Lunch & Learn

Lunch & Learn student led discussion and presentations are held on Thursdays from Noon-1:30 in the Howey Interaction Zone (next to the front office). These sessions are an informal gathering of PoLS students and faculty in which one student presentation will be given followed by a discussion. If you would like to sign up to give a talk this semester please ask Curtis Balusek to add your name in the spreadsheet below.

Spring 2015 Schedule

Date	Speaker
15 January	Karl Lundquist --- Gumbart Lab
22 January	Kerry McGill --- Schmidt-Krey
29 January	Michael Tennenbaum --- Fernandez-Nieves Lab
5 February	Feifei Qian --- Goldman Lab
12 February	open
19 February	Farzan Beroz --- Princeton University
26 February	Dr. Anton Souslov --- Goldbart Lab --- Snow Day, Campus Closed
5 March	APS Meeting --- San Antonio, TX (No PoLS)
12 March	Diandian "Diana" Chen --- Fenton Group
19 March	Spring Break (No PoLS)
26 March	James "Jim" Waters --- Kim Lab
2 April	Travis Tune --- Sponberg Lab
9 April	Douglas 'Bo' Broadwater --- Kim Lab
16 April	Dr. Joey Leung --- Weitz Lab
23 April	Casey Trimble --- Fenton Lab
30 April	Post-doc Candidate --- Sponberg Lab

Spring 2015 Abstracts

16 April 2015

Chung Yin "Joey" Leung

Conflicting Attachment and the Growth of Bipartite Networks

Abstract: Network growth models have become an indispensable part of the study of networks. In these models, the network grows by sequential addition of new nodes, where the connectivity of each newly added node is determined by the existing network connectivity and a set of predefined rules describing the network growth mechanisms. A number of network growth mechanisms has been proposed to explain the emergence of structural properties observed in real networks. For example, the widely-studied preferential attachment mechanism assumes that a newly added node is more likely to link to an existing node that is already well-connected. Such a mechanism can explain the power-law degree distribution observed in complex scale-free networks [1]. However, the growth mechanisms of many networks are incompatible with preferential attachment. In many bipartite systems composed of two types of agents that interact, there exists a fundamental conflict of interests as to the preferred level of connectivity. For example, in an interaction network between virus (phage) and microbe (bacteria) where a link denotes the ability for a given phage to infect a bacteria, a high level of connectivity may be beneficial for a phage but detrimental to a bacteria. Recent studies have revealed intriguing structural properties in these infection networks. They exhibit a nested pattern where relatively highly-resistant bacteria are infected by generalist phages and relatively susceptible bacteria are infected by generalist and specialist phages [2]. In addition, they can exhibit modular patterns with groups consisting of phages and bacteria that interact strongly within the group but not between groups [3]. The mechanism for the emergence of these properties is not well understood. We propose a network growth model with a conflicting attachment mechanism inspired by the evolution of phage-bacteria interactions. We find that the resulting networks reproduce realistic patterns found in empirical data including nestedness, modularity, and a nested-modular pattern where modularity is observed at the network scale and nestedness is observed at the module scale. We study the role of conflicting interests in shaping network structure and discuss ways to incorporate greater realism in linking growth process to pattern.

References

(1) A. L. Barabási and R. Albert, "Emergence of scaling in random networks" Science 1999, 286(5439), 509-512.

(2) C. Flores, J. Meyer, L. Farr, S. Valverde, and J. S. Weitz, "The statistical structure of host-phage interactions" Proceedings of the National Academy of Sciences 2011, 108, E288-E297.

(3) C. Flores, S. Valverde, and J. S. Weitz, "Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages" ISME Journal 2013, 7, 520-532.

9 April 2015

Douglas "Bo" Broadwater --- Kim Lab

The Effects of Mismatch Position on DNA Strand Displacement Rate

DNA strand displacement is a reaction involving three single strands of DNA. It occurs when one single strand of DNA fully hybridizes to a partially duplexed complement. DNA strand displacement is essential to two of the most critical operations in biology, DNA repair and homologous recombination. It is also utilized in the field of nanotechnology in diverse areas such as DNA motors and DNA computation. In this week's PoLS meeting, I will discuss our work towards tuning the overall rate of strand displacement by varying the position of a single nucleotide mismatch. The ability to tune the displacement rate is important because it has applications in identifying single nucleotide variants in mRNA transcripts. I will provide experimental evidence of a non-trivial relationship between strand displacement rate and mismatch position. Finally, I will posit a model that explains the origins of the complex rate behavior as being due to both secondary structure and mismatch position.

2 April 2015

Travis Tune --- Sponberg Lab

Energetic Versatility of Muscle

Muscle is a unique material which has the ability to operate as a spring, motor, brake, or strut which are characterized by a muscle’s workloop. In a typical workloop experiment, force and length of a muscle are plotted against each other while the muscle undergoes oscillation while being activated under physiological conditions. A muscle’s workloop can be altered by changing any of a number of physiological inputs such as temperature, phase or frequency of activation, or operating length. This is what is meant by “Energetic Versatility of Muscle”- the ability of muscle to alter its role quickly and with low energy cost. In this talk I will give an overview of what parameters are known to alter muscle workloops and then will introduce a system of two muscles whose workloops are not explained by our current understanding of muscle physiology. I will then discuss the structure of the muscle as a potential source of variation of workloops. Because skeletal muscle is a highly ordered structure, we can use the technique of x-ray diffraction to examine the lattice structure of muscle. To do this, we traveled to Argonne National Lab to make use of the Advanced Photon Source x-ray beamline. Our early results show what may be a difference in the lattice spacing of the two muscles. We also will perform a frequency analysis on muscle, from which we can extract rates which are related to the molecular processes which are responsible for muscle’s force generation.

26 March 2015

James Waters --- Kim Lab

Simulation of fluctuating entropic force by kinetic sampling

Abstract: A polymer chain when pinned to a point or a plane exerts a force on the pinning point in thermal equilibrium. From a thermodynamic point of view, this force arises as the chain tries to minimize its free energy at constant temperature. Due to the hard constraint at the pinning point, calculation of this entropic force is not a trivial problem in statistical mechanics. Here, we introduce a novel kinetic sampling method that can produce the equilibrium distribution of instantaneous forces exerted by a terminally pinned polymer. We represent a generic flexible chain using the canonical bead-rod model and perturb both the positions and momenta of the beads compatible with the spatial constraints and the Boltzmann distribution of total energy. We then calculated the constraint force for each conformation using Lagrangian dynamics. The mean of this force distribution is consistent with the force estimated from the partition function. Unlike the mean that quickly plateaus at tens of monomers, the skewness of the distribution keeps increasing in the range of chain lengths tested. This result suggests that longer chains exert large pulling forces at the pinning point more frequently than short chains. Our work provides insights into the mechanistic origin of entropic forces, and a computational tool applicable to simulations of constrained systems

12 March 2015

Diandian Chen --- Fenton Lab

Cellular mechanisms for QRS alternans in the heart

Abstract: Alternans in the electrocardiogram of the heart often precede sudden cardiac death. To analyze the conditions that allow for alternans, scientists examine dynamics at the cellular level. For T-wave alternans, it has been confirmed that the source is due to an alternating action potential duration at the cellular level. However, the cellular mechanisms for QRS alternans have not been well studied. We propose that the source of QRS alternans is due to action potential amplitude alternation at the cellular level. First, we created a simple model that reproduces this effect. Next, we derived a method to analyze the criteria for amplitude alternation in this simple model. Our results show that our method of analysis is correct in predicting the conditions for alternans.

5 February 2015

Feifei Qian --- Goldman Lab (Physics)

Legged locomotion on homogeneous and heterogeneous granular ground

Flowable substrates like sand, snow, leaf litter and gravel can be especially challenging for terrestrial locomotors. The objective of our research is to discover principles of ambulatory locomotion on homogeneous and heterogeneous granular substrates and create models of animal and robot interaction with such environments. Since interaction with natural substrates is complicated to model, we take a robophysics approach – we create a terrain generation system that allows systematic exploration of substrate properties, and we use bio-inspired robots as simplified model locomotors to vary morphological and kinematic parameters. We find that terradynamic performance on homogeneous deformable substrates was determined by the leg penetration ratio. Locomotors with smaller foot pressure were less sensitive to ground stiffness variation, and thus could passively maintain relatively effective performance on low resistance ground. At low gait frequencies, hydrostatic-like forces generated during the yielding of the granular material ultimately led to solidification of the material, allowing locomotors to move as if they were walking on a solid surface. At high frequencies, the inertia of the grains being accelerated became important and granular forces became hydrodynamic-like, allowing lightweight locomotors to achieve high locomotor performance by exploiting fluid properties of the granular material.

29 January 2015

Michael Tennenbaum --- Fernandez-Nieves Lab (Physics)

Rheological Properties of Fire Ant Aggregations

Fire ants, Solenopsis invicta, form aggregations that are able to drip and spread like simple liquids, but that can also store energy and maintain a shape like elastic solids. They are an active material where the constituent particles constantly transform chemical energy into work. We find that fire ant aggregations shear thin and exhibit a stress cutoff below which they are able to oppose the applied stress. In the linear regime, the dynamics is fractal-like with both storage and shear moduli that overlap for over three orders of magnitude and that are power law with frequency. This dynamic behavior, characteristic of polymer gels and the gelation point, gives way to a predominantly elastic regime at higher ant densities. In comparison, dead ants are always solid-like.

