A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.

Vertical uplift resistance of two closely spaced horizontal strip anchors embedded in cohesive-frictional weightless medium

The vertical uplift resistance of two closely spaced horizontal strip plate anchors has been investigated by using lower and upper bound theorems of the limit analysis in combination with finite elements and linear optimization. The interference effect on uplift resistance of the two anchors is evaluated in terms of a nondimensional efficiency factor (eta(c)). The variation of eta(c) with changes in the clear spacing (S) between the two anchors has been established for different combinations of embedment ratio (H/B) and angle of internal friction of the soil (phi). An interference of the anchors leads to a continuous reduction in uplift resistance with a decrease in spacing between the anchors. The uplift resistance becomes a minimum when the two anchors are placed next to each other without any gap. The critical spacing (S-cr) between the two anchors required to eliminate the interference effect increases with an increase in the values of both H/B and phi. The value of S-cr was found to lie approximately in the range 0.65B-1.5B with H/B = 1 and 11B-14B with H/B = 7 for phi varying from 0 degrees to 30 degrees.

Supersolid in a one-dimensional model of hard-core bosons

We study a system of hard-core boson on a one-dimensional lattice with frustrated next-nearest-neighbor hopping and nearest-neighbor interaction. At half filling, for equal magnitude of nearest- and next-nearest-neighbor hopping, the ground state of this system exhibits a first-order phase transition from a bond-ordered solid to a charge-density-wave solid as a function of the nearest- neighbor interaction. Moving away from half filling we investigate the system at incommensurate densities, where we find a supersolid phase which has concurrent off-diagonal long-range order and density-wave order which is unusual in a system of hard-core bosons in one dimension. Using the finite-size density-matrix renormalization group method, we obtain the complete phase diagram for this model.

Partial Integrated Guidance and Control of Interceptors for High-Speed Ballistic Targets

A new partial integrated guidance and control design approach is proposed in this paper, which combines the benefits of both integrated guidance and control as well as the conventional guidance and control design philosophies. The proposed technique essentially operates in a two-loop structure. In the outer loop, an optimal guidance problem is formulated considering the nonlinear six degrees-of-freedom equation of motion of the interceptor. From this loop, the required pitch and yaw rates are generated by solving a nonlinear suboptimal guidance formulation in a computationally efficient manner while simultaneously assuring roll stabilization. Next, the inner loop tracks these outer loop body rate commands. This manipulation of the six degrees-of-freedom dynamics in both loops preserves the inherent time scale separation property between the translational and rotational dynamics, while retaining the philosophy of integrated guidance and control design as well. Because of this, the tuning process is quite straightforward and nontedious as well. Extensive six degrees-of-freedom simulations studies have been carried out, considering three-dimensional engagement geometry, to demonstrate the effectiveness of the proposed new design approach engaging high-speed ballistic targets. A variety of comparison studies have also been carried out to demonstrate the effectiveness of the proposed approach.

Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions

Background: The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating these findings into biomedically useful information is to find out the mechanism of the action of these genes. However, GWAS studies often implicate genes whose functions are currently unknown; for example, MYEOV, ANKLE1, TMEM45B and ORAOV1 are found to be associated with breast cancer, but their molecular function is unknown. Results: We carried out Bayesian inference of Gene Ontology (GO) term annotations of genes by employing the directed acyclic graph structure of GO and the network of protein-protein interactions (PPIs). The approach is designed based on the fact that two proteins that interact biophysically would be in physical proximity of each other, would possess complementary molecular function, and play role in related biological processes. Predicted GO terms were ranked according to their relative association scores and the approach was evaluated quantitatively by plotting the precision versus recall values and F-scores (the harmonic mean of precision and recall) versus varying thresholds. Precisions of similar to 58% and similar to 40% for localization and functions respectively of proteins were determined at a threshold of similar to 30 (top 30 GO terms in the ranked list). Comparison with function prediction based on semantic similarity among nodes in an ontology and incorporation of those similarities in a k nearest neighbor classifier confirmed that our results compared favorably. Conclusions: This approach was applied to predict the cellular component and molecular function GO terms of all human proteins that have interacting partners possessing at least one known GO annotation. The list of predictions is available at http://severus.dbmi.pitt.edu/engo/GOPRED.html. We present the algorithm, evaluations and the results of the computational predictions, especially for genes identified in GWAS studies to be associated with diseases, which are of translational interest.

