Stability of synchronization in a multi-cellular system

Networks of biochemical reactions regulated by positive-and negative-feedback processes underlie functional dynamics in single cells. Synchronization of dynamics in the constituent cells is a hallmark of collective behavior in multi-cellular biological systems. Stability of the synchronized state is required for robust functioning of the multi-cell system in the face of noise and perturbation. Yet, the ability to respond to signals and change functional dynamics are also important features during development, disease, and evolution in living systems. In this paper, using a coupled multi-cell system model, we investigate the role of system size, coupling strength and its topology on the synchronization of the collective dynamics and its stability. Even though different coupling topologies lead to synchronization of collective dynamics, diffusive coupling through the end product of the pathway does not confer stability to the synchronized state. The results are discussed with a view to their prevalence in biological systems. Copyright (C) EPLA, 2010

Prediction of the Indian summer monsoon rainfall using a state-of-the-art coupled ocean-atmosphere model

A state-of-the-art model of the coupled ocean-atmosphere system, the climate forecast system (CFS), from the National Centres for Environmental Prediction (NCEP), USA, has been ported onto the PARAM Padma parallel computing system at the Centre for Development of Advanced Computing (CDAC), Bangalore and retrospective predictions for the summer monsoon (June-September) season of 2009 have been generated, using five initial conditions for the atmosphere and one initial condition for the ocean for May 2009. Whereas a large deficit in the Indian summer monsoon rainfall (ISMR; June-September) was experienced over the Indian region (with the all-India rainfall deficit by 22% of the average), the ensemble average prediction was for above-average rainfall during the summer monsoon. The retrospective predictions of ISMR with CFS from NCEP for 1981-2008 have been analysed. The retrospective predictions from NCEP for the summer monsoon of 1994 and that from CDAC for 2009 have been compared with the simulations for each of the seasons with the stand-alone atmospheric component of the model, the global forecast system (GFS), and observations. It has been shown that the simulation with GFS for 2009 showed deficit rainfall as observed. The large error in the prediction for the monsoon of 2009 can be attributed to a positive Indian Ocean Dipole event seen in the prediction from July onwards, which was not present in the observations. This suggests that the error could be reduced with improvement of the ocean model over the equatorial Indian Ocean.

Density-matrix renormalization-group studies of the spin-1/2 Heisenberg system with dimerization and frustration

Using the density-matrix renormalization-group technique, we study the ground-state phase diagram and other low-energy properties of an isotropic antiferromagnetic spin-1/2 chain with both dimerization and frustration, i.e., an alternation delta of the nearest-neighbor exchanges and a next-nearest-neighbor exchange J(2). For delta = 0, the system is gapless for J(2) < J(2c) and has a gap for J(2) > J(2c) where J(2c) is about 0.241. For J(2) = J(2c) the gap above the ground state grows as delta to the power 0.667 +/- 0.001. In the J(2)-delta plane, there is a disorder line 2J(2) + delta = 1. To the left of this line, the peak in the static structure factor S(q) is at q(max) = pi (Neel phase), while to the right of the line, q(max) decreases from pi to pi/2 as J(2) is increased to large values (spiral phase). For delta = 1, the system is equivalent to two coupled chains as on a ladder and it is gapped for all values of the interchain coupling.

Peristaltic transport of a biofluid in a pipe of elliptic cross section

Peristaltic transport of two fluids occupying the peripheral layer and the core in an elliptic tube is, investigated in elliptic cylindrical co-ordinate system, under long wavelength and low Reynolds number approximations. The effect of peripheral-layer viscosity on the flow rate and the frictional force for a slightly elliptic tube is discussed. The limiting results for the one-fluid model are obtained for different eccentricities of the undisturbed tube cross sections with the same area. As a result of non-uniformity of the peristaltic wave, two different amplitude ratios are defined and the time-averaged flux and mechanical efficiency are studied for different eccentricities. It is observed that the time-averaged flux is not affected significantly by the pressure drop when the eccentricity is large. For the peristaltic waves with same area variation, the pumping seems to improve with the eccentricity.

Two-Parameter Uniformly Elliptic Sturm–Liouville Problems With Eigenparameter-Dependent Boundary Conditions

We consider the two-parameter Sturm–Liouville system $$ -y_1''+q_1y_1=(\lambda r_{11}+\mu r_{12})y_1\quad\text{on }[0,1], $$ with the boundary conditions $$ \frac{y_1'(0)}{y_1(0)}=\cot\alpha_1\quad\text{and}\quad\frac{y_1'(1)}{y_1(1)}=\frac{a_1\lambda+b_1}{c_1\lambda+d_1}, $$ and $$ -y_2''+q_2y_2=(\lambda r_{21}+\mu r_{22})y_2\quad\text{on }[0,1], $$ with the boundary conditions $$ \frac{y_2'(0)}{y_2(0)} =\cot\alpha_2\quad\text{and}\quad\frac{y_2'(1)}{y_2(1)}=\frac{a_2\mu+b_2}{c_2\mu+d_2}, $$ subject to the uniform-left-definite and uniform-ellipticity conditions; where $q_{i}$ and $r_{ij}$ are continuous real valued functions on $[0,1]$, the angle $\alpha_{i}$ is in $[0,\pi)$ and $a_{i}$, $b_{i}$, $c_{i}$, $d_{i}$ are real numbers with $\delta_{i}=a_{i}d_{i}-b_{i}c_{i}>0$ and $c_{i}\neq0$ for $i,j=1,2$. Results are given on asymptotics, oscillation of eigenfunctions and location of eigenvalues.

