Curriculum Vitae

Prasanth P. Jose

• Educational Qualifications and Work Experience:
  • Education:
    1. Bachelor of Science in Physics (Major: Physics and Minors: Mathematics and Computer Science) from University of Calicut, Kozhikode, India, 1996.
    2. Master of Science in Physics (Specialization: Solid state physics) from Cochin University of Science and Technology, Kochi, India, 1999.
    3. Ph.D in Statistical Mechanics (Specialization: Soft condensed matter, Phase transitions, Computational Physics/Chemistry) from Indian Institute of Science, Bangalore, Karnataka, India, 2006.
    4. Title of the thesis: Dynamics of liquid crystals near Isotropic-Nematic phase transition and some contributions to density relaxation in non-equilibrium systems.
    5. Thesis Supervisor : Prof. Biman Bagchi
  • Work Experience:
    1. Post-doctoral Fellow at Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
    2. Duration-Jan 2006 - July 2008.
    3. Project Title: Structure and dynamics of semidilute polymer solution under steady shear flow
    4. Duties: model and simulate the system, identify microscopic processes and verify the existing theoretical models.
    5. Post-Doctoral Advisor: Prof. Grzegorz Szamel
    6. Post-doctoral Fellow at Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA.
    7. Duration-Aug 2008 - July 2010.
    8. Project Title: Molecular simulations of protein unfolding
    9. Post-Doctoral Advisor: Prof. Ioan Andricioaei
• Research Interests :
  • Theoretical and computational studies of simple liquids, liquid crystals, polymer melts and solutions, bio-molecules. Computational studies of protein folding. Phase transitions and study of microscopic dynamics and transport properties during phase transitions. Modelling of polymer melt and solutions using model potentials. Another area of interest is in modelling of phase transition of bulk and confined water; also modeling of water in biological systems. Study of dynamics of phase transitions in liquid crystals is another area of interest.
  • List of Publications:
    1. Similarities between protein folding and granular jamming, Prasanth P. Jose and Ioan Andricioaei, Nature Communications 3, 1161 (2012).
    2. Thermodynamic and transport anomalies near isotropic-nematic phase transition, Prasanth P. Jose, and Biman Bagchi, Phys., arXiv:0802.2167v1[cont-mat.soft].
    3. Single-chain dynamics in a semidilute polymer solution under steady shear, Prasanth P. Jose, and Grzegorz Szamel, J. Chem. Phys. 128, 224910 (2008).
    4. Structure of a semi-dilute polymer solution under steady shear, Prasanth P. Jose, and Grzegorz Szamel, J. Chem. Phys. 127 114905 (2007).
    5. Multiple short time power laws in the orientational relaxation of nematic liquid crystals, Prasanth P. Jose, and Biman Bagchi, J. Chem. Phys. 125, 184901 (2006).
    6. Complete breakdown of the Debye model of rotational relaxation near the isotropic-nematic phase boundary: Effects of intermolecular correlations in orientational dynamics, Prasanth P. Jose, Dwaipayan Chakrabarti, and Biman Bagchi, Phys. Rev. E, 73, 31705 (2006).
    7. Universal power law in the orientational relaxation in thermotropic liquid crystals, Dwaipayan Chakrabarti, Prasanth P. Jose, Suman Chakrabarty and Biman Bagchi, Phys. Rev. Lett. 95, 197801 (2005).
    8. Anomalous glassy relaxation near the isotropic-nematic phase transition, Prasanth P. Jose, Dwaipayan Chakrabarti and Biman Bagchi, Phys. Rev. E 71, 030701(R) (2005).
    9. Anomalous viscoelasticity near the isotropic-nematic phase transition in liquid crystals, Prasanth P. Jose and Biman Bagchi, J. Chem. Phys. 121, 6978 (2004).
    10. In search of temporal power laws in the orientational relaxation near isotropic-nematic phase transition in model nematogens, Prasanth P. Jose and Biman Bagchi, J. Chem. Phys.120, 11256 (2004).
    11. Density and energy relaxation in an open one-dimensional system, Prasanth P. Jose and Biman Bagchi J. Chem. Phys. 120, 8327 (2004).
    12. Formation of nano-clusters under radiation pressure in solution: A Brownian dynamics simulation study, Prasanth P. Jose and Biman Bagchi, J. Chem. Phys. 116, 2556 (2002).
  • Contributions in Workshops and Conferences:
    1. Oral presentation at 2008 APS March Meeting titled: Chain dynamics in a semidilute polymer solution under steady shear, on March 10, 2008, held at New Orleans, Louisiana, U.S..
