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BEGIN:VEVENT
SUMMARY:Cristian Micheletti (International School for Advanced Studies)
DTSTART;VALUE=DATE-TIME:20210614T150000Z
DTEND;VALUE=DATE-TIME:20210614T153000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/1
DESCRIPTION:Title: Knots and links in channel and slit confinement: static and dynamics<
/a>\nby Cristian Micheletti (International School for Advanced Studies) as
part of BIRS workshop : Novel Mathematical Methods in Material Science: A
pplications to Biomaterials\n\nView-only livestream: https://www.birs.ca/l
ive\n\nAbstract\nI will report on a series of studies where we looked at h
ow the static and dynamics of entangled polymers is affected by confinemen
t. Specifically\, I will first by consider the knotting of semi-flexible c
hains inside channels of different size and discuss how the size and compl
exity evolves during the free or externally-driven dynamics of the chain[1
\,2]. Next\, I will turn to the case of linked rings inside channels and s
lits and discuss how the size and dynamics of their linked portion respond
s to different types of confinement[3\,4].\n\nReferences\n[1] C. Michelett
i and E. Orlandini\, ”Knotting and unknotting dynamics of DNA strands in
nanochannels”\, ACS Macro Letters\, 3 \, 876-880 (2014)\n[2] D. Michiel
etto\, E. Orlandini\, M.S. Turner and C. Micheletti\, ”Separation of Geo
metrical and Topological entangle- ment in Confined polymers Driven out of
Equilibrium”\, ACS Macro Letters\, 9 \, 1081-1085 (2020)\n[3] G. D’Ad
amo\, E. Orlandini and C. Micheletti\, ”Linking of ring polymers in slit
-like confinement”\, Macromolecules\,\, 50 \, 1713-1718 (2017)\n[4] G. A
mici\, M. Caraglio\, E. Orlandini and C. Micheletti\, ”Topologically Lin
ked Chains in Confinement”\, ACS Macro Lett.\, 8 \, 442-446 (2019)\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/1/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Fred MacKintosh (Rice University)
DTSTART;VALUE=DATE-TIME:20210614T153000Z
DTEND;VALUE=DATE-TIME:20210614T160000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/2
DESCRIPTION:Title: Mechanical phase transitions and elastic anomalies in biopolymer gels
\nby Fred MacKintosh (Rice University) as part of BIRS workshop : Nove
l Mathematical Methods in Material Science: Applications to Biomaterials\n
\nView-only livestream: https://www.birs.ca/live\n\nAbstract\nThe mechanic
s of cells and tissues are largely governed by scaffolds of filamentous pr
oteins that make up the cytoskeleton\, as well as extracellular matrices.
Evidence is emerging that such networks can exhibit rich mechanical phase
behavior. A classic example of a mechanical phase transition was identifie
d by Maxwell for macroscopic engineering structures: networks of struts or
springs exhibit a continuous\, second-order phase transition at the isost
atic point\, where the number of constraints imposed by connectivity just
equals the number of mechanical degrees of freedom. We will present recent
theoretical predictions and experimental evidence for a strain-controlled
mechanical phase transition in biopolymer networks below Maxwell’s isos
tatic point. We will outline a theoretical framework to understand and qua
ntify the critical phenomena associated with this transition. As we show\,
this transition also governs elastic anomalies\, including an anomalously
large Poisson ratio and inverse Poynting effect.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/2/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Wilma Olson (Rutgers University)
DTSTART;VALUE=DATE-TIME:20210614T160000Z
DTEND;VALUE=DATE-TIME:20210614T163000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/3
DESCRIPTION:Title: Surprising Twists in Nucleosomal DNA with Implication for Higher-orde
r Chromatin Folding\nby Wilma Olson (Rutgers University) as part of BI
RS workshop : Novel Mathematical Methods in Material Science: Applications
to Biomaterials\n\nView-only livestream: https://www.birs.ca/live\n\nAbst
ract\nWhile nucleosomes are dynamic entities that must undergo structural
deformations to perform their functions\, the general view from available
high-resolution structures is a largely static one. Even though numerous e
xamples of twist defects have been documented\, the DNA wrapped around the
histone core is generally thought to be overtwisted. Analysis of availabl
e high-resolution structures reveals a heterogeneous distribution of twist
along the nucleosomal DNA\, with clear patterns that are consistent with
