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Search Results: 1 - 10 of 463 matches for " Nagarajan Vaidehi "
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Factors That Affect the Computational Prediction of Hot Spots in Protein-Protein Complexes  [PDF]
Jianping Lin, Pi Liu, Hua-Zheng Yang, Nagarajan Vaidehi
Computational Molecular Bioscience (CMB) , 2012, DOI: 10.4236/cmb.2012.21003
Abstract: Protein-protein complexes play an important role in the physiology and the pathology of cellular functions, and therefore are attractive therapeutic targets. A small subset of residues known as “hot spots”, accounts for most of the protein-protein binding free energy. Computational methods play a critical role in identifying the hotspots on the proteinprotein interface. In this paper, we use a computational alanine scanning method with all-atom force fields for predicting hotspots for 313 mutations in 16 protein complexes of known structures. We studied the effect of force fields, solvation models, and conformational sampling on the hotspot predictions. We compared the calculated change in the protein-protein interaction energies upon mutation of the residues in and near the protein-protein interface, to the experimental change in free energies. The AMBER force field (FF) predicted 86% of the hotspots among the three commonly used FF for proteins, namely, AMBER FF, Charmm27 FF, and OPLS-2005 FF. However, AMBER FF also showed a high rate of false positives, while the Charmm27 FF yielded 74% correct predictions of the hotspot residues with low false positives. Van der Waals and hydrogen bonding energy show the largest energy contribution with a high rate of prediction accuracy, while the desolvation energy was found to contribute little to improve the hot spot prediction. Using a conformational ensemble including limited backbone movement instead of one static structure leads to better predicttion of hotpsots.
Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
Peter Spijker,Bram Van Hoof,Michel Debertrand,Albert J. Markvoort,Nagarajan Vaidehi,Peter A. J. Hilbers
International Journal of Molecular Sciences , 2010, DOI: 10.3390/ijms11062393
Abstract: Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.
Identification of Anti-Malarial Compounds as Novel Antagonists to Chemokine Receptor CXCR4 in Pancreatic Cancer Cells
Joseph Kim, M. L. Richard Yip, Xiaoming Shen, Hubert Li, Li-Yu Charlie Hsin, Samuel Labarge, Eileen L. Heinrich, Wendy Lee, Jianming Lu, Nagarajan Vaidehi
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031004
Abstract: Despite recent advances in targeted therapies, patients with pancreatic adenocarcinoma continue to have poor survival highlighting the urgency to identify novel therapeutic targets. Our previous investigations have implicated chemokine receptor CXCR4 and its selective ligand CXCL12 in the pathogenesis and progression of pancreatic intraepithelial neoplasia and invasive pancreatic cancer; hence, CXCR4 is a promising target for suppression of pancreatic cancer growth. Here, we combined in silico structural modeling of CXCR4 to screen for candidate anti-CXCR4 compounds with in vitro cell line assays and identified NSC56612 from the National Cancer Institute's (NCI) Open Chemical Repository Collection as an inhibitor of activated CXCR4. Next, we identified that NSC56612 is structurally similar to the established anti-malarial drugs chloroquine and hydroxychloroquine. We evaluated these compounds in pancreatic cancer cells in vitro and observed specific antagonism of CXCR4-mediated signaling and cell proliferation. Recent in vivo therapeutic applications of chloroquine in pancreatic cancer mouse models have demonstrated decreased tumor growth and improved survival. Our results thus provide a molecular target and basis for further evaluation of chloroquine and hydroxychloroquine in pancreatic cancer. Historically safe in humans, chloroquine and hydroxychloroquine appear to be promising agents to safely and effectively target CXCR4 in patients with pancreatic cancer.
Approximate Controllability of Fractional Order Retarded Semilinear Control Systems  [PDF]
Simegne Tafesse, Nagarajan Sukavanam
International Journal of Modern Nonlinear Theory and Application (IJMNTA) , 2013, DOI: 10.4236/ijmnta.2013.23020
Abstract:

In this paper, approximate controllability of fractional order retarded semilinear systems is studied when the nonlinear term satisfies the newly formulated bounded integral contractor-type conditions. We have shown the existence and uniqueness of the mild solution for the fractional order retarded semilinear systems using an iterative procedure approach. Finally, we obtain the approximate controllability results of the system under simple condition.