22 January 2015

Kerry McGill --- Schmidt-Krey Lab (Biology)

Electron crystallography: A method for protein structure determination

Membrane proteins occupy a variety of functional niches in the cell including structural support, regulation, and communication; understanding how these proteins accomplish their role in the cell can be enhanced with the knowledge of the membrane protein structure. One method of membrane protein structure determination is 2D crystallography. In this method, solubilized membrane proteins are crystallized in lipid membranes via manipulation of the dialysis conditions, like lipid to protein ratio (LPR), salt type and concentration, dialysis length, lipid type and concentration, etc. As these conditions are changed, 2D crystals are screened for via uranyl acetate negative staining and imaging with a transmission electron microscope. Once crystallization conditions are optimized for membrane formation, high resolution images are taken via electron cryo-microscopy (cryo-EM). A crystal structure is determined with the help of image processing. Both membrane bound and membrane associated membranes can be studied by 2D crystallography. Understanding the structure of membrane proteins can lead to insight on how proteins function within the cell.

15 January 2015

Karl Lundquist --- Gumbart Lab (Physics)

Insertion of β-barrel proteins in gram-negative bacteria

Gram-negative bacteria possess two phospholipid membranes, the inner and outer of which are composed primarily α-helix and β-barrel proteins respectively. In recent years, significant progress has been made in understanding insertion and assembly of proteins into the inner membrane, while the same process in the outer membrane has remained elusive. In 2013, the crystal structure of BamA, the central and essential component of the β-barrel assembly machinery (BAM), was released, paving the way for rapid progress in understanding the insertion and assembly process. All-atom molecular dynamics simulations have been performed, revealing many novel features including lateral gate opening between the first and last barrel strands, and a destabilized membrane region near the putative insertion site caused by a decreased hydrophobic band. However, many questions remain, including the role of the periplasmic domains, the mode of substrate recognition, and the energetic factors driving function in the absence of both ATP and an electrochemical gradient. Currently, we are performing novel equilibrium simulations of the protein in its native LPS environment, and calculating the free energy of lateral-gate opening for native systems, as well as systems with strand modifications and/or augmentations designed to yield insight into driving energetics and substrate recognition.

Fall 2014 Schedule

Date	Speaker
28 August	Anthony Hazel (Gumbart Lab)
4 September	Bradford Taylor (Weitz Lab)
11 September	Guillermo Amador (Hu Lab)
18 September	Vlad Levenfeld (Goldman Lab)
25 September	Bye Week
2 October	Paul Cardenas Lizana (Zhu Lab)
9 October	Jairo Rodriguez Padilla (Fenton Lab)
16 October	Will Ratcliff - School of Biology, Georgia Tech
23 October	Dan Kovari (Curtis Lab)
30 October	Perrin Schiebel (Dan Goldman)
6 November	Yanyan 'Claire' Ji (Fenton Lab)
13 November	Alexis Noel (Hu Lab)
20 November	Kahye Song - Pohang University of Science & Technology, Pohang, KOR
27 November	Thanksgiving Break
4 December	Sulisay Phonekeo (Hu Lab)

Fall 2014 Abstracts

20 November 2014

Kahye Song --- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH),

What enables the plants to move?

Most plants have been considered as non-motile organisms. However, plants move in response to environmental changes for survival. In addition, some species drive dynamic motions in a short period of time. Mimosa pudica is a plant that rapidly shrinks its body in response to external stimuli. It has specialized organs that are omnidirectionally activated due to morphological features. In addition, scales of pinecone open or close up depending on humidity for efficient seed release. A number of previous studies on the dynamic motion of plants have been investigated in a biochemical point of view. However, an interdisciplinary study on the structural characteristics of the motile plant should be accompanied by biophysical research to explain the principles underlying such movements. In this study, the motions of plants were analyzed and morphological characteristics of those motile organs were investigated by using X-ray CT and micro-imaging techniques. The results show that the dynamic motions of motile plants are supported by structural features related with water transport. These studies would provide new insight for better understanding the moving mechanism of motile plant in morphological point of view.

13 October 2014

Alexis Noel --- Hu Lab

To catch a fly: The role of saliva adhesivity during prey capture in frog tongue projection.

There are many organisms that utilize a sticky biological fluid to capture prey, such as amphibians, pitcher plants, sundew plants and spider silk. At a molecular scale, these bio-adhesives are composed of long chain glycoprotein networks, which give the fluids unique adhesive properties through viscoelasticity. Strain hardening is observed in these fluids during normal separation; extensional viscosity increases by orders of magnitude as strain rate increases. In the field, there is not currently a method to test and compare biological adhesives. While professional extensional rheometers, such as the CaBER or FiSER, provide accurate measurements, they are expensive and not portable. Many biological samples (such as saliva) degrade within hours; once the sample reaches the machine, the fluid properties may have changed dramatically. We have designed and built a portable extensional rheometer (titled Elo-Rheo) which allows us to analyze biological fluid properties in the field, minimizing degradation of the fluid sample. The machine is lightweight, user-friendly and costs less than $1500. By analyzing these bio-adhesives, we can determine forces apparent in the fluid during prey capture. In this experimental study, we investigate how a frog’s sticky saliva enables high-speed prey capture. At the Atlanta zoo, we use high-speed video to film the trajectory of frog tongues during projection; post analysis of the video allows us to calculate acceleration during insect impact and retraction. Using a frog saliva sample in Elo-Rheo, we can mimic separation rates present during prey capture and so infer the adhesive force between tongue and prey. High speed collection using soft, adhesive materials has numerous applications. Current actuated systems in the field of soft robotics operate at low speeds, and are mostly used for machine movement. This work will inspire new methods to quickly collect an object with non-uniform surface texture in such a way that minimizes destructive collision forces.

6 November 2014

Yanyan 'Claire' Ji --- Fenton Lab

Modeling on Calcium Dynamics and Contraction

At present, there are close to a hundred mathematical models describing the electrophysiology and dynamics of single cardiomyocytes. However, most of them focus only on ion channels and sarcoplasmic reticulum (SR) dynamics without including the equations to simulate their contraction. This is a considerable drawback since electrical activities and mechanics are closely related. In this study, we present a systematical methodology to incorporate a contraction model (Negroni_Lascano_1996) into fourteen well known electrophysiological (EP) cell models. To evaluate how well these coupled electromechanical (EM) models behave, we study them using a postextrasystolic pacing (PESP) protocol. We first compare the dynamics between the new EM models and the original EP models to quantify the effects of the inclusion of contraction on the EP models. Then we compare the contractile strength of the new EM models with previously published experiments (Yue et al 1985). Finally we compare results from the Negroni_Lascano_1996 model with two other contraction models. We discover that the original EP models with dynamic troponin buffers show little change in dynamics after the implementation of contraction, and these models also better match the experimental contractile strength data than models originally with instantaneous or no troponin buffers. We conclude and describe how EP models with dynamic buffers are better candidates to incorporate contraction.

30 October 2014

Perrin Schiebel --- Goldman Lab

Limbless locomotion in heterogeneous terrestrial substrates

Snakes can traverse heterogeneous terrain composed of rocks, foliage, soil and/or sand. Previous research elucidated how rigid obstacles influence snake locomotion by studying a model heterogeneous terrain—symmetric lattices of obstacles placed in hard ground. We want to understand the benefits and tradeoffs of different substrate-body interaction modes during transit of substrates composed of rigid obstacles and flowable (granular) substrates in desert-adapted snakes. We hypothesize that, due to these snakes’ ability to utilize granular resistive forces, introducing a granular medium (GM) to a peg lattice will improve performance (in terms of snake speed) compared to that in the same lattice on a hard substrate. We tested Chionactis occipitalis, the Mojave shovel-nosed snake, in a square lattice of 0.64 cm diameter obstacles arrayed on both a hard, slick substrate and in a GM of 270±4 μm diameter glass particles (comparable in size to natural sand). We challenged the snakes to move through lattices of different densities such that nearest-neighbor spacing ranged from slightly wider than the body diameter to larger than the snakes’ natural amplitude. Performance was a function of both lattice spacing and substrate. Kinematics were similar for both substrates but depended on lattice density: at low density, undulatory locomotion was typically used while at high density a more complicated time-dependent body shape emerged.

23 October 2014

Daniel Kovari --- Curtis Lab

Modeling Phagocytosis: Using Hydrodynamics to Predict Cell Behavior

Phagocytosis is the process by which individual cells engulf foreign bodies. It is the hallmark behavior of white blood cells, being the process through which those cells ingest and degrade pathogens and debris. Comprehensive models of phagocytosis hold the promise of providing key insights into processes such as infection, wound repair and drug delivery. The cascade of biochemical signals which trigger phagocytosis is expansive. Furthermore, it is often unclear how to integrate the results of purified molecular experiments into a larger whole-cell model. Consequently, modeling phagocytosis from the ground up is not only computationally expensive but also ill-posed. As an alternative, our work seeks to model phagocytosis as a mechanical process. I present physical characterizations of phagocytosis and our efforts to develop a simple hydrodynamic model built around physical properties which can be measured on intact living cells. The model predicts phagocyte behavior in a planar geometry, termed frustrated phagocytosis, and can be extended to make predictions for other cell-substrate interactions.