The knight of sugar industry: T. S. Venkatraman (1884-1963)

Tiruvadi Sambasiva Venkatraman (TSV) was a plant breeder. In response to a call from Pundit Madan Mohan Malaviya, he made it his mission to develop high-yielding varieties of sugarcane for manufacturing sugar and making it available as a sweetening agent and an energy source for the malnourished children of India. Using Saccharum officinarum, then under cultivation in India, as the female parent, he artificially fertilized it with pollen from S. barberi, which grew wild in Coimbatore. After 4-5 recurrent backcrossings of S. officinarum Chi wild Sorghum spontaneum with S. officinarum as the female parent, TSV selected the `rare' interspecies hybrid cane varieties that resembled sugarcane and had approximately 2.5 cm thick juicy stems containing 16-18% sucrose - nearly 35 times more than what occurred in parent stocks. The hybrid canes matured quickly, were resistant to waterlogging, drought, and to the red-rot disease caused by Glomerella tucumanensis (Sordariomycetes: Glomerellaceae), and to the sereh-virus disease. Most importantly, they were amenable for propagation using stem cuttings. In recognition of the development of high-yielding sugarcane varieties, TSV was conferred the titles Rao Bahadur, Rao Sahib, and Sir by the British Government, and Padma Bhushan by the Republic of India. In the next few decades, consequent to TSV's work, India turned into the second largest sugar producer in the world, after Brazil. The hybrid sugarcane varieties developed are the foundational stocks for new sugarcane x bamboo hybrids, and for possible resistance to Puccinia megalocephala (Pucciniomycetes: Pucciniaceae) and Ustilago scitaminea (Ustilaginomycetes: Ustilaginaceae) using molecular techniques.

Facile synthesis of reduced graphene oxide/Pt-Ni nanocatalysts: their magnetic and catalytic properties

The catalytic performance of metals can be enhanced by intimately alloying different metals with Reduced Graphene Oxide (RGO). In this work, we have demonstrated a simplistic in situ one-step reduction approach for the synthesis of RGO/Pt-Ni nanocatalysts with different atomic ratios of Pt and Ni, without using any capping agent. The physical properties of the as-synthesized nanocatalysts have been systematically investigated by XRD, FTIR, Raman spectroscopy, XPS, EDX, ICP-AES, and TEM. The composition dependent magnetic properties of the RGO/Pt-Ni nanocatalysts were investigated at 5 and 300 K, respectively. The results confirm that the RGO/Pt-Ni nanocatalysts show a super-paramagnetic nature at room temperature in all compositions. Furthermore, the catalytic activities of the RGO/Pt-Ni nanocatalysts were investigated by analyzing the reduction of p-nitrophenol, and the reduction rate was found to be susceptible to the composition of Pt and Ni. Moreover, it has been found that RGO/Pt-Ni nanocatalysts show superior catalytic activity compared with the bare Pt-Ni of the same composition. Interestingly, the nanocatalysts can be readily recycled by a strong magnet and reused for the next reactions.

On the Utility of Microscopy and C-Scan Techniques in the Study of Defects Arising From Resin Infusion Process and a Study on the Influence of Voids on the Impact Behavior of CFRP Composites

Carbon Fiber Reinforced Plastic composites were fabricated through vacuum resin infusion technology by adopting two different processing conditions, viz., vacuum only in the first and vacuum plus external pressure in the next, in order to generate two levels of void-bearing samples. They were relatively graded as higher and lower void-bearing ones, respectively. Microscopy and C-scan techniques were utilized to describe the presence of voids arising from the two different processing parameters. Further, to determine the influence of voids on impact behavior, the fabricated +45 degrees/90 degrees/-45 degrees composite samples were subjected to low velocity impacts. The tests show impact properties like peak load and energy to peak load registering higher values for the lower void-bearing case where as the total energy, energy for propagation and ductility indexes were higher for the higher void-bearing ones. Fractographic analysis showed that higher void-bearing samples display lower number of separation of layers in the laminate. These and other results are described and discussed in this report.

