Complexation of siRNA with Dendrimer: A Molecular Modeling Approach

This paper reports the structural behavior and thermodynamics of the complexation of siRNA with poly(amidoamine) (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) through fully atomistic molecular dynamics (MD) simulations accompanied by free energy calculations and inherent structure determination. We have also done simulation with one siRNA and two dendrimers (2 x G3 or 2xG4) to get the microscopic picture of various binding modes. Our simulation results reveal the formation of stable siRNA-dendrimer complex over nanosecond time scale. With the increase in dendrimcr generation, the charge ratio increases and hence the binding energy between siRNA and dendrimer also increases in accordance with available experimental measurements. Calculated radial distribution functions of amines groups of various subgenerations in a given generation of dendrimer and phosphate in backbone of siRNA reveals that one dendrimer of generation 4 shows better binding with siRNA almost wrapping the dendrimer when compared to the binding with lower generation dendrimer like G3. In contrast, two dendrimers of generation 4 show binding without siRNA wrapping the den-rimer because of repulsion between two dendrimers. The counterion distribution around the complex and the water molecules in the hydration shell of siRNA give microscopic picture of the binding dynamics. We see a clear correlation between water. counterions motions and the complexation i.e. the water molecules and counterions which condensed around siRNA are moved away from the siRNA backbone when dendrimer start binding to the siRNA back hone. As siRNA wraps/bind to the dendrimer counterions originally condensed onto siRNA (Na-1) and dendrimer (Cl-) get released. We give a quantitative estimate of the entropy of counterions and show that there is gain in entropy due to counterions release during the complexation. Furthermore, the free energy of complexation of IG3 and IG4 at two different salt concentrations shows that increase in salt concentration leads to the weakening of the binding affinity of siRNA and dendrimer.

Impact of climate change on Indian forests: a dynamic vegetation modeling approach

We make an assessment of the impact of projected climate change on forest ecosystems in India. This assessment is based on climate projections of the Regional Climate Model of the Hadley Centre (HadRM3) and the dynamic global vegetation model IBIS for A2 and B2 scenarios. According to the model projections, 39% of forest grids are likely to undergo vegetation type change under the A2 scenario and 34% under the B2 scenario by the end of this century. However, in many forest dominant states such as Chattisgarh, Karnataka and Andhra Pradesh up to 73%, 67% and 62% of forested grids are projected to undergo change. Net Primary Productivity (NPP) is projected to increase by 68.8% and 51.2% under the A2 and B2 scenarios, respectively, and soil organic carbon (SOC) by 37.5% for A2 and 30.2% for B2 scenario. Based on the dynamic global vegetation modeling, we present a forest vulnerability index for India which is based on the observed datasets of forest density, forest biodiversity as well as model predicted vegetation type shift estimates for forested grids. The vulnerability index suggests that upper Himalayas, northern and central parts of Western Ghats and parts of central India are most vulnerable to projected impacts of climate change, while Northeastern forests are more resilient. Thus our study points to the need for developing and implementing adaptation strategies to reduce vulnerability of forests to projected climate change.

Multiscale Modeling Approach to Acoustic Emission during Plastic Deformation

We address the long-standing problem of the origin of acoustic emission commonly observed during plastic deformation. We propose a framework to deal with the widely separated time scales of collective dislocation dynamics and elastic degrees of freedom to explain the nature of acoustic emission observed during the Portevin-Le Chatelier effect. The Ananthakrishna model is used as it explains most generic features of the phenomenon. Our results show that while acoustic emission bursts correlated with stress drops are well separated for the type C serrations, these bursts merge to form nearly continuous acoustic signals with overriding bursts for the propagating type A bands.

Image reconstruction from incomplete projections data: A multiresolution modeling approach

Computerized tomography is an imaging technique which produces cross sectional map of an object from its line integrals. Image reconstruction algorithms require collection of line integrals covering the whole measurement range. However, in many practical situations part of projection data is inaccurately measured or not measured at all. In such incomplete projection data situations, conventional image reconstruction algorithms like the convolution back projection algorithm (CBP) and the Fourier reconstruction algorithm, assuming the projection data to be complete, produce degraded images. In this paper, a multiresolution multiscale modeling using the wavelet transform coefficients of projections is proposed for projection completion. The missing coefficients are then predicted based on these models at each scale followed by inverse wavelet transform to obtain the estimated projection data.

