Charge Transport in DNA-Based Devices

Charge migration along DNA molecules has attracted scientific interest for over half a century. Reports on possible high rates of charge transfer between donor and acceptor through the DNA, obtained in the last decade from solution chemistry experiments on large numbers of molecules, triggered a series of direct electrical transport measurements through DNA single molecules, bundles and networks. These measurements are reviewed and presented here. From these experiments we conclude that electrical transport is feasible in short DNA molecules, in bundles and networks, but blocked in long single molecules that are attached to surfaces. The experimental background is complemented by an account of the theoretical/computational schemes that are applied to study the electronic and transport properties of DNA-based nanowires. Examples of selected applications are given, to show the capabilities and limits of current theoretical approaches to accurately describe the wires, interpret the transport measurements, and predict suitable strategies to enhance the conductivity of DNA nanostructures.Comment: A single pdf file of 52 pages, containing the text and 23 figures. Review about direct measurements of DNA conductivity and related theoretical studies. For higher-resolution figures contact the authors or retrieve the original publications cited in the caption

Intermediate coherent-incoherent charge transport: DNA as a case study

We study an intermediate quantum coherent-incoherent charge transport mechanism in metal-molecule-metal junctions using B\"uttiker's probe technique. This tool allows us to include incoherent effects in a controlled manner, and thus to study situations in which partial decoherence affects charge transfer dynamics. Motivated by recent experiments on intermediate coherent-incoherent charge conduction in DNA molecules [L. Xiang {\it et al.}, Nature Chem. 7, 221-226 (2015)], we focus on two representative structures: alternating (GC)$_n$ and stacked G$_n$C$_n$ sequences; the latter structure is argued to support charge delocalization within G segments, and thus an intermediate coherent-incoherent conduction. We begin our analysis with a highly simplified 1-dimensional tight-binding model, while introducing environmental effects through B\"uttiker's probes. This minimal model allows us to gain fundamental understanding of transport mechanisms and derive analytic results for molecular resistance in different limits. We then use a more detailed ladder-model Hamiltonian to represent double-stranded DNA structures---with environmental effects captured by B\"uttiker's probes. We find that hopping conduction dominates in alternating sequences, while in stacked sequences charge delocalization (visualized directly through the electronic density matrix) supports significant resonant-ballistic charge dynamics reflected by an even-odd effect and a weak distance dependence for resistance. Our analysis illustrates that lessons learned from minimal models are helpful for interpreting charge dynamics in DNA.Comment: 16 pages, 14 figure

Dissipative Effects in the Electronic Transport through DNA Molecular Wires

We investigate the influence of a dissipative environment which effectively comprises the effects of counterions and hydration shells, on the transport properties of short \DNA wires. Their electronic structure is captured by a tight-binding model which is embedded in a bath consisting of a collection of harmonic oscillators. Without coupling to the bath a temperature independent gap opens in the electronic spectrum. Upon allowing for electron-bath interaction the gap becomes temperature dependent. It increases with temperature in the weak-coupling limit to the bath degrees of freedom. In the strong-coupling regime a bath-induced {\it pseudo-gap} is formed. As a result, a crossover from tunneling to activated behavior in the low-voltage region of the $I$-$V$ characteristics is observed with increasing temperature. The temperature dependence of the transmission near the Fermi energy, $t(E_{\rm F})$, manifests an Arrhenius-like behavior in agreement with recent transport experiments. Moreover, $t(E_{\rm F})$ shows a weak exponential dependence on the wire length, typical of strong incoherent transport. Disorder effects smear the electronic bands, but do not appreciably affect the pseudo-gap formation