16 October 2014

Will Ratcliff --- School of Biology, Georgia Inst. of Technology

Experimental Evolution of Multicellularity

The evolution of multicellularity was one of the most significant innovations in the history of life, but early steps in this transition remain poorly understood. Using experimental evolution, we demonstrate that keys steps in this transition evolve far more easily than previously thought. Starting with the unicellular yeast Saccharomyces cerevisiae, we evolved clustering genotypes characterized by production of multicellular propagules, a juvenile phase, and determinate growth. We observe a shift in the level of selection, such that clusters evolve as multicellular individuals, resulting in the evolution of simple among-cell division of labor. Over thousands of generations of adaptation, we see the emergence of morphological complexity in our multicellular yeast (though they are still quite simple).

9 October 2014

Jairo Rodriguez --- Fenton Lab

Interaction of Scroll Rings in Reaction Diffusion Equations

2 October 2014

Paul Cardenas Lizana --- Zhu Lab

Mechanically-regulated pathways employed by viruses to escape immune recognition: An atomistic study

One subset of leukocytes is cytotoxic T lymphocytes (CD8+ T cells) that are capable of inducing cytolytic activity on cells presenting foreign antigen peptide. T cell receptors (TCR) expressed on CD8+ T cells interacts with peptide and class I Major Histocompatibility Complex (MHC) molecule on antigen presenting cells. TCR found on each T cell is unique in that they are specific in scanning pMHC complexes. Antigens are foreign substances that induce immune response. Antigens are composed of several antigenic determinants, known as epitopes, and the epitopes can bind to a specific TCR and/or antibody.

Viral persistence is observed in Cytomegalovirus (CMV) and Hepatitis C (HCV) infection. CMV does not pose a threat to an immune competent subject in terms of developing a life-threatening disease; however infected subject with HCV evolves to chronic state during the course of infection. The development into chronic condition is linked in part to the rise of "viral mutations" that have decreased functional effects as those of the wild type (WT) thereby escaping recognition from the immune system. Nevertheless, the true extent of TCR-pMHC interaction, its role in the molecular mechanism of antigen recognition, and the tolerance of leukocytes to viral epitopes upon infection, still remain a speculative issue, largely due to the lack of experimental approaches that could definitively address this question. TCR/pMHC interaction must also stand mechanical forces in order to prevent dissociation from external fluid flow or substrate stresses.

MD simulation combined with experiments are employed to understand the mechanically-regulated pathways of TCR-pMHC interaction in the context of viral infection and epitope recognition. It will be described the molecular mechanisms by which mutant epitopes escape detection by the immune system and correlate this loss of recognition by the TCR with a characteristic mechanical behavior of TCR-pMHC response (catch-slip/slip-only bond) This kind of study is novel and provides a unique means for elucidating the mechanical regulation of bio-molecular interactions at the atomic resolution.

18 September 2014

Vlad Levenfeld --- Goldman Lab

The role of ground-reaction forces in martial arts striking techniques

The human body is capable of generating powerful impact forces through elaborate combinations of movements, which is particularly evident in combat sports such as boxing and mixed martial arts. In order to understand the complex dynamics of such movements, studies have been done on the kinematics and impact forces of various punches. In other sports, notably running and gymnastics, the features of ground reaction forces in time are used to understand the biomechanical strategies used by the athlete. However, there is little in the way of such analysis for combat sports. Most combat sports studies involving dynamometry focus on the impact force of the punch. The overall contribution of the legs to the force of the punch has been examined, but little research has been done on the features of the GRF trajectory in time. We hypothesize that there are signatures in these time-domain signals that can qualitatively and quantitatively differentiate the strikes of experienced fighters versus less experienced fighters. To observe the GRF during an athlete's strike, we constructed a platform with a force plate at the center and synchronized the recorded signals with two high-speed cameras. We predict that careful analysis of the GRF signature and synchronized video will yield a deeper understanding of the biomechanical strategies used during punching, as it has for other sports.

11 September 2014

Guillermo Amador --- Hu Lab

Arrayed bristles reduce soiling of compound eyes

While the presence of bristle arrays on insect compound eyes has been known for quite some time, there hasn’t been a study analyzing the effect of bristles on airborne particle deposition. Our hypothesis is that bristles affect incoming airflows to reduce airborne particle deposition to the eye surface. Through collaboration with Dr. Isao Shimoyama’s lab at the University of Tokyo, micron-scaled sensors are used to probe the effect of bristle arrays on incoming airflows. The sensors are comprised of piezo-resistive cantilevers that deflect when acted upon by the dynamic pressure exerted by flowing air. When deflected, the electrical resistance of the cantilever is changed. The change in resistance of the cantilever is proportional to the dynamic pressure exerted by the airflow, so it can be used as a metric for the intensity of the airflow. Through the use of these sensors, we find that bristle arrays greatly affect airflow penetration for shearing flows, reducing the dynamic pressure by 40-60%. The decrease in flow penetration observed in this study may motivate bio-inspired solutions for reducing airborne particle deposition onto sensitive surfaces.

4 September 2014

Bradford Taylor --- Weitz Lab

A Hitchhiker's Guide to Coinfection: Ecology and Evolution of Virophage

Virophage are viruses of viruses that serve a hyperparasitic role. In order to reproduce, the virophage must coinfect a eukaryotic host along with a giant virus. There are two ways for the virophage to hitchhike into coinfection: by adhering to the virus and the pair later entering the host, or by entering the host and lying in wait for the virus. I will address the different effects between these modes of coinfection on the population dynamics of the system. I will also look at the feasibility of multiple virophage strains coexisting and the existence of virophage capable of both modes of coinfection.

28 August 2014

Anthony Hazel --- Gumbart Lab

Molecular Dynamics Simulations of Small Protein Structures

Molecular dynamics (MD) simulations provide atomistic detail to biological and chemical processes. It is used extensively in the study of protein structure and folding. Here, I use the power of MD simulations to determine the folding pathway and energetics of small protein structures, namely α-helices and β-turns. Extensive computational work has been performed on small Ala-based peptides due to Ala's high helical propensity amongst the 20 common amino acids. The free energy of α-helix formation of deca-alanine in vacuum is often used as a benchmark for free energy calculation methods. A common reaction coordinate used to describe the folding pathway and the stability of the helical and extended states is the end-to-end distance of the peptide, which shows a helical minimum around 14-15 Å which is ~20-25 kcal/mol more stable than the fully extended state. We first calculated this folding free energy in water to get a better description of α-helix formation in vivo. We discovered that near the α-helical minimum, end-to-end distance becomes highly degenerate. Therefore, we introduced a second reaction coordinate – α-helical content – and calculated a 2D free energy surface, which revealed the extended states to be of comparable free energy to the helical state due to hydrogen bonding from the surrounding water molecules, a result not seen in previous free energies calculated for deca-alanine in water using only end-to-end distance. Lastly, I will show how these results can be extended to other folding systems, e.g. α-helix formation inside the protein exit tunnel of the ribosome during translation, β-turn formation of the GB1 protein, and β-helix formation of the virulence factors for autotransporters in the outer membrane of gram-negative bacteria.

Spring 2014 Schedule

Date	Speaker
1/17	NA
1/24	Zhenhai Li (Zhu lab)
1/31	Tung Le (Kim lab)
2/7	Ben McInroe (Goldman lab)
2/14	Henry Astley (Goldman & Hu Lab)
2/21	Patrick Chang (Curtis lab)
2/28	James Waters (Kim lab)
3/7	APS meeting, NA
3/14	Sridhar Ravi (Stacey Combes's Lab)
3/21	Spring Break, NA
3/28	Jiyoun Jeong (Kim lab)
4/4	Andrea Welsh (Fenton lab)
4/11	Daria Monaenkova (Goldman lab)
4/18	Bo Broadwater (Kim lab)

Link to editable google doc here.

Spring 2014 Abstracts

04/18/2014

Bo Broadwater Kim's Lab

Creating long, bespoke DNA with tandem repeats

Regulation of gene expression is an essential process for all forms of ife. The most common mode of gene regulation occurs at the level of transcription with the initiation of messenger RNA. Transcription factors (TFs) can specifically bind to the operator sequence thereby inhibiting or activating RNA polymerase. Despite a preference for binding to the operator sequence, experiments have shown the surprising result that TFs do not saturate a tandem array of binding sites. This suggest that there is a negative allosteric interaction between TFs through DNA. In this week's PoLS meeting, I will talk about our plans to investigate the suspected contribution of the 3D configuration of DNA to the anti-cooperative allostery in TetR binding. I will also present a novel method for the creation of bespoke DNA with tandem repeats using rolling circle replication. Finally, I will present preliminary data evidencing early success in attempting this new method.

04/11/2014

Daria Monaenkova

Goldman's Lab

SOCIAL EXCAVATION IN SUBTERRANEAN ENVIRONMENTS

Many social insects construct underground nests composed of networks of tunnels and chambers. Such cooperative construction is a challenge: individuals must effectively manipulate soil in confined, crowded, dark conditions without interfering with the flow and functioning of the collective. To begin to discover principles by which colonies balance these competing demands, we studied excavation strategies employed by fire ants during nest construction in substrates composed of particles of different sizes and moisture content. Ants constructed tunnels through the repetitive excavation and transport of cohesive soil pellets. Individual ants used complex, coordinated motion of limbs, mandibles and antennae to create pellets. Mean pellet size was comparable to head width, differed slightly depending on soil moisture and particle size, and was significantly smaller than the maximum pellet size an ant could form. We hypothesize that these intermediate-sized pellets are actively shaped by ants and passively shaped by the tunnel to optimally balance individual carrying capacity against clogging, pellet disruption and locomotor hindrance, which could diminish the transport efficacy of the collective.