the literature\, and a significant fraction of structures that are undertw
isted. The subtle differences in nucleosomal DNA folding\, which extend be
yond twist\, have implications for nucleosome disassembly and modeled high
er-order structures. Simulations of oligonucleosome arrays built with unde
rtwisted models behave very differently from those constructed from overtw
isted models\, in terms of compaction and inter-nucleosome contacts\, intr
oducing configurational changes equivalent to those associated with 2-3 ba
se-pair changes in nucleosome spacing. Differences in the nucleosomal DNA
pathway\, which underlie the way that DNA enters and exits the nucleosome\
, give rise to different nucleosome-decorated minicircles and affect the t
opological mix of configurational states.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/3/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Louis Kauffman (University of Illinois at Chicago)
DTSTART;VALUE=DATE-TIME:20210614T164500Z
DTEND;VALUE=DATE-TIME:20210614T171500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/4
DESCRIPTION:Title: Knotoids and Their Applications\nby Louis Kauffman (University of
Illinois at Chicago) as part of BIRS workshop : Novel Mathematical Method
s in Material Science: Applications to Biomaterials\n\nView-only livestrea
m: https://www.birs.ca/live\n\nAbstract\nA knotoid is a generalization of
a 1-1 tangle in classical knot theory to a diagram with ends so that the e
nds can be in distinct regions.\nSuch diagrams are taken up to Reidemeiste
r moves that do not allow passage of strands across the ends of the diagra
m. In this way one obtains\na concept of an open ended diagram that can be
classified topologically just as are the closed diagrams of classical kno
t theory. By constructions due to Vladimir Turaev\n(for diagrams on the tw
o-sphere) and the author and Neslihan Gugumcu (for diagrams in the plane)
one can interpret knotoids as projections from open-ended curves in three
dimsensional space.\nBy natural restrictions of the isotopies of such spac
e curves (in relation to the projection) one then has a way to handle the
topology of open-ended curves in three dimensional space. This talk will d
iscuss\nthe relationship between open-ended curves in three dimensional sp
ace and their corresponding knotoid classes. We will discuss basic invaria
nts such as the Jones polynomial\, relationships of knotoids with viritual
\nknot theory and aspects of our joint work with Nesilhan Gugumcu\, Sofia
Lambropoulou\,Manos Manouras and with Eleni Panagiotou.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/4/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Eleni Panagiotou (University of Tennessee at Chattanooga)
DTSTART;VALUE=DATE-TIME:20210614T171500Z
DTEND;VALUE=DATE-TIME:20210614T174500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/5
DESCRIPTION:by Eleni Panagiotou (University of Tennessee at Chattanooga) a
s part of BIRS workshop : Novel Mathematical Methods in Material Science:
Applications to Biomaterials\n\nView-only livestream: https://www.birs.ca/
live\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/5/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Slobodan Zumer (Jozef Stefan Institute & University of Ljubljana)
DTSTART;VALUE=DATE-TIME:20210615T140000Z
DTEND;VALUE=DATE-TIME:20210615T143000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/6
DESCRIPTION:Title: Topological analysis of 3D active nematic turbulence in droplets\
nby Slobodan Zumer (Jozef Stefan Institute & University of Ljubljana) as p
art of BIRS workshop : Novel Mathematical Methods in Material Science: App
lications to Biomaterials\n\nView-only livestream: https://www.birs.ca/liv
e\n\nAbstract\nIn confined active anisotropic soft mater\, the interplay o
f ordering\, elasticity\, chirality\, confinement\, surface anchoring\, ex
ternal fields\, flows\, and activity leads to numerous complex static and
dynamic structures. Their orientational ordering fields include singular t
opological defects and nonsingular solitonic deformations. Increasing inte
rest in active systems stimulated us to model topology of three-dimensiona
l extensile activity driven nematodynamics in a spherical confinement prov
iding a topological constrain [1\,2]. We used a simple mesoscopic modellin
g of active nematic fluids [3] that enables numerical simulations of activ
e nematodynamics. It reasonably well describes experiments in thin layers
and shells with active complex fluids that are mostly biological systems d
riven by internal conversion of stored chemical energy into motion [3\,4].
