Abstract

In this paper we deduce the evolution of a four wheeled active suspension rover from a five wheeled passive suspension rover. The aim of this paper is to design a suspension mechanism which utilizes the advantages of both passive suspension and active suspension rover. Both the design considered here are simpler than the existing suspension mechanisms in the sense that the number of links as wells as the number of joints have been significantly reduced without compromising the climbing capability of the rover. We first analyze the kinematics of the five wheeled rover and its motion pattern while climbing an obstacle and try to deduce the same motion pattern and capability in the four wheeled rover. Both the suspension mechanism consists of two planar closed kinematic chains on each side of the rover. We also deduce the control strategy for the active suspension rover wherein only two actuators are used to control the internal configuration of the rover. To the best of author's knowledge this is the minimum number of actuators required to control the internal configuration of a active suspension while operating on a fully 3D rough terrain. Extensive uneven terrain simulations are performed for both 5-wheeled and 4-wheeled rover and a comparative analysis has been done on maximum coefficient of friction and torque requirements.

Abstract

Incorporating ferromagnetic materials into integrated microwave devices is a promising approach for the development of on-chip high-performance circuit components. Therefore, high-frequency domain-wall motion and magnetization rotation, which yield permeability, are of primary interest. However, so far it has not been attempted to physically separate high-frequency domain-wall motion and magnetization rotation driven by external magnetic field excitation. Nor have attempts for the corresponding characterizations. In this work, patterned permalloy films are integrated with on-chip microstrip lines. Domain-wall motion and magnetization rotation are separated through aspect ratio and dimension control. The measured results show that high-frequency-field driven domain-wall motion is fast, different from current driven domain-wall motion. It is also shown that coupling effects are not important when the distance between two adjacent permalloy films is~ 1 μm despite their large lateral dimensions. Finally, surface topography affects domain structures and corresponding dynamic processes.

Abstract

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Abstract

Identification of base pairs which can participate, through multimodality of edge interactions, in conformational switching events, and evaluation of possible environmental factors responsible for the switching can lead to greater understanding of RNA functional dynamics. Moleculardynamics studies by Schneider et al involving multimodality in C:U W:W cis interactions in aqueous medium, arguments forwarded by Van Dongen et al in support of a pH dependent G:C W:W cis to G:C H:W cis conformational switch and the postulation of putative role of a minor motifs in ribosomal dynamics through structure analysis, are examples of efforts in this section. Here we discuss the computational analysis of a putative pH dependant conformational switching of G:G base pairs in RNA structures.

Abstract

In this paper, we have computationally described the interaction of yDNA bases with small gold clusters through a variety of aspects including geometrical, spectroscopic and energetic one. To get insights in to essential elements of this interaction, the contribution of typical energy interaction components have also been investigated.

Abstract

Controlling dynamics at the atomic level is a primary goal of chemists. In the last decade, Optimal control theory (OCT) has emerged as one comprehensive means of designing laser pulses for achieving prescribed dynamical goals. We have used OCT to obtain infrared laser pulses for the selective vibrational excitation of several different systems, from a simple diatomic to triatomic systems located in complex molecular environments. We will present our results obtained for the diatomic system HF applying OCT using different algorithmic methods, namely an iterative method, conjugate gradient method and genetic algorithms. The results of a new dynamic method for applying the penalty term needed to keep the power in the electric field of the laser within reasonable bounds will be discussed. For the triatomic FeCO, we use a two mathematical dimensional model of carboxy-myoglobin. Density functional theory is used to obtain the potential energy and dipole moment surfaces of the active site model. The Conjugate gradient method is employed to optimize the cost functional and to obtain the optimized laser pulses. Optimized laser fields are found which give virtually 100% excitation probability to preselected vibrational levels. Similar application to hydrogen bonding in a complex system will also be presented.

Abstract

The synthesis of modified versions of DNA is an area that is receiving much attention because of their potential applications in biotechnology and nanotechnology. Recently, Eric Kool et al have re-engineered an expanded version of DNA by pairing size expanded x-bases with normal bases in a complementary manner, which they called as xDNA. xDNA bases are analogues of natural bases that are formed by insertion of benzene ring into the natural bases. Recently, there was arisen a huge interest in conducting properties of metal bound DNA structures. We use quantum chemistry methods to investigate the structural and electronic properties of x-bases and their interaction with gold atoms, in order to explore develop insight into the nature of binding between gold atoms and size expanded DNA.