04/04/2014

Andrea Welsh

Flavio Fenton's Lab

COUPLING INDUCED SYNCHRONIZATION OF MEXICAN JUMPING BEANS

Synchronization and de-synchronization are important phenomena that occur in many biological systems, including the heart and brain. Therefore, understanding how to better control and induce synchronization or de-synchronization may be vital in the area of cardiac and brain dynamics. For this project, we seek to study spatially extended synchronization through a mechanical-induced coupling of Mexican jumping beans. The frequency of their jumps, set by temperature gradients, display a bursting behavior with periods of jumping and periods of rest. We experimentally characterize their ability to synchronize after inducing nearest neighbor coupling through the attachment of string. We compare the resulting jumping behavior to simulations of oscillators undergoing a similar bursting pattern whose time evolution is governed by an adaptation of the Kuramoto model. We also use Arduino electronics for visual representations of these simulations for outreach and education.

03/28/2014

HOW DNA MELTING INFLUENCES FLEXIBILITY

Jiyoun Jeong (Kim lab)

Thermal fluctuations within double-stranded DNA (dsDNA) can lead to transient, local opening of base pairs known as bubbles. Bubble formation (or "melting") of dsDNA plays an important role in gene regulation; for example, RNA polymerases require single-stranded DNA in the genome to initiate transcription. Despite numerous theoretical and computational studies on thermodynamics and kinetics of bubble formation, experimental demonstration of bubble formation well below the melting temperature remains elusive. Nevertheless, bubble formation has been invoked as a mechanism to enhance DNA flexibility. In this week's PoLS meeting, I will talk about how we experimentally study the effect of melting on dsDNA flexibility. We calculate the probability of bubble formation along a given DNA sequence using statistical mechanical models and design short DNA molecules that are highly likely to form a bubble near their center. Bubble formation in such DNA would cause a dramatic increase in the looping probability, which we measure using single-molecule fluorescent resonance energy transfer (FRET). We are investigating how the looping rate increases as a function of temperature to test the prediction of the meltable worm-like chain model.

03/14/2014

INSECT AND BIRD FLIGHT IN UNSTEADY WINDS

Sridhar Ravi (Stacey Combes Lab)

Insects and birds reside in the outdoor environment where the wind can be very unsteady and complex. Due to various factors, including terrain, meteorological conditions, etc. the wind profile within the Atmospheric Boundary Layer can be very turbulent, i.e. wind speed and direction changes rapidly, rendering very unfavorable conditions for flight. Insects and birds seem to be capable of flying even in such adverse conditions by utilizing various flight control strategies. In this talk, I will be presenting on some of these strategies, in particular, I will be presenting on the flight of bumblebees in von Karman streets, hummingbirds flying in discrete vortices and fully mixed turbulence.

02/28/2014

COARSE-GRAINED LAGRANGIAN MODELS FOR SEMIFLEXIBLE POLYMERS

James Waters (Kim Lab)

The looping of short segments of DNA plays an important role in gene regulation. The stability of the loop will be affected by the restoring force arising from bending elasticity of DNA. In thermal equilibrium, this force fluctuates in time, but the time-dependent force is only accessible from a dynamics simulation, which is computationally expensive. An alternative approach to obtain instantaneous forces is to generate an ensemble of looped chains and measure the force of constraint for each conformation using Lagrangian dynamics. In this talk, I will introduce a microscopic approach to explore the conformational phase space of an end-constrained polymer and calculate the force distribution about the mean that would be lacking from a purely thermodynamic approach. By applying this method to polymers attached to a surface at one end, we design a simple experiment that can measure the persistence length of a semiflexible chain.

02/21/2014

PROTEOGLYCAN IN PERICELLULAR MATRIX MEDIATES BIOPHYSICAL INTERACTION WITH THE ENVIRONMENT

Patrick Chang (Curtis Lab)

The pericellular matrix (PCM) is a polymer coat grafted on the membrane surface of many eukaryotic cells. The PCM is known to associate with different physiological processes of the cells, such as adhesion, migration and proliferation. After investigating the structure of the PCM through different biophysical assays we developed, it is found that the proteoglycan, protein with sugar chains, in the matrix plays an important role in determining the structure, more so then the polymer backbone the proteoglycan attached to. When the PCM is acting as a chemical reservoir, it is the proteoglycan that sequester the chemical and later release at specific condition to change the cells' state. Before particles, such as drug, from the outside enter the cell, they have to go through the PCM, and it is the distribution of the proteoglycan that determines the opening of the matrix that let the particles through. In the process of cell migration, it is the proteoglycan's conformation in the PCM that affects the adhesion and detachment of the cell. Although the key player has been identified, little is known on the mechanism of proteoglycan during different biophysical processes. In our research, we aim to start uncovering the role of proteoglycan in pericellular matrix and its interaction with the cells' environment.

02/14/2014

TURNING AND MANEUVERABILITY DURING SIDEWINDING LOCOMOTION

Henry Astley, Goldman and Hu Labs

Sidewinding is an unusual form of snake locomotion used to move rapidly on yielding substrates such as desert sands. Posteriorly propagating waves alternate between static contact with the substrate and elevated motion, resulting in a "stepping" motion of body segments. Unlike lateral undulation, the direction of travel is not collinear with the axis of the body wave, and posterior body segments do not follow the path of anterior segments. Field observations indicate that sidewinding snakes are highly maneuverable, but the mechanisms by which these snakes change direction during this complex movement are unknown. Motion capture data from four Colorado Desert sidewinder rattlesnakes (Crotalus cerastes laterorepens) shows a variety of turn magnitudes and behaviors. Shallow turns are achieved via "differential sidewinding", in which the motion is altered such that the head moves further than the tail. Additionally, sidewinders are capable of "reversals" in which the snakes halts forward progress and begins locomotion in the opposite direction without rotation of the body. Because the head is re-oriented with respect to the body during these reversals, the snake is able to reverse direction without rotation yet continue moving in the new direction without impediment to perception or mechanics, a rare level of maneuverability in animals. We are able to reproduce these turning mechanics on a sidewinding robot snake, and have begun investigation into sidewinding in other snake species.

02/07/2014

USING A ROBOT TO STUDY THE EVOLUTION OF LEGGED LOCOMOTION

Ben McInroe, Goldman Lab

Throughout history, many organisms have used flipper-like limbs for both aquatic and terrestrial locomotion. Modern examples include mudskippers and sea turtles; extinct examples include walkers such as the early tetrapod\textit{ Ichthyostega}. In the transition from an aquatic to a terrestrial environment, early walkers had to adapt to the challenges of locomotion over flowable media like sand and mud. Previously, we discovered that a flipper with an elbow-like joint that could passively flex and extend toward and away from the body aided crawling on dry granular media [Mazouchova et. al. 2013], a result related to the jamming of material behind and beneath the flipper. To gain insight into how an additional degree of freedom of this joint affects flipper-based locomotors, we have built a robotic model with limb-joint morphology inspired by \textit{Ichthyostega}. We add to our previous limb design a passive degree of freedom that allows for supination/pronation of the flipper about a variable insertion angle. Springs at the joints restore the flippers to equilibrium positions after interaction with the media. We study the crutching locomotion of the robot performing a symmetric gait, varying flipper-joint degrees of freedom and limb cycle frequency.

01/31/2014

USING SMALL DNA LOOPS TO STUDY ENERGETICS OF DNA KINKING

Tung Le, Kim lab

Elevated temperature or sharp bending can induce disruptions in the double helix of DNA, which are known as kinks. Recent experiments using small circular and teardrop-shaped DNA loops demonstrate that DNA can experience local disruptions solely by strong bending. However, energetics and sequence-dependence of kink formation remains unexplored. In this preliminary study, we investigated kink distribution in small circular and teardrop-shaped DNA loops using Monte Carlo simulation. We found that both a circular and teardrop loops less than 70 bp readily develop kinks by thermal excitation. Kinks are delocalized in a circular loop, but in a teardrop loop, a single kink tends to be localized near the bottom and efficiently relaxes the bending stress of the loop. Our result suggests that stability of a teardrop loop is most sensitive to the sequence located near the bottom, which can be exploited to measure sequence-dependent kinkability in the sharp bending regime.

01/24/2014

THREE STATES MODEL FOR CYCLIC MECHANICAL REINFORCEMENT

Zhenhai Li, Zhu lab

Many biomolecular interactions are regulated by mechanical force. Bell model indicates the mechanical force applied to the interactions accelerate the bond dissociation. However recent research shows some biomolecular interactions exhibit a mechanical strengthening under mechanical force, which is termed as catch bond. Using atomic force microscopy, we observed catch bond in integrin/FNIII7-10 interaction. Furthermore the strengthening effect became stronger after cyclic mechanical force applied to integrin/FNIII7-10 interaction, indicating the force history is memorized by the molecules. This phenomenon is termed as cyclic mechanical reinforcement (CMR). Comparing to the previous two-state two pathway model which explain the mechanism for catch bond, the molecules need an additional memory state and pathway to store and present the mechanical force history information. Herein we propose a three-state three-pathway model, in which loading and unloading regulate the molecular interactions switch among three states. Cyclic mechanical force trap more bonds in the memory state, and by assuming the memory states has low off-rate, the model provide a mechanism for the CMR.

