Prashant Purohit

Phone: 215.898.3870
Email: purohit @ seas (.upenn.edu)
Office: 210 Towne Building

Website: http://www.seas.upenn.edu/~purohit/

RESEARCH INTERESTS:

EDUCATION:

Ph.D. Applied Mechanics November, 2001.California Institute of Technology, Pasadena, California, USA.
Thesis title: Dynamics of phase boundaries in strings, beams and atomic chains.
Thesis Advisor: Prof. Kaushik Bhattacharya

B.Tech. Mechanical Engineering July, 1997.
Indian Institute of Technology, Delhi, India.

AWARDS:

RESEARCH: SOFT MATTER THEORY:

Mechanics of DNA packaging and ejection in viruses: Ingenious experiments have led to the quantitative characterization of the force exerted by the portal motor of a virus as it packages DNA into the viral head. In this project we present an analytical model for the process based on a rod like model for DNA coupled with its electrostatic interactions in solution. The structural strength of the viral capsid is estimated using a cohesive model for protein interactions based on data obtained from molecular simulations. We also use the model to predict the length of DNA ejected from a virus as a function of applied osmotic pressure. We show that the extremely tight packaging of the viral genome is crucial in determining its infectiousness.

Kinetics of protein mediated DNA loop formation: Protein mediated DNA loops are highly recurrent structural motifs in biology. They are used for gene regulation and mechanical manipulation of DNA (for example, cutting by restriction enzymes) in many prokaryotes and eukaryotes. The kinetics of the formation of these loops
is of interest in many experiments. The main ingredient in determining the kinetics is the free-energy of the protein-DNA complex.The goal of this project is to determine the elastic and entropic part of the free energy using analytical methods of statistical mechanics. In particular, we are using a functional integrals based technique to
obtain the free energy the DNA by modeling it as a semi-flexible polymer. We will then use Kramer’s rate theory to determine the kinetics and apply this knowledge to tethered particle experiments.

Mechanics of mitochondrial membranes: Traditional wisdom about the structure of the interior of mitochondria (the energy producing oranelles in our cells) has been questioned by recent cryo-electron microscopy experiments. In order to better understand the results of these experiments we use the spontaneous curvature model of lipid membranes coupled with the eect of protein interactions to determine energetically favorable configurations of biological membranes in confined spaces. We are using these models to understand the process of crista formation in mitochondria since this could have implications in the study of mitochodrial diseases.

RESEARCH: MARTENSITIC MATERIALS

Mechanics of shape memory beams and rods: Shape memory alloys, such as Nitinol, are used in a variety of medical instruments such as stents, guide-wires, dental wires, etc. These devices employ them in slender configurations like rods or ribbons where bending and shearing are the principal modes of deformation. But, most quantitative theories for these materials treat only extensional deformations. We develop a simple and practical engineering theory for shape memory beams starting from the Cosserat theory of rods complemented with a constitutive law motivated by crystallography. We then propose simple experiments that enable easy tracking of the moving phase boundaries that are principally responsible for the superelastic properties of these materials.

Biologically inspired shape memory based device for propulsion at small scales: The goal of this work was to test the feasibility of using shape-memory materials for the fabrication of a small scale device capable of propelling itself through a fluid. We wanted to mimic the string like flagella of certain microorganisms. The idea was to generate movement by eecting shape changes by nucleating and propagating a new material phase using energy supplied by an outside source such as a laser. We showed that it is possible to generate motion by moving a phase boundary from one end of a shape-memory beam to the other.

Discrete model for phase boundaries in solids: Continuum theories for phase boundary motion in solids argue that the temporal evolutiuon of the phase boundary depends critically on a kinetic law. Our discrete simulations are motivated by the view that this kinetic law is a manifestation of the physics of rearrangement of atoms at the phase boundary that is neglected in a continuum theory. We explore this possiblity through simulations on a chain of masses with bi-stable springs much like the models used for studying the propagation of electrical impulses in axons. We reproduce much of the continuum results and find that the discrete model
is actually much richer.

Dynamics of phase boundary motion in strings: Phase boundary motion had hitherto been formally treated in 3D continua with specific problems solved in the one-dimensional context of bars. We studied the problem in strings and observed a rich class of phenomena arising as a result of the interplay of geometric nonlinearity of the string and material nonlinearity associated with change of phase. We also developed a computational method to solve initial boundary value problems for strings made of phase transforming materials.