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  • Title: PoLSWiki
    Descriptive info: Main Page.. From PoLSWiki.. Jump to:.. navigation.. ,.. search.. This is the homepage of the Georgia Tech node of the international.. Physics of Living Systems (PoLS).. student research network.. The goal of this network is to foster interaction and collaboration among.. PoLS.. researchers within Georgia Tech and across institutes.. Six core faculty members from the Schools of Biology, Physics, and Mechanical Engineering lead the Georgia Tech.. node.. Contents.. 1.. Postdoc positions.. 2.. Announcements.. 3.. Signing-up for the email list.. 4.. Core faculty list.. 5.. Support.. The NSF.. Physics of Living Systems.. program sponsors research.. exploring the most fundamental physical processes that living systems utilize to perform their functions in dynamic and diverse environments.. The aim of PoLS research is to advance our understanding of the living world in a quantitative way, while also seeking to expand the intellectual range of physics paying through the lessons learned from the biological study.. For more information about the PoLS virtual institute program see the main PoLS website at.. http://pols.. rice.. edu/.. At Georgia Tech PoLS research is carried out across a diversity of biological scales: single-molecule.. cellular.. organismal biophysics.. Both theoretical and experimental biophysics research is conducted by core faculty members and affiliated faculty.. The Physics of Living Systems (PoLS) Student Research Network at the Georgia Institute of Technology (GT) invites applications for multiple PoLS Postdoctoral Fellowships.. The successful applicants will join the GT node of the National Science Foundation funded Student Research Network.. Successful applicants will work with faculty in the GT node on projects at the interface of physics and biology.. Candidates with backgrounds in biological physics, biorobotics, soft condensed matter, and nonlinear dynamics are encouraged to apply.. Candidates are expected to have a Ph.. D.. in physics, biophysics, applied mathematics, mechanical engineering, or a related field.. Ideal candidates will have a demonstrated ability to conduct independent high-impact research.. Appointments are available immediately.. To apply, please e-mail [mailto:info@pols.. gatech.. edu info@pols.. edu] with a curriculum vitae (CV) along with a one page statement of how your research interests are related to this position.. In addition, please arrange to have two letters of recommendation e-mailed to the same address.. Applications will be considered immediately and the search will continue until all positions are filled.. Georgia Tech is a unit of the University System of Georgia and an Affirmative Action/Equal Opportunity Employer and requires compliance with the Immigration Control  ...   27- July 5, 2013.. Registration opens in February 2013.. See.. flier.. for details.. 01-22-13: The PoLS web site, which includes the BLOG is now ready for use, but it requires you to register first.. If you have not already registered, visit:.. edu.. 11-16-12 there will be two talks given by Prof.. Robert Dudley entitled.. From Ants to Hummingbirds: The Evolution of Flight.. Information about the talk can be found.. here.. and.. A lunch for PoLS student members and the speaker will be provided after the talk.. 11-15-12: For those students interested, the Siements Competition in Math, Science Technology will be held on the Georgia Tech campus this weekend.. As described on the competition website "America’s next generation of young innovators presents their awe-inspiring research projects to expert university judges.. " More information can be found.. To receive email notification about upcoming GaTech-PoLS events and reminders about the weekly talks, sign-up for the email list.. You can sign-up by simply sending a message.. To: pols-request@lists.. edu Subject: subscribe.. After you have requested subscription the list moderators can approve you.. Once that happens you will get a confirmation email.. Core faculty list.. Core Faculty.. PI.. Website.. Contact.. Daniel I.. Goldman.. http://crablab.. daniel.. goldman[at]physics.. Jennifer Curtis.. http://curtisresearch.. jennifer.. curtis[at]physics.. Kurt Wiesenfeld.. Department profile.. kurt.. wiesenfeld[at] physics.. Joshua Weitz.. physics.. edu/user/joshua-weitz.. jsweitz[at] gatech.. Harold Kim.. edu/user/harold-kim.. harold.. kim [at] physics.. Flavio Fenton.. https://www.. edu/user/flavio-fenton.. flavio.. fenton [at] physics.. David Hu.. http://www-old.. me.. edu/hu/.. hu [at] me.. James Gumbart.. mcs.. anl.. gov/~gumbart/index.. html.. gumbart[at]physics.. Support.. This network is supported by the NSF.. program within the physics division.. The student research network is a part of the NSF.. Science across virtual institutes.. program to encourage interaction among researchers across many universities.. Retrieved from ".. https://pols.. edu/pols/index.. php?title=Main_Page oldid=529.. ".. Views.. Page.. Discussion.. View source.. History.. Personal tools.. Log in.. Navigation.. News.. Lunch Learn.. Job Listings.. Courses.. Upcoming Conferences.. Upcoming Seminars.. About PoLS.. Student directory.. Other nodes.. Internal.. Contact.. Core faculty.. Goldman.. Jennifer Curtis.. Kurt Wiesenfeld.. Joshua Weitz.. Harold Kim.. Flavio Fenton.. David Hu.. James Gumbart.. Links.. Georgia Tech.. School of Physics.. School of Biology.. School of Mechanical Engineering.. PoLS Home base.. NSF Physics of Living Systems.. Search.. Toolbox.. What links here.. Related changes.. Special pages.. Printable version.. Permanent link.. This page was last modified on 23 July 2013, at 08:45.. This page has been accessed 3,067 times.. Privacy policy.. About PoLSWiki.. Disclaimers..