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Molecule Modeling of Human Pentameric alpha(7) Neuronal Nicotinic Acetylcholine Receptor and Its Interaction with its Agonist and Competitive Antagonist

The nicotinic Acetylcholine Receptor (nAChR) is the major class of neurotransmitter receptors that is involved in many neurodegenerative conditions such as schizophrenia, Alzheimer's and Parkinson's diseases. The N-terminal region or Ligand Binding Domain (LBD) of nAChR is located at pre- and post-synaptic nervous system, which mediates synaptic transmission. nAChR acts as the drug target for agonist and competitive antagonist molecules that modulate signal transmission at the nerve terminals. Based on Acetylcholine Binding Protein (AChBP) from Lymnea stagnalis as the structural template, the homology modeling approach was carried out to build three dimensional model of the N-terminal region of human alpha(7)nAChR. This theoretical model is an assembly of five alpha(7) subunits with 5 fold axis symmetry, constituting a channel, with the binding picket present at the interface region of the subunits. alpha-netlrotoxin is a potent nAChR competitive antagonist that readily blocks the channel resulting in paralysis. The molecular interaction of alpha-Bungarotoxin, a long chain alpha-neurotoxin from (Bungarus multicinctus) and human alpha(7)nAChR seas studied. Agonists such as acetylcholine, nicotine, which are used in it diverse array of biological activities, such as enhancements of cognitive performances, were also docked with the theoretical model of human alpha(7)nAChR. These docked complexes were analyzed further for identifying the crucial residues involved i interaction. These results provide the details of interaction of agonists and competitive antagonists with three dimensional model of the N-terminal region of human alpha(7)nAChR and thereby point to the design of novel lead compounds.

Constitutive modeling of shape memory alloy wire with non-local rate kinetics

A constitutive modeling approach for shape memory alloy (SMA) wire by taking into account the microstructural phase inhomogeneity and the associated solid-solid phase transformation kinetics is reported in this paper. The approach is applicable to general thermomechanical loading. Characterization of various scales in the non-local rate sensitive kinetics is the main focus of this paper. Design of SMA materials and actuators not only involve an optimal exploitation of the hysteresis loops during loading-unloading, but also accounts for fatigue and training cycle identifications. For a successful design of SMA integrated actuator systems, it is essential to include the microstructural inhomogeneity effects and the loading rate dependence of the martensitic evolution, since these factors play predominant role in fatigue. In the proposed formulation, the evolution of new phase is assumed according to Weibull distribution. Fourier transformation and finite difference methods are applied to arrive at the analytical form of two important scaling parameters. The ratio of these scaling parameters is of the order of 10(6) for stress-free temperature-induced transformation and 10(4) for stress-induced transformation. These scaling parameters are used in order to study the effect of microstructural variation on the thermo-mechanical force and interface driving force. It is observed that the interface driving force is significant during the evolution. Increase in the slopes of the transformation start and end regions in the stress-strain hysteresis loop is observed for mechanical loading with higher rates.

Modeling the Field Emission Current Fluctuation in Carbon Nanotube Thin Films

Owing to their distinct properties, carbon nanotubes (CNTs) have emerged as promising candidate for field emission devices. It has been found experimentally that the results related to the field emission performance show variability. The design of an efficient field emitting device requires the analysis of the variabilities with a systematic and multiphysics based modeling approach. In this paper, we develop a model of randomly oriented CNTs in a thin film by coupling the field emission phenomena, the electron-phonon transport and the mechanics of single isolated CNT. A computational scheme is developed by which the states of CNTs are updated in time incremental manner. The device current is calculated by using Fowler-Nordheim equation for field emission to study the performance at the device scale.

Vaporization and collision modeling of liquid fuel sprays in a co-axial fuel and air pre-mixer

Droplet collision occurs frequently in regions where the droplet number density is high. Even for Lean Premixed and Pre-vaporized (LPP) liquid sprays, the collision effects can be very high on the droplet size distributions, which will in turn affect the droplet vaporization process. Hence, in conjunction with vaporization modeling, collision modeling for such spray systems is also essential. The standard O'Rourke's collision model, usually implemented in CFD codes, tends to generate unphysical numerical artifact when simulations are performed on Cartesian grid and the results are not grid independent. Thus, a new collision modeling approach based on no-time-counter method (NTC) proposed by Schmidt and Rutland is implemented to replace O'Rourke's collision algorithm to solve a spray injection problem in a cylindrical coflow premixer. The so called ``four-leaf clover'' numerical artifacts are eliminated by the new collision algorithm and results from a diesel spray show very good grid independence. Next, the dispersion and vaporization processes for liquid fuel sprays are simulated in a coflow premixer. Two liquid fuels under investigation are jet-A and Rapeseed Methyl Esters (RME). Results show very good grid independence in terms of SMD distribution, droplet number distribution and fuel vapor mass flow rate. A baseline test is first established with a spray cone angle of 90 degrees and injection velocity of 3 m/s and jet-A achieves much better vaporization performance than RME due to its higher vapor pressure. To improve the vaporization performance for both fuels, a series of simulations have been done at several different combinations of spray cone angle and injection velocity. At relatively low spray cone angle and injection velocity, the collision effect on the average droplet size and the vaporization performance are very high due to relatively high coalescence rate induced by droplet collisions. Thus, at higher spray cone angle and injection velocity, the results expectedly show improvement in fuel vaporization performance since smaller droplet has a higher vaporization rate. The vaporization performance and the level of homogeneity of fuel-air mixture can be significantly improved when the dispersion level is high, which can be achieved by increasing the spray cone angle and injection velocity. (C) 2012 Elsevier Ltd. All rights reserved.

