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

In last years, low-dimensional and high-dimensional chaotic systems have been implemented in cryptography. The efficiency and performance of these nonlinear systems play an important role in limited hardware implementations. In this context, low-dimensional chaotic systems are more attractive than high-dimensional chaotic systems to produce the pseudorandom key stream used for encryption purposes. Although low-dimensional chaotic maps present some security disadvantages when they are used in cryptography, they are highly attractive due its simple structure, discrete nature, less arithmetic operations, high output processing, and relatively easy to implement in a digital system. In this paper, we proposed both a pseudorandomly enhanced logistic map (PELM) and its application in a novel pseudorandom number generator (PRNG) algorithm, which produces pseudorandom stream with excellent statistical properties. The proposed PELM is compared with logistic map by using histograms and Lyapunov exponents to show its higher benefits in pseudorandom number generator. In contrast to recent schemes in the literature, we present a comprehensive security analysis over the proposed pseudorandom number generator based on pseudorandomly enhanced logistic map (PRNG–PELM) from a cryptographic point of view to show its potential use in secure communications. In addition, the randomness of the PRNG–PELM is verified with the most complete random test suit of National Institute of Standards and Technology (NIST 800-22) and with TestU01. Based on security results, few arithmetic operations required, and high output rate, the proposed PRNG–PELM scheme can be implemented in secure encryption applications, even in embedded systems with limited hardware resources.

A novel pseudorandom number generator based on pseudorandomly enhanced logistic map

A color image encryption with heterogeneous bit-permutation and correlated chaos

Atomically thin two-dimensional (2D) materials face significant energy barriers for synthesis and processing into functional metastable phases such as Janus structures. Here, the controllable implantation of hyperthermal species from pulsed laser deposition (PLD) plasmas is introduced as a top-down method to compositionally engineer 2D monolayers. The kinetic energies of Se clusters impinging on suspended monolayer WS2 crystals were controlled in the <10 eV/atom range with in situ plasma diagnostics to determine the thresholds for selective top layer replacement of sulfur by selenium for the formation of high quality WSSe Janus monolayers at low (300 °C) temperatures and bottom layer replacement for complete conversion to WSe2. Atomic-resolution electron microscopy and spectroscopy in tilted geometry confirm the WSSe Janus monolayer. Molecular dynamics simulations reveal that Se clusters implant to form disordered metastable alloy regions, which then recrystallize to form highly ordered structures, demonstrating low-energy implantation by PLD for the synthesis of 2D Janus layers and alloys of variable composition.

Low Energy Implantation into Transition-Metal Dichalcogenide Monolayers to Form Janus Structures

In order to overcome the disadvantages of logistic map in designing chaos-based cipher, the piecewise logistic map (PLM) is presented. Some properties related to cryptography of the PLM, such as ergodicity, Lyapunov exponent, and bifurcation, are analyzed and compared with the logistic map. From the view of cryptography, the PLM owns better properties than the logistic map. Then, a novel pseudorandom number generator (PRNG) based on the PLM is proposed. Since the cryptographic properties of the PLM are enhanced, the presented PRNG achieves a trade-off between efficiency and security. Both performance analysis and simulation test confirm that our scheme is simple, secure, and efficient, with high potential to be adopted as a stream cipher for secure communication.

A pseudorandom number generator based on piecewise logistic map

Pseudo random number generator based on quantum chaotic map

Validation of inter-atomic potential for WS2 and WSe2 crystals through assessment of thermal transport properties

Predicting the mechanical and thermal properties of quasi-two-dimensional (2D) transition metal dichalcogenides (TMDs) is an essential task necessary for their implementation in device applications. Although rigorous density-functional-theory--based calculations are able to predict mechanical and electronic properties, mostly they are limited to zero temperature. Classical molecular dynamics facilitates the investigation of temperature-dependent properties, but its performance highly depends on the potential used for defining interactions between the atoms. In this study, we calculated temperature-dependent phonon properties of single-layer TMDs, namely, ${\mathrm{MoS}}_{2}$, ${\mathrm{MoSe}}_{2}$, ${\mathrm{WS}}_{2}$, and ${\mathrm{WSe}}_{2}$, by utilizing Stillinger-Weber--type potentials with optimized sets of parameters with respect to the first-principles results. The phonon lifetimes and contribution of each phonon mode in thermal conductivities in these monolayer crystals are systematically investigated by means of the spectral-energy-density method based on molecular dynamics simulations. The obtained results from this approach are in good agreement with previously available results from the Green-Kubo method. Moreover, detailed analysis of lattice thermal conductivity, including temperature-dependent mode decomposition through the entire Brillouin zone, shed more light on the thermal properties of these 2D crystals. The LA and TA acoustic branches contribute most to the lattice thermal conductivity, while ZA mode contribution is less because of the quadratic dispersion around the Brillouin zone center, particularly in ${\mathrm{MoSe}}_{2}$ due to the phonon anharmonicity, evident from the redshift, especially in optical modes, by increasing temperature. For all the considered 2D crystals, the phonon lifetime values are compelled by transition metal atoms, whereas the group velocity spectrum is dictated by chalcogen atoms. Overall, the lattice thermal conductivity is linearly proportional with inverse temperature.

https://link.aps.org/accepted/10.1103/PhysRevB.100.035402

Temperature-dependent phonon spectrum of transition metal dichalcogenides calculated from the spectral energy density: Lattice thermal conductivity as an application

Multifractal properties of denaturation process based on Peyrard–Bishop model

The theory of DNA dynamics is exceedingly complex and not easily explained. In the past two decades, by adapting methods of statistical physics, the dynamics of DNA in contact with a thermal bath is widely studied. In this paper, the thermal denaturation of DNA in the framework of the Peyrard-Bishop-Dauxois (PBD) model through the Renyi dimension is investigated. As a result, the Renyi dimension spectrum of the melting transition process reveals the multifractal nature of the dynamics of the Peyrard-Bishop-Dauxois model. Also, it can be concluded that the Renyi dimension (D(q)) at negative values of q is the characteristic signature of pre-melting and thermal denaturation of DNA. Furthermore, this approach is in excellent agreement with previous experimental studies.

Arash Mobaraki

Papers

Pseudo random number generator based on quantum chaotic map

Validation of inter-atomic potential for WS2 and WSe2 crystals through assessment of thermal transport properties

Temperature-dependent phonon spectrum of transition metal dichalcogenides calculated from the spectral energy density: Lattice thermal conductivity as an application

Multifractal properties of denaturation process based on Peyrard–Bishop model

Multifractal analysis of thermal denaturation based on the Peyrard-Bishop-Dauxois model.