    2. Oral presentation at 2007 APS March Meeting titled: Steady state structure factor and stress in sheared semi-dilute polymer solutions, on March 8, 2007, held at Colorado Convention Center - 203, Denver, Colorado, U.S.A.
    3. Presented a poster at International Symposium on Spectroscopy, Structure and Dynamics December 12-13, 2002, held at Indian Association for the Cultivation of Science, Jadavpur, Culcutta-700032, India.
    4. Presented a poster at 22nd International Conference on Statistical Physics July 4-9, 2004, titled: Power laws in the orientational relaxation of model nematogens near isotropic to nematic phase transition held at Department of Physics, Indian Institute of Science, Bangalore-560012, India.
    5. Presented a poster at DAE-BRNS Symposium on Theoretical Chemistry (TCS-2004) December 9-12, 2004, held at Bhabha Atomic Research Centre, Trombay, Mumbai - 400 085, India.
  • List of Projects
    1. Dynamics of protein unfolding(On going)
       1. Molecular dynamics simulations are used to study the dynamics of protein unfolding. We look into this problem in the context of jamming transition, well-known in the literature of granular materials. Data obtained from the equilibrium simulations is analyzed to identify the existence of force chains in this bio-molecular systems. We also simulate the non-equilibrium molecular dynamics experiments to understand the atomic force microscopy experiments that can give shed light on the energy landscape of the bio-molecules and also helpful in construction of the force-temperature phase diagram of the bio-molecules. We also study the protein translocation through the pore. These computer experiments are used to understand underlying energy landscape of the protein and jamming of protein dynamics in their folded state.
    2. Formation of anisotropic scattering patterns (Butterfly patterns) in semi-dilute polymer solution under shear (On going)
       1. Brownian dynamics simulations are used to reproduce variation of anisotropic scattering patterns in semi-dilute polymer solutions under uniform laminar shear that is observed in the light scattering experiments (Wu et al., Phys. Rev. Lett. 66, 2408 (1991)) and to elucidate the role of intra and inter chain correlations in the formation of these patterns. We find that while in equilibrium solutions the contributions to structure factor from intra and inter chain correlations cancel each other almost completely, under shear these contributions are modified in different ways resulting in incomplete cancellation and the formation of anisotropic scattering patterns. We compare these scattering patterns with that obtained in the dilute solution. We also investigate the contribution of intra and inter chain correlations to shear stress and viscosity, and to the shear stress relaxation. Dependence of normal viscosity on the shear rate is also investigated.
       2. In order to elucidate the microscopic origin of this behavior, we have investigated the change in the single-chain dynamics in the solution: we have focused on the relaxation of the end-to-end vector, the Rouse modes and the radius of gyration tensor. In equilibrium and for small shear rates, these quantities show double exponential relaxation. With increasing shear rate they show oscillatory relaxation, which hints at the tumbling motion of the chain. In the high shear rate regime the frequency of the oscillations of the end-to-end vector autocorrelation function shows a power law dependence on the shear rate. We have compared the single-chain dynamics in the semidilute solution with that in a dilute solution. An analysis of the instantaneous values of the radius of gyration tensor, the end-to-end distance, and the normal stress along the system's trajectory reveals a synchronization of the fluctuations of these quantities.
       3. Next we study the wavevector dependent dynamics of this model system at equilibrium. We characterize the concentration fluctuations dynamics through intermediate scattering functions. At the lowest wave vector available in our simulation study the collective intermediate scattering function exhibits an exponential relaxation whereas at higher wave vectors it shows a bi-exponential relaxation. The wave vector dependence of the relaxation rates agrees qualitatively with the prediction of Brochard-de Gennes two-fluid model (Macromolecules 10, 1157 (1977)). The wave vector dependence of both the relaxation rates and the amplitudes agrees with the microscopic theory of collective diffusion in polymer solutions proposed by Genz (Macromolecules 25, 3501 (1994)).