We demonstrated that at low activity stationary dynamic structures occur
that with increasing activity undergo transitions from stationary to chaot
ic 3D motions - active nematic turbulence. In this talk I will present how
in a such regime the time evolution can be for a specific confinement cha
racterized by a series of elementary topological events where nematic disc
linations divide\, merge\, annihilate\, and crossover. I will focus to hom
eotropic anchoring\, no-slip surface\, and for selected activities illustr
ate our findings by simulated dynamics of nematic disclinations & flows ac
companied by simulated optical microscopy. Our simple confined system coul
d be a nice test ground for recently introduced machine learning approach
to active nematics [5]. \nThe research was done in collaboration with S.
Čopar\, J. Aplinc\, Ž. Kos\, and M. Ravnik.\n\n[1] S. Čopar\, J. Aplinc
\, Ž. Kos\, S. Žumer\, and M. Ravnik\, Topology of three-dimensional act
ive nematic turbulence confined to droplets\, Physical Review X 9\, 031051
(2019)\,\n[2] J. Binysh\, Z. Kos\, S. Čopar\, M. Ravnik\, and G. P. Alex
ander\, Three-dimensional active defect loops\, Physical Review Letters 12
4\, 088001 (2020). \n[3] A. Doostmohammadi\, J. Ignés-Mullol\, and J. M.
Yeomans\, F. Sagúes\, Active nematics\, Nature Communications 9: 3246\, 1
(2018).\n[4] G. Duclos\, R. Adkins\, D. Banerjee\, M. S. Peterson\, M. Va
rghese\, I. Kolvin\, A. Baskaran\, R. A. Pelcovits\, T. R. Powers\, A. Bas
karan\, F. Toschi\, M. F. Hagan\, S.J. Streichan\, V. Vitelli\, D. A. Bel
ler\, and Z. Dogic\, Topological structure and dynamics of three dimension
al active nematics\, Science 367\, 1120 (2020).\n[5] J. Colen\, M.Han\, R.
Zhang\, S. A. Redford\, L. M. Lemma\, L. Morgan\, P. V Ruijgrok\, R.Adkin
s\, Z. Bryant\, Z. Dogic\, M. L. Gardel\, J. J de Pablo\, V. Vitelli\, Mac
hine learning active-nematic hydrodynamics\, Proc. Natl. Acad. Sci. USA 11
8\, e2016708118 (2021).\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/6/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Rajeev Kumar (Oak Ridge National Laboratories)
DTSTART;VALUE=DATE-TIME:20210615T143000Z
DTEND;VALUE=DATE-TIME:20210615T150000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/7
DESCRIPTION:Title: Generating Knotted Configurations in Polymers using Field Theory Appr
oach\nby Rajeev Kumar (Oak Ridge National Laboratories) as part of BIR
S workshop : Novel Mathematical Methods in Material Science: Applications
to Biomaterials\n\nView-only livestream: https://www.birs.ca/live\n\nAbstr
act\nIn this talk\, I will present our on-going work related to understand
ing topological effects in polymer melts and solutions. In particular\, is
sue of Gauge invariance in the field theory of polymers will be discussed
and it will be shown that Gauge fixing can be used to discover topological
invariants. A specific example using the Coulomb gauge will be used to de
monstrate that the helicity is one of the topological invariants for both\
, linear and ring polymers. Furthermore\, a numerical recipe to generate k
notted vector fields will be presented for studying topological configurat
ions near equilibrium using the self-consistent field theory of polymers.\
n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/7/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Alexandra Zidovska (New York University)
DTSTART;VALUE=DATE-TIME:20210615T150000Z
DTEND;VALUE=DATE-TIME:20210615T153000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/8
DESCRIPTION:Title: Interphase Chromatin Undergoes a Local Sol-Gel Transition Upon Cell D
ifferentiation\nby Alexandra Zidovska (New York University) as part of
BIRS workshop : Novel Mathematical Methods in Material Science: Applicati
ons to Biomaterials\n\nView-only livestream: https://www.birs.ca/live\n\nA
bstract\nCell differentiation\, the process by which stem cells become spe
cialized cells\, is associated with chromatin reorganization inside the ce
ll nucleus. Here\, we measure the chromatin distribution and dynamics in e
mbryonic stem cells in vivo before and after differentiation. We find that
undifferentiated chromatin is less compact\, more homogeneous and more dy
namic than differentiated chromatin. Further\, we present a noninvasive rh
eological analysis using intrinsic chromatin dynamics\, which reveals that