Demarcation of coding and non-coding regions of DNA using linear transforms

Deoxyribonucleic Acid (DNA) strand carries genetic information in the cell. A strand of DNA consists of nitrogenous molecules called nucleotides. Nucleotides triplets, or the codons, code for amino acids. There are two distinct regions in DNA, the gene and the intergenic DNA, or the junk DNA. Two regions can be distinguished in the gene- the exons, or the regions that code for amino acid, and the introns, or the regions that do not code for amino acid. The main aim of the thesis is to study signal processing techniques that help distinguish between the regions of the exons and the introns. Previous research has shown the fact that the exons can be considered as a sequence of signal and noise, whereas introns are noise-like sequences. Fourier Transform of an exonic sequence exhibits a peak at frequency sample value k N/3 where N is the length of the FFT transform. This property is referred to as the period -3 property. Unlike exons, introns have a noise-like spectrum. The factor that determines the performance efficiency of a transform is the figure of merit, defined as the ratio of the peak value to the arithmetic mean of all the values. A comparative study was conducted for the application of the Discrete Fourier Transform and the Karhunen Loeve Transform. Though both DFT and KLT of an exon sequence produce a higher figure of merit than that for an intron sequence, it is interesting to note that the difference in the figure of merits of exons and introns was higher when the KLT was applied to the sequence than when the DFT was applied. The two transforms were also applied on entire sequences in a sliding window fashion. Finally, the two transforms were applied on a large number of sequences from a variety of organisms. A Neyman Pearson based detector was used to obtain receiver operating curves, i.e., probability of detection versus probability of false alarm. When a transform is applied as a sliding window, the values for exons and introns are taken separately. The exons and the introns served as the two hypotheses of the detector. The Neyman Pearson detector helped indicate the fact the KLT worked better on a variety of organisms than the DFT

Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of wire model vs. extended ladder model

We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the on-site energies of the bases and the hopping integrals between neighboring bases, i.e., an \textit{extended} ladder model since we also include diagonal hoppings. We solve a system of $MD$ ("matrix dimension") coupled equations [(I) $MD$ = $N$, (II) $MD$ = $2N$] for the time-independent problem, and a system of $MD$ coupled $1^\text{st}$ order differential equations for the time-dependent problem. We study the HOMO and the LUMO eigenspectra, the occupation probabilities, the Density of States (DOS) and the HOMO-LUMO gap as well as the mean over time probabilities to find the carrier at each site [(I) base pair or (II) base)], the Fourier spectra, which reflect the frequency content of charge transfer (CT) and the pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.Comment: 20 pages, 23 figure

Molecular Studies in Mercury Toxicity Using X-ray Absorption Spectroscopy and High Energy Resolution Fluorescence Detection X-ray Absorption Spectroscopy

The abstract of this item is unavailable due to an embargo

Electrical Conductance in Biological Molecules

Nucleic acids and proteins are not only biologically important polymers: They have recently been recognized as novel functional materials surpassing in many aspects the conventional ones. Although Herculean efforts have been undertaken to unravel fine functioning mechanisms of the biopolymers in question, there is still much more to be done. This particular paper presents the topic of biomolecular charge transport, with a particular focus on charge transfer/transport in DNA and protein molecules. Here the experimentally revealed details, as well as the presently available theories, of charge transfer/transport along these biopolymers are critically reviewed and analyzed. A summary of the active research in this field is also given, along with a number of practical recommendations.Comment: v2: This paper has been withdrawn by the authors due to a serious complaints from one author whose work we cite. v3: After clarifying the issue we are herewith republishing our paper

Protein sequencing strategy in nanotechnology by classical and quantum atomistic models

