Atomistic insights into solvation dynamics and conformational transformation in thermo-sensitive and non-thermo-sensitive oligomers

Solvation dynamics and conformational transformation in oligomers with varying degree of temperature sensitivity is studied using molecular dynamics (MD) simulations. Conformational transformation in three model systems namely poly(N-isopropylacrylamide) (PNIPAM), poly(acrylamide) (PAA), and poly(ethylene glycol) (PEG) are compared and contrasted to understand the origin of a coil-to-globule transformations across the lower critical solution temperature (LCST) in thermo-sensitive oligomers. PNIPAM, PAA, and PEG are water-soluble oligomers. However, for the temperature range used in these simulations, PNIPAM shows an LCST whereas PAA and PEG are non-thermo-sensitive. Oligomers of PNIPAM, PAA, and PEG consisting of 30 monomer units (30-mer) each were simulated at 5 °C (278 K) and 37 °C (310 K). Conformational transformations in the oligomers are evaluated using structural and dynamical correlation functions such as radius of gyration, radial distribution function, residence time probabilities and hydrogen-bonding life-times. Our simulations suggest that the solubility, solvation dynamics, and conformation of the oligomers are dictated by two factors: (a) the local structure of proximal water and (b) the diffusion and exchange kinetics of proximal water with bulk water. In thermo-sensitive oligomer such as PNIPAM, we find that the coil-to-globule transition is closely related to the local ordering and solvation dynamics of PNIPAM. We have identified stable configurations of proximal water molecules for an oligomer undergoing conformational transition. The slow diffusional properties of proximal water molecules near PNIPAM oligomers suggests that water forms a stable network near hydrophilic groups of PNIPAM as compared to the hydrophilic groups of PAA and PEG. Thermal perturbation of this solvated structure results in significant reduction in local ordering of water, which contributes to the globular collapse and the reduced solubility of PNIPAM above its LCST. On the other hand, non-thermo-sensitive oligomers such as PAA and PEG are characterized by much faster diffusion and exchange kinetics of proximal water at the two simulated temperatures compared to PNIPAM. This faster exchange kinetics helps in maintaining higher hydration level of the oligomers and is responsible for the apparent hydrophilic character and thereby the observed solubility at the two simulated temperatures.     

Performance of cellular packet CDMA in an integrated voice/data network

This paper presents a simulation-based study of cellular packet CDMA systems operating in an integrated voice/data traffic scenario. Spread-spectrum CDMA provides a suitable framework for resource-shared packet transport capable of combining isochronous (voice, ISDN) and bursty data services. In this work, a general network model for cellular packet CDMA with mixed voice/data traffic is described and used to evaluate the capacity/performance impact of several key system parameters. First, the effect of spreading factor (N) and forward error correction (FEC) rate are studied, confirming earlier work indicating a weak dependence onN and a well-defined optimum code rate in the range of 0.5–0.7 (with BCH coding). Next, the effect of propagation loss coefficient () on network capacity is investigated over a range of possible assumptions for, including both constant and distance-dependent models. The results show that system capacity depends strongly on, varying by as much as a factor of 2 over the range of parameters considered. For a given distance-dependent assumption, performance results are also obtained for different cell sizes in order to understand the overall spatial reuse efficiency achievable in different cellular and microcellular scenarios. This is followed by an investigation of traffic source model effects: first the capacity improvement from voice activity detection VAD) is presented, showing the expected 21 gains. Results for varying proportions of voice and data traffic intensities indicate that the operating efficiency does not change significantly as the proportion of bursty data relative to voice is varied.     

The role of tackifiers on the auto-adhesion behavior of EPDM rubber

The article describes the effect of hydrocarbon (HC) and coumarone-indene (CI) resin tackifiers on autohesion behavior of ethylene propylene diene polymethylene (EPDM) rubber. The viscoelastic behavior and nature of compatibility of EPDM/tackifier blends were studied by means of dynamic mechanical analysis. Furthermore, scanning electron microscopy and atomic force microscopy were used to understand the compatibility of the EPDM/tackifier blends. The HC tackifying resin modified the viscoelastic properties of the EPDM rubber in such a way that it behaved as a plasticizer at lower frequency by reducing the storage modulus and filler at higher frequency by increasing the storage modulus. On the contrary, the CI modified EPDM rubber did not show similar behavior; the modulus enhanced throughout the entire frequency range. The viscosity of the matrix was found to be highly governed by the compatibility as well as amount of tackifier present in the blend. In order to explain the tack behavior, several tack governing factors such as green strength, creep compliance, entanglement molecular weight, relaxation time, self-diffusion coefficient, and monomer friction coefficient (ζ₀) were investigated. The tack strength increased with HC tackifier loading up to 24 parts per hundred grams of rubber (phr), beyond which a plateau region was observed. A maximum of 196% improvement was observed at 24 phr HC loaded sample as compared to gum EPDM rubber devoid of tackifier. Conversely, there was a marginal improvement of tack strength (36%) up to 8 phr loading for the system containing CI, beyond which it dropped.     

