Monte Carlo Computer Simulations Research Articles

Confined Quantum Hard Spheres.

We present computer simulation and theoretical results for a system of N Quantum Hard Spheres (QHS) particles of diameter and mass m at temperature T, confined between parallel hard walls separated by a distance , within the range . Semiclassical Monte Carlo computer simulations were performed adapted to a confined space, considering effects in terms of the density of particles , where V is the accessible volume, the inverse length and the de Broglie’s thermal wavelength , where k and h are the Boltzmann’s and Planck’s constants, respectively. For the case of extreme and maximum confinement, and , respectively, analytical results can be given based on an extension for quantum systems of the Helmholtz free energies for the corresponding classical systems.

Two-dimensional core-softened model with water like properties: solvation of non-polar solute

ABSTRACT Monte Carlo simulations and integral equation theory were used to study the thermodynamics and structure of mixture of particles interacting through the smooth version of Stell–Hemmer interaction and non-polar particles interacting through Lennard–Jones interaction in two dimensions. The theoretical results are tested against the Monte Carlo computer simulations. Very good agreement between the integral equation theory results and exact computer simulations is obtained. We showed that some versions of the integral equation theory completely fail to predict structure of such system at some state points so caution has to be taken when applying them but in comparison with results for pure component results are better. We also checked how position of critical point changes with content of non-polar particles.

Reliability analysis of the optimized carrying door frame based on six-sigma

The door frame is a key component of the track door system. This paper uses the Six-sigma Analysis module in the finite element software ANSYS Workbench to analyze the reliability of the door frame, and regards its geometric dimensions and materials as random variables. Test design, Latin hypercube sampling, and Monte Carlo simulation calculations respectively obtained the reliability values of static strength and static stiffness of the door frame. The reliability values were analyzed to verify the rationality of the design.

An assessment of contamination pickup on ground robotic vehicles for nuclear surveying application

Ground robotic vehicles are often deployed to inspect areas where radioactive floor contamination is a prominent risk. However, the accuracy of detection could be adversely affected by enhanced radiation signal through self-contamination of the robot occurring over the course of the inspection. In this work, it was hypothesised that a six-legged robot could offer advantages over the more conventional ground robotic devices such as wheeled and tracked rovers. To investigate this, experimental contamination testing and computational Monte Carlo simulation techniques (GEANT4) were employed to understand how radioactive contamination pick-up on three different robotic vehicles would affect their detection accuracy. Two robotic vehicles were selected for comparison with the hexapod robot based on their type of locomotion; a wheeled rover and a tracked rover. With the aid of a non-toxic fluorescent tracer dust, the contamination received by the all three vehicles when traversing a contaminated area was initially compared through physical inspection using high definition cameras. The parametric results from these tests where used in the computational study carried out in GEANT4. A cadmium zinc telluride detector was simulated at heights ranging from 10 to 50 cm above each contaminated vehicle, as if it were mounted on a plinth. Assuming a uniform activity of 60 Bq cm−2 on all contaminated surfaces, the results suggested that due to the hexapod’s small ground-contacting surface area and geometry, radiation detection rates using an uncollimated detector are likely to be overestimated by between only 0.07%–0.12%, compared with 3.95%–8.43% and 1.75%–14.53% for the wheeled and tracked robot alternatives, respectively.

Energy Scaling of Compositional Disorder in Ternary Transition‐Metal Dichalcogenide Monolayers

AbstractAlloying semiconductors is often used to tune the material properties desired for device applications. The price for this tunability is the extra disorder caused by alloying. In order to reveal the features of the disorder potential in alloys of atomically thin transition‐metal dichalcogenides (TMDs) such as MoxW1−xSe2, the exciton photoluminescence is measured in a broad temperature range between 10 and 200 K. In contrast to the binary materials MoSe2 and WSe2, the ternary system demonstrates non‐monotonous temperature dependences of the luminescence Stokes shift and of the luminescence linewidth. Such behavior is a strong indication of a disorder potential that creates localized states for excitons and affects the exciton dynamics responsible for the observed non‐monotonous temperature dependences. A comparison between the experimental data and the results obtained by Monte Carlo computer simulations provides information on the energy scale of the disorder potential and also on the shape of the density of localized states created by disorder. Statistical spatial fluctuations in the distribution of the chemically different material constituents are revealed to cause the disorder potential responsible for the observed effects. A deeper understanding of the disorder‐induced effects is vital for prospective TMD alloy‐based devices.