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  • Title: JobBoard - PoLSWiki
    Descriptive info: JobBoard.. This is a listing of open positions and research opportunities either directly, or closely, related to the physics of living systems.. GaTech Positions.. 1.. Postdoc Positions.. Other Institutions.. Postdoc Positions Grants.. GaTech Positions.. Below are a listing of Post-Doc positions available in the Physics of Living Systems research groups at Georgia Tech.. Postdoc Positions.. PoLS Postdoctoral Fellowships (multiple available).. To apply, please e-mail.. info@pols.. with a curriculum vitae (CV) along with a one page statement of how your research interests are related to this position.. Other Institutions.. The following are open positions at non-GaTech institutions.. If you are interested in posting a position contact the GaTech-PoLS web master.. Postdoc Positions Grants..  ...   of theoretical and mathematical tools contributing to the science of complex, adaptive, nonlinear systems.. While the program's emphasis is on the development and application of the theory and tools used in the study of complex research questions and not on particular fields of research per se, JSMF is particularly interested in the continued development of complex systems science, and in projects attempting to apply complex systems approaches to coherently articulated questions.. For more information see the website:.. jsmf.. org/apply/fellowship/index.. php.. Note: The deadline is June 14, 2013, 15:59 Central Time (20:59 UTC).. php?title=JobBoard oldid=525.. This page was last modified on 18 April 2013, at 15:34.. This page has been accessed 692 times..

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  • Title: PoLSWiki
    Descriptive info: Revision as of 08:45, 23 July 2013 by.. Ashleyjeter.. (.. Talk.. |.. contribs.. ).. diff.. ).. ← Older revision.. | Latest revision (diff) | Newer revision → (diff).. This page has been accessed 3,068 times..

