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

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

Since the discovery of mechanically exfoliated graphene in 2004, research on ultrathin two-dimensional (2D) nanomaterials has grown exponentially in the fields of condensed matter physics, material science, chemistry, and nanotechnology. Highlighting their compelling physical, chemical, electronic, and optical properties, as well as their various potential applications, in this Review, we summarize the state-of-art progress on the ultrathin 2D nanomaterials with a particular emphasis on their recent advances. First, we introduce the unique advances on ultrathin 2D nanomaterials, followed by the description of their composition and crystal structures. The assortments of their synthetic methods are then summarized, including insights on their advantages and limitations, alongside some recommendations on suitable characterization techniques. We also discuss in detail the utilization of these ultrathin 2D nanomaterials for wide ranges of potential applications among the electronics/optoelectronics, electrocat...

Recent Advances in Ultrathin Two-Dimensional Nanomaterials

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Heteroatom doped carbon materials represent one of the most prominent families of materials that are used in energy related applications, such as fuel cells, batteries, hydrogen storage or supercapacitors. While doping carbons with nitrogen atoms has experienced great progress throughout the past decades and yielded promising material concepts, also other doping candidates have gained the researchers' interest in the last few years. Boron is already relatively widely studied, and as its electronic situation is contrary to the one of nitrogen, codoping carbons with both heteroatoms can probably create synergistic effects. Sulphur and phosphorus have just recently entered the world of carbon synthesis, but already the first studies published prove their potential, especially as electrocatalysts in the cathodic compartment of fuel cells. Due to their size and their electronegativity being lower than those of carbon, structural distortions and changes of the charge densities are induced in the carbon materials. This article is to give a state of the art update on the most recent developments concerning the advanced heteroatom doping of carbon that goes beyond nitrogen. Doped carbon materials and their applications in energy devices are discussed with respect to their boron-, sulphur- and phosphorus-doping.

/pdf/doping-carbons-beyond-nitrogen-an-overview-of-advanced-2volpel94i.pdf

Doping carbons beyond nitrogen: an overview of advanced heteroatom doped carbons with boron, sulphur and phosphorus for energy applications

Herein, we investigate sulfur substitutional defects in single-walled carbon nanotubes (SWCNTs) and graphene by using first-principles calculations. The estimated formation energies for the (3,3), (5,5), and (10,0) SWCNTs and graphene lie between 0.9 and 3.8 eV, at sulfur concentrations of 1.7-4 atom %. Thus, from a thermodynamic standpoint, sulfur doping is not difficult. Indeed, these values can be compared with that of 0.7 eV obtained for a nitrogen-doped (5,5) SWCNT. We suggest that it may be possible to introduce sulfur into the SWCNT framework by employing sulfur-containing heterocycles. Our simulations indicate that sulfur doping can modify the electronic structure of the SWCNTs and graphene, depending on the sulfur content. In the case of graphene, sulfur doping can induce different effects: the doped sheet can be a small-band-gap semiconductor, or it can have better metallic properties than the pristine sheet. Thus, S-doped graphene may be a smart choice for constructing nanoelectronic devices, since it is possible to modulate the electronic properties of the sheet by adjusting the amount of sulfur introduced. Different synthetic routes to produce sulfur-doped graphene are discussed.

Is It Possible to Dope Single-Walled Carbon Nanotubes and Graphene with Sulfur?

Herein, we investigate the structural, electronic and mechanical properties of zigzag graphene nanoribbons upon the presence of stress applying Density Functional Theory within the GGA-PBE approximation. The uniaxial stress is applied along the periodic direction, allowing a unitary deformation in the range of +/- 0.02%. The mechanical properties show a linear-response within that range while the non-linear dependence is found for higher strain. The most relevant results indicate that Young's modulus is considerable higher than those determined for graphene and carbon nanotubes. The geometrical reconstruction of the C-C bonds at the edges hardness the nanostructure. Electronic structure features are not sensitive to strain in this linear elastic regime, being an additional promise for the using of carbon nanostructures in nano-electronic devices in the near future.

Mechanical properties of Graphene Nanoribbons

Herein, we investigate the structural, electronic and mechanical properties of zigzag graphene nanoribbons in the presence of stress by applying density functional theory within the GGA-PBE (generalized gradient approximation-Perdew–Burke–Ernzerhof) approximation. The uniaxial stress is applied along the periodic direction, allowing a unitary deformation in the range of ± 0.02%. The mechanical properties show a linear response within that range while a nonlinear dependence is found for higher strain. The most relevant results indicate that Young's modulus is considerable higher than those determined for graphene and carbon nanotubes. The geometrical reconstruction of the C–C bonds at the edges hardens the nanostructure. The features of the electronic structure are not sensitive to strain in this linear elastic regime, suggesting the potential for using carbon nanostructures in nano-electronic devices in the near future.

https://iopscience.iop.org/article/10.1088/0953-8984/21/28/285304/pdf

Mechanical properties of graphene nanoribbons.

We present an ab initio—DFT/GGA—study on the structural and electronic distortions of modified graphene by the creation of vacancies, the inclusion of boron atoms, and the coexistence of both, by means of total energy and band structure calculations In the case of coexistence of boron atoms and vacancy, the modified graphene presents spin polarization only when B atoms locate far from vacancy Thus, when a boron atom fills single and divacancies, it suppresses the spin polarization of the charge density In particular, when B atoms fill a divacancy, a new type of rearrangement occurs, where a stable BC4 unit is formed inducing important out-of-plane distortions to graphene All these findings suggest that new chemical modifications to graphene and new types of vacancies can be used to modify its electronic properties

http://www.diva-portal.org/smash/get/diva2:374223/FULLTEXT01

Electronic and Structural Distortions in Graphene Induced by Carbon Vacancies and Boron Doping

We present an ab initio study on the structural and electronic distortions of modified graphene by creation of vacancies, inclusion of boron atoms, and the coexistence of both, by means of thermodynamics and band structure calculations. In the case of coexistence of boron atoms and vacancy, the modified graphene presents spin polarization only when B atoms locate far from vacancy. Thus, when a boron atom fills single- and di-vacancies, it suppresses the spin polarization of the charge density. In particular when B atoms fill a di-vacancy a new type of rearrangement occurs, where a stable BC4 unit is formed inducing important out of plane distortions to graphene. All these findings suggest that new chemical modifications to graphene and new type of vacancies can be used for interesting applications such as sensor and chemical labeling.

Alvaro W. Mombrú

Papers

Is It Possible to Dope Single-Walled Carbon Nanotubes and Graphene with Sulfur?

Mechanical properties of Graphene Nanoribbons

Mechanical properties of graphene nanoribbons.

Electronic and Structural Distortions in Graphene Induced by Carbon Vacancies and Boron Doping

Electronic and structural distortions in graphene induced by carbon vacancies and boron doping