Department of Physics

Indian Institute of Technology Palakkad&nbsp;(IIT Palakkad or IIT PKD) is a public autonomous&nbsp;engineering&nbsp;and&nbsp;research&nbsp;institute located in&nbsp;Palakkad,&nbsp;Kerala. It was&nbsp;one of the five new&nbsp;IITs&nbsp;proposed in the&nbsp;2014 Union budget of India. The campus was inaugurated on 3 August 2015. The institute has 94 faculty, 978 students, and 63 non-teaching staffs.

IT Palakkad currently offers four-year Bachelor of Technology (B.Tech) and two years MS programmes in 8 different engineering disciplines including&nbsp;Computer Science, Electrical, Mechanical, Civil among others.

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IIT Palakkad

The currently accepted model of biological membranes involves a heterogeneous, highly dynamic organization, where certain lipids and proteins associate to form cooperative platforms ("rafts") for cellular signaling or transport processes. Ceramides, a lipid species occurring under conditions of cellular stress and apoptosis, are considered to stabilize these platforms, thus modulating cellular function. The present study focuses on a previously unrecognized effect of ceramide generation. In agreement with previous studies, we find that ceramide leads to a depletion of sphingomyelin from mixtures with palmitoyl oleoyl phosphatidylcholine bilayers, forming a ceramide-sphingomyelin-rich gel phase that coexists with a fluid phase rich in palmitoyl oleoyl phosphatidylcholine. Interestingly, however, this latter phase has an almost fourfold smaller bending rigidity compared to a sphingomyelin-palmitoyl oleoyl phosphatidylcholine mixture lacking ceramide. The significant change of membrane bulk properties can have severe consequences for conformational equilibria of membrane proteins. We discuss these effects in terms of the lateral pressure profile concept for a simple geometric model of an ion channel and find a significant inhibition of its activity. © 2009 Springer Science+Business Media, LLC.

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Journal of Membrane Biology

Effect of ceramide on nonraft proteins

Fulltext

Acta Crystallographica Section A Foundations of Crystallography

Coexisting lipid domains

We present an exact result for the nonadiabatic transition probability and hence the defect density in the final state of a one-dimensional Kitaev model following a slow quench of the parameter J-, which estimates the anisotropy between the interactions, as J- (t) ∼- | t/τ |. Here, time t goes from - to + and τ defines the rate of change in the Hamiltonian. In other words, the spin chain initially prepared in its ground state is driven by changing J- linearly in time up to the quantum critical point, which in the model considered here occurs at t=0, reversed and then gradually decreased to its initial value at the same rate. We have thoroughly compared the reverse quenching with its counterpart forward quenching, i.e., J- ∼t/τ. Our exact calculation shows that the probability of excitations is zero for the wave vector at which the instantaneous energy gap is zero at the critical point J- =0 as opposed to the maximum value of unity in the forward quenching. It is also shown that the defect density in the final state following a reverse quenching, we propose here, is nearly half of the defects generated in the forward quenching. We argue that the defects produced when the system reaches the quantum critical point get redistributed in the wave-vector space at the final time in case of reverse quenching whereas it keeps on increasing until the final time in the forward quenching. We study the entropy density and also the time evolution of the diagonal entropy density in the case of the reverse quenching and compare it with the forward case. © 2009 The American Physical Society.

Physical Review B - Condensed Matter and Materials Physics

Reverse quenching in a one-dimensional Kitaev model

We investigated the mechanism by which heparin enhances the binding of vascular endothelial growth factor (VEGF) to the extracellular matrix protein fibronectin. In contrast to other systems, where heparin acts as a protein scaffold, we found that heparin functions catalytically to modulate VEGF binding site availability on fibronectin. By measuring the binding of VEGF and heparin to surface-immobilized fibronectin, we show that substoichiometric amounts of heparin exposed cryptic VEGF binding sites within fibronectin that remain available after heparin removal. Measurement of association and dissociation kinetics for heparin binding to fibronectin indicated that the interaction is rapid and transient. We localized the heparin-responsive element to the C-terminal 40-kDa Hep2 domain of fibronectin. A mathematical model of this catalytic process was constructed that supports a mechanism whereby the heparin-induced conformational change in fibronectin is accompanied by release of heparin. Experiments with endothelial extracellular matrix suggest that this process may also occur within biological matrices. These results indicate a novel mechanism whereby heparin catalyzes the conversion of fibronectin to an open conformation by transiently interacting with fibronectin and progressively hopping from molecule to molecule. Catalytic activation of the extracellular matrix might be an important mechanism for heparin to regulate function during normal and disease states. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Journal of Biological Chemistry

A catalytic role of heparin within the extracellular matrix

In this paper we review the quenching dynamics of a quantum XY spin-1/2 chain in the presence of a transverse field, when the transverse field or the anisotropic interaction is quenched at a slow but uniform rate. We also extend the results to the cases in which the system starts with any arbitrary initial condition as opposed to the initial fully magnetically aligned state which has been extensively studied earlier. The evolution is non-adiabatic in the time interval when the parameters are close to their critical values, and is adiabatic otherwise. The density of defects produced due to non-adiabatic transitions is calculated by mapping the many-particle system to an equivalent Landau-Zener problem. We show that in one dimension the density of defects in the final state scales as 1/√τ irrespective of the initial condition, where τ is the quenching time-scale. However, the magnitude of density of defects is found to depend on the initial condition. © Indian Academy of Sciences.