undifferentiated chromatin behaves like a Maxwell fluid\, while different
iated chromatin shows a coexistence of fluid-like (sol) and solid-like (ge
l) phases. Our data suggest that chromatin undergoes a local sol-gel trans
ition upon cell differentiation\, corresponding to the formation of the mo
re dense and transcriptionally inactive heterochromatin (Eshghi I\, Eaton
JA and Zidovska A\, Phys. Rev. Lett.\, 2021).\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/8/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:David Swigon (University of Pittsburgh)
DTSTART;VALUE=DATE-TIME:20210615T154500Z
DTEND;VALUE=DATE-TIME:20210615T161500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/9
DESCRIPTION:Title: Dynamical and stochastic simulations of knotted and linked DNA\nb
y David Swigon (University of Pittsburgh) as part of BIRS workshop : Novel
Mathematical Methods in Material Science: Applications to Biomaterials\n\
nView-only livestream: https://www.birs.ca/live\n\nAbstract\nPresented wil
l be two methods that allow the study of the stochastic and dynamical beha
vior of knotted and confined DNA molecules. One method is based on exact s
tatistical sampling of closed configurations\, the other on dynamical simu
lations performed using on generalized immersed boundary method. The equat
ions of motion of the rod include the fluid–structure interaction\, sequ
ence-dependent elasticity and a combination of two interactions that preve
nt self-contact\, namely the electrostatic interaction and hard-core repul
sion. I will discuss the dynamics of DNA trefoils and configurations of DN
A Hopf links with relevance to kinetoplast DNA.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/9/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Javier Arsuaga (University of California\, Davis)
DTSTART;VALUE=DATE-TIME:20210615T161500Z
DTEND;VALUE=DATE-TIME:20210615T164500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/10
DESCRIPTION:Title: DNA knots and liquid crystals in icosahedral bacteriophages\nby
Javier Arsuaga (University of California\, Davis) as part of BIRS workshop
: Novel Mathematical Methods in Material Science: Applications to Biomate
rials\n\nView-only livestream: https://www.birs.ca/live\n\nAbstract\nThe t
hree dimensional organization of genomes is a key player in multiple biolo
gical processes including the genome packaging and release in viruses. The
genome of some viruses\, such as bacteriophages or human herpes\, is a do
uble stranded DNA (dsDNA) molecule that is stored inside a viral protein c
apsid at a concentration of 200 mg/ml-800mg/ml and an osmotic pressure of
70 atmospheres. The organization of the viral genome under these extreme p
hysical conditions is believed to be liquid crystalline but remains to be
properly understood. A general picture of this organization has been recen
tly given by cryoelectron microscopy (cryoEM) studies that show a series o
f concentric layers near the surface of the viral capsid followed by a dis
ordered arrangement of DNA fibers near the center of the capsid.\nIn this
talk I will present computational and experimental results modeling the st
ructure and packing of DNA in bacteriophage P4. P4 is characterized for pr
oducing DNA knots and for being one of the smallest bacteriophages with on
ly 45nm in diameter. I will discuss experimental results concerning the st
ructure of P4 and how liquid crystal models can help predict the propertie
s of DNA in P4 and the formation of knots.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/10/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Tetsuo Deguchi (Ochanomizu University)
DTSTART;VALUE=DATE-TIME:20210616T140000Z
DTEND;VALUE=DATE-TIME:20210616T143000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/11
DESCRIPTION:Title: Exact evaluation of the mean-square fluctuation of the position vect
or of a crosslinking point in the Gaussian network\nby Tetsuo Deguchi
(Ochanomizu University) as part of BIRS workshop : Novel Mathematical Meth
ods in Material Science: Applications to Biomaterials\n\nView-only livestr
eam: https://www.birs.ca/live\n\nAbstract\nThe Gaussian network plays a ce
ntral role in the study on the fundamental elastic behavior\nof various po
lymer networks such as rubbers and gels [1\, 2]. Here we remark that many\
nbio-materials are made of gels. Recently\, a new method has been introduc