Abstract

The problem of predicting the 3D native conformation of a polypeptide given the primary sequence is of fundamental importance in contemporary biology. Here we present a novel Genetic algorithm method to obtain the optimal geometry of a pentapeptide. The pentapeptide moiety is found in wide set of configurations in protein databases. A genetic algorithm utilizes optimization procedure similar to natural genetic evolution. Unlike other genetic algorithms, which are constrained to operate on bit strings, the algorithm used here operates on real values. A random population of conformations is generated taking into account the constraints of Ramachandran plot. This population advances through successive generations in which the solutions evolve via genetic operators (Mutate, Variate and Crossover); in such a way that it gives both better survival chance to fitter soluctions and a larger diversity within the population. More attention will be given to favorable local structures while unfavorable local structures will be rapidly abandoned on the basis of their fitness functions (potential energy), which are calculated using the GROMOS-96 force field of Spdbv version-3.7. The SCWRL3.0 program developed at Dunbrack lab is used for placing side chains to a fixed backbone coordinates. This algorithm proved to be very efficient for the penta-peptide Met-Enkephalin, a natural Opioid polypeptide produced in the brain. The algorithm converged only in 41 minutes and in 23 generations keeping the population size fixed (20 individual per population). The converged structure is energetically as stable as the native conformation of the protein. Its shows a RMSD of 5.9 from the original native conformation.

Abstract

With availability of fast computers, electronic structure and properties calculations of small to medium sized systems using quantum chemical methods are now commonplace. Several options in addition to obtaining structures with energy optimisation are now easily realisable, e.g., carrying out calculations of electrostatic potential interations, atoms in molecule approach of Bader, Natural Bonding orbital method, etc. We discuss results obtained in specific cases using these options. We have recently carried out studies on several such systems including amino-methyl furan carboxylic acid system and binding of gold nanoclusters with size expanded DNA bases, xA, xC, xG, and xT. We will present the motivation behind such works and discuss the results obtained using different methods. Geometries of these molecular systems were fully optimized using the Hartree Fock SCF method and using B3LYP density functional method (DFT). The calculations provide a theoretical understanding beyond a phenomenological observation of the preferential cyclotrimerization of 5- (aminomethyl)-2-furancarboxylic acid (AMFC). Other than calculations of thermodynamic free energy, a detailed analysis of the molecular properties is carried out. The electrostatic potentials (ESP) in the region around molecular skeletons are investigated to provide justication for the preferential formation of the cyclic tripeptide over the cyclic dipeptide from the building block, AMFC. The ESP are calculated and computed on the molecular surfaces of the oligopeptides. There are repulsions observed in the dimer due to the proximity of the ethereal oxygen atoms of the furan rings. Natural bond orbital (NBO) analysis is done to find the second-order interactions, and atoms in molecules (AIM) calculations are performed to explore the interactions between the donor and acceptor moieties in the molecule. Our results on the gold complexed x-bases show that the gold clusters around xA and xT adopt triangular geometries, whereas irregular structures are obtained in the case of gold clusters complexed around xC and xG. The lengths of the bonds between atoms in the x-bases increase on gold complexation. The aromaticcharacter of the x-bases also increases on gold complexation except for the five member rings. A significant charge transfer from the x-base to gold atoms is seen in these complexes. Second-order interactions are observed in addition to direct covalent bonds between gold atoms and x bases.

Abstract

The last two decades have seen increasing interest in the area of controlling dynamics at the atomic level. Among the several approaches used, Optimal Control Theory (OCT) has emerged as a powerful method for designing laser pulses to achieve prescribed dynamical goals. We have used OCT to obtain infrared laser pulses for the selective vibrational excitation of several different systems, from a simple diatomic to triatomics located in complex molecular environments. We use time dependent quantum mechanics to monitor the evolution of the system subject to a varying laser field. We have obtained fields for vibrational control of the diatomic system HF applying OCT using different algorithms, namely an iterative method, conjugate gradient method and genetic algorithms. The time-dependent quantum mechanical propagation of the system is achieved using the split operator form of the time evolution operator together with Fast Fourier transforms and grid methods. For the modelling of FeCO in carboxy-myoglobin, we use a two mathematical dimensional model. Density functional theory is used to obtain the potential energy and dipole moment surfaces of the active site model, while the conjugate gradient method is employed within the OCT optimization procedure to obtain the laser pulses. Optimized laser fields are found which give virtually 100% excitation probability to preselected vibrational levels. A similar application to a hydrogen bonded system of biological significance will also be presented. In all cases, detailed analyses of the field are carried out in terms of its power spectrum and the time variation of the contributions from the frequencies involved.