Congestion notification and probing mechanisms for endpoint admission control

There has been much interest in admission control schemes that place the burden of admission control decisions on the end users. In these schemes, referred to as Endpoint Admission Control, the decision to join the network is taken by the user, based on the probing of the network using probe packets. Depending on the level of congestion, routers mark the probe packets and thus inform the user of the state of the network. In this paper, we analyze three mechanisms for providing Endpoint Admission Control: virtual-queue marking, random-early marking and tail drop. For each scheme, we analyze the probing duration necessary to guarantee the required QoS and achieve high link utilization. Our main conclusion is that very few probe packets have to be sent when early marking is used, whereas tail drop requires a large number of probe packets.     

A Comparative Study of Methods of Clock Ensemble Development

An ensemble of clocks is the first step towards the realization of a timescale. A timescale is the estimate of phase and frequency of the “perfect” clock derived from the phase and frequency of the clocks which participate in the ensemble. Three methods of clock ensembling viz. a Kalman filter based formulation, a multi-scale ensemble timescale based on minimizing the ADEV and an ensemble using artificial neural networks have been discussed in this paper and a comparative study has been performed.     

SMTIBEA: a hybrid multi-objective optimization algorithm for configuring large constrained software product lines

Software and Systems Modeling - A key challenge to software product line engineering is to explore a huge space of various products and to find optimal or near-optimal solutions that satisfy all...     

Studies on the growth and stability of silver nanoparticles synthesized by electron beam irradiation

Stable Ag nanoparticles have been synthesized by irradiating an aqueous solution of AgNO₃ and Poly-vinyl alcohol (PVA) with 8 MeV electrons from a Microtron. The rate of formation of nanoparticles could be controlled by changing either the irradiation dosage or the relative concentration of the precursors. The size, shape, and the rate of formation of the nanoparticles depend on the final dosage, as well as the weight ratio of AgNO₃ and PVA. The formation of Ag nanoparticles and their size were established through UV–Vis spectroscopy and Transmission electron microscopy (TEM) analysis, respectively. Increasing the irradiation dosage seem to favour the formation of polygonal nanostructures. Differential scanning calorimetry (DSC) measurements show that there exists a strong interaction between the PVA matrix and the Ag nanoparticles.     

A Physics-driven Neural Networks-based Simulation System (PhyNNeSS) for multimodal interactive virtual environments involving nonlinear deformable objects

BACKGROUND: While an update rate of 30 Hz is considered adequate for real time graphics, a much higher update rate of about 1 kHz is necessary for haptics. Physics-based modeling of deformable objects, especially when large nonlinear deformations and complex nonlinear material properties are involved, at these very high rates is one of the most challenging tasks in the development of real time simulation systems. While some specialized solutions exist, there is no general solution for arbitrary nonlinearities. METHODS: In this work we present PhyNNeSS - a Physics-driven Neural Networks-based Simulation System - to address this long-standing technical challenge. The first step is an off-line pre-computation step in which a database is generated by applying carefully prescribed displacements to each node of the finite element models of the deformable objects. In the next step, the data is condensed into a set of coefficients describing neurons of a Radial Basis Function network (RBFN). During real-time computation, these neural networks are used to reconstruct the deformation fields as well as the interaction forces. RESULTS: We present realistic simulation examples from interactive surgical simulation with real time force feedback. As an example, we have developed a deformable human stomach model and a Penrose-drain model used in the Fundamentals of Laparoscopic Surgery (FLS) training tool box. CONCLUSIONS: A unique computational modeling system has been developed that is capable of simulating the response of nonlinear deformable objects in real time. The method distinguishes itself from previous efforts in that a systematic physics-based pre-computational step allows training of neural networks which may be used in real time simulations. We show, through careful error analysis, that the scheme is scalable, with the accuracy being controlled by the number of neurons used in the simulation. PhyNNeSS has been integrated into SoFMIS (Software Framework for Multimodal Interactive Simulation) for general use.     

Electrostatic assembly of nanoparticles and biomacromolecules

The controlled assembly of nanoparticles in thin film form on solid supports, both as monolayers and as superlattice structures, is a problem of considerable topical interest. Among the many interactions used to program the assembly of nanoparticles, electrostatic forces are particularly interesting for many reasons. This Account deals with assembling surface-modified nanoparticles in thin film form using electrostatic interactions at the air-water interface and in thermally evaporated lipid films. The generality of the electrostatic assembly protocol is demonstrated in the immobilization of DNA and proteins in lipid films.     

Triplex formation at physiological pH by oligonucleotides incorporating 5-Me-dC-(N4-spermine)

Oligonucleotide (ODN) directed triplex formation has therapeutic importance and depends on Hoogsteen hydrogen bonds between a duplex DNA and a third strand. While T*A:T triplets are formed at neutral pH, C+*G:C are favoured at acidic pH. Herein it is shown that 18-mer ODN containing spermine conjugated to 5-Me-dC at N4 (1-5), form triplexes with complementary 24-mer duplex 8:9 at neutral pH (7.3, 100 mM NaCl). Under such conditions, control ODN's carrying dC (6) or 5-Me-dC (7) did not show any triple helix formation. Remarkably, the triplexes from spermine-conjugates (1-5) have foremost stability at neutral pH (7.1), unlike the behavior of normal ODN's where optimal stability is at acidic pH (5.5). These results have importance in designing oligonucleotides for antigene applications.