ed for generating\nan ensemble of random conformations of graph-shaped pol
ymers in terms of topologically constrained\nGaussian random walks (TCRW)
or Gaussian random graph embeddings [3]. It is one\nof the key properties
of TCRW that the probability distribution function of the bond vectors in\
npolymer conformations of TCRW is composed of the normal distributions wit
h unit variance.\nIn this talk we critically study Flory’s approximate e
xpression for the mean square fluctuation\nof the end-to-end vector r arou
nd its average value \\(r\\) with functionality \\(f\\) [4]\n\n$$⟨2 ⟨(
r − ⟨r⟩) ⟩2 2Nb f$$\n\nHere N is the number of the Kuhn segmen
ts in the network subchain connecting a crosslinking\npoint to another one
.\nWe express the fluctuation ⟨(Δr)2⟩ in terms of resistance distance
s\, and evaluate it rigorously.\nWe argue that Flory’ s expression shoul
d be valid if the functionality f is very large\,\nbased on the numerical
experiments of large random graphs with functionality f\, i.e.\, regular\n
graphs with functionality f. We also discuss the results of Ref. [5].\nThe
results of the present talk should be important not only in materials sci
ence but also\nin applications of biomaterials.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/11/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Stefanie Redemann (University of Virginia)
DTSTART;VALUE=DATE-TIME:20210616T143000Z
DTEND;VALUE=DATE-TIME:20210616T150000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/12
DESCRIPTION:Title: Integrated 3D tomography and computational modeling to study mechani
cs in mitotic and meiotic spindles\nby Stefanie Redemann (University o
f Virginia) as part of BIRS workshop : Novel Mathematical Methods in Mater
ial Science: Applications to Biomaterials\n\nView-only livestream: https:/
/www.birs.ca/live\n\nAbstract\nThe faithful segregation of chromosomes dur
ing mitosis is a fundamental and important process. Errors in mitosis hav
e severe implications and are often detrimental to development\, health an
d survival of the organism. We know that microtubules\, in particular kine
tochore microtubules\, exert forces on chromosomes to initially position t
hem on the metaphase plate and consequently divide them to the two daughte
r cells. The forces generated by microtubules are in balance during metaph
ase resulting in a mechanical steady-state and a stable long-lived spindle
shape and length. Previous studies have identified the proteins involved
in metaphase spindle assembly. Yet\, we do not understand how those protei
ns lead to force generation through interactions of microtubules\, motor p
roteins and chromosomes in submicron scale\, and the collective effect of
these forces on spindle shape function at larger scales. One major barrier
in answering this question is the limitation of light microscopy in visua
lizing details of spindle microstructure in submicron resolutions. We have
developed a novel approach of visualizing entire spindles in 3D by electr
on tomography and automatic microtubule segmentation. Using this approach\
, we can resolve single microtubules\, which provides a unique perspective
and offers a plethora of completely new information about the microstruct
ure of spindles. Specifically\, we can resolve chromosome surfaces\, ident
ify microtubules that are in contact with chromosomes (kinetochore microtu
bules)\, determine microtubules’ nucleation profile\, length distributio
n and local curvature. We combine electron tomography\, light microcopy\,
biophysical modeling and large-scale simulations to develop a detailed and
unprecedented understanding of force generation inside the spindle from i
ndividual microtubules to the mitotic spindle composed of thousands of mic
rotubules.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/12/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Oleg Lavrentovich (University of Virginia)
DTSTART;VALUE=DATE-TIME:20210616T150000Z
DTEND;VALUE=DATE-TIME:20210616T153000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/13
DESCRIPTION:Title: Tactoid-to-Toroid Topological Transition (4T-transition ot T5) in Li
quid Crystal Nuclei\nby Oleg Lavrentovich (University of Virginia) as
part of BIRS workshop : Novel Mathematical Methods in Material Science: Ap
plications to Biomaterials\n\nView-only livestream: https://www.birs.ca/li
