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I am post doctorate fellow at the University of California Merced (UCM). I received my PhD in condensed matter physics from Syracuse University under the guidance of Professor Jennifer Schwarz in 2011. Currently I am working on several research topics which are all connected by one common theme, biology. My graduate research focused on passive biological materials (explained more in detail below). Now my research interests have broadened quite a bit to include systems of active interacting particles and regulating protein pores that are found in the nuclear envelope, the NPC (Nuclear Pore Complex). Aside from these new excited research areas I am also still interested in biological materials and their mechanical properties. These new research interests have also allowed me to learn and implement new computational tools such as large scale molecular dynamics simulations using the LAMMPS ( link ) and Gromacs ( link ) which are both amazing versatile simulation packages. On top of learning new computational tools I have also helped design and build a new cluster for High Performance Computation (HPC) for our group which incorporates the use of GPUs. 


Post Doc Work:


To elaborate a bit more on my research interestes there are 3 projects which I am currently working on. The first of which deals with a an interesting problem in bacteria. Bacteria, such as E. Coli, are known to have structural proteins which are similar (homologous) to eukaryotes . In eukaryotes, actin and tubulin are two proteins which are important for forming what is called the cytoskeleton. The cytoskeleton is what gives single cell there mechanical integrity as well as providing in some cases a method for preforming locomotion (see below my graduate work). It consists of a tightly regulated network of inter-crossing and cross-linked biopolymers made of actin and tubulin. Not only does this cytoskeleton provide rigidity to the cell, it also forms a system of highways in which cargo is transported by molecular motors. In bacteria, the two homologs of actin and tubulin are MreB and FtsZ. Not very much is know of these two structural polymers but they are both extremely important for bacterial life and reproduction. MreB has been suggested by previous studies to facilitate in the regulation of cell wall growth (another fascinating subject). However, MreB's exact role is still unknown and more experiments are needed to sort this out. Even more curious, from a structural point of view, is that MreB as been known to form helical-like structures which are bound to the inner bacterial cell wall. For a polymer or another elongated object to wrap around a cylindrical structure like that of the baterial cell wall, it must twist ( Frenet-Torsion ). You can demonstrate this but taking a thick cord and wrapping it around your arm to form a helix and you will see that inorder to form this helix the cord must twist around its own center line. This is purely a geometric effect. The importance if this twisting can lead to interesting behavior when a polymer like MreB is adsorbed to a surface. Like all biopolymers MreB has its own preferred twist which is due to how the monomers stack on each other. The competition between the Frenet torsion and the  intrinsic twist of the polymer can have a huge effect on the structural conformation of the polymer when it is bound to the cell membrane.  We have recently published a paper detailing this effect and it can be found HERE. We are still carrying out a more detailed analysis of this work and it will be published soon.


My second project is concerned with the function of the Nuclear Pore Complex (NPC) ( link ). The NPC is really fascinating in how it functions as well on how efficiently it works. Plainly stated the NPC is responsible for all traffic of protein material in and out of the nucleus as well as exporting RNA out of the nucleus. It can transport material through the nuclear envelop at a rate of 1000 translocations per second! Not only is it fast at what it does but it is highly selective about what is allowed into the nucleus. The diameter of the pore is 45-50 nm in the narrowest parts and is about 90 nm is length. Cargo which is less than 20 kDa can freely diffuse through the pore. However, cargo which is roughly the size of the narrowest part of the pore itself can pass through! This is an amazing fact when you realize that the pore is not just an empty tube, but it also has tethered proteins inside (Nucleoporins =nups) the pore which act as the gate for cargo to pass. All the while the process of transport in and out of the pore requires no energy source, ie. no ATP is consumed in the process. This all leads to the natural question of, How in the hell does this think function? This is essentially what my research involving the NPC is centered around. To attempt to answer this question I will be creating my own NPC "in silico" ( on a computer ) and passing cargo through my simulated NPC so that we can disentangle how cargo passes through the protein gate mesh at such a high rate.


My final project is focused on the phenomena of swarming, flocking or crowding. Have you ever seen a flock of birds flying in the sky together? (see video below) It seems that the flock has a mind of its own, which is separate from the individuals which make up the flock. The flock can move cohesively in free space and remain in this cohesive state for long periods of time. This phenomena is quite common in nature, we see this pattern not only in birds but also fish and people as well as on smaller length scales like microbial colonies, swimming bacteria and even non-living systems such as biopolymers which sit on a bed of motor proteins. All of the these differing types of animal and non-animal motion is what is known as collective motion. The types of individuals  and the interactions which govern the individuals are not important for collective motion to occur, which makes the a universal phenomena. I am interested in studying this phenomena using large scale simulations to try to understand what are the fundamental features which allow this phenomena to occur on widely different length scales. 


YouTube Video


Here is a cool web based interactive flocking program to get a feel of how flocking may work.


Flocking Algoritm


Graduate Work:


My graduate research focused on modeling biological materials specifically focusing on the interplay between network morphology and material mechanics of the cellular cytoskeleton found in the singled cell organisms. The spherical cow of single cell mechanics and the study of single locomotion via crawling is the keratocyte. 


Keratocytes exist in the epithelial tissue of most animals and promote wound healing. To move around in its environment (to heal a wound or search for food), keratocytes utilize their cytoskeleton to change their shape. The cytoskeleton is composed mainly of biopolymers called actin filaments. These filaments are dynamic in that they assemble at one end and dissemble at the other, and, therefore, the filaments exhibit directed motion. Using this directed motion, the cell can extend itself to crawl along a surface to heal a wound. 

 

I am mostly interested in the mechanics of the cytoskeleton network at the leading edge of the cell. This region is significant for the crawling cell because the cell must maintain and rearrange this network of filaments at a rate that is comparable to the rate of crawling (0.05-0.5 micron/sec). The cell must "build" a structure that can maintain a high degree of mechanical stability. In other words, the cell is continually constructing  and maintaining a support structure, much like a bridge. This bridge is constantly being rearranged and redesigned to accommodate any type of forces that the cell might encounter. Moreover, the morphology of this network couples to its mechanical function, just as there are different bridge architectures for different applications. The cell accomplishes this continual bridge building within a "short" time and with finite resources. 


Understanding these types of "dynamic" materials may provide us with some understanding of the many phases of biomaterials that can be found in Nature. We will also better understand how "life" has been using a mixture of simple engineering principles to construct these materials for a very diverse set of applications. Studying these systems theoretically can provide a general understanding of all materials that utilizing particular design principles. 


 

YouTube Video