Computer simulation of protein—carbohydrate complexes: application to arabinose-binding protein and pea lectin

The CCEM method (Contact Criteria and Energy Minimisation) has been developed and applied to study protein-carbohydrate interactions. The method uses available X-ray data even on the native protein at low resolution (above 2.4 Å) to generate realistic models of a variety of proteins with various ligands.The two examples discussed in this paper are arabinose-binding protein (ABP) and pea lectin. The X-ray crystal structure data reported on ABP-β-l-arabinose complex at 2.8, 2.4 and 1.7 Å resolution differ drastically in predicting the nature of the interactions between the protein and ligand. It is shown that, using the data at 2.4 Å resolution, the CCEM method generates complexes which are as good as the higher (1.7 Å) resolution data. The CCEM method predicts some of the important hydrogen bonds between the ligand and the protein which are missing in the interpretation of the X-ray data at 2.4 Å resolution. The theoretically predicted hydrogen bonds are in good agreement with those reported at 1.7 Å resolution. Pea lectin has been solved only in the native form at 3 Å resolution. Application of the CCEM method also enables us to generate complexes of pea lectin with methyl-α-d-glucopyranoside and methyl-2,3-dimethyl-α-d-glucopyranoside which explain well the available experimental data in solution.

Sliding Modes for the Simulation of Mechanical and Electrical Systems Defined by Differential-Algebraic Equations

We offer a technique, motivated by feedback control and specifically sliding mode control, for the simulation of differential-algebraic equations (DAEs) that describe common engineering systems such as constrained multibody mechanical structures and electric networks. Our algorithm exploits the basic results from sliding mode control theory to establish a simulation environment that then requires only the most primitive of numerical solvers. We circumvent the most important requisite for the conventionalsimulation of DAEs: the calculation of a set of consistent initial conditions. Our algorithm, which relies on the enforcement and occurrence of sliding mode, will ensure that the algebraic equation is satisfied by the dynamic system even for inconsistent initial conditions and for all time thereafter. [DOI:10.1115/1.4001904]

Monte carlo simulation for molecular gas dynamics

The dynamics of low-density flows is governed by the Boltzmann equation of the kinetic theory of gases. This is a nonlinear integro-differential equation and, in general, numerical methods must be used to obtain its solution. The present paper, after a brief review of Direct Simulation Monte Carlo (DSMC) methods due to Bird, and Belotserkovskii and Yanitskii, studies the details of theDSMC method of Deshpande for mono as well as multicomponent gases. The present method is a statistical particle-in-cell method and is based upon the Kac-Prigogine master equation which reduces to the Boltzmann equation under the hypothesis of molecular chaos. The proposed Markoff model simulating the collisions uses a Poisson distribution for the number of collisions allowed in cells into which the physical space is divided. The model is then extended to a binary mixture of gases and it is shown that it is necessary to perform the collisions in a certain sequence to obtain unbiased simulation.

Optimal reservoir operation for irrigation of multiple crops using genetic algorithms

This paper presents a genetic algorithm (GA) model for obtaining an optimal operating policy and optimal crop water allocations from an irrigation reservoir. The objective is to maximize the sum of the relative yields from all crops in the irrigated area. The model takes into account reservoir inflow, rainfall on the irrigated area, intraseasonal competition for water among multiple crops, the soil moisture dynamics in each cropped area, the heterogeneous nature of soils. and crop response to the level of irrigation applied. The model is applied to the Malaprabha single-purpose irrigation reservoir in Karnataka State, India. The optimal operating policy obtained using the GA is similar to that obtained by linear programming. This model can be used for optimal utilization of the available water resources of any reservoir system to obtain maximum benefits.

Study Of The Hvdc-Torsional Interactions Through Digital Dynamic Simulation

This paper presents the detailed dynamic digital simulation for the study of phenomenon of torsional interaction between HVDC-Turbine generator shaft, dynamics using the novel converter model presented in [ 1 ] The system model includes detailed representation of the synchronous generator and the shaft dynamics, the ac and dc network transients. The results of a case study indicate the various factors that influence the torsional interaction.

Numerical simulation of solidification of liquid aluminum alloy flowing on cooling slope

Preparation of semisolid slurry using a cooling slope is increasingly becoming popular, primarily because of the simplicity in design and ease control of the process. In this process, liquid alloy is poured down an inclined surface which is cooled from underneath. The cooling enables partial solidification and the incline provides the necessary shear for producing semisolid slurry. However, the final microstructure of the ingot depends on several process parameters such as cooling rate, incline angle of the cooling slope, length of the slope and initial melt superheat. In this work, a CFD model using volume of fluid (VOF) method for simulating flow along the cooling slope was presented. Equations for conservation of mass, momentum, energy and species were solved to predict hydrodynamic and thermal behavior, in addition to predicting solid fraction distribution and macrosegregation. Solidification was modeled using an enthalpy approach and a volume averaged technique for the different phases. The mushy region was modeled as a multi-layered porous medium consisting of fixed columnar dendrites and mobile equiaxed/fragmented grains. The alloy chosen for the study was aluminum alloy A356, for which adequate experimental data were available in the literature. The effects of two key process parameters, namely the slope angle and the pouring temperature, on temperature distribution, velocity distribution and macrosegregation were also studied.