ve\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/13/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Christine Soteros (University of Saskatchewan)
DTSTART;VALUE=DATE-TIME:20210616T154500Z
DTEND;VALUE=DATE-TIME:20210616T161500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/14
DESCRIPTION:Title: Characterizing linking in lattice models of polymers in nanochannels
\nby Christine Soteros (University of Saskatchewan) as part of BIRS wo
rkshop : Novel Mathematical Methods in Material Science: Applications to B
iomaterials\n\nView-only livestream: https://www.birs.ca/live\n\nAbstract\
nMotivated in part by experimental and molecular dynamics studies of the
entanglement characteristics of DNA in nanonchannels\, we have been studyi
ng the statistics of knotting and linking for equilibrium lattice models o
f polymers confined to lattice tubes. In this talk I will present our the
orems and transfer-matrix-based numerical results for the link statistics
for self-avoiding polygon models in small tubes. The main focus will be
on the special case of pairs of polygons which span a lattice tube. In thi
s case\, it is known that all but exponentially few of the configurations
will be linked as the span of the polygons goes to infinity. However ther
e are many interesting open questions about configurational statistics for
pairs of polygons with fixed link type and I will introduce some of those
.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/14/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Franziska Weber (Carnegie Mellon University)
DTSTART;VALUE=DATE-TIME:20210616T161500Z
DTEND;VALUE=DATE-TIME:20210616T164500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/15
DESCRIPTION:Title: A Convergent Numerical Method for a Model of Liquid Crystal Director
Coupled to An Electric Field\nby Franziska Weber (Carnegie Mellon Uni
versity) as part of BIRS workshop : Novel Mathematical Methods in Material
Science: Applications to Biomaterials\n\nView-only livestream: https://ww
w.birs.ca/live\n\nAbstract\nStarting from the Oseen-Frank theory\, we deri
ve a simple model for the dynamics of a nematic liquid crystal director fi
eld under the influence of an electric field. The resulting nonlinear syst
em of partial differential equations consists of the electrostatics equati
ons for the electric field coupled with the damped wave map equation for t
he evolution of the liquid crystal director field\, which is a normal vect
or pointing in the direction of the main orientation of the liquid crystal
molecules. The liquid crystal director field enters the electrostatics eq
uations in the constitutiverelations while the electric field enters the w
ave map equation in the form of a nonlinear source term. Since it is a nor
mal vector\, the variable for the liquid crystal director field has to sat
isfy the constraint that it takes values in the unit sphere. We derive an
energy-stable and constraint preserving numerical method for this system a
nd prove convergence of a subsequence of approximations to a weak solution
of the system of partial differential equations. In particular\, this imp
lies the existence of weak solutions for this model.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/15/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Koya Shimokawa (Saitama University)
DTSTART;VALUE=DATE-TIME:20210617T140000Z
DTEND;VALUE=DATE-TIME:20210617T143000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/16
DESCRIPTION:Title: Handlebody decompositions of the 3-torus and polycontinuous patterns
\nby Koya Shimokawa (Saitama University) as part of BIRS workshop : No
vel Mathematical Methods in Material Science: Applications to Biomaterials
\n\nView-only livestream: https://www.birs.ca/live\n\nAbstract\nPolycontin
uous patterns appear as microphase separation of block\ncopolymers. In thi
s talk\, we discuss handlebody decompositions of the\n3-torus and their ap
plication to the study of polycontinuous patterns.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/16/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Myfanwy Evans (University of Potsdam)
DTSTART;VALUE=DATE-TIME:20210617T143000Z
DTEND;VALUE=DATE-TIME:20210617T150000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/17
DESCRIPTION:Title: Triply-periodic tangling\nby Myfanwy Evans (University of Potsda
