Molecular-scale Computers Research Articles

Suzuki coupling derived indolocarbazole based macromolecule as a solid phase/solution phase sensor for Hg2+: Experimental and theoretical explorations

We present a study on an indolo[3,2-b]carbazole derived macromolecule viz; ICZP5 formed through Suzuki coupling reaction. The synthesized polymer exhibits good thermal and photophysical properties. The semiconducting nature of the polymer has been confirmed by cyclic voltammetric and current-voltage analyses. Its ground-state optimized structure has been achieved by DFT/B3LYP/6-31G* calculations. ONIOM method has been used for the optimization of its dimer and tetramer structures. A well- organized ICZP5 immobilized filter paper strip has subsequently been designed which could sense Hg2+ under UV light; as a solid state sensor. Moreover, for the development of automated chemical systems and molecular scale computers, a reversible INHIBIT logic gate has been put forward which extends the scope of the designed polymer. The theoretical calculations on the sensing mechanism have also been highlighted.

DNA-mediated gold nanoparticle signal transducers for combinatorial logic operations and heavy metal ions sensing.

Herein, the structure of two DNA strands which are complementary except fourteen T-T and C-C mismatches was programmed for the design of the combinatorial logic operation by utilizing the different protective capacities of single chain DNA, part-hybridized DNA and completed-hybridized DNA on unmodified gold nanoparticles. In the presence of either Hg(2+) or Ag(+), the T-Hg(2+)-T or C-Ag(+)-C coordination chemistry could lead to the formation of part-hybridized DNA which keeps gold nanoparticles from clumping after the addition of 40 μL 0.2M NaClO4 solution, but the protection would be screened by 120 μL 0.2M NaClO4 solution. While the coexistence of Hg(2+), Ag(+) caused the formation of completed-hybridized DNA and the protection for gold nanoparticles lost in either 40 μL or 120 μL NaClO4 solutions. Benefiting from sharing of the same inputs of Hg(2+) and Ag(+), OR and AND logic gates were easily integrated into a simple colorimetric combinatorial logic operation in one system, which make it possible to execute logic gates in parallel to mimic arithmetic calculations on a binary digit. Furthermore, two other logic gates including INHIBIT1 and INHIBIT2 were realized to integrated with OR logic gate both for simultaneous qualitative discrimination and quantitative determination of Hg(2+) and Ag(+). Results indicate that the developed logic system based on the different protective capacities of DNA structure on gold nanoparticles provides a new pathway for the design of the combinatorial logic operation in one system and presents a useful strategy for development of advanced sensors, which may have potential applications in multiplex chemical analysis and molecular-scale computer design.

Introduction to IEEE Transactions on Multiscale Computing Systems (TMSCS)

Reports on the introduction of the IEEE Transactions on Multiscale Computing Systems (TMSCS). IEEE TMSCS is a new journal devoted to computing systems that exploit multiscale and multi-functionality. Multiscale and multi-functionality computing are very rich fields. The traditional computing domain is transitioning in to exciting new directions due to several emerging technologies and advanced applications such as: massive many core processing platforms, nano architectures, big data driven applications, mapping of the brain, and molecular-scale computing. Consequently, multiscale and multi-functional computing have become a topic of increasing importance and emphasis in both research and graduate/undergraduate computer science and computer engineering education.

Molecular dynamics study of carbon-nanotube shuttle-memory on graphene nanoribbon array

Carbon nanomaterials, such as fullerenes, graphenes, and nanotubes, have a unique place in nanoscience, owing to their exceptional electrical, thermal, chemical and mechanical properties, and the number of their potential applications continues to grow. Conjugated carbon nanomaterials, such as fullerene–nanotube, fullerene–graphene, and nanotube–graphene hybrids, also have great potential applications. In this work, we present the schematics and the energetics of a nonvolatile memory based on nanotube–graphene hybrid, serving as the key building blocks for molecular-scale computers, and investigated the dynamic operations of a double-walled carbon nanotube (CNT) memory element, by using classical molecular dynamics simulations. The localized potential energy wells, achieved from the vdW energies between the outer CNT and two graphene-nanoribbons (GNRs), cause bi-stability of the outer CNT positions; and the alternative driving forces lead to the reversibility of this shuttle memory. Since the attractive vdW potential energies between the outer CNT and GNR make the outer CNT keep its position, the proposed shuttle-memory device can retain its stored data, without recharging processes.