    3. Temporal power laws in the in the dynamics of model nematogens near Isotropic-Nematic (I-N) phase transition.
       1. The motivation for this study comes from recent Kerr relaxation experiments by Gottke et al. (J. Chem. Phys. 116, 360 (2002) and 116, 6339 (2002)) which revealed the existence of a pronounced temporal power law decay in the orientational relaxation (as probed by Kerr relaxation) near the I-N transition. We have carried out very long molecular dynamics simulations of model (Gay-Berne) prolate ellipsoids with aspect ratio 3 in order to investigate the origin of this power law. The distance dependence of the calculated angular pair correlation function correctly shows the emergence of a long range correlation as the I-N transition is approached along the density axis. In the vicinity of I-N transition, the single particle second rank orientational time correlation function exhibits power law decay, of the form with exponent a approximately 2/3. More importantly, we find the sudden appearance of a pronounced power-law decay in the collective part of the second rank orientational time correlation function at short times when the density is very close to the transition density. The power law has an exponent close to unity, that is, the correlation function decays almost linearly with time. At long times, the decay is exponential-like, as predicted by Landau-de Gennes mean field theory. Since Kerr relaxation experiments measure the time derivative of the collective second rank orientational pair correlation function, the simulations recover the near independence of the signal on time which is observed in the experiments. In order to capture the microscopic essence of the dynamics of pseudo-nematic domains inside the isotropic phase, we introduce and calculate a dynamic orientational pair correlation function (DOPCF) obtained from the coefficients in the expansion of the distinct part of orientational van Hove time correlation function in terms of spherical harmonics. The DOPCF exhibits power law relaxation when the pair separation length is below certain critical length.
       2. We further studied the analogies between the supercooled liquid and a nematogen in the pre-transition region of I-N transition at the level of the single particle dynamics. The translational mean square displacement (MSD) show ordinary liquid like behaviour for a liquid near I-N transition; but, the rotational MSD show prolonged sub-diffusive behavior, which is a signature of dynamical heterogeneity in the orientational dynamics. The orientational dynamical heterogeneity is further quantified using the non-Gaussian parameter and orientational van Hove correlation function.
       3. Now, we study the collective conserved modes of this system of nematogens usually hidden under the non-conserved director modes in the light scattering experiments. The coherent intermediate scattering function show marked anisotropy in the structural relaxation as the system approaches I-N transition; this is reflected in the relaxation of the transverse and the longitudinal currents also. The transport coefficients and the thermodynamic parameters obtained from fit of the linearized hydrodynamic model at the smallest wavenumber to the correlation function of collective relaxation shows divergence like behaviour across I-N transition. Another relaxation function which deserves study is the wave vector dependent relaxation of angular currents. The structural relaxation of the nematogens near I-N transition behaves similar to that of a simple liquid, however, the relaxation function shows anisotropy with respect to the direction of the wavevector.
       4. We have also investigated the correlation of viscoelasticity with orientational relaxation. It is found that although the viscosity indeed undergoes a somewhat sharper than normal change near the I-N transition, it is not characterized by any divergence-like behaviour (like the ones observed in the supercooled liquid). The rotational friction, on the other hand, shows a much sharper rise as the I-N transition is approached.
       5. We have further studied this system in the nematic phase. Transient optical Kerr signal obtained from molecular dynamics simulations of the nematic phase reveal, two distinct power laws, with a cross-over region, in the decay of the orientational time correlation function at short to intermediate times (in the range of a few ps to few ns). In addition, the simulation results seem to indicate an absence of any long time exponential decay component. Theoretical analysis suggests that the two power laws may originate from local fluctuations of the nematic director.
    4. Density and energy relaxation in an one-dimensional lattice: a random walk model.
       1. This model, consists of a one-dimensional lattice and the random walkers in the lattice interact through excluded volume interaction (single-file system); and the total number of walkers in the lattice can fluctuate because of exchange with a bath. In addition, the movement of the random walkers is biased by an external perturbation. The movement of the random walkers in the lattice is simulated using grand canonical Monte Carlo moves. Two models for the latter are considered: (1) an inverse potential , where r is the distance between the center of the perturbation and the random walker and (2) an inverse of sixth power potential. The calculated density of the walkers and the total energy show interesting dynamics. When the size of the system is comparable to the range of the perturbing field, the energy relaxation is found to be highly non-exponential.
    5. Dynamics of cluster formation under radiation pressure
       1. This work is based on Brownian dynamics simulation of solute molecules under the perturbation induced by laser radiation. Here the force field generated by a laser beam in the fundamental mode is modeled as a two dimensional harmonic oscillator. An explicit analysis of the nature of these clusters is done by calculating density-density correlation functions in the plane perpendicular to beam direction and along the direction of beam that gives an average picture of shell structure formation in the different directions. The relaxation time of the first shell structure calculated from Van Hove correlation function is found to be relatively large in the perturbed solution giving the signature of stable clusters in the presence of radiation field.