m) as part of BIRS workshop : Novel Mathematical Methods in Material Scien
ce: Applications to Biomaterials\n\nView-only livestream: https://www.birs
.ca/live\n\nAbstract\nUsing periodic surfaces as a scaffold is a convenien
t route to making periodic entanglements. I will present a systematic way
of building new tangled periodic structures\, using low-dimensional topol
ogy and combinatorics\, posing the question of how to characterise the str
uctures more completely.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/17/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Elisabetta Matsumoto (Georgia Tech)
DTSTART;VALUE=DATE-TIME:20210617T150000Z
DTEND;VALUE=DATE-TIME:20210617T153000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/18
DESCRIPTION:by Elisabetta Matsumoto (Georgia Tech) as part of BIRS worksho
p : Novel Mathematical Methods in Material Science: Applications to Biomat
erials\n\nView-only livestream: https://www.birs.ca/live\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/18/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Radmila Sazdanovic (NC State University)
DTSTART;VALUE=DATE-TIME:20210617T154500Z
DTEND;VALUE=DATE-TIME:20210617T161500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/19
DESCRIPTION:Title: TDA applications in cancer genomics\nby Radmila Sazdanovic (NC S
tate University) as part of BIRS workshop : Novel Mathematical Methods in
Material Science: Applications to Biomaterials\n\nView-only livestream: ht
tps://www.birs.ca/live\n\nAbstract\nCancer is a polygenic disease in which
genomic events are selected in order to produce a sophisticated and coord
inated outcome. Determining when two events are co-occurring is at the hea
rt of finding possible genetic treatments and also an important open quest
ion in data science. This work focuses on further analysis and modificatio
n of the existing topological data analysis approach to breast cancer data
. In particular we will address the stability of proposed methods and poss
ible generalizations to other contexts.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/19/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Sarah Harris (NC State University)
DTSTART;VALUE=DATE-TIME:20210617T161500Z
DTEND;VALUE=DATE-TIME:20210617T164500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/20
DESCRIPTION:Title: Multiscale Simulations of Biological Polymers\nby Sarah Harris (
NC State University) as part of BIRS workshop : Novel Mathematical Methods
in Material Science: Applications to Biomaterials\n\nView-only livestream
: https://www.birs.ca/live\n\nAbstract\nPolymeric structures are ubiquitou
s in biology\, and perform diverse functions at multiple length-scales. D
NA carries the genetic code through the chemistry of the constituent bases
at an atomic level\, but also plays an active role in its own regulation
through its ability to store and transmit mechanical stress over genomic l
ength-scales. Long polymeric coiled-coils are a common protein structural
motif\, and as well as forming the basis of robust super-macromolecular h
ierarchical structures such as collagen\, also have an active role in regu
lating the chemo-mechanical cycle of molecular motors such as dynein and m
yosin. Intrinsically disordered proteins present a particular enigma\; som
e undergo disorder to order transitions on encountering their binding part
ner and so participate in highly specific molecular recognition in spite o
f their apparent lack of structure\, whereas others appear to generate vit
al emergent behaviour over far longer length-scales than their own structu
re\, such as the self-assembly of membraneless organelles.\nHere I will co
mpare and contrast multi-scale representations of polymeric biomacromolecu
les from the fully atomistic up to the continuum level. I will discuss ope
n challenges to development and biological questions that would benefit fr
om robust mathematical and computational models of biological polymers.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/20/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Eric Rawdon (University of Saint Thomas)
DTSTART;VALUE=DATE-TIME:20210618T143000Z
DTEND;VALUE=DATE-TIME:20210618T150000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/21
DESCRIPTION:Title: Accumulated knot probability\nby Eric Rawdon (University of Sain