Self-Assembled Structures of Colloidal Dimers and Disks on a Spherical Surface.

We study self-assembly on a spherical surface of a model for a binary mixture of amphiphilic dimers in the presence of guest particles via Monte Carlo (MC) computer simulation. All particles had a hard core, but one monomer of the dimer also interacted with the guest particle by means of a short-range attractive potential. We observed the formation of aggregates of various shapes as a function of the composition of the mixture and of the size of guest particles. Our MC simulations are a further step towards a microscopic understanding of experiments on colloidal aggregation over curved surfaces, such as oil droplets.

Calculation of the Free Energy of Mixing as a Tool for Assessing and Improving Potential Models: The Case of the N,N-Dimethylformamide-Water System.

The Helmholtz free energy, energy, and entropy of mixing of N,N-dimethylformamide (DMF) and water are calculated in the entire composition range by means of Monte Carlo computer simulations and thermodynamic integration using all possible combinations of five DMF and three widely used water models. Our results reveal that the mixing of DMF and water is highly non-ideal. Thus, in their dilute solutions, both molecules induce structural ordering of the major component, as evidenced by the concomitant decrease in the entropy. Among the 15 model combinations considered, only 4 reproduce the well-known full miscibility of DMF and water, 3 of which strongly exaggerate the thermodynamic driving force of the miscibility. Thus, the combination of the CS2 model of DMF and the TIP4P/2005 water model reproduces the properties of the DMF-water mixtures far better than the other combinations tested. Our results also reveal that moving a fractional negative charge from the N atom to the O atom of the DMF molecule, leading to the increase in its dipole moment, improves the miscibility of the model with water. Starting from the CS2 model and optimizing the charge to be moved, we propose a new model of DMF that reproduces very accurately both the Helmholtz free energy of mixing of aqueous DMF solutions in the entire composition range (when used in combination with the TIP4P/2005 water model) and also the internal energy of neat DMF.

Long-Range Supercoiling-Mediated RNA Polymerase Cooperation in Transcription.

It is widely believed that DNA supercoiling plays an important role in the regulation of transcriptional dynamics. Recent studies show that it could affect transcription not only through the buildup and relaxation of torsional strain on DNA strands but also via effective long-range supercoiling-mediated interactions between RNA polymerase (RNAP) molecules. Here, we present a theoretical study that quantitatively analyzes the effect of long-range RNAP cooperation in transcription dynamics. Our minimal chemical-kinetic model assumes that one or two RNAP molecules can simultaneously participate in the transcription, and it takes into account their binding to and dissociation from DNA. It also explicitly accounts for competition between the supercoiling buildup that reduces the RNA elongation speed and gyrase binding that rescues the RNA synthesis. The full analytical solution of the model accompanied by Monte Carlo computer simulations predicts that the system should exhibit transcriptional bursting dynamics, in agreement with experimental observations. The analysis also revealed that when there are two polymerases participating in the elongation rather than one, the transcription process becomes much more efficient since the level of stochastic noise decreases while more RNA transcripts are produced. Our theoretical investigation clarifies molecular aspects of the supercoiling-mediated RNAP cooperativity during transcription.