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  • Title: View source for Main Page - PoLSWiki
    Descriptive info: View source for Main Page.. ←.. You do not have permission to edit this page, for the following reason:.. The action you have requested is limited to users in the group:.. Users.. You can view and copy the source of this page:.. This is the homepage of the Georgia Tech node of the international '''Physics of Living Systems (PoLS)''' student research network.. The goal of this network is to foster interaction and collaboration among '''PoLS''' researchers within Georgia Tech and across institutes.. Six core faculty members from the Schools of Biology, Physics, and Mechanical Engineering lead the Georgia Tech '''PoLS''' node.. __TOC__ The NSF [http://www.. nsf.. gov/funding/pgm_summ.. jsp?pims_id=6673 '''Physics of Living Systems'''] program sponsors research nowiki>" /nowiki>''exploring the most fundamental physical processes that living systems utilize to perform their functions in dynamic and diverse environments.. '' nowiki>" /nowiki> The aim of PoLS research is to advance our understanding of the living world in a quantitative way, while also seeking to expand the intellectual range of physics paying through the lessons learned from the biological study.. For more information about the PoLS virtual institute program see the main PoLS website at [http://pols.. edu/ http://pols.. edu/].. At Georgia Tech PoLS research is carried out across a diversity of biological scales: single-molecule ''' rArr;''' cellular ''' rArr;''' organismal biophysics.. == span style="color:#eeb211">Postdoc positions /span> == pre style="background-color:#99ccff;white-space:pre-wrap"> The Physics of Living Systems (PoLS) Student Research Network at the Georgia Institute of Technology (GT) invites applications for multiple PoLS Postdoctoral Fellowships.. /pre> == Announcements == *07-22-13 Gabriel Mitchell presented his thesis defense entitled, "Quantifying Enzymatic Lysis in Gram-positive Bacteria," in the ES T Building, room L1125.. *05-08-13 Tung Le from Harold Kim's lab has recently published a publication, entitled, Measuring Shape-Dependent Looping Probability of DNA.. *04-18-13: The James S.. For more information see the listing in the newly created [[JobBoard|job board]].. *02-15-13: Sarah Sharpe (Goldman Lab) placed 2nd for Best Student Presentation in the  ...   and [http://www.. biology.. edu/seminars/ here].. * 11-15-12: For those students interested, the Siements Competition in Math, Science Technology will be held on the Georgia Tech campus this weekend.. " More information can be found [https://www.. ceismc.. edu/student-competitionsiemens here].. == Signing-up for the email list== To receive email notification about upcoming GaTech-PoLS events and reminders about the weekly talks, sign-up for the email list.. You can sign-up by simply sending a message pre> To: pols-request@lists.. edu Subject: subscribe /pre> After you have requested subscription the list moderators can approve you.. == Core faculty list == {| class="wikitable" style="text-align:center; font-size: 12px; width:80%;" |+ Core Faculty ! PI ! Website ! Contact |- ! Daniel I.. Goldman ! [http://crablab.. edu http://crablab.. edu] ! [mailto:daniel.. goldman@physics.. edu daniel.. goldman nowiki>[ /nowiki>at nowiki>] /nowiki>physics.. edu] |- ! Jennifer Curtis ! [http://curtisresearch.. edu/ http://curtisresearch.. edu/] ! [mailto:jennifer.. curtis@physics.. edu jennifer.. curtis nowiki>[ /nowiki>at nowiki>] /nowiki>physics.. edu] |- ! Kurt Wiesenfeld ! [https://www.. edu/user/kurt-wiesenfeld Department profile] ! [mailto:kurt.. wiesenfeld@physics.. edu kurt.. wiesenfeld nowiki>[ /nowiki>at nowiki>] /nowiki> physics.. edu] |- ! Joshua Weitz ! [http://www.. edu/user/joshua-weitz http://www.. edu/user/joshua-weitz] ! [mailto:jsweitz@gatech.. edu jsweitz nowiki>[ /nowiki>at nowiki>] /nowiki> gatech.. edu] |- ! Harold Kim ! [http://www.. edu/user/harold-kim http://www.. edu/user/harold-kim] ! [mailto:harold.. kim@physics.. edu harold.. kim nowiki>[ /nowiki>at nowiki>] /nowiki> physics.. edu] |- ! Flavio Fenton ! [https://www.. edu/user/flavio-fenton https://www.. edu/user/flavio-fenton] ! [mailto:flavio.. fenton@physics.. edu flavio.. fenton nowiki>[ /nowiki>at nowiki>] /nowiki> physics.. edu] |- ! David Hu ! [http://www-old.. edu/hu/ http://www-old.. edu/hu/] ! [mailto:hu@me.. edu hu nowiki>[ /nowiki>at nowiki>] /nowiki> me.. edu] |- ! James Gumbart ! [http://www.. html http://www.. html] ! [mailto:gumbart@physics.. edu gumbart nowiki>[ /nowiki>at nowiki>] /nowiki>physics.. edu] |- |} == Support == This network is supported by the NSF [http://www.. jsp?pims_id=6673 '''Physics of Living Systems'''] program within the physics division.. The student research network is a part of the NSF [http://www.. gov/news/special_reports/savi/index.. jsp Science across virtual institutes] program to encourage interaction among researchers across many universities.. Return to.. php?title=Main_Page..