Pramana - Journal of Physics

Quenching dynamics of a quantum XY spin-1/2 chain in the presence of transverse field by the application of a generalized Landau-Zener formula

In many intracellular processes, the length distribution of microtubules is controlled by depolymerizing motor proteins. Experiments have shown that, following non-specific binding to the surface of a microtubule, depolymerizers are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. We develop a quantitative model to study the depolymerizing action of such a generic motor protein, and its possible effects on the length distribution of microtubules. We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the length distribution is, in general, non-monotonic with a single peak. However, for highly processive motors and large motor densities, this distribution effectively becomes an exponential decay. Our findings suggest that such motor proteins may be selectively used by the cell to ensure precise control of MT lengths. The model is also used to analyze experimental observations of motor-induced depolymerization. © 2008 Europhysics Letters Association.

Length control of microtubules by depolymerizing motor proteins

We use a quenching scheme to study the dynamics of a one-dimensional anisotropic XY spin-1/2 chain in the presence of a transverse field which alternates between the values h+δ and h-δ from site to site. In this quenching scheme, the parameter denoting the anisotropy of interaction (γ) is linearly quenched from -∞ to +∞ as γ=t/τ, keeping the total strength of interaction J fixed. The system traverses through a gapless phase when γ is quenched along the critical surface h2 = δ2 + J2 in the parameter space spanned by h, δ, and γ. By mapping to an equivalent two-level Landau-Zener problem, we show that the defect density in the final state scales as 1/ τ1/3, a behavior that has not been observed in previous studies of quenching through a gapless phase. We also generalize the model incorporating additional alternations in the anisotropy or in the strength of the interaction and derive an identical result under a similar quenching. Based on the above results, we propose a general scaling of the defect density with the quenching rate τ for quenching along a gapless critical line. © 2008 The American Physical Society.

Quenching along a gapless line: A different exponent for defect density

We study the breakdown of a random fiber bundle model (RFBM) with n discontinuities in the threshold distribution using the global load sharing scheme. In other words, n+1 different classes of fibers identified on the basis of their threshold strengths are mixed such that the strengths of the fibers in the ith class are uniformly distributed between the values σ2i-2 and σ2i-1, where 1≤i≤n+1. Moreover, there is a gap in the threshold distribution between ith and (i+1) -th class. We show that although the critical stress depends on the parameter values of the system, the critical exponents are identical to that obtained in the recursive dynamics of a RFBM with a uniform distribution and global load sharing. The avalanche size distribution, on the other hand, shows a nonuniversal, non-power-law behavior for smaller values of avalanche sizes which becomes prominent only when a critical distribution is approached. We establish that the behavior of the avalanche size distribution for an arbitrary n is qualitatively similar to a RFBM with a single discontinuity in the threshold distribution (n=1), especially when the density and the range of threshold values of fibers belonging to strongest (n+1) -th class is kept identical in all the cases. © 2008 The American Physical Society.

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Random fiber bundle with many discontinuities in the threshold distribution

We study the quantum dynamics of a one-dimensional spin- 1 2 anisotropic XY model in a transverse field when the transverse field or the anisotropic interaction is quenched at a slow but uniform rate. The two quenching schemes are called transverse and anisotropic quenching, respectively. Our emphasis in this paper is on the anisotropic quenching scheme, and we compare the results with those of the other scheme. In the process of anisotropic quenching, the system crosses all the quantum critical lines of the phase diagram where the relaxation time diverges. The evolution is nonadiabatic in the time interval when the parameters are close to their critical values, and is adiabatic otherwise. The density of defects produced due to nonadiabatic transitions is calculated by mapping the many-particle system to an equivalent Landau-Zener problem and is generally found to vary as 1 τ, where τ is the characteristic time scale of quenching, a scenario that supports the Kibble-Zurek mechanism. Interestingly, in the case of anisotropic quenching, there exists an additional nonadiabatic transition, in comparison to the transverse quenching case, with the corresponding probability peaking at an incommensurate value of the wave vector. In the special case in which the system passes through a multicritical point, the defect density is found to vary as 1 τ1 6. The von Neumann entropy of the final state is shown to maximize at a quenching rate around which the ordering of the final state changes from antiferromagnetic to ferromagnetic. © 2007 The American Physical Society.

Quenching dynamics of a quantum XY spin- 1 2 chain in a transverse field

In this article, we briefly review the critical behaviour of a long-range percolation model in which any two sites are connected with a probability that falls off algebraically with the distance. The results of this percolation transition are used to describe the quantum phase transitions in a dilute transverse Ising model at the percolation threshold pc of the long-range connected lattice. In the similar spirit, we propose a new model of a contact process defined on the same long-range diluted lattice and explore the transitions at pc. The long-range nature of the percolation transition allows us to evaluate some critical exponents exactly in both the above models. Moreover, mean field theory is valid for a wide region of parameter space. In either case, the strength of Griffiths McCoy singularities are tunable as the range parameter is varied. © 2007 Elsevier B.V. All rights reserved.