Coupled Climate Model on Grids

Community Climate System Model (CCSM) is a Multiple Program Multiple Data (MPMD) parallel global climate model comprising atmosphere, ocean, land, ice and coupler components. The simulations have a time-step of the order of tens of minutes and are typically performed for periods of the order of centuries. These climate simulations are highly computationally intensive and can take several days to weeks to complete on most of today’s multi-processor systems. ExecutingCCSM on grids could potentially lead to a significant reduction in simulation times due to the increase in number of processors. However, in order to obtain performance gains on grids, several challenges have to be met. In this work,we describe our load balancing efforts in CCSM to make it suitable for grid enabling.We also identify the various challenges in executing CCSM on grids. Since CCSM is an MPI application, we also describe our current work on building a MPI implementation for grids to grid-enable CCSM.

Adaptive Executions of Multi-Physics Coupled Applications on Batch Grids

Long running multi-physics coupled parallel applications have gained prominence in recent years. The high computational requirements and long durations of simulations of these applications necessitate the use of multiple systems of a Grid for execution. In this paper, we have built an adaptive middleware framework for execution of long running multi-physics coupled applications across multiple batch systems of a Grid. Our framework, apart from coordinating the executions of the component jobs of an application on different batch systems, also automatically resubmits the jobs multiple times to the batch queues to continue and sustain long running executions. As the set of active batch systems available for execution changes, our framework performs migration and rescheduling of components using a robust rescheduling decision algorithm. We have used our framework for improving the application throughput of a foremost long running multi-component application for climate modeling, the Community Climate System Model (CCSM). Our real multi-site experiments with CCSM indicate that Grid executions can lead to improved application throughput for climate models.

A Flexible Crypto-system Based upon the REDEFINE Polymorphic ASIC Architecture

The highest levels of security can be achieved through the use of more than one type of cryptographic algorithm for each security function. In this paper, the REDEFINE polymorphic architecture is presented as an architecture framework that can optimally support a varied set of crypto algorithms without losing high performance. The presented solution is capable of accelerating the advanced encryption standard (AES) and elliptic curve cryptography (ECC) cryptographic protocols, while still supporting different flavors of these algorithms as well as different underlying finite field sizes. The compelling feature of this cryptosystem is the ability to provide acceleration support for new field sizes as well as new (possibly proprietary) cryptographic algorithms decided upon after the cryptosystem is deployed.

Synchronization of globally coupled two-state stochastic oscillators with a state-dependent refractory period

We present a model of identical coupled two-state stochastic units, each of which in isolation is governed by a fixed refractory period. The nonlinear coupling between units directly affects the refractory period, which now depends on the global state of the system and can therefore itself become time dependent. At weak coupling the array settles into a quiescent stationary state. Increasing coupling strength leads to a saddle node bifurcation, beyond which the quiescent state coexists with a stable limit cycle of nonlinear coherent oscillations. We explicitly determine the critical coupling constant for this transition.

How good are the simulations of tropical SST-rainfall relationship by IPCC AR4 atmospheric and coupled models?

The failure of atmospheric general circulation models (AGCMs) forced by prescribed SST to simulate and predict the interannual variability of Indian/Asian monsoon has been widely attributed to their inability to reproduce the actual sea surface temperature (SST)-rainfall relationship in the warm Indo-Pacific oceans. This assessment is based on a comparison of the observed and simulated correlation between the rainfall and local SST. However, the observed SSTconvection/rainfall relationship is nonlinear and for this a linear measure such as the correlation is not an appropriate measure. We show that the SST-rainfall relationship simulated by atmospheric and coupled general circulation models in IPCC AR4 is nonlinear, as observed, and realistic over the tropical West Pacific (WPO) and the Indian Ocean (IO). The SST-rainfall pattern simulated by the coupled versions of these models is rather similar to that from the corresponding atmospheric one, except for a shift of the entire pattern to colder/warmer SSTs when there is a cold/warm bias in the coupled version.

