developed for metal-mediated DNA (mmDNA) structures, using ab-initio methods to parameterize metal coordination. Two mmDNA were considered, comprising of a cytosine/thymine mismatch with coordinated Ag/Hg metal atoms. These basepairs were parameterized with the proposed computational framework and subjected to multiple validation steps. The generated force fields result in enhanced structural stability, with metallated basepairs rotating into the major groove. Our findings show a higher propeller angle associated with metalated base pair, which agrees with previously reported experimental data. Molecular dynamics (MD) simulations showed that the metallated basepairs stabilized the DNA structure, with the mismatch bases locking together via metal coordination. We anticipate the developed force fields can help in unveiling the structural dynamics of long metallo-DNA nanowires. 

This article explores how conformational fluctuations influence the conductance of a single-stranded RNA (ssRNA) and the means to harness its inherent structural variabilityviasalt concentration regulation. 

Topology has emerged as a field for describing and controlling order and matter, and thereby the physical properties of materials. There are several largely disparate fields focused on examining and manipulating topology. One of these arenas is in the realm of real space, manipulating systems in terms of their spatial properties, to control the corresponding structural, mechanical, and self- assembling responses. Much of the work in soft matter topology falls within this domain. A second arena is in the domain of momentum or k-space wherein topology controls the features of the electronic band structure of materials, and topologically non-trivial features result in the development of materials with truly unique properties. This work focuses squarely on the realm of condensed matter physics. Here, we review concepts of real- and k-space topology and propose areas for convergence between these two disparate fields. 

Abstract Deoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage devices is currently hindered by limitations such as expensive and complex fabrication processes and time-consuming read–write operations. In this article, we propose the use of a DNA crossbar array architecture for an electrically readable read-only memory (DNA-ROM). While information can be ‘written’ error-free to a DNA-ROM array using appropriate sequence encodings its read accuracy can be affected by several factors such as array size, interconnect resistance, and Fermi energy deviations from HOMO levels of DNA strands employed in the crossbar. We study the impact of array size and interconnect resistance on the bit error rate of a DNA-ROM array through extensive Monte Carlo simulations. We have also analyzed the performance of our proposed DNA crossbar array for an image storage application, as a function of array size and interconnect resistance. While we expect that future advances in bioengineering and materials science will address some of the fabrication challenges associated with DNA crossbar arrays, we believe that the comprehensive body of results we present in this paper establishes the technical viability of DNA crossbar arrays as low power, high-density storage devices. Finally, our analysis of array performance vis-à-vis interconnect resistance should provide valuable insights into aspects of the fabrication process such as proper choice of interconnects necessary for ensuring high read accuracies. 

Deoxyribonucleic acid (DNA) has emerged as a promising building block for designing next-generation ultra-high density storage devices. Although DNA is highly durable and extremely high density in nature, its potential as the basis of storage devices is currently hindered by limitations such as expensive and complex fabrication processes and time-consuming read-write operations. In this article, we propose the use of a DNA crossbar array architecture for an electrically-readable Read-Only Memory (DNA-ROM). For DNA-ROM, we have chosen two DNA strands for representing Bit 1 and Bit 0 respectively. DNA charge transport has been studied through a contact-DNA-contact setup. The results obtained from the DNA charge transport study have been used to analyze the crossbar array. The performance has been analyzed by loading an image onto a 128×128 crossbar. For this application, we have observed a bit error rate of 4.52% and power consumption of 6.75 µW. 

Abstract The rational design of molecular electronics remains a grand challenge of materials science. DNA nanotechnology has offered unmatched control over molecular geometry, but direct electronic functionalization is a challenge. Here a generalized method is presented for tuning the local band structure of DNA using transmetalation in metal‐mediated base pairs (mmDNA). A method is developed for time‐resolved X‐ray diffraction using self‐assembling DNA crystals to establish the exchange of Ag⁺ and Hg²⁺ in T:T base pairs driven by pH exchange. Transmetalation is tracked over six reaction phases as crystal pH is changed from pH 8.0 to 11.0, and vice versa. A detailed computational analysis of the electronic configuration and transmission in the ensuing crystal structures is then performed. This findings reveal a high conductance contrast in the lowest unoccupied molecular orbitals (LUMO) as a result of metalation. The ability to exchange single transition metal ions as a result of environmental stimuli heralds a means of modulating the conductance of DNA‐based molecular electronics. In this way, both theoretical and experimental basis are established by which mmDNA can be leveraged to build rewritable memory devices and nanoelectronics.