Fall 2013 Schedule

Date	Speaker
8/29	Tung Le (Kim Lab)
9/5	--
9/12	Ilija Uzelac (Fenton Lab)
9/19	Keith Carroll (Curtis Lab)
9/26	Henry Astley (Goldman & Hu Lab)
10/3	Mark Kingsbury (Goldman Lab)
10/10	Curtis Malusek (Gumbart Lab)
10/17	Fall Break
10/24	Gable Wadsworth (Kim Lab)
10/31	Luis Jover (Weitz Lab)
11/7	Guillermo Amador (Hu Lab)
11/14	Jeff Aguilar (Goldman Lab)
11/21	Karl Lundquist (Curtis Lab)
11/28	Thanksgiving Break
12/5	Patricia Yang (Hu Lab)

Link to editable google doc here.

Fall 2013 Abstracts

11/21/2013

INVESTGATING THE BIOMECHANICAL PROPERTIES OF THE PERICELLULAR MATRIX USING NOVEL ASSAYS

Karl Lundquist, Curtis Lab

The pericellular matrix (PCM) is a large polymer mesh which is grafted to the surface of many Eukaryotic cells. This coat is composed primarily of a Hyaluronan backbone and proteoglycans such as aggrecan and versican. Studies have shown that the PCM plays a critical role in various cellular processes including migration, mechanotransduction, molecular sequestration, and virtually every other cell process which requires communication between the outside and inside of the cell. However, due to the extremely high water content in the coat, the PCM cannot be visualized using traditional imaging methods. Considering this, and the contribution of the PCM to countless cellular processes, it is empirical to develop novel assays for probing the properties of the matrix. Work in our laboratory has generated such assays but has yet to apply them to characterize the differences in cellular coats that exist between distinct cell types and during physiological transformations like migration and mitosis. I will discuss future work addressing the role that the PCM plays in cellular processes, as well as provide a summary of results obtained in the Curtis lab.

11/14/2013

A SIMPLE JUMPING ROBOT ON HARD AND FLOWABLE GROUND

Jeff Aguilar, Goldman's Lab

Various animals exhibit locomotive behaviors involving fast impulsive interactions with granular media, such as sprinting, jumping and hopping. On hard ground, these behaviors can be piece-wise described as transient bursts of actuation coupled with internal elastic elements to generate movement. On granular media, however, the performance of these behaviors is subject to the reaction forces of the media upon foot intrusion. The laws that govern these forces are not fully understood and vary with size and shape of foot, volume fraction and speed of intrusion. To better understand these interactions, we study the performance of vertical jumping on granular media of an actuated spring mass robot. The robot performs single jumps via one-cycle sine-wave relative trajectory. We systematically vary the forcing frequency and volume fraction and find that, at 8 Hz forcing, there is 743% increase in jump height with only a 5% increase in volume fraction using a 2” diameter flat foot. Additionally, including a short, high speed downward push prior to the main sine-wave movement nearly doubles the jump height at high volume fractions.

11/07/2013

HOW INSECTS KEEP THEIR SENSORY ORGANS CLEAN

Guillermo Amador, Hu's Lab

Flying insects face a barrage of foreign particles such as dust and pollen, which threaten to coat their eyes and antennae, limiting their sensing abilities. In this study, we elucidate novel aerodynamic and elastic mechanisms by which insects keep these organs clean. The compound eye of many species of insects is covered by an array of short bristles, or setae, evenly spaced between photoreceptor units. Among these insect species, setae length is roughly equal to their spacing. We conduct numerical simulations and wind tunnel experiments using an insect eye mimic to show setae of this length reduce shear rate at the eye surface by up to 90%. Thus, the setae create a stagnant zone in front of the eye, which diverts airflow to reduce deposition of particles. Setae can also act as springboards to catapult accumulated particles. In high speed videography of insects using their legs to clean themselves, we observe deflected setae and antennae hurling micron scale particles at accelerations 100-1000 times earth's gravity. The dual abilities of setae to divert airflow and catapult particles may motivate bio-inspired designs for dust-controlling lenses, sensors, and solar panels.

10/31/2013

THE ELEMENTAL COMPOSITION OF VIRAL PARTICLES: IMPLICATIONS FOR MARINE BIOGEOCHEMICAL CYCLES

Luis Jover, Weitz's Lab

Viral lysis of host cells in marine environments leads to the release of cellular carbon and nutrients and is hypothesized to be a major driver of carbon recycling at global scales. However, prior efforts to characterize the effect of viruses on carbon recycling have focused on materials in the host and overlooked the geochemical potential of viral particles themselves, particularly with respect to their nitrogen (N) and phosphorus (P) content. In this Analysis article, we propose a biophysical scaling model of the elemental stoichiometry of intact bacteriophage particles, finding that bacteriophage differ strongly in terms of their elemental stoichiometry from that of their host microorganisms. In conjunction with comparisons to the genomic and proteomic content of known virus isolates, we extrapolate this particle-scale model to ecosystem scales and predict that, despite their typically sub-femtogram total mass, bacteriophage particles – and virus particles more generally – are stronger contributors than previously recognized to both the reservoir and recycling of marine organic N and P.

10/24/2013

QUANTIFYING GENE EXPRESSION AT THE mRNA LEVEL

Gable Wadsworth, Kim's Lab

Gene expression is an ongoing process in all living organisms. Genetically identical cells can exhibit different gene expression patterns. Understanding the origin of this diversification is one of the main research goals in biology. To study how structure and dynamics of the physical genome affects stochastic gene expression, we have to measure either transcriptional dynamics of a single cell over time, or transcriptional statistics of a cell population at a fixed time from different genomic architectures. By implementing changes in the genetic code of the Pho5 promoter and open reading frame, gene expression can be quantified by measuring the amount of mRNA expressed by the cell. I will explain a technique called Fluorescence in Situ Hybridization (FISH), which is used to measure the number of mRNA in single cells. I will present improvements we made to this technique to achieve a true single-probe, single-fluorophore sensitivity in the model organism Saccharomyces Cerevisiae. Our technique allows the quantification of mRNA with a 1:1 ratio between mRNA molecule and FISH probe. To obtain this, mRNA spots are characterized in order to perform deconvolution and obtain super resolution images.

10/03/2013

EXPERIMENTAL ICHNOLOGY USING A ROBOTIC BIPED

Mark Kingsbury, Stephen Gatesy, Daniel I. Goldman, Brown, Georgia Tech

In the mid 1800s, Edward Hitchcock founded the field of ichnology, or the branch of paleontology that studies traces of organismal behavior through burrows and footprints in substrates like mud and sand that flowed hundreds of millions of years ago. Initially, well preserved tracks of extinct animals like dinosaurs were measured with a ruler and protractor to help identify species and morphological characteristics of the organisms' feet. Modern investigations study the intrusion of foot-shaped objects into laboratory mud (mimicking ancient beds) and observations of the footprints of living avian dinosaurs (like Guinea fowl) in prepared trackways. However, forced intrusions cannot capture how tracks emerge from the dynamical interactions of foot shape, ground properties and locomotion mechanics. And live organism studies suffer from controllability and repeatability. To systematically study how features of footprint formation are related to mass, gait, foot shape and size and substrate properties, we have built a self-supporting bipedal robot (39cm tall, 1.6 kg) that walks over prepared ground. We use an air fluidized bed of poppy seeds as our model substrate. Each leg is composed of four motors connected by segments which mimic avian limb morphology. The feet are 3D printed into different fixed shapes; we also test the effects of toe compliance. The robot is constrained by nearly frictionless horizontal and vertical air bearings; this structure allows translation but not pitching and avoids the need for feedback control to maintain the robot upright. The limbs and feet can be controlled to step in a specified trajectory. The entire system is under computer control, and we can systematically vary parameters, recording several hundred experiments per day. We present some preliminary data from our apparatus.