RNA nanotechnology for computer design and in vivo computation.

Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.

Easy Design of Colorimetric Logic Gates Based on Nonnatural Base Pairing and Controlled Assembly of Gold Nanoparticles

Utilizing the principles of metal-ion-mediated base pairs (C-Ag-C and T-Hg-T), the pH-sensitive conformational transition of C-rich DNA strand, and the ligand-exchange process triggered by DL-dithiothreitol (DTT), a system of colorimetric logic gates (YES, AND, INHIBIT, and XOR) can be rationally constructed based on the aggregation of the DNA-modified Au NPs. The proposed logic operation system is simple, which consists of only T-/C-rich DNA-modified Au NPs, and it is unnecessary to exquisitely design and alter the DNA sequence for different multiple molecular logic operations. The nonnatural base pairing combined with unique optical properties of Au NPs promises great potential in multiplexed ion sensing, molecular-scale computers, and other computational logic devices.

A Visual Dual-Aptamer Logic Gate for Sensitive Discrimination of Prion Diseases-Associated Isoform with Reusable Magnetic Microparticles and Fluorescence Quantum Dots

Molecular logic gates, which have attracted increasing research interest and are crucial for the development of molecular-scale computers, simplify the results of measurements and detections, leaving the diagnosis of disease either “yes” or “no”. Prion diseases are a group of fatal neurodegenerative disorders that happen in human and animals. The main problem with a diagnosis of prion diseases is how to sensitively and selectively discriminate and detection of the minute amount of PrPRes in biological samples. Our previous work had demonstrated that dual-aptamer strategy could achieve highly sensitive and selective discrimination and detection of prion protein (cellular prion protein, PrPC, and the diseases associated isoform, PrPRes) in serum and brain. Inspired by the advantages of molecular logic gate, we further conceived a new concept for dual-aptamer logic gate that responds to two chemical input signals (PrPC or PrPRes and Gdn-HCl) and generates a change in fluorescence intensity as the output signal. It was found that PrPRes performs the “OR” logic operation while PrPC performs “XOR” logic operation when they get through the gate consisted of aptamer modified reusable magnetic microparticles (MMPs-Apt1) and quantum dots (QDs-Apt2). The dual-aptamer logic gate simplifies the discrimination results of PrPRes, leaving the detection of PrPRes either “yes” or “no”. The development of OR logic gate based on dual-aptamer strategy and two chemical input signals (PrPRes and Gdn-HCl) is an important step toward the design of prion diseases diagnosis and therapy systems.

Nanoscale Optical Computing Using Resonance Energy Transfer Logic

Drawing on the nanometer-placement capabilities of self-assembly fabrication methods, the authors propose a new nanoscale device based on a single-molecule optical phenomenon called resonance energy transfer. This device enables a complete integrated technology, providing a potential path to molecular-scale computing. The authors present several important circuit elements, show how to compose these elements into computational nodes, and outline initial steps toward a prototype system.

Schematics and Simulations of a Nanotube Shuttle Nonvolatile Memory Device

We propose a novel carbon-nanotube (CNT)-based nonvolatile memory, which can serve as a key building block for molecular-scale computers and perform molecular dynamics simulations to investigate the dynamic operation of a double-walled CNT memory. We find that the most important physical characteristics of the proposed nanometer-scale memory device are the bi-stability achieved by using the CNT inter-wall van der Waals interaction , the CNT-metal binding energies and the reversibility caused by the electrostatic attractive forces. Since the CNT shuttle can have a high kinetic energy during the transition, the dynamical collisions between the CNT and the metal electrodes are very important factors to be considered for design of a electrostatically telescoping CNT memory. The long collision time and the several rebounds cause a delay in the state transition.

