Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Motivated by experiments in which a polynucleotide is driven through a proteinaceous pore by an electric field, we study the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions. We show that there is a range of polymer lengths in which the system is approximately translationally invariant, and we develop a coarse-grained description of this regime. From this description, general features of the distribution of times for the polymer to pass through the pore may be deduced. We also introduce a more microscopic model. This model provides a physically reasonable scenario in which, as in experiments, the polymer's speed depends sensitively on its chemical composition, and even on its orientation in the channel. Finally, we point out that the experimental distribution of times for the polymer to pass through the pore is much broader than expected from simple estimates, and speculate on why this might be.

Driven Polymer Translocation Through a Narrow Pore

We report an ab initio density functional theory study of the interaction of four nucleobases, cytosine, thymine, adenine, and guanine, with a novel graphene nanopore device for detecting the base sequence of a single-stranded nucleic acid (ssDNA or RNA). The nucleobases were inserted into a pore in a graphene nanoribbon, and the electrical current and conductance spectra were calculated as functions of voltage applied across the nanoribbon. The conductance spectra and charge densities were analyzed in the presence of each nucleobase in the graphene nanopore. The results indicate that due to significant differences in the conductance spectra the proposed device has adequate sensitivity to discriminate between different nucleotides. Moreover, we show that the nucleotide conductance spectrum is affected little by its orientation inside the graphene nanopore. The proposed technique may be extremely useful for real applications in developing ultrafast, low-cost DNA sequencing methods.

http://absimage.aps.org/image/MAR10/MWS_MAR10-2009-001318.pdf

Detection of Nucleic Acids with Graphene Nanopores: Ab Initio Characterization of a Novel Sequencing Device

Herein, we explore the main features and the prospect of plasmonics with two-dimensional semiconductors. Plasmonic modes in each class of van der Waals semiconductors have their own peculiarities, along with potential technological capabilities. Plasmons of transition-metal dichalcogenides share features typical of graphene, due to their honeycomb structure, but with damping processes dominated by intraband rather than interband transitions, unlike graphene. Spin-orbit coupling strongly affects the plasmonic spectrum of buckled honeycomb lattices (silicene and germanene), while the anisotropic lattice of phosphorene determines different propagation of plasmons along the armchair and zigzag directions. Black phosphorus is also a suitable material for ultrafast plasmonics, for which the active plasmonic response can be initiated by photoexcitation with femtosecond pulses. We also review existing applications of plasmonics with two-dimensional materials in the fields of thermoplasmonics, biosensing, and plasma-wave Terahertz detection. Finally, we consider the capabilities of van der Waals heterostructures for innovative low-loss plasmonic devices.

Plasmonics with two-dimensional semiconductors: from basic research to technological applications

We have investigated the electronic response of single crystals of indium selenide by means of angle-resolved photoemission spectroscopy, electron energy loss spectroscopy and density functional theory. The loss spectrum of indium selenide shows the direct free exciton at ~1.3 eV and several other peaks, which do not exhibit dispersion with the momentum. The joint analysis of the experimental band structure and the density of states indicates that spectral features in the loss function are strictly related to single-particle transitions. These excitations cannot be considered as fully coherent plasmons and they are damped even in the optical limit, i.e. for small momenta. The comparison of the calculated symmetry-projected density of states with electron energy loss spectra enables the assignment of the spectral features to transitions between specific electronic states. Furthermore, the effects of ambient gases on the band structure and on the loss function have been probed.

Indium selenide: an insight into electronic band structure and surface excitations.

We propose a potential sensing mechanism for DNA nucleotides using the interband π surface plasmon resonance (SPR) of graphene nanopores. The SPR and field-enhancement properties were investigated using the discrete dipole approximation (DDA) and the finite-difference-time-domain (FDTD) methods, respectively. For graphene nanopores smaller than 10 nm in length, increasing the pore diameter red shifts the SPR peak wavelength, and for larger sheets, the SPR peak wavelength is essentially unchanged by variations in the pore diameter. Presentation of a single nucleotide to the pore significantly changes the SPR properties of the graphene nanopore, and each nucleotide has unique SPR properties. Each nucleotide induces a shift of 2–12 nm in the peak wavelength of each SPR mode, and if all of the modes are considered simultaneously, the type of DNA nucleotide present can be clearly determined. Our results show that the small-size-sensitive interband π plasmon in graphene nanopore is probably applicable as a new ...

Interband π Plasmon of Graphene Nanopores: A Potential Sensing Mechanism for DNA Nucleotides

We propose a new DNA sensing mechanism based on optical properties of graphene oxide (GO) and molybdenum disulphide (MoS2) nanopores. In this method, GO and MoS2 is utilized as quantum dot (QD) nanopore and DNA molecule translocate through the nanopore. A recently-developed hybrid quantum/classical method (HQCM) is employed which uses time-dependent density functional theory and quasi-static finite difference time domain approach. Due to good biocompatibility, stability and excitation wavelength dependent emission behavior of GO and MoS2 we use them as nanopore materials. The absorption and emission peaks wavelengths of GO and MoS2 nanopores are investigated in the presence of DNA nucleobases. The maximum sensitivity of the proposed method to DNA is achieved for the 2-nm GO nanopore. Results show that insertion of DNA nucleobases in the nanopore shifts the wavelength of the emitted light from GO or MoS2 nanopore up to 130 nm. The maximum value of the relative shift between two different nucleobases is achieved by the shift between cytosine (C) and thymine (T) nucleobases, ~111 nm for 2-nm GO nanopore. Results show that the proposed mechanism has a superior capability to be used in future DNA sequencers.

/pdf/a-potential-sensing-mechanism-for-dna-nucleobases-by-optical-3ujhjhckgr.pdf

A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS 2 Nanopores

Taking advantage of a nanopore-based DNA sequencing concept, a variety of recognition approaches have been intensively explored. We have recently presented a potential mechanism for DNA sequencing based on interband π plasmons of graphene nanopores. In this paper, a realistic ab initio analysis of the proposed method based on π and also π+σ plasmons is investigated making use of graphene quantum dots (GQDs) with a nanopore. The plasmonic properties are studied by post processing the density functional theory (DFT) calculations. The first principle study provides an unprecedented fully theoretical description of the proposed structure. The critical features such as passivating atoms, structure relaxation, DNA-graphene interactions, and nucleobase rotations are considered, which result in a more accurate and realistic description of the presented method. Our calculations show a 0.04 to 0.28 eV shift to the energy of the plasmonic modes related to each inserted nucleobase in the nanopore of GQD, which demons...

DNA Nucleobases Sensing by Localized Plasmon Resonances in Graphene Quantum Dots with Nanopore: A First Principle Approach

http://scientiairanica.sharif.edu/article_20419_bac2c3634f39ab0bb9b98122a247e654.pdf

Controlling DNA translocation speed through graphene nanopore via plasmonic fields

http://scientiairanica.sharif.edu/article_4143_289fd8fbb52e203abcc17e9cbe553bb6.pdf

Mostafa Abasifard

Papers

Interband π Plasmon of Graphene Nanopores: A Potential Sensing Mechanism for DNA Nucleotides

A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS 2 Nanopores

DNA Nucleobases Sensing by Localized Plasmon Resonances in Graphene Quantum Dots with Nanopore: A First Principle Approach

Controlling DNA translocation speed through graphene nanopore via plasmonic fields

Petahertz-frequency plasmons in graphene nanopore and their application to nanoparticle sensing