On the holographic simulation of non-circular zone plates

New methods involving the manipulation of fundamental wavefronts (e.g., plane and spherical) with simple optical components such as pinholes and spherical lenses have been developed for the fabrication of elliptic, hyperbolic and conical holographic zone plates. Also parabolic zone plates by holographic techniques have been obtained for the first time. The performance behaviour of these zone plates has been studied. Further a phenomenological explanation is offered for the observed improved fringe contrast obtained with a spherical reference wave.

Large Eddy Simulation

Large eddy simulation (LES) is an emerging technique for obtaining an approximation to turbulent flow fields It is an improvement over the widely prevalent practice of obtaining means of turbulent flows when the flow has large scale, low frequency, unsteadiness An introduction to the method, its general formulation, and the more common modelling for flows without reaction, is discussed Some attempts at extension to flows with combustion have been made Examples from present work for flows with and without combustion are given The final example of the LES of the combustor of a helicopter engine illustrates the state-of-the-art in application of the technique

Analytical and simulation studies of a multiprocessor system for high-speed numerical computations

This paper describes the architecture of a multiprocessor system which we call the Broadcast Cube System (BCS) for solving important computation intensive problems such as systems of linear algebraic equations and Partial Differential Equations (PDEs), and highlights its features. Further, this paper presents an analytical performance study of the BCS, and it describes the main details of the design and implementation of the simulator for the BCS.

Structure of the Indian southwesterly pre-monsoon and monsoon boundary layers: Observations and numerical simulation

Characteristics of pre-monsoon and monsoon boundary layer structure and turbulence were studied in New Delhi and Bangalore, India during the summer of 1987. Micrometeorological towers were installed and instrumented at these locations to provide mean and turbulent surface layer measurements, while information on the vertical structure of the atmosphere was obtained using miniradiosondes. Thermal structures of the pre-monsoon and monsoon boundary layers were quite distinct. The daytime, pre-monsoon boundary layer observed over New Delhi was much deeper than that of the monsoon boundary layer observed over Bangalore and at times was characterized by multiple inversions. Surface, turbulent sensible heat fluxes at both sites were approximately the same (235 and 200 Wm−2 for New Delhi and Bangalore, respectively). Diurnal variations in the monsoon boundary layer at Bangalore were more regular compared to those under pre-monsoon conditions at New Delhi. One-dimensional numerical simulations of the pre-monsoon boundary layer using a turbulent energy closure scheme show good agreement with observations.

A Numerical-Simulation Of The Gneiss-Charnockite Transformations In Southern India

This paper presents a numerical simulation of the well-documented, fluid-controlled Kabbal and Ponmudi type gneiss-chamockite transformations in southern India using a free energy minimization method. The computations have considered all the major solid phases and important fluid species in the rock - C-O-H and rock - C-O-H-N systems. Appropriate activity-composition relations for the solid solutions and equations of state for the fluids have been included in order to evaluate the mineral-fluid equilibria attending the incipient chamockite development in the gneisses. The C-O-H fluid speciation pattern in both the Kabbal and Ponmudi type systems indicates that CO2 and H2O make up the bulk of the fluid phase with CO, CH4, H-2 and O2 as minor constituents. In the graphite-buffered Ponmudi-system, the abundance of CO, CH4 and H-2 is orders of magnitude higher than that in the graphite-free Kabbal system. Simulation with C-O-H-N fluids of varying composition demonstrates the complementary role of CO2 and N2 as rather inert dilutants of H2O in the fluid phase. The simulation, carried out on available whole-rock data, has demonstrated the dependence of the transformation X(H2O) on P,T, and phase and chemical composition of the precursor gneiss.

Cell-dynamical simulation of magnetic hysteresis in the two-dimensional Ising system

We present results from numerical simulations using a ‘‘cell-dynamical system’’ to obtain solutions to the time-dependent Ginzburg-Landau equation for a scalar, two-dimensional (2D), (Φ2)2 model in the presence of a sinusoidal external magnetic field. Our results confirm a recent scaling law proposed by Rao, Krishnamurthy, and Pandit [Phys. Rev. B 42, 856 (1990)], and are also in excellent agreement with recent Monte Carlo simulations of hysteretic behavior of 2D Ising spins by Lo and Pelcovits [Phys. Rev. A 42, 7471 (1990)].

Influence of Die Surface Textures during Metal Forming-A Study Using Experiments and Simulation

Friction plays an important role in metal forming processes, and the surface texture of the die is a major factor that influences friction. In the present investigation, experiments were conducted to understand the role of surface texture of the harder die surface and load on coefficient of friction. The data analysis showed that the coefficient of friction is highly dependent on the surface texture of the die surface. Assigning different magnitude of coefficients of friction, obtained in the experiments, at different regions between the die and the workpiece, Finite element (FE) simulation of a compression test was carried out to understand the effect of friction on deformation and stress/strain-rate distribution. Simulation results revealed that, owing to the difference in coefficient of friction, there is a change in metal flow pattern. Both experimental and simulation results confirmed that the surface texture of the die surface and thus coefficient of friction directly affects the strain rate and flow pattern of the workpiece.