9/26/2013

PERFORMANCE, MECHANICS, AND DIVERSITY OF ANURAN JUMPING

Henry C. Astley, Goldman's Lab

Locomotion is an essential component of animal life history, and is strongly linked to morphology and physiology. Frog locomotion represents an ideal system in which to study locomotor performance, mechanics, and evolution. The exceptional jumping performance of anurans exceeds the capability of muscle due to a “catapult mechanism” in which an elastic element is slowly loaded by muscle, then rapidly recoils. Furthermore, anuran species employ a wide diversity of locomotor modes, with numerous independent evolutionary convergences and divergences. In this dissertation, I examined the performance and jump mechanics of a model taxon, followed by examining the evolution of muscle properties across the anuran phylogeny. Using X-ray Reconstruction of Moving Morphology (XROMM), I tested a candidate muscle-tendon unit for elastic energy storage by comparing muscle fascicle length change and ankle extension. These results showed that the muscle shortened early in the jump, stretching the elastic tendon, followed by rapid ankle extension without corresponding muscle shortening, indicating elastic recoil. However, prior laboratory performance measurements for this species (Rana pipiens) and congenerics suggested that no catapult mechanism was needed. To test this, I quantified jump distance of over 3000 bullfrog jumps at the Calaveras County Jumping Frog Jubilee. The majority of the jumps (58%) exceeded the maximum recorded in the scientific literature, in one case by almost a meter (2.2 m total), requiring the use of a catapult mechanism. To determine how this catapult mechanism was loaded prior to recoil, I used XROMM and force-plate data to compute inverse dynamics of frog jumping. Early in the jump, the hip moment and poor mechanical advantage impede joint motion, allowing the tendon to be loaded, after which hip moment declines and mechanical advantage improves, allowing tendon recoil. Examination of anatomical, performance, and muscle contractile property data across the frog phylogeny revealed that the evolution of performance was strongly linked to changes in anatomy, but minimally linked to changes in muscle properties. These result show that anurans do employ catapult mechanisms to produce high jump performance, using loading mechanisms widespread among vertebrates, and that the evolution of muscle properties is decoupled from locomotor performance.

9/12/2013

Controlled Nano-scale Reactions with Thermochemical Nanolithography

Keith Carroll, Curtis Lab

ThermoChemical NanoLithography (TCNL) is a lithographic technique based on an Atomic Force Microscope (AFM) modified with a semi-conducting thermal cantilever. When brought into contact with a surface and heated, thermal cantilevers induce a narrow temperature profile and with a well-designed substrate, this localized heating can cause a chemical or physical transformation. While previous works focused primarily on different materials, there is limited research on controlling and understanding the underlying mechanisms governing the technique. In this talk, we show that by coupling the technique with a chemical kinetics model, surface reactions can be controlled down to the nano-scale. Having demonstrated excellent control, applications for biophysics are discussed.

9/12/2013

CARDIAC NON-LINEAR DYNAMICS AND STABILIZATION OF CARDIAC ARRHYTMIAS WITH SINUS RESTORATION USING LOW-ENERGY FEEDBACK CONTROL

Ilija Uzelac, Fenton's Lab

Disruption of the normal heart rhythm can lead to a chaotic cardiac dynamic driven by the multiple scroll waves. If ventricular fibrillation (VF) develops, the cardiac intrinsic control system is unable to terminate it, and without any external control, death is imminent. In a phase space, the cardiac dynamic during normal heart rhythm is represented as a set of overlapping closed orbits that are destabilized during cardiac arrhythmias, mostly notably during VF. From the perspective of chaos theory and control theory of chaotic dynamics, parallels can be made with cardiac chaotic behavior and control methods can be devised. Time-delayed feedback control is well known as a practical method for stabilizing unstable periodic orbits embedded in chaotic attractors. The method is based on applying feedback perturbation proportional to the deviation of the current state of the system from its state one period in the past, so that the feedback signal vanishes when the stabilization of the target orbit is attained. Presented is the experimental implementation of the time- delayed feedback control to stabilize cardiac arrhythmias during VF. Second feedback control method is based on a proportional control where the feedback signal depends only on the present state of the system. In both control methods stabilization is achieved by forcing the dynamical system back to “maintain” the correct orbit by administering a defibrillation shock as an electrical current. In the first method, the control signal stabilizes the period of the chaotic orbit during VF, while the second control method terminates VF by forcing the system back into phase space orbits during sinus rhythm. Feedback signals are obtained in real time with the optical electrocardiogram and processed with the feedback controller which drives the custom made voltage-to-current converter that is able to produce arbitrary waveforms. The experimental results showed that proposed continuous feedback control methods can stabilize VF converting it into monomorphic tachycardia and sinus rhythm by administering low energy shocks.

8/29/2013

MEASURING ENERGETICS OF SHARP DNA BENDING FROM BREAKAGE KINETICS OF SMALL DNA LOOPS

Tung Le, Kim's Lab

The bending energetics of double stranded DNA (dsDNA) at short length scales remains controversial. Notably, recent single-molecule experiments on DNA looping in the absence of proteins suggest that the wormlike chain (WLC) model fails to predict the looping probability of dsDNA shorter than its persistence length. However, measurement of the looping probability of short dsDNA is subject to significant statistical error because looping events are extremely rare in physiological salt conditions, and comparison to the WLC model is ambiguous because of the unknown geometry requirement for loop stabilization. In this work, we used a novel unlooping assay to investigate energetics of small DNA loops in physiological salt conditions. Based on the measured loop breakage rate vs. loop length, we find that the free energy stored in DNA loops can be well described by the WLC model down to 60 bp. We also observe strong signs of structural transitions below 60 bp, reminiscent of kink formation.

Spring 2013 Abstracts

Lunch & Learn 4/18/2013

EFFECT OF SOIL WETNESS ON NEST ARCHITECTURE BY FIRE ANTS
Daria Monaenkova (Goldman's Lab)

Large underground nests are crucial for fire ants survival, providing protection from severe weather and predators. Although, the fire ants nests are found in all soil types in both North America and South
America, the areas with excessive soil moisture as well as the dry areas seems to be less favorable for a colony foundation. In this work we use x-ray computed tomography to study the effect of soil moisture
content on the growth and architecture of fire ants nests.  Because capillary cohesion in wet soils leads to the competition between tunnel stability and the labor-intensity of the excavation, we expect
to find an optimal soil wetness, which allows the most effective nest construction. We prepared digging containers (3.8 cm diameter by 14.5 cm deep aluminum tubes) with 3 types of simulated soil (50, 210 and
595 um glass particles). The prepared moisture content W varied from 0.01 to 0.2 by mass. Hundred ants were allowed to dig in the containers for 20 hours. Although, the ants were able to construct tunnels in all moisture levels, the maximum tunnel depth, H, and tunnels volume, V,  were significantly affected by W. At moderate moisture content (W=0.1) H and V were at least twice greater than at the lowest moisture content (W=0.01) for all tested colonies (n=9) for all particle sizes. The increase in H mirrors the dependence of the soil cohesion on W and we therefore conclude that the tunnel stability is a key factor influencing the digging strategy of fire ants.  In this presentation we will also discuss the influence of moisture content and particle size on nest geometry, excavation techniques employed by fire ants, and show in-progress work on social aspects of nest construction.

Lunch & Learn 4/11/2013

DEGRADATION OF LAMP1 and LAMP2 DECREASES LYSOSOME MOBILITY THROUGH ENLARGEMENT OF LYSOSOMES AND CELLULAR CROWDING
Austin Cyphersmith
Payne Laboratory, Chemistry and Biochemistry

The lysosome associated membrane proteins (LAMP1 and LAMP2) are the major lysosomal membrane proteins. Although the majority of the protein is contained within the lumen of the lysosome, the knockout or degradation of LAMPs significantly decreases lysosome mobility. Our goal was to degrade LAMP1 and LAMP2 in BS-C-1 cells and characterize lysosome transport to determine the underlying cause of decreased mobility. LAMP1 and LAMP2 were degraded using endoglycosidase H (endo H). Endo H cleaves oligosaccharides from LAMP1 and LAMP2 resulting in their degradation by lysosomal enzymes. Fluorescently labeled lysosomes were tracked during intracellular transport using live cell imaging and single particle tracking. Endo H treatment results in two populations of lysosomes; normal, punctate lysosomes and lysosomes with an increased diameter. The punctate lysosomes undergo standard long-range, microtubule-dependent transport throughout the cell. The enlarged lysosomes show highly localized motion and little long-range transport. To determine if this change in mobility was biochemical, due to LAMP degradation, or physical, due to the greater diameter of the lysosomes, single particle tracking experiments were carried out with sucrose-swollen lysosomes. These experiments show that the increased diameter of the lysosomes, and associated cellular crowding, results in the decreased mobility of the enlarged lysosomes.

Lunch & Learn 4/04/2013

MICROENVIRONMENT MATTERS: HOW FORCE AFFECTS MACROMOLECULE ASSEMBLIES AND THEIR FUNCTION IN LIVING CELLS
Jan Scrimgeour (Curtis Lab)

The behavior of macromolecules in living cells and their extracellular matrix can be dramatically modified by their local physical and chemical environment.  The formation, or breakdown, of macromolecular assemblies in response to the microenvironment can be interrogated using fluorescence microscopy, where techniques such as fluorescence recovery after photobleaching (FRAP) allow the measurement of molecular mobilities.  In combination with lab-on-a-chip devices, which allow precise control or measurement of environmental conditions, FRAP is a powerful experimental tool for studying macromolecule behavior.  Specifically, I will discuss the internal mechanics of cellular adhesion, probing how force can alter the function of proteins inside the adhesive complexes of living cells.  Through the use of force sensitive substrates, the protein vinculin was shown to exhibit anomalous behavior in response to applied force, suggesting it may play a mechanosensitive role during cell adhesion.