High-conductance states and A-type K+ channels are potential regulators of the conductance-current balance triggered by HCN channels

An increase in the hyperpolarization-activated cyclic nucleotide-gated (HCN) channel conductance reduces input resistance, whereas the consequent increase in the inward h current depolarizes the membrane. This results in a delicate and unique conductance-current balance triggered by the expression of HCN channels. In this study, we employ experimentally constrained, morphologically realistic, conductance-based models of hippocampal neurons to explore certain aspects of this conductance-current balance. First, we found that the inclusion of an experimentally determined gradient in A-type K+ conductance, but not in M-type K+ conductance, tilts the HCN conductance-current balance heavily in favor of conductance, thereby exerting an overall restorative influence on neural excitability. Next, motivated by the well-established modulation of neuronal excitability by synaptically driven high-conductance states observed under in vivo conditions, we inserted thousands of excitatory and inhibitory synapses with different somatodendritic distributions. We measured the efficacy of HCN channels, independently and in conjunction with other channels, in altering resting membrane potential (RMP) and input resistance (R-in) when the neuron received randomized or rhythmic synaptic bombardments through variable numbers of synaptic inputs. We found that the impact of HCN channels on average RMP, R in, firing frequency, and peak-to-peak voltage response was severely weakened under high-conductance states, with the impinging synaptic drive playing a dominant role in regulating these measurements. Our results suggest that the debate on the role of HCN channels in altering excitability should encompass physiological and pathophysiological neuronal states under in vivo conditions and the spatiotemporal interactions of HCN channels with other channels.

Transverse single spin asymmetry in e plus p up arrow -> e plus J/psi plus X and Q(2) evolution of Sivers function-II

We present estimates of single spin asymmetry in the electroproduction of J/psi taking into account the transverse momentum-dependent (TMD) evolution of the gluon Sivers function. We estimate single spin asymmetry for JLab, HERMES, COMPASS and eRHIC energies using the color evaporation model of J/psi. We have calculated the asymmetry using recent parameters extracted by Echevarria et al. using the Collins-Soper-Sterman approach to TMD evolution. These recent TMD evolution fits are based on the evolution kernel in which the perturbative part is resummed up to next-to-leading logarithmic accuracy. We have also estimated the asymmetry by using parameters which had been obtained by a fit by Anselmino et al., using both an exact numerical and an approximate analytical solution of the TMD evolution equations. We find that the variation among the different estimates obtained using TMD evolution is much smaller than between these on one hand and the estimates obtained using DGLAP evolution on the other. Even though the use of TMD evolution causes an overall reduction in asymmetries compared to the ones obtained without it, they remain sizable. Overall, upon use of TMD evolution, predictions for asymmetries stabilize.

On the Two-Step Mechanism for Synthesis of Transition-Metal Nanoparticles

The two-step particle synthesis mechanism, also known as the Finke-Watzky (1997) mechanism, has emerged as a significant development in the field of nanoparticle synthesis. It explains a characteristic feature of the synthesis of transition metal nanoparticles, an induction period in precursor concentration followed by its rapid sigmoidal decrease. The classical LaMer theory (1950) of particle formation fails to capture this behavior. The two-step mechanism considers slow continuous nucleation and autocatalytic growth of particles directly from precursor as its two kinetic steps. In the present work, we test the two-step mechanism rigorously using population balance models. We find that it explains precursor consumption very well, but fails to explain particle synthesis. The effect of continued nucleation on particle synthesis is not suppressed sufficiently by the rapid autocatalytic growth of particles. The nucleation continues to increase breadth of size distributions to unexpectedly large values as compared to those observed experimentally. A number of variations of the original mechanism with additional reaction steps are investigated next. The simulations show that continued nucleation from the beginning of the synthesis leads to formation of highly polydisperse particles in all of the tested cases. A short nucleation window, realized with delayed onset of nucleation and its suppression soon after in one of the variations, appears as one way to explain all of the known experimental observations. The present investigations clearly establish the need to revisit the two-step particle synthesis mechanism.