Formulation and Evaluation of Mucoadhesive Microspheres of Pioglitazone Hydrochloride Prepared by Ionotropic External Gelation Technique  [PDF]
Nagarajan Sriram, Prakash Katakam
Journal of Encapsulation and Adsorption Sciences (JEAS) , 2016, DOI: 10.4236/jeas.2016.61003
Abstract: Microspheres containing Pioglitazone hydrochloride were prepared by the ionotropic external gelation method, using sodium alginate with four mucoadhesive polymers namely sodium carboxy methyl cellulose, hydroxy propyl methyl cellulose, carbopol 934 P and cellulose acetate phthalate as coat materials. Ionotropic gelation is a method to prepare microspheres using combination of Ca2+ as cationic components and alginate as anion. The practical yield of prepared microspheres using the ionotropic gelation technique was between 172 mg and 604 mg. The result of the Chi-squared test carried out between the actual (practical) and expected (theoretical) yields showed no significant difference (P < 0.05) which indicated that the ionotropic gelation technique could be successfully employed to prepare pioglitazone microspheres using sodium alginate, sodium carboxy methyl cellulose, carbopol 934 P, HPMC, cellulose acetate butyrate polymers. The drug entrapment efficiency of prepared microspheres showed between 56.12% ± 3.86% to 84.68% ± 2.93% which was significantly higher for ionotropic gelation technique. The highest drug entrapment was found in formulation PMI 8. Swelling index is the capability of a polymer to swell before the drug is released which influences the rate and mechanism of drug release from the polymer matrix. The swelling index of prepared microspheres was in the range of 68% ± 4.52% to 87% ± 0.98%. Pioglitazone HCl microspheres showed controlled release of drug without initial peak level achieving. This type of properties in Pioglitazone HCl microspheres used to decrease side effects, reduce dosing frequency and improve patient compliances. From the all batches PMI 8 is considered the best formulation, because among all other formulations, it shows better extent of drug release up to 82.12% (18 h), good entrapment efficiency (84.68%) and the ex-vivo wash-off test shows the best mucoadhesive property. The in vitro drug release studies do up to 18 h. As observed from the various plots, most of the formulations followed the Korsmeyer-Peppas model.
Triple-Polarized Multi-User Mimo-Idma System under Correlated Fading Channel  [PDF]
B. Partibane, V. Nagarajan
Circuits and Systems (CS) , 2016, DOI: 10.4236/cs.2016.78141
Abstract: A multiple-input multiple-output interleave division multiple access (MIMO-IDMA) system withTriple Polarized Division Multiplexing (TPDM) is presented in this paper. The present methodology replaces three independent linearly polarized antennas with a single triple polarized antenna at both the transmitter and receiver. The users in the communication link are accommodated and separated using a user-specific interleaver combined with low rate spreading sequence. To eliminate the effects of multi-stream interference (MSI), minimum mean square error (MMSE) algorithm based on successive interference cancellation (SIC) Multi-user detection (MUD) technique is employed at the receiver. Furthermore, log-maximum a posteriori probability (MAPP) decoding algorithm is implemented at the mobile stations (MSs) to overcome the effects of multi-user interference (MUI) effects. The paper also evaluates the effects of coded MIMO-IDMA in the downlink communication by adopting the Stanford University Interim (SUI) and Long-term Evolution (LTE)channel model specifications. In comparison with the traditional uncoded system, the presentsolution considering turbo coded triple-polarized MIMO-IDMA system with iterative decoding algorithm provides better bit error rate (BER) with reduced signal to noise ratio (SNR). The simulation results also show that though the SNR requirement is higher for the proposed technique compared to the conventional uni-polarized antenna based MIMO-IDMA system, it gives the advantages of achieving higher data rate with reduced cost and space requirements in the context of a downlink (DL).