Electrostatically telescoping nanotube nonvolatile memory device

We propose a nonvolatile memory based on carbon nanotubes (CNTs) serving as the keybuilding blocks for molecular-scale computers and investigate the dynamic operations of adouble-walled CNT memory element by classical molecular dynamics simulations. Thelocalized potential energy wells achieved from both the interwall van der Waals energy andCNT–metal binding energy make the bistability of the CNT positions and the electrostaticattractive forces induced by the voltage differences lead to the reversibility of this CNTmemory. The material for the electrodes should be carefully chosen to achieve thenonvolatility of this memory. The kinetic energy of the CNT shuttle experiences severalrebounds induced by the collisions of the CNT onto the metal electrodes, and this iscritically important to the performance of such an electrostatically telescoping CNTmemory because the collision time is sufficiently long to cause a delay of the statetransition.

An Overview of Molecular Computing Approaches (Part I)

Abstract This article reviews recent developments in the area of molecular-scale computing. It describes the construction and operating characteristics of molecular wires, rectifiers, switches, and transistors. It also discusses the concept of molecular gain. Molecular computing architectures based on crosspoint arrays, randomized nanocells, and cellular automata will be discussed in Part II of this article in the November 2004 issue of EDFA.

COMPUTER SIMULATION OF STRUCTURAL CHANGES IN PHOSPHOLIPID BILAYERS

Using molecular-scale computer simulation, we show that structural changes may take place in phospholipid bilayers in an aqueous solution as we vary the relative concentration of water to phospholipids, the bilayer thickness, the inclination angle of the choline, dipole molecular fragment with respect to the bilayer surface, and the conformation of hydrocarbon chains of phospholipid in the hydrophobic volume of the bilayer. It is shown that in the hydrophobic volume of the bilayer, an interpenetration of the hydrocarbon chains located on opposite sides of the phospholipid bilayer takes place.

Switch turns molecular wire signal on and off

By astutely varying the building blocks of molecular wires that transmit light energy, a team of chemists has devised a way to switch the signal on and off at will. Their new molecular optoelectronic gates are a step toward components that could be used to build future molecular-scale computers. Molecular photonic wires that absorb a photon of light at one end of an array of porphyrins, then emit a different photon at the other end, were developed a few years ago by chemistry professor Jonathan S. Lindsey and postdoctoral fellow Richard W. Wagner at Carnegie Mellon University, Pittsburgh (C&EN, Oct. 31,1994, page 5). Now, working with chemistry professor David F. Bocian's group at the University of California, Riverside, they have devised a way to interrupt transmission of the light energy by adding a magnesium porphyrin that can be selectively oxidized [ J. Am. Chem. Soc , 118,3996 (1996)]. If we are ever going to make molecular devices ...

Determination of Excess Gibbs Free Energy from Computer Simulation: Multiple-Parameter Charging Approach

We devise a general procedure for determining the excess Gibbs free energy from molecular-scale computer simulations of binary mixtures. The method is based upon Kirkwood's coupling-parameter interpretation of the chemical potential. We show that, by a suitable choice of integration path, coupling involving any number of parameters can be represented by a single independent parameter. Thus for (rigid-molecule) solutions made nonideal by differences among several potential parameters, the determination of the excess free energy generally requires little more effort than if all the differences reside in one potential parameter. The development here is an extension of the recent revision of the coupling-parameter approach that avoids the need for the pure component free energies in obtaining the excess free energy of the mixture.

Computer simulation of fluid mixtures

Molecular-scale computer simulations can contribute to the development of correlations for properties of fluid mixtures. This point is illustrated here by sample results from three problems: (1) determination of the excess Gibbs free energy for fluid mixtures, (2) determination of inter- and intramolecular structure in fluids of short-chain molecules, and (3) tests of the fundamental hypothesis of group contribution methods for correlating thermodynamic properties.