Chemical Functionalization of Graphene To Augment Stem Cell Osteogenesis and Inhibit Biofilm Formation on Polymer Composites for Orthopedic Applications

Toward designing the next generation of resorbable biomaterials for orthopedic applications, we studied poly(epsilon-caprolactone) (PCL) composites containing graphene. The role, if any, of the functionalization of graphene on mechanical properties, stem cell response, and biofilm formation was systematically evaluated. PCL composites of graphene oxide (GO), reduced GO (RGO), and amine-functionalized GO (AGO) were prepared at different filler contents (1%, 3%, and 5%). Although the addition of the nanoparticles to PCL markedly increased the storage modulus, this increase was largest for GO followed by AGO and RGO. In vitro cell studies revealed that the AGO and GO particles significantly increased human mesenchymal stem cell proliferation. AGO was most effective in augmenting stem cell osteogenesis leading to mineralization. Bacterial studies revealed that interaction with functionalized GO induced bacterial cell death because of membrane damage, which was further accentuated by amine groups in AGO. As a result, AGO composites were best at inhibiting biofilm formation. The synergistic effect of oxygen containing functional groups and amine groups on AGO imparts the optimal combination of improved modulus, favorable stem cell response, and biofilm inhibition in AGO-reinforced composites desired for orthopedic applications. This work elucidates the importance of chemical functionalization of graphene in polymer composites for biomedical applications.

One-pot synthesis of a TiO2-CdS nano-heterostructure assembly with enhanced photocatalytic activity

An unprecedented morphology of a titanium dioxide (TiO2) and cadmium sulfide (CdS) self-assembly obtained using a `truly' one-pot and highly cost effective method with a multi-gram scale yield is reported here. The TiO2-CdS assembly, comprising of TiO2 and CdS nanoparticles residing next to each other homogeneously self-assembling into `woollen knitting ball' like microspheres, exhibited remarkable potential as a visible light photocatalyst with high recyclability.

A predictive approach to CVD of crystalline layers of TMDs: the case of MoS2

Layered transition metal dichalcogenides (TMDs), such as MoS2, are candidate materials for next generation 2-D electronic and optoelectronic devices. The ability to grow uniform, crystalline, atomic layers over large areas is the key to developing such technology. We report a chemical vapor deposition (CVD) technique which yields n-layered MoS2 on a variety of substrates. A generic approach suitable to all TMDs, involving thermodynamic modeling to identify the appropriate CVD process window, and quantitative control of the vapor phase supersaturation, is demonstrated. All reactant sources in our method are outside the growth chamber, a significant improvement over vapor-based methods for atomic layers reported to date. The as-deposited layers are p-type, due to Mo deficiency, with field effect and Hall hole mobilities of up to 2.4 cm(2) V-1 s(-1) and 44 cm(2) V-1 s(-1) respectively. These are among the best reported yet for CVD MoS2.

Conceptualization of a Behavior Modification Tool for University Systems and Doctoral Students

This paper describes a university based system relevant to doctoral students who have problems with themselves, their peers and research supervisors. Doctoral students have various challenges to solve and these challenges contribute to delays in their thesis submission. This tool aims at helping them think through their problem in a pre-counseling stage. The tool uses narratives and hypothetical stories to walk a doctoral student through options of responses he or she can make given the situation in the narrative. Narratives were developed after a preliminary survey (n=57) of doctoral students. The survey indicated that problems they experienced were: busy supervisors, negative competition from peers and laziness with self. The narrative scenarios in the tool prompt self-reflection and provide for options to chose from leading to the next scenario that will ensue. The different stages of the stimulus-response cycles are designed based on Thomas-Kilmann conflict resolution techniques (collaboration and avoidance). Each stimulus-response cycle has a score attached that reflects the student's ability to judge a collaborative approach. At the end of all the stages a scorecard is generated indicating either a progressive or regressive outcome of thesis submission.