Enhanced algorithms to ensure the success of rendezvous maneuvers using aerodynamic forces

A common practice in the field of differential lift and drag controlled satellite formation flight is to analytically design maneuver trajectories using linearized relative motion models and the constant density assumption. However, the state-of-the-art algorithms inevitably fail if the initial condition of the final control phase exceeds an orbit and spacecraft-dependent range, the so-called feasibility range. This article presents enhanced maneuver algorithms for the third (and final) control phase which ensure the overall maneuver success independent of the initial conditions. Thereby, all maneuvers which have previously been categorized as infeasible due to algorithm limitations are rendered feasible. An individual algorithm is presented for both possible control options of the final phase, namely differential lift or drag. In addition, a methodology to precisely determine the feasibility range without the need of computational expensive Monte Carlo simulations is presented. This allows fast and precise assessments of possible influences of boundary conditions, such as the orbital inclination or the maneuver altitude, on the feasibility range.

Cluster Morphology of Colloidal Systems With Competing Interactions

Reversible aggregation of purely short-ranged attractive colloidal particles leads to the formation of clusters with a fractal dimension that only depends on the second virial coefficient. The addition of a long-ranged repulsion to the potential modifies the way in which the particles aggregate into clusters and form intermediate range order structures, and have a strong influence on the dynamical and rheological properties of colloidal dispersions. The understanding of the effect of a long-ranged repulsive potential on the aggregation mechanisms is scientifically and technologically important for a large variety of physical, chemical and biological systems, including concentrated protein solutions. In this work, the equilibrium cluster morphology of particles interacting through a short-ranged attraction plus a long-ranged repulsion is extensively studied by means of Monte Carlo computer simulations. Our findings point out that the addition of the repulsion affects the resulting cluster morphology and allows one to have a full control on the compactness or fractal dimension of the aggregates at a given thermodynamic condition. This allows us to manipulate the reversible aggregation process and, therefore, to finely tune the resulting building blocks of materials at large length scales.

Extended Lifetime of Molecules Adsorbed onto Excipients Drives Nucleation in Heterogeneous Crystallization.

Monte Carlo (MC) and molecular dynamics (MD) computer simulations were used to investigate the role of adsorption during seeded and heterogeneous crystallization. The simulations characterized the range of adsorption energies and configurations encountered during adsorption of individual molecules of active pharmaceutical ingredients (APIs), with varying hydrogen-bonding tendencies, onto seed and heterosurfaces. Specifically, the adsorption of acetaminophen (AAP), carbamazepine (CBMZ), fenofibrate (FF), phenylbutazone (PBZ), clozapine (CPB), and risperidone (RIS) was simulated on selected crystallographic facets of their own crystals as examples of seeded crystallizations and on lactose or microcrystalline cellulose (MCC) substrates as heterosurfaces. The MC screening provided adsorption enthalpies in the range of −59 to −155 kJ mol–1 for these APIs on lactose, generally increasing as the molar mass of the API increased. The corresponding values predicted for adsorption of each API onto its own crystal were in the range of −92 to −201 kJ mol–1. More detailed MD simulations performed in methanol showed adsorption free energies for RIS on MCC in the range of −37 to −50 kJ mol–1 with strong molecule–surface complexation lifetime of tens of nanoseconds on the (010) face of MCC. This extended lifetime is a key feature in understanding the mechanism of heterogeneous crystallization. A well-formed nucleus is generated on the surface starting with a single adsorbed molecule. Individual or small clusters add to the adsorbed species. This addition is facilitated by the extended lifetime of the adsorbed molecule, which is several orders of magnitude greater than the time required for additional molecules to assemble and grow into a stable nucleus attached to the heterosurface.

ViewSq, a Visual Molecular Dynamics (VMD) module for calculating, analyzing, and visualizing X-ray and neutron structure factors from atomistic simulations

viewSq, a Visual Molecular Dynamics (VMD) module for calculating, analyzing, and visualizing X-ray and neutron structure factors from atomistic simulations