Hybrid Segment Approximate Multiplication for Image Processing Applications  [PDF]
Jamuna Ramasamy, Sathishkumar Nagarajan
Circuits and Systems (CS) , 2016, DOI: 10.4236/cs.2016.78147
Abstract: It is critical in terms of approximate computation errors in VLSI multiplier circuits are increasing with technology scaling. The most common method for fast and energy efficient execution of multiplication result is approximation of operands. But this traditional approximate result is not suitable for image processing applications. This paper proposes the two architectures of high accurate hybrid segment approximate multiplier (HSAM) and enhanced HSAM for image compression. Existing static segment method based approximate multiplier is not suitable for certain accurate applications and dynamic segment method based approximate multiplier is not suitable for cost efficient applications. The proposed work combines the advantages of both static segment method and dynamic segment method to drive the efficiency in accuracy and cost. The proposed approximate multipliers HSAM8 × 8 and EHSAM8 × 8 provide 99.85% and 99.999% accuracy respectively for various inputs. The proposed HSAM consumes less energy with small increase of area overhead. The proposed EHSAM consumes less energy without any area overhead. The proposed HSAM and EHSAM is improved the speed by 40% and 85% compared to the existing SSM8 × 8 technique.
Performance Analysis of UWB Channels for Wireless Personal Area Networks
C. Ramesh,V. Vaidehi
Information Technology Journal , 2006,
Abstract: Ultra-wide Band (UWB) communication is one of the most promising technology for high data rate networks over short-range communication. The ultra-wide bandwidth offers pulses with very short duration that provides frequency diversity and multipath resolution. UWB channels raise new effects in the receiver, the amplitude fading statistics being different compared to the conventional narrow band wireless channels. Here we focus on modeling of ultra-wide band channels, especially for simulation of personal area networks and also discuss the benefits, application potential and technical challenges in wideband communication. The concept of Orthogonal Frequency Division Multiplexing (OFDM) has recently been applied in wireless communication systems due to its high data rate transmission capability with high bandwidth efficiency and its robustness to multi-path delay. UWB OFDM communication was proposed for physical layer in the IEEE 802.15.3a standard which covers wideband communication in wireless personal area networks. Since the channel model for multicarrier UWB communication is different from that of plain ultra-wide band channel, a novel modification method in UWB channel model is proposed with specific center frequency and multipath resolution. Moreover, dynamic channel estimation is necessary before demodulation of UWB OFDM signals since the radio channel is time varying and frequency selective for wideband systems. The performance of the proposed method is statistically analyzed using LS and MMSE based channel estimation methods.
Effective Voice Calls Admission for Authorized User in Inter VOIP Network
Subashri T,Vaidehi V
International Journal of Network Security & Its Applications , 2010,
Abstract: IP based voice transmission technology is a flexible, simpler and a cost effective implementation of voicetransmission. It provides a real convergence of various networks. This voice transmission technology doesnot support a quality that is equivalent to digitized voice, which is available in the existing PSTN networks.In addition to this, data network vulnerabilities affect the VOIP service causing a drop in the utilization ofvoice communication. In this paper, the quality of service for voice calls is ensured with the integration ofCAC mechanism with the bandwidth link utilization which makes an estimation of the demandedbandwidth. In terms of security, prevention of ARP cache poisoning attack is achieved by use of the signedMAC address response in local area networks. It makes the network confident that the admitted user is anauthorized user and also it verifies that only the authorized users’ information is exchanged over the localarea network. Also an approach that makes it difficult for the hacker’s to hack the data exchanged over thequality channel has been proposed.
Performance Analysis of Soft Computing Based Anomaly Detectors
N. Srinivasan,V. Vaidehi
International Journal of Network Security , 2008,
Abstract: Anomaly detectors have become a necessary component of the computer and information security framework. Some of the numerous drawbacks experienced by the current Anomaly detectors are large number of false positive and false negative alarms, difficulty in processing huge amount of traffic in real time, inadequacy in novel attack recognition and non-scalability. Consequently their efficacy in protecting against anomalies is limited. The use of soft computing techniques like Genetic algorithms, Neural networks and Fuzzy logic in implementing Anomaly detection is perused in this paper. Additionally, a few novel approaches for the detection of anomalies by identifying user actions and network traffic that might compromise a system's secure state, is also proposed. A potential solution to the problem has been contemplated, by comparing the performance of these systems based on various criteria. Characterization of the behavior of a single user (Host based) or a network (Network based) and recognition of anomalies through observation of deviation from normal behavior patterns are conducted to arrive at the solution. The implementations of Genetic algorithm based Anomaly detection system (GAAD), Neural network based Anomaly detection system (NNAD) and Fuzzy Logic based system (FLAD) are reported. Interesting conclusions are deduced from an exhaustive evaluation and comparison of the performance of these systems enabling an administrator to choose the best solution for a given scenario.
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