Basin Scale Water Resources Systems Modeling Under Cascading Uncertainties

Global change in climate and consequent large impacts on regional hydrologic systems have, in recent years, motivated significant research efforts in water resources modeling under climate change. In an integrated future hydrologic scenario, it is likely that water availability and demands will change significantly due to modifications in hydro-climatic variables such as rainfall, reservoir inflows, temperature, net radiation, wind speed and humidity. An integrated regional water resources management model should capture the likely impacts of climate change on water demands and water availability along with uncertainties associated with climate change impacts and with management goals and objectives under non-stationary conditions. Uncertainties in an integrated regional water resources management model, accumulating from various stages of decision making include climate model and scenario uncertainty in the hydro-climatic impact assessment, uncertainty due to conflicting interests of the water users and uncertainty due to inherent variability of the reservoir inflows. This paper presents an integrated regional water resources management modeling approach considering uncertainties at various stages of decision making by an integration of a hydro-climatic variable projection model, a water demand quantification model, a water quantity management model and a water quality control model. Modeling tools of canonical correlation analysis, stochastic dynamic programming and fuzzy optimization are used in an integrated framework, in the approach presented here. The proposed modeling approach is demonstrated with the case study of the Bhadra Reservoir system in Karnataka, India.

Fatigue Laws Via Functional Equations

In routine industrial design, fatigue life estimation is largely based on S-N curves and ad hoc cycle counting algorithms used with Miner's rule for predicting life under complex loading. However, there are well known deficiencies of the conventional approach. Of the many cumulative damage rules that have been proposed, Manson's Double Linear Damage Rule (DLDR) has been the most successful. Here we follow up, through comparisons with experimental data from many sources, on a new approach to empirical fatigue life estimation (A Constructive Empirical Theory for Metal Fatigue Under Block Cyclic Loading', Proceedings of the Royal Society A, in press). The basic modeling approach is first described: it depends on enforcing mathematical consistency between predictions of simple empirical models that include indeterminate functional forms, and published fatigue data from handbooks. This consistency is enforced through setting up and (with luck) solving a functional equation with three independent variables and six unknown functions. The model, after eliminating or identifying various parameters, retains three fitted parameters; for the experimental data available, one of these may be set to zero. On comparison against data from several different sources, with two fitted parameters, we find that our model works about as well as the DLDR and much better than Miner's rule. We finally discuss some ways in which the model might be used, beyond the scope of the DLDR.

Field Emission Properties of Carbon Nanotube Arrays with Defects and Impurities

It has been found experimentally that the results related to the collective field emission performance of carbon nanotube (CNT) arrays show variability. The emission performance depends on the electronic structure of CNTs (especially their tips). Due to limitations in the synthesis process, production of highly pure and defect free CNTs is very difficult. The presence of defects and impurities affects the electronic structure of CNTs. Therefore, it is essential to analyze the effect of defects on the electronic structure, and hence, the field emission current. In this paper, we develop a modeling approach for evaluating the effect of defects and impurities on the overall field emission performance of a CNT array. We employ a concept of effective stiffness degradation for segments of CNTs, which is due to structural defects. Then, we incorporate the vacancy defects and charge impurity effects in our Green's function based approach. Simulation results indicate decrease in average current due to the presence of such defects and impurities.

Electromechanical interactions in a carbon nanotube based thin film field emitting diode

Carbon nanotubes (CNTs) have emerged as promising candidates for biomedical x-ray devices and other applications of field emission. CNTs grown/deposited in a thin film are used as cathodes for field emission. In spite of the good performance of such cathodes, the procedure to estimate the device current is not straightforward and the required insight towards design optimization is not well developed. In this paper, we report an analysis aided by a computational model and experiments by which the process of evolution and self-assembly (reorientation) of CNTs is characterized and the device current is estimated. The modeling approach involves two steps: (i) a phenomenological description of the degradation and fragmentation of CNTs and (ii) a mechanics based modeling of electromechanical interaction among CNTs during field emission. A computational scheme is developed by which the states of CNTs are updated in a time incremental manner. Finally, the device current is obtained by using the Fowler–Nordheim equation for field emission and by integrating the current density over computational cells. A detailed analysis of the results reveals the deflected shapes of the CNTs in an ensemble and the extent to which the initial state of geometry and orientation angles affect the device current. Experimental results confirm these effects.

Local texture and microstructure in cube-oriented nickel single crystal deformed by equal channel angular extrusion

Local texture and microstructure was investigated to study the deformation mechanisms during equal channel angular extrusion of a high purity nickel single crystal of initial cube orientation. A detailed texture and microstructure analysis by various diffraction techniques revealed the complexity of the deformation patterns in different locations of the billet. A modeling approach, taking into account slip system activity, was used to interpret the development of this heterogeneous deformation.