Il mio lavoro di ricerca ha avuto l’obiettivo di studiare le proprietà principali dell’interazione tra materiale biologico e superfici inorganiche. Per tale scopo è stato utilizzato uno approccio basato sulla teoria del funzionale densità (DFT), lo studio è stato svolto nell’ambito del calcolo ad alte prestazioni utilizzando un approccio quanto-meccanico da principi primi, in modo da poter descrivere al meglio le interazioni chimico-fisiche a livello molecolare e sub-molecolare. Il tutto è stato applicato in dispositivi di ultima generazione per sequenziamento di catene biologiche, basate sulla tecnologia a nano-poro; in questi sensori nano-strutturati vi è un analisi detta a singola-molecola, il tipo e i modi d’interazioni tra dispositivo e target d’analizzare sono fondamentali e determinano la variazione del nostro segnale in uscita. Il funzionamento è relativamente semplice: si applica agli estremi della superfice con il poro una differenza di potenziale, e si misura la variazione della corrente quando il foro è occupato; le dimensioni del poro fanno si che si possa analizzare una molecola alla volta. Il materiale scelto per la realizzazione di questi dispositivi è stato il grafene per le sue proprietà elettroniche e la sua geometria; le catene biologiche scelte sono sequenze di amminoacidi; questa scelta si basa sulla possibile evoluzione di questi dispositivi, finora utilizzati per il sequenziamento di DNA (commercializzato dalla Oxford Nanopores Technologies), e sull’importanza dell’identificazione della sequenza e della struttura delle proteine, visto la connessione a patologie neurodegenerative come Parkinson e Alzheimer. Più in dettaglio il mio lavoro di ricerca è partito da studi precedenti dove venivano analizzate filamenti di DNA con la traslazione di basi nucleiche in nano-pori biologici per il sequenziamento; si sono studiati i cambiamenti caratteristici di corrente quando il target si avvicina alla superficie o attraversava il poro in modo da ottenere un'analisi rapida a singola-molecola. Si è provato, così, ad applicare lo stesso principio su sequenze di peptidi, per la loro importanza a livello medico-scientifico, con nanostrutture allo stato solido, visti i vantaggi di quest'ultimi rispetto a quelli biologici (miglior rapporto segnale rumore e una vita media più lunga). Sono state effettuate simulazioni Ab-Initio per caratterizzare sia le proprietà elettroniche superficiali, osservando la densità degli stati (DOS), e sia l'effetto quantistico del tunneling degli elettroni al variare della molecola interagente con la superficie. Per fare ciò si è studiata la corrente elettronica trasversale al piano del poro, su un ribbon di grafene, correlando le variazioni della nube elettronica con la molecola target. Per raggiungere questi obiettivi abbiamo: • definito modelli atomistici di interazione tra amminoacidi e bordi di un nano-poro di grafene; • utilizzato simulazioni atomistiche/molecolari per ottimizzare la morfologia (grandezza) e struttura (forma) più adeguata del poro; • studiato il funzionamento elettronico del nano-poro in fase di traslocazione degli amminoacidi attraverso esso. In particolare ci si è concentrati sul calcolo della conduttività trasversale attraverso la metodologia della Non-Equilibrium Green Function (NEGF) e l'approccio Landauer-Buttiker La ricerca è stata articolata in due fasi: I Fase: Design del nano-poro di grafene Nonostante diversi nano-pori siano già studiati con tecniche sperimentali, l’approccio teorico-modellistico basato su simulazioni molecolari atomistiche della struttura del nano-poro ha reso possibile avere una rigorosa caratterizzazione fisica e chimica del sistema; questa caratterizzazione è diventata la base per il successivo processo di ottimizzazione del dispositivo (passando da un nano-poro a un nano-gap). Dal punto di vista teorico-computazionale, si è confrontato il comportamento, strutturale del passaggio all’interno del sensore di diversi amminoacidi e si è progettato un nano-gap adatto alla valutazione degli effetti di traslocazione. II Fase: Caratterizzazione del segnale Si è studiata la variazione del “segnale” ottenuto, per caratterizzarlo al meglio e abbassare il rapporto segnale rumore. Attraverso varie analisi di post-processing si è andata a vedere la corrente elettronica elastica ed anelastica e si è aggiunta l’analisi della corrente ionica con simulazioni di dinamica molecolare classica

Molecular Mechanisms and Design of Hydrogen-Bonded Materials for Thermal Applications

Heat transfer at the nanoscale plays an important role in determining the reliability and performance of many innovative advanced materials technologies such as nanoelectronics, semiconductor, biomedical devices, polymers, and composites. Extensive efforts have been made to design materials with extraordinary thermal properties. However, fundamental understanding of heat transfer in many of these materials is still not lacking, because the thermal transport processes are governed by several factors including molecular morphology and chemical bonding. Among these factors, the atomic bonding between two dissimilar materials or within single materials is of particular interest due to its ubiquity and importance in physical processes. This work will focus on the demonstration and fundamental understanding of nanoscale thermal transport enhanced by incorporating hydrogen bonds in materials design. Molecular dynamics is performed for studying heat transfer processes in two typical hydrogen-bonded materials: (1) protein secondary structures, and (2) electrode/electrolyte composites in lithium ion batteries. Theoretical calculation and analysis show that heat transfer can be tuned in a wide range by modifying the hydrogen bonds. Results will not only provide new physical insights, but will also guide the rational design of materials for desired thermal properties towards many applications