Lunch & Learn 3/28/2013

A TERRADYNAMICS OF LEGGED LOCOMOTION ON GRANULAR MEDIA[1]
Tingnan Zhang (Goldman Lab)

The theories of aero- and hydrodynamics form the bases for prediction of animal movement and device design in flowing air and water. For example, they allow computation of lift, thrust, and drag on wings and fins of a diversity of shapes and kinematics in a variety of flying and swimming animals. In contrast, we know little about how limb morphology and kinematics affect legged locomotion on natural substrates like sand and gravel which also flow in response to
movement. This is largely because predictive models for such flowing ground have been unavailable. Our recently developed “terradynamics” (Li et al, in review)—predictive force laws for legged locomotion on granular media (sand)—allow us to begin to investigate the role of limb morphology in locomotor performance on granular media. Using terradynamics, we develop a multi-body dynamic simulation of a small six-legged robot (13 cm, 150 g) moving on granular media, and predict the speed of the robot for c-shaped legs of a range of curvatures (1/R < 1/r < 1/R, where 2R = 4.1 cm is maximal leg length) and a range of stride frequencies (0 < f < 5 Hz). Our simulation reveals that the robot moves faster using positive curvature legs than negative curvature legs, because the former’s leg elements can access larger stresses and penetrate less deeply but generate larger thrust given the same average lift (robot weight). Further, our model
predicts that using an optimal c-shaped leg of curvature 1/r = 0.86/R, the robot can achieve maximal speed of ~70 cm/s (~5 BL/s) at 5 Hz. Our study demonstrates the power of terradynamics in the design of bio-inspired devices and promises to aid understanding of the functional morphology of sand-dwelling organisms.

Lunch & Learn 3/07/2013

CREATING CONTROLLED STATES OF WET GRANULAR MEDIA
Robyn Kuckuk (Goldman Lab)

Wet granular media, such as soil and beach sand, is abundant in nature.Numerous animals live on and within these soils and must cope with resistive forces which vary depending on wetness and compaction. Though
many studies have investigated animal kinematics in dry media, little work has been done that quantifies the effects of water content on animal locomotion. This study focused on the development of a method for the preparation of homogenous wet granular media states that are similar to naturally wet sand. In order to be biologically relevant in studying the mechanics of animals, water was used as the wetting medium. The independent variable was wetness content of the medium.   The compaction of the medium was also controllable. This method provides a technique for researchers in the field of biomechanics and robotics to create homogenous wet granular media systems with controlled compaction for use in other experiments. Next, we characterized the compaction of the system after initial shaking as well as prolonged shaking. A robot arm was used to drag an intruder of comparative size and shape to the animal to characterize how the resistive force changes with compaction and wetness content. We have successfully
used this technique in our studies of sandfish locomotion in dry granular media. We varied parameters such as speed of movement through the media and depth of movement, which helped us to further understand the characteristics of wet granular media. Additionally, we studied the Ocellated skink (figure 1) as a model animal to test how ground water affects locomotion strategy.  Building on our previous work studying sandfish lizard locomotion, we used x-ray imaging to visualize subsurface locomotion in the wet granular media so that we could track kinematics.

Lunch & Learn 2/28/2013

MODELING VIRUSES OF VIRUSES
Bradford Taylor (Weitz Lab)

IIn 2008 it was discovered that large viruses (size and genome comparable to bacteria) can have their own viruses called virophages.  While the large virus can reproduce within a eukaryotic host, the virophage requires coinfecting the host with the virus.  Two different modes for coinfection have been postulated.  As more and more examples of virophages are being discovered the importance of understanding the interactions between host, virus, and virophage is increasing.  Here we model the two different modes of coinfection in order to address how virophages control host and virus populations and to explore what dynamics are possible.

Lunch & Learn 2/21/2013

DNA EJECTION FROM BACTERIPHAGES TO BACTERIAL CELLS: A COMPUTATIONAL STUDY
Anton Petrov (Harvey Lab)

In the current presentation, we report on simulations of double-stranded DNA (dsDNA) ejection from bacteriophage φ29 into a bacterial cell. The ejection was studied with a coarse-grained model, in which viral dsDNA was represented by beads on a torsionless string. Our simplest simulations (involving constant viscosity and no external biasing forces) produced results compatible with the push-pull model of DNA ejection, with an ejection rate significantly higher in the first part of ejection than in the latter parts. Additionally, we performed more complicated simulations, in which we included additional factors such as external forces, osmotic pressure, condensing agents, and ejection-dependent viscosity. We found that, in general, the dependency of ejection forces and ejection rates on the amount of DNA ejected becomes more complex if the ejection is modeled with a broader, more realistic set of parameters and influences (such as variation in the solvent’s viscosity and the application of an external force). However, certain combinations of factors and numerical parameters led to the opposition of some ejection-driving and ejection-inhibiting influences, ultimately causing an apparent simplification of the ejection profiles.

Lunch & Learn 2/14/2013

BIOARTIFICIAL MATRICES TO MODULATE EPITHELIAL MORPHOGENESIS
Nduka Enemchukwu (Garcia Lab, Mech. Eng.)

We have developed synthetic polymer-based hydrogels with well-defined mechanical and cell-signaling properties to study the impact of the physical and chemical microenvironment on epithelial morphogenesis. In three-dimensional (3D) cell cultures of kidney epithelial cells, we found that hydrogel stiffness and cell adhesion peptide concentration control cell proliferation and cluster formation. Furthermore, we discovered a hydrogel stiffness that promotes assembly of spherical, hollow cyst structures that display physiological apical-basal polarity and laminin basement membrane assembly. Together, these findings establish a synthetic bioactive hydrogel platform for investigating epithelial morphogenesis.

Lunch & Learn 2/7/2013

WHAT IS HOLDING MY MAGNETIC MORTAR TOGETHER?
Carlos Orellana (Guest)

Magnetorheological (MR) fluids are colloidal suspensions of magnetizable particles that show an increment the yield stress and in the apparent viscosity in the presence of a magnetic field. It has been shown previously that MR fluids can be used for field-controlled static adhesion to non-magnetic surfaces [Phys. Fluids 23, 073104(2011)]. Here we demonstrate the important role the surface tension and viscosity play in this adhesion effect and that the adhesive property is not related to the shear resistance of the field-dependent yield stress suspension.

Lunch & Learn 1/31/2013

 
REAL-TIME OBSERVATIONS OF INTEGRIN CONFORMATIONAL CHANGES ON LIVING CELLS
Wei (Jack) Chen (Zhu Lab)

As adhesion molecules, integrins connect a cell to its environment and transduce signals across the membrane. Their different functional states correspond to distinct conformations. Using a biomembrane force probe, we observed real-time reversible switches between bent and extended conformations of a single integrin, aLb2, on the surface of a living cell by measuring its nanometer-scale headpiece displacements, bending and unbending frequencies, and molecular stiffness changes. We determined the stabilities of these conformations, their dynamic equilibrium, speeds and rates of conformational changes, and the impact of divalent cations and tensile forces. We quantified how initial and subsequent conformations of aLb2 regulate the force-dependent kinetics of dissociation from intercellular adhesion molecule-1 (ICAM-1). Our findings provide new insights into how integrins function as nano-machines to precisely control cell adhesion and signaling.

Lunch & Learn 1/24/2013

ANT TOWER
Nathan Mlot (Hu Lab)

Fire ants are capable of linking together to form bivouacs that serve as temporary shelter when alternatives cannot be found.  While the presence of army ant bivouacs has long been known, little to no studies have been carried out on the fire ant bivouac.  Much remains to be learned about the factors that limit the shape and speed of construction.  In this combined experimental and theoretical study, we use time-lapse video to investigate the construction of fire ant bivouacs that are built against a supporting Teflon rod.  We hypothesize that fire ants construct towers to uniformly distribute stress throughout the tower.  We test this hypothesis by designing an experiment to control tower building, gather data on tower shape and construction rate, and compare our findings to our uniform stress tower model.  We find that ants build towers into a shape that uniformly distributes stress with each ant supporting on average the weight of 3 neighbors.  We also test the effects of increasing gravity on the ant strength.  Finally we compare our model to self-assembled human towers to find the strength humans support within the towers.  Our future work involves developing an agent-based simulation for bivouac disassembly.

Lunch & Learn 1/17/2013

 
NEUROMECHANICS OF SAND-SWIMMING
Sarah Sharpe (Goldman Lab)

Animals like the sandfish lizard (Scincus scincus) that live in desert sand locomote on and within a granular medium whose resistance to intrusion is dominated by frictional forces. Recent kinematic studies reveal that the sandfish utilizes a wave of body undulation during swimming. Models predict that a particular combination of wave amplitude and wavelength yield maximum speed for a given frequency, and experiments have suggested that the sandfish targets this kinematic waveform. To investigate the neuromechanical strategy of the sandfish during sand-swimming, we used high speed x-ray and visible light imaging with synchronized electromyogram (EMG) recordings of epaxial muscle activity. During subsurface sand-swimming, EMG revealed an anterior-to-posterior traveling wave of muscle activation that travels faster than the wave of curvature. Muscle activation intensity increased as the animal swam deeper into the material but was insensitive to undulation frequency. These findings were in accord with empirical force measurements, which showed that resistance force increased with depth but was independent of speed. The change in EMG intensity with depth indicates that the sandfish targets a kinematic waveform (a template) which models predict maximizes swimming speed and minimizes mechanical cost of transport as it descends into granular media. In addition, we use a simple model of undulatory sand-swimming to explain the timing differences between muscle activation and curvature along the body. The differences in the EMG pattern as compared to undulatory swimmers in fluids can be attributed to the friction-dominated intrusion forces of granular media.