Improvement of the passive efficiency calibration of the segmented gamma scanner

Abstract The Segmented Gamma Scanner(SGS) technology is specially used for type identification and activity quantitative analysis of radioactive material in sealed containers, which mainly divided into the transmission measurement and the emission measurement. In actual measurement process, it cannot meet the need for rapid analysis because the efficiency calibration time takes up more than 60% of the whole detect time in the data analysis. Whereas most previous research have focused on theory or specific applications, this research groups aim to different aspects of the SGS technique and direct it at an audience with interests in the need for rapid analysis. The Monte Carlo simulation calculation models were established by the passive efficiency calibration method, and then the detection efficiency database was carried out based on the experimental verification. Lots of work was used to analysis the influence of crosstalk between layers and interpolation step. Furthermore, the database was implanted into the control and analysis system to complete the measurement experiments. The results show the measuring time of single waste drums is about 30 min, and the average relative deviation is less than 10%, so the problem that the time taken to calibrate the detection efficiency is too long has been solved effectively. The efficiency in the use of SGS technology has been increased.

A combination of modeling and experimental approaches to investigate the novel nicotinohydrazone Schiff base and its complexes with Zn(II) and ZrO(II) as inhibitors for mild-steel corrosion in molar HCl

Two novel metal-complexes of 5-sodium sulfonate-2-hydroxybenzylidene)nicotinohydrazone (H2LCs) with Zn2+ and ZrO2+ ions were synthesized and characterized (ZnLCs and ZrOLCs), respectively. Condensation of nicotinohydrazide with salicylaldehyde-5-sodium sulfonate salt afforded H2LCs. Inhibition effectiveness of H2LCs and its complexes with Zn(II) and Zr(II) for M-steel in a 1.0 M HCl solution was examined by electrochemical (EOCP vs. time, impedance spectroscopy (EIS) and potentiodynamic polarization (PDP)) methods. In comparison with H2LCs, ZnLCs and ZrOLCs display enhanced protection capacities. Particularly, the ZrOLCs compound displays higher protection power, and the efficacy is up to 97.4% at 5 × 10−4 mol L − 1 at 303 K. PDP studies exhibited that the as-prepared additives act as inhibitors of the mixed-kind, and adsorbed on M-steel surface via chemisorption following the Langmuir isotherm model. The surface morphology inspections (FE-SEM/EDX, and FT-IR) display that the M-steel interface was inhibited by titled compounds. To get a preferable comprehension of the adsorption of compound species on the steel interface, a detailed modeling investigation was accomplished using Monte Carlo (MC) simulation and DFT calculations. QSAR model also investigated via multiple linear regression method. The current report delivers very significant outcomes in designing and fabricating sustainable inhibitors with high protection capacity.

Generalized equation of state for fluids: From molecular liquids to colloidal dispersions

In this work, a new parameterization for the Statistical Association Fluid Theory for potentials of Variable Range (SAFT-VR) is coupled to the discrete potential theory to represent the thermodynamic properties of several fluids, ranging from molecular liquids to colloidal-like dispersions. In this way, this version of the SAFT-VR approach can be straightforwardly applied to any kind of either simple or complex fluid. In particular, two interaction potentials, namely, the Lennard-Jones and the hard-core attractive Yukawa potentials, are discretized to study the vapor-liquid equilibrium properties of both molecular and complex liquids, respectively. Our results are assessed with Monte Carlo computer simulations and available and accurate theoretical results based on the self-consistent Ornstein-Zernike approximation.

Ab initio Monte Carlo simulations of structure and electronic properties of copper-tin clusters

This study investigated the structural and electronic properties of (CuSn)n clusters with n = 1–6 using ab initio Monte Carlo Simulations and density functional theory calculations. Monte Carlo simulations were performed using a large number of initial structures of neutral, cationic, and anionic copper-tin clusters. Their stable structures were determined using B3LYP/def2-TZVP model chemistry and the most stable structures of neutral, cationic, and anionic copper-tin clusters were established. The values of bond angles and bond lengths, atomization energies, second differences of the energies, HOMO-LUMO gaps, Mulliken population analysis, adiabatic ionization potentials, and adiabatic electronic affinities were determined as a function of n.

DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search.