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  • Title: Revision history of "Main Page" - PoLSWiki
    Descriptive info: Revision history of "Main Page".. View logs for this page.. Browse history.. From year (and earlier):.. From month (and earlier):.. all.. January.. February.. March.. April.. May.. June.. July.. August.. September.. October.. November.. December.. Deleted only.. Diff selection: Mark the radio boxes of the revisions to compare and hit enter or the button at the bottom.. Legend:.. (cur).. = difference with latest revision,.. (prev).. = difference with preceding revision,.. m.. = minor edit.. (Latest |.. Earliest.. ) View (newer 50 |.. older 50.. ) (.. 20.. 50.. 100.. 250.. 500.. (cur |.. prev.. 08:45, 23 July 2013.. (+159).. →.. cur.. 11:50, 21 May 2013.. DKovari.. (+2).. 15:50, 8 May 2013.. (+264).. 15:32, 18 April 2013.. (+1).. 15:31, 18 April 2013..  ...   09:23, 22 January 2013.. (+182).. 15:28, 11 December 2012.. Admin.. (+137).. 17:12, 6 December 2012.. (+53).. 16:05, 6 December 2012.. (-62).. (-909).. 10:54, 28 November 2012.. 13:58, 27 November 2012.. (-15).. 13:57, 27 November 2012.. (+15).. 13:56, 27 November 2012.. (+21).. 13:55, 27 November 2012.. (+46).. 13:54, 27 November 2012.. (+4).. 13:48, 27 November 2012.. (+20).. 13:46, 27 November 2012.. (+11).. 09:58, 27 November 2012.. (+240).. 00:44, 27 November 2012.. (+1,287).. 00:43, 27 November 2012.. (+26).. (-6).. 00:42, 27 November 2012.. 00:40, 27 November 2012.. 00:39, 27 November 2012.. (+3).. (+61).. 00:37, 27 November 2012.. (+163).. 00:30, 27 November 2012.. 10:12, 16 November 2012.. (+64).. 18:28, 15 November 2012.. 18:26, 15 November 2012.. (+307).. 12:49, 15 November 2012.. (+10).. Atom..

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  • Title: Log in - PoLSWiki
    Descriptive info: You must have cookies enabled to log in to PoLSWiki.. Username:.. Password:.. Remember my login on this browser (for a maximum of 180 days).. Forgotten your login details?.. php?title=Special:UserLogin.. Special page.. 213.. 175.. 86.. 38.. Talk for this IP address..

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  • Title: News - PoLSWiki
    Descriptive info: 04-08-13.. 3-21-13.. 02-15-13.. 2.. 02-01-13.. 3.. 01-31-13.. 4.. 01-22-13.. 5.. 11-16-12.. 6.. 11-15-12.. 7.. 10/7/2012.. 8.. 9/21/2012.. 04-08-13.. Visiting researcher at CrabLab: Christopher Topp, Postdoctoral Associate at the Department of Biology, Duke University.. Dates: April 29-th-30th 2013.. Christopher is interested in studying the plants roots networks in soil.. Visiting researcher: Jessica Kurth, Graduate Student at the Department of Biology, UNC Chapel Hill.. Dates: April 22-nd- 24-th 2013.. Jessica plans to study burrowing behavior of earthworms.. 3-21-13.. PoLS students from Georgia Tech, The University of Maryland, and The University of Maryland gathered for lunch at March Meeting.. 02-15-13.. Sarah Sharpe (Goldman Lab) placed 2nd for Best Student Presentation in the Division of Comparative Biology at the.. 02-01-13.. The University of Illinois, Urbana-Champaign will be hosting the 2013.. 01-31-13.. The Lake Como  ...   it requires you to register first.. 11-16-12.. There will be a talk given by Prof.. Lunch for PoLS student members will be provided after the talk.. 11-15-12.. For those students interested, the Siements Competition in Math, Science Technology will be held on the Georgia Tech campus this weekend.. 10/7/2012.. The first of nine.. student led presentation and discussion sections will begin this Thursday, 10/11/2012.. sessions will be held on Thursdays from 12-1:30 in Howey.. A full schedule and sign up sheet for the lunch and learns can be found on the.. page.. 9/21/2012.. Georgia Tech joins other North American.. Nodes.. in the.. For more information see the Georgia Tech press release.. php?title=News oldid=517.. This page was last modified on 17 April 2013, at 10:24.. This page has been accessed 316 times..