Fall 2012 Schedule

Date	Speaker	PPT
10/11	Tung Le (Kim Lab)	-
10/18	Nick Gravish (Goldman lab)	-
10/25	Louis McLane (Curtis Lab)	-
11/1	Gabriel Mitchel (Weitz Lab)	-
11/8	James Waters (Kim Lab)	-
11/15	Hamid Marvi (Hu Lab)	-
11/29	Dan Kovari (Curtis Lab)	-
12/6	César Flores (Weitz Lab)	-

Fall 2012 Abstracts

Lunch & Learn 12/06/2012

 
PHAGE-BACTERIA INFECTION NETWORKS: FROM NESTEDNESS TO MODULARITY
César Flores (Weitz lab)

Bacteriophages (viruses that infect bacteria) are the most abundant biological
life-forms on Earth.  However, very little is known regarding the structure of
phage-bacteria infections. In a recent study we re-evaluated 38 prior studies
and demonstrated that phage-bacteria infection networks tend to be
statistically nested in small scale communities (Flores et al 2011).
Nestedness is consistent with a hierarchy of infection and resistance within
phages and bacteria, respectively.  However, we predicted that at large
scales, phage-bacteria infection networks should be typified by a modular
structure.

We evaluate and confirm this hypothesis using the most extensive study of
phage-bacteria infections (Moebus and Nattkemper 1981). In this study, cross-
infections were evaluated between 215 marine phages and 286 marine bacteria.
We develop a novel multi-scale network analysis and find that the Moebus and
Nattkemper (1981) study, is highly modular (at the whole network scale), yet
also exhibits nestedness and modularity at the within-module scale. We examine
the role of geography in driving these modular patterns and find evidence that
phage-bacteria interactions can exhibit strong similarity despite large
distances between sites.

 
Lunch & Learn 11/29/2012


INVESTIGATION OF PHAGOCYTOSIS WITH PHYSICAL TOOLS
Daniel Kovari (Curtis Lab)

Phagocytosis has traditionally been investigated in terms of the relevant biochemical signaling pathways.  However, a growing number of studies have investigated how the physical attributes of cells affect phagocytosis.  In this talk I provide an overview of phagocytosis, highlighting how physical reasoning has been used to explain some of the hallmark behaviors of phagocytes.  I go on to describe some of the novel, physic-inspired, tools we (the Curtis group) have been developing to investigate phagocytosis.  These tools include: micro-pipette manipulators, traction force-microscopy, and the development of a photo-switchable fluorescent actin protein for use in molecular dynamics studies.   The work I present is ongoing and contributes to our long term effort of developing a physics based model of phagocytosis.

 
Lunch & Learn 11/15/2012

THE MECHANICS OF SNAKE LOCOMOTION
Hamid Marvi (Hu Lab)

Snakes are one of the worlds most versatile locomotors, at ease slithering through rubble or ratcheting up vertical tree trunks. In our experimental study, we measured the frictional properties of several species of snakes as well as the kinematics of their locomotion. We conducted experiments to show that snakes’ scales can dig into the underlying surface to prevent sliding. We used this novel paradigm, the active control of scales to modify frictional properties, to build Scalybot 1 and 2, two snake-like robots with individually controlled sets of belly scales. In our supporting theoretical study, we developed a dynamic model of snakes’ locomotion to predict its speed and the forces it applies to its environment. We focus on common modes of a snake’s motion such as concertina, rectilinear, and sidewinding.

 
Lunch & Learn 11/08/2012

TRANSCRIPTIONAL BURST GENERATION VIA CLUSTERING
James Waters (Kim Lab)

Certain gene transcription events occur in interesting temporal patterns, inadequately described by first-order kinetics, while still being governed by inherently stochastic processes. For instance, the production of messenger RNA in yeast cells is characterized by large bursts as opposed to individual uncorrelated events. We are investigating the co-localization or clustering of active sites as a mechanism to control this effect and we attempt to reproduce these bursts through numerical simulation of transcription factors diffusing in a model yeast nucleus. We present a detailed introduction to the development of our computational model, as well as preliminary results describing the effect of clustering sites on transcriptional bursting.

 
Lunch & Learn 11/01/2012

THE BIOPHYSICS OF ENZYMATIC LYSIS: DETERMINING A CRITICAL HOLE SIZE
Gabriel Mitchell (Weitz Lab)

Gram-positive bacteria transport molecules necessary for their survival through holes in their cell wall. The holes in cell walls need to be large enough to let critical nutrients pass through. However, the cell wall must also function to prevent the bacteria's membrane from protruding through a large hole into the environment and lysing the cell. As such, we hypothesize that there exists a range of cell wall hole sizes that allow for molecule transport but prevent membrane protrusion. Here we (Gabriel Mitchell, Kurt Kurt Wiesenfeld, Joshua Wetiz) develop and analyze a biophysical theory of the response of a Gram-positive cell's membrane to the formation of a hole in the cell wall. We determine a critical hole size beyond which lysis occurs. Our prediction is corroborated by experiments (conducted by our collaborator Daniel Nelson) in that provide lower bounds on cell wall hole sizes that result in lysis. Together, the theory and experiments provide a means to quantify the mechanisms of death of Gram-positive cells via enzymatically mediated lysis and provides insight into the range of cell wall hole sizes compatible with bacterial homeostasis.

 
Lunch & Learn 10/25/2012

OPTICAL FORCE PROBE STUDIES OF THE PERICELLULAR COAT
Louis McLane (Curtis Lab)

A voluminous polymer coat adorns the surface of many eukaryotic cells. Although the pericellular matrix (PCM) often extends several microns from the cell surface, its macromolecular structure remains elusive. This massive cellular organelle negotiates the cell’s interaction with surrounding tissue, influencing important processes including cell adhesion, mitosis, locomotion, molecular sequestration, and mechanotransduction.  Investigations of the PCM’s architecture and function have been hampered by the difficulty of visualizing this invisible hydrated structure without disrupting its integrity. In this work, we establish several assays to non-invasively measure the ultrastructure of the PCM. Optical force probe assays show that the PCM of chondrocytes (RCJ-P) is not crosslinked and that it easily reconfigures around microparticles. We report distinct changes in forces measured from PCMs treated with exogenous aggrecan, illustrating the assay’s potential to probe proteoglycan distribution. Measurements detect an exponentially-increasing osmotic force in the PCM arising from an inherent concentration gradient. With this result, we estimate the variation of the PCM’s mesh size (correlation length) to range from approximately 100 nm at the surface to 500 nm at its periphery. Quantitative particle exclusion assays confirm this prediction, and show that the PCM acts like a sieve. These assays provide a much needed tool to study PCM ultrastructure and its poorly defined but important role in fundamental cellular processes.

 
10/18/2012

STABILIZING FALLS IN CONFINED ENVIRONMENTS
Nick Gravish (Goldman lab)

Subterranean animals must rapidly navigate unpredictable and perilous underground environments. Nests of the fire ant \em{Solenopsis invicta} (average body length 0.35  \pm 0.05 cm) consist of a subterranean network of large chambers and tunnels which can reach 2 meters into the earth and house up to 250,000 workers. Laboratory investigations of fire ants reveal that digging workers typically climb up and down tunnels slightly wider than the largest ant hundreds of times per hour. However the principles of locomotion within confined environments such as tubes have been largely unexplored. We hypothesize that the ability to engineer underground habitats provides opportunities to facilitate movement. We conducted laboratory experiments to monitor upward and downward tube climbing of isolated fire ant workers. Fire ants were challenged to climb in 9.4 cm long glass tunnels (diameter D = 0.1 – 0.9 cm) that separated a nest from an open arena with food and water. During ascending and descending climbs we induced falls by a rapid, short, translation of the tunnels downward. We monitored induced falls over 24 hours in groups from five separate colonies. The tunnel diameter has a significant affect on the ability of ants to rapidly recover from perturbations. Falls in smaller diameter tunnels were arrested through the use of rapid jamming of limbs, body and antennae against the tunnel walls, arresting in as low 30 ms. Falls in larger diameter tunnels were not arrested. We find that the transition to stable fall arrest occurs in tunnels equal to 1.4 BL. This tunnel size is  comparable to the natural tunnel diameter found near nest entrances. Our data indicates that fire ants moving through natural tunnels can employ antennae, limbs, and body to rapidly stabilize falls.

 
10/11/2012

MEASURING LOOPING KINETICS OF SHORT DOUBLE-STRANDED DNA
Tung Le (Kim Lab)

Bending of double-stranded DNA (dsDNA) is associated with fundamental biological processes such as genome packaging and gene regulation, and
therefore studying sequence-dependent dsDNA bending is a key to understanding biological impact of DNA sequence beyond the genetic code. Average mechanical behavior of long dsDNA is well described by the wormlike chain model, but the behavior of dsDNA at length scales
around or below the persistence length remains controversial. Here we used single-molecule FRET (Förster Resonance Energy Transfer) to measure spontaneous looping kinetics of 100~200 bp dsDNA in the absence of proteins. We showed that in this length regime, the apparent looping rate increased as dsDNA became more curved and longer, suggesting that the energy component dominates the free energy of looping. We also calculated the predicted dependence of looping rate as a function of deflection angle and length based on a dinucleotide wormlike chain model, and showed that the observed length and curvature dependence is much weaker than predicted. Our results suggest that dynamics of dsDNA deviates from the wormlike chain behavior below 200 bp.