Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250 K, 300 K and 350 K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between B_I and B_II forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.     

Model development in scientific discovery learning with a computer-based physics task

Based on theories of scientific discovery learning (SDL) and conceptual change, this study explores students' preconceptions in the domain of torques in physics and the development of these conceptions while learning with a computer-based SDL task. As a framework we used a three-space theory of SDL and focused on model space, which is supposed to contain the current conceptualization/model of the learning domain, and on its change through hypothesis testing and experimenting. Three questions were addressed: (1) What are students' preconceptions of torques before learning about this domain? To do this a multiple-choice test for assessing students' models of torques was developed and given to secondary school students (N = 47) who learned about torques using computer simulations. (2) How do students' models of torques develop during SDL? Working with simulations led to replacement of some misconceptions with physically correct conceptions. (3) Are there differential patterns of model development and if so, how do they relate to students’ use of the simulations? By analyzing individual differences in model development, we found that an intensive use of the simulations was associated with the acquisition of correct conceptions. Thus, the three-space theory provided a useful framework for understanding conceptual change in SDL.     

Self-swarming robots that exploit hydrodynamical interaction

Although numerous swarm robotic systems have already been developed, they have exhibited limited adaptability. This was partly because the previous researchers designed the control schemes on the basis of informational interaction, without considering the physical effects of the environment. To tackle this problem, we employ an unconventional approach: we design a control scheme for swarm robots based on their physical interaction in a hydrodynamic field, inspired by biological swarming. Through simulations using a smoothed particle hydrodynamics method, we show that the proposed control scheme allows agents to form an ordered swarm in response to their environment.     

RHEED intensities from two-dimensional heteroepitaxial nanoscale systems

A practical computing algorithm has been developed for calculating the reflection high-energy electron diffraction (RHEED) from the molecular beam epitaxy growing surface. The calculations are based on the use of the dynamical diffraction theory in which the electrons are taken to be diffracted by a potential, which is periodic in the dimension perpendicular to the surface. The computer program presented in this paper enables calculations for three basic types of diffuse potential for crystalline heteroepitaxial structures, including the possible existence of various diffuse scattering models through the layer parallel to the surface.     

Plasmonic and photonic scattering and near fields of nanoparticles

We theoretically compare the scattering and near field of nanoparticles from different types of materials, each characterized by specific optical properties that determine the interaction with light: metals with their free charge carriers giving rise to plasmon resonances, dielectrics showing zero absorption in wide wavelength ranges, and semiconductors combining the two beforehand mentioned properties plus a band gap. Our simulations are based on Mie theory and on full 3D calculations of Maxwell’s equations with the finite element method. Scattering and absorption cross sections, their division into the different order electric and magnetic modes, electromagnetic near field distributions around the nanoparticles at various wavelengths as well as angular distributions of the scattered light were investigated. The combined information from these calculations will give guidelines for choosing adequate nanoparticles when aiming at certain scattering properties. With a special focus on the integration into thin film solar cells, we will evaluate our results.     

Effects of seismic and aerodynamic load interaction on structural dynamic response of multi-megawatt utility scale horizontal axis wind turbines

Horizontal axis wind turbines can experience significant time varying aerodynamic loads that has the potential to cause adverse effects on structural, mechanical, and power production. The progress in the wind industry has caused the construction of wind farms in areas prone to high seismic activity. With the advances in computational tools, a more realistic representation of the behavior of wind turbines should be performed. One of the simulation platforms was developed using the 5 MW NREL utility scale reference turbine model. The performed simulations will be used to evaluate the effects of aerodynamic and seismic load coupling on the power generation and structural dynamics behavior of this structure. Different turbine operational scenarios such as (i) normal operational condition with no earthquake, (ii) idling condition with the presence of seismic loads, (iii) normal operational condition with earthquake, and (iv) earthquake-induced emergency shutdown will be simulated with various loading conditions to show the differences in generated power and dynamic response. The results of this paper provide formulations for calculating generated power and design deriving parameters by considering different intensity measures. Moreover, the effects of aerodynamic damping and pitch control system are presented to shows reduction in the resulting design demand loads.     

Evaluation of log‐of‐power extremum seeking control for wind turbines using large eddy simulations

The extremum seeking control (ESC) algorithm has been proposed to determine operating parameters that maximize power production below rated wind speeds (region II). This is usually done by measuring the turbine's power signal to determine optimal values for parameters of the control law or actuator settings. This paper shows that the standard ESC with power feedback is quite sensitive to variations in mean wind speed, with long convergence time at low wind speeds and aggressive transient response, possibly unstable, at high wind speeds. The paper also evaluates the performance, as measured by the dynamic and steady state response, of the ESC with feedback of the logarithm of the power signal (LP‐ESC). Large eddy simulations (LES) demonstrate that the LP‐ESC, calibrated at a given wind speed, exhibits consistent robust performance at all wind speeds in a typical region II. The LP‐ESC is able to achieve the optimal set‐point within a prescribed settling time, despite variations in the mean wind speed, turbulence, and shear. The LES have been conducted using realistic wind input profiles with shear and turbulence. The ESC and LP‐ESC are implemented in the LES without assuming the availability of analytical gradients.     

Practical benefits for the separation process of drying that can be realized from novel multiscale modeling procedures that utilize the scientific information and results obtained from molecular dynamics modeling and simulation studies

Novel multiscale modeling procedures are constructed and presented that use the scientific information and results determined from microscopic molecular dynamics (MD) modeling and simulation studies to calculate local effective values for the parameters that characterize the heat and mass transfer mechanisms of dynamic macroscopic continuum models (Euler physics of continua) that are used in practice to describe and predict the dynamic behavior of large scale in time and space (e.g., industrial scale), separation (e.g., drying; adsorption), and chemical and biochemical reaction engineering (e.g., chemical catalysis; biocatalysis; immobilized cell bioreactor systems) processes involving porous media whose pore structure is formed either by a solid rigid matter or by a solid soft matter. Furthermore, the results determined from MD modeling and simulation studies with regard to the energies of interaction between the molecules of the different species of the porous media during the time evolution (time varying) of the drying process can be used to design a time optimally controlled heat input system that could appropriately and accurately supply at any time during drying the amount of heat necessary to provide a desired drying rate with respect to both free and bound water and to satisfy the constraints that safeguard the quality properties of the product.     

Hydrodynamic behaviour of a new permeable pavement material under high rainfall conditions

Permeable pavements are among the most effective alternative solutions for sustainable stormwater management. They decrease impervious surfaces in urban areas, reduce the risk of flooding under high rainfall conditions and protect the natural environment against stormwater pollution. In a view to ensuring sustainable stormwater management, a new eco-material has been designed for producing permeable pavements. This material is a mixture of construction wastes (crushed concrete) and organic matter (compost). The crushed concrete is the structural support and the compost is used for retention and the biological treatment of stormwater pollution. The purpose of the research work presented in this paper was to evaluate the hydrodynamic behaviour of a new permeable pavement material under high rainfall conditions. The experimental approach adopted for this research study is a temporal moment analysis. Therefore, for the experimental study, we simulated high rainfall with a return period of 10 years (Torreilles in 2001, France). The rainfall data were provided by Meteo France. The rainfall was maintained at an intensity of 126 mm/h, corresponding to a flow rate of 16 l/h at laboratory apparatus scale. Then, the flow rate was increased three times, to 25 l/h, 50 l/h and finally 100 l/h to subject the material to extreme conditions.