Modeling the vulnerability of an urban groundwater system due to the combined impacts of climate change and management scenarios

Climate change impact on a groundwater-dependent small urban town has been investigated in the semiarid hard rock aquifer in southern India. A distributed groundwater model was used to simulate the groundwater levels in the study region for the projected future rainfall (2012-32) obtained from a general circulation model (GCM) to estimate the impacts of climate change and management practices on groundwater system. Management practices were based on the human-induced changes on the urban infrastructure such as reduced recharge from the lakes, reduced recharge from water and wastewater utility due to an operational and functioning underground drainage system, and additional water extracted by the water utility for domestic purposes. An assessment of impacts on the groundwater levels was carried out by calibrating a groundwater model using comprehensive data gathered during the period 2008-11 and then simulating the future groundwater level changes using rainfall from six GCMs Institute of Numerical Mathematics Coupled Model, version 3.0 (INM-CM. 3.0); L'Institut Pierre-Simon Laplace Coupled Model, version 4 (IPSL-CM4); Model for Interdisciplinary Research on Climate, version 3.2 (MIROC3.2); ECHAM and the global Hamburg Ocean Primitive Equation (ECHO-G); Hadley Centre Coupled Model, version 3 (HadCM3); and Hadley Centre Global Environment Model, version 1 (HadGEM1)] that were found to show good correlation to the historical rainfall in the study area. The model results for the present condition indicate that the annual average discharge (sum of pumping and natural groundwater outflow) was marginally or moderately higher at various locations than the recharge and further the recharge is aided from the recharge from the lakes. Model simulations showed that groundwater levels were vulnerable to the GCM rainfall and a scenario of moderate reduction in recharge from lakes. Hence, it is important to sustain the induced recharge from lakes by ensuring that sufficient runoff water flows to these lakes.

CUDA-for-clusters: a system for efficient execution of CUDA kernels on multi-core clusters

Rapid advancements in multi-core processor architectures coupled with low-cost, low-latency, high-bandwidth interconnects have made clusters of multi-core machines a common computing resource. Unfortunately, writing good parallel programs that efficiently utilize all the resources in such a cluster is still a major challenge. Various programming languages have been proposed as a solution to this problem, but are yet to be adopted widely to run performance-critical code mainly due to the relatively immature software framework and the effort involved in re-writing existing code in the new language. In this paper, we motivate and describe our initial study in exploring CUDA as a programming language for a cluster of multi-cores. We develop CUDA-For-Clusters (CFC), a framework that transparently orchestrates execution of CUDA kernels on a cluster of multi-core machines. The well-structured nature of a CUDA kernel, the growing popularity, support and stability of the CUDA software stack collectively make CUDA a good candidate to be considered as a programming language for a cluster. CFC uses a mixture of source-to-source compiler transformations, a work distribution runtime and a light-weight software distributed shared memory to manage parallel executions. Initial results on running several standard CUDA benchmark programs achieve impressive speedups of up to 7.5X on a cluster with 8 nodes, thereby opening up an interesting direction of research for further investigation.

A spectral multiscale method for wave propagation analysis: Atomistic-continuum coupled simulation

In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a 2D square Bravais lattice, and a 2D triangular lattice with microcrack demonstrate the accuracy and the robustness of the method. In addition, under certain conditions, this method can simulate complex dynamics of crystalline solids involving different spatial and/or temporal scales with sufficient accuracy and efficiency. (C) 2014 Elsevier B.V. All rights reserved.

Solar driven Adsorption Desalination system

Desalination is one of the most traditional processes to generate potable water. With the rise in demand for potable water and paucity of fresh water resources, this process has gained special importance. Conventional thermal desalination processes involves evaporative methods such as multi-stage flash and solar distils, which are found to be energy intensive, whereas reverse osmosis based systems have high operating and maintenance costs. The present work describes the Adsorption Desalination (AD) system, which is an emerging process of thermal desalination cum refrigeration capable of utilizing low grade heat easily obtainable from even non-concentrating type solar collectors. The system employs a combination of flash evaporation and thermal compression to generate cooling and desalinated water. The current study analyses the system dynamics of a 4-bed single stage silica-gel plus water based AD system. A lumped model is developed using conservation of energy and mass coupled with the kinetics of adsorption/desorption process. The constitutive equations for the system components viz. evaporator, adsorber and condenser, are solved and the performance of the system is evaluated for a single stage AD system at various condenser temperatures and cycle times to determine optimum operating conditions required for desalination and cooling. (C) 2013 P. Dutta. Published by Elsevier Ltd.

Optimal error estimate using mesh equidistribution technique for singularly perturbed system of reaction-diffusion boundary-value problems

In this article, we study the problem of determining an appropriate grading of meshes for a system of coupled singularly perturbed reaction-diffusion problems having diffusion parameters with different magnitudes. The central difference scheme is used to discretize the problem on adaptively generated mesh where the mesh equation is derived using an equidistribution principle. An a priori monitor function is obtained from the error estimate. A suitable a posteriori analogue of this monitor function is also derived for the mesh construction which will lead to an optimal second-order parameter uniform convergence. We present the results of numerical experiments for linear and semilinear reaction-diffusion systems to support the effectiveness of our preferred monitor function obtained from theoretical analysis. (C) 2014 Elsevier Inc. All rights reserved.