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  • Title: Lunch & Learn - PoLSWiki
    Descriptive info: Lunch Learn student led discussion and presentations are held on Thursdays from 12-1:30 in the Howey Physics Building.. 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 fill in your name in the spreadsheet below.. Fall 2013 Schedule.. Fall 2013 Abstracts.. Spring 2013 Abstracts.. Fall 2012 Schedule.. Fall 2012 Abstracts.. Fall 2013 Schedule.. Date.. Speaker.. 8/29.. Tung Le (Kim Lab).. 9/5.. --.. 9/12.. Ilija Uzelac (Fenton Lab).. 9/19.. 9/26.. 10/3.. 10/10.. 10/17.. Fall Break.. 10/24.. 10/31.. 11/7.. 11/14.. 11/21.. 11/28.. Thanksgiving Break.. 12/5.. Link to editable google doc.. Fall 2013 Abstracts.. Lunch Learn 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.. Lunch Learn 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.. 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  ...   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.. 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.. php?title=Lunch_%26_Learn oldid=540.. This page was last modified on 11 September 2013, at 10:04.. This page has been accessed 1,051 times..

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  • Title: Courses - PoLSWiki
    Descriptive info: Spring 2013 Courses.. Course name.. Information.. Statistical Mechanics II.. An approximate syllabus:.. http://phweb.. edu/academics/Classes/fall2010/7123/index.. Readings in Viral Ecology.. Link to syllabus:.. php?title=File:Syllabus_8801.. pdf#file.. php?title=Courses oldid=407.. This page was last modified on 9 January 2013, at 11:41.. This page has been accessed 71 times..

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  • Title: Conferences & Meetings - PoLSWiki
    Descriptive info: Conferences Meetings.. For information on upcoming conferences and meetings that are relavent to physics of living systems research, see the items below.. "Quantitative Laws of Genome Evolution" Workshop (Como, Italy) -- June 27-July 5, 2013.. Lake Como School of Advanced Studies in Complex Systems (Villa del Grumello, Como, Italy) will be hosting a workshop discussing "Quantitative Laws of Genome Evolution".. Registrations will open in February 2013.. Scholarships will be available on a selection basis.. Contact: ev.. genome.. workshop@gmail.. com.. Quantitative approaches to evolutionary genomics, systems biology, and ecology unravel several universal regularities connecting genome-scale observables, phenotypes and physiological traits.. Putting aside any irrealistic ambitions of a all-inclusive theories, some of these universal empirical trends might qualify as “biological laws” in a similar sense as “law” is understood in modern physics.. Consequently, a current challenge for theoreticians is understanding how different universal features emerging empirically can be accounted for by simple mathematical models exploring quantitative laws at different levels, from physiology  ...   open to anyone with background in (evolutionary) genomics, (evolutionary) biology, bioinformatics, ecology, interested in quantitative work.. See the announcement flier for more details:.. https://docs.. com/file/d/0B5KqyPAOnU9CQTF0eXdNMlRfLWs/edit?usp=sharing.. 2013 Physics of Living Systems Summer School -- June 15-20, 2013 (Champaign, IL).. On behalf of the Center for the Physics of Living Cells (CPLC), an NSF Physics Frontier Center at the University of Illinois, Urbana-Champaign, we are writing to announce the 2013 Physics of Living Cells Summer School being offered from July 15 – 20, 2013 at the University of Illinois at Urbana-Champaign.. This one-week program is designed for graduate students, postdoctoral fellows and researchers in the chemical and life sciences, biophysics, physics, and engineering who would like to expand their training into the areas of single-molecule and live-cell experimental and computational biophysics.. For more information and to.. apply by March 15.. , please visit:.. php?title=Conferences_%26_Meetings oldid=458.. This page was last modified on 1 February 2013, at 11:21.. This page has been accessed 131 times..

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