Protein searching and binding to specific sites on DNA is a fundamentally important process that marks the beginning of all major cellular transformations. While the dynamics of protein-DNA interactions in in vitro settings is well investigated, the situation is much more complex for in vivo conditions because the DNA molecules in live cells are packed into chromosomal structures where they are undergoing strong dynamic and conformational fluctuations. In this work, we present a theoretical investigation on the role of DNA looping and DNA conformational fluctuations in the protein target search. It is based on a discrete-state stochastic analysis that allows for explicit calculations of dynamic properties, which is also supplemented by Monte Carlo computer simulations. It is found that for stronger nonspecific interactions between DNA and proteins the search occurs faster on the DNA looped conformation in comparison with the unlooped conformation, and the fastest search is observed when the loop is formed near the target site. It is also shown that DNA fluctuations between the looped and unlooped conformations influence the search dynamics, and this depends on the magnitude of conformational transition rates and on which conformation is more energetically stable. Physical-chemical arguments explaining these observations are presented. Our theoretical study suggests that the geometry and conformational changes in DNA are additional factors that might efficiently control the gene regulation processes.

Adaptive Optics pre-compensated laser uplink to LEO and GEO.

We present the results from a Monte Carlo computer simulation of adaptive optics (AO) pre-compensated laser uplink propagation through the Earth's atmospheric turbulence from the ground to orbiting satellites. The simulation includes the so-called point-ahead angle and tests several potential AO mitigation modes such as tip/tilt or full AO from the downlink beam, and a laser guide star at the point ahead angle. The performance of these modes, as measured by metrics relevant for free-space optical communication, are compared with no correction and perfect correction. The aim of the study is to investigate fundamental limitations of free-space optical communications with AO pre-compensation and a point-ahead angle, therefore the results represent an upper bound of AO corrected performance, demonstrating the potential of pre-compensation technology. Performance is assessed with varying launch aperture size, wavelength, launch geometry, ground layer turbulence strength (i.e. day/night), elevation angle and satellite orbit (Low-Earth and Geostationary). By exploring this large parameter space we are able examine trends on performance with the aim of informing the design of future optical ground stations and demonstrating and quantifying the potential upper bounds of adaptive optics performance in free-space optical communications.

Throughput Maximization Based on Optimized Frame-Aggregation Levels for IEEE 802.11 WLANs

To improve the throughput via frame aggregation (FA), the number of aggregate medium access control service data unit (A-MSDU) and protocol data unit (A-MPDU) subframes must be set appropriately under the IEEE 802.11 standards. In this letter, we construct an optimization problem that maximizes theoretical throughput considering bit error in A-MSDU under the IEEE 802.11ac standard based on the detailed structure of FA. Further, we propose a scheme to determine the optimal subframe sets through an exhaustive search for not only A-MPDU but also A-MSDU. The proposed scheme is validated through numerical calculations and Monte Carlo computer simulations. Although the computational complexity of the proposed scheme is larger than that of the conventional scheme, it leads to a significant throughput improvement.

Free energy and segregation dynamics of two channel-confined polymers of different lengths.

Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere polymers under confinement in a cylindrical channel. We focus on the effects of using polymers of different lengths. We measure the variation of the conformational free energy, F, with the center-of-mass separation distance, λ. The simulations reveal four different separation regimes, characterized by different scaling properties of the free energy with respect to the polymer lengths and the channel diameter, D. We propose a regime map in which the state of the system is determined by the values of the quantities N_{2}/N_{1} and λ/(N_{1}+N_{2})D^{-β}, where N_{1} and N_{2} are the polymer lengths, and where β≈0.64. The observed scaling behavior of F(λ) in each regime is in reasonable agreement with predictions using a simple theoretical model. In addition, we use MC dynamics simulations to study the segregation dynamics of initially overlapping polymers by measurement of the incremental mean first-passage time with respect to λ. For systems characterized by a wide range of λ in which a short polymer is nested within a longer one, the segregation dynamics are close to that expected for two noninteracting one-dimensional random walkers undergoing unbiased diffusion. When the free-energy gradient is large, segregation is rapid and characterized by out-of-equilibrium effects.