t Thomas) as part of BIRS workshop : Novel Mathematical Methods in Materia
l Science: Applications to Biomaterials\n\nView-only livestream: https://w
ww.birs.ca/live\n\nAbstract\nMany knots in nature are open knots\, not the
closed knots from knot theory. There are several definitions of knotting
in open curves\, each of which have their own advantages and disadvantage
s. The speaker's favorite open knot definition involves extending rays to
infinity in a common direction from the endpoints to create a closed knot
for each such direction. In such a case\, the knotting in an open chain
is classified as the distribution of knot types seen over the different di
rections of closure. In most cases\, there is a knot type that appears in
over 50% of the closure directions\, in which case we might all be able t
o agree that the open knot has the essence of that closed knot type. Howe
ver\, there are many cases where there is no knot type that appears in ove
r 50% of the closure directions\, especially near transitions between diff
erent knot types. We present the accumulated knot probability as a way of
making sense of these more ambiguous situations. The short story is that
\, for a given knot type K\, we compute the probability that the closures
are a knot type which "includes" K in some sense. In this talk\, we use t
he partial ordering on knots developed by Diao\, Ernst\, and Stasiak based
on crossing changes in minimal knot diagrams\, which creates a sort of fa
mily tree of knots. However\, any sort of family tree could be substitute
d here depending on what one is trying to model. We show how some of the
knotting classifications change for some proteins and tight knot configura
tions.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/21/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Pei Liu (University of Minnesota)
DTSTART;VALUE=DATE-TIME:20210618T150000Z
DTEND;VALUE=DATE-TIME:20210618T153000Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/22
DESCRIPTION:by Pei Liu (University of Minnesota) as part of BIRS workshop
: Novel Mathematical Methods in Material Science: Applications to Biomater
ials\n\nView-only livestream: https://www.birs.ca/live\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/22/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Kenneth Millett (University of California\, Santa Barbara)
DTSTART;VALUE=DATE-TIME:20210618T154500Z
DTEND;VALUE=DATE-TIME:20210618T161500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/23
DESCRIPTION:Title: Using the HOMFLY-PT polynomial to quantuantify the entanglement of c
ollections of open chains\nby Kenneth Millett (University of Californi
a\, Santa Barbara) as part of BIRS workshop : Novel Mathematical Methods i
n Material Science: Applications to Biomaterials\n\nView-only livestream:
https://www.birs.ca/live\n\nAbstract\nThe superposition of HOMFLY-PT polyn
omials of collections of open chains provides an "average" of the\npolynom
ials associated to individual closures and\, consequently\, a HOMFLY-PT po
lynomial for the open\nlink. Following a bri\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/23/
URL:https://www.birs.ca/live
END:VEVENT
BEGIN:VEVENT
SUMMARY:Andrew Rechnitzer (University of California\, Santa Barbara)
DTSTART;VALUE=DATE-TIME:20210618T161500Z
DTEND;VALUE=DATE-TIME:20210618T164500Z
DTSTAMP;VALUE=DATE-TIME:20210612T231709Z
UID:BIRS_21w5232/24
DESCRIPTION:Title: Trials and tribulations of preserving topology\nby Andrew Rechni
tzer (University of California\, Santa Barbara) as part of BIRS workshop :
Novel Mathematical Methods in Material Science: Applications to Biomateri
als\n\nView-only livestream: https://www.birs.ca/live\n\nAbstract\nMonte C
arlo simulations are a big part of understanding the statistical propertie
s of knots. Unfortunately\, if one wishes to study curves of fixed knot ty
pes then there are very few methods available. This work\, with Nick Beato
n and Nathan Clisby\, is an attempt to adapt existing algorithms to polygo
ns in R3 of fixed topology. It is very much a work in progress\, but I wil
l report on our work adapting BFACF to polygons in R3\, and also our attem
pts at trying to coerce the (very fast) pivot algorithm to respect topolog
y.\n
LOCATION:https://researchseminars.org/talk/BIRS_21w5232/24/
URL:https://www.birs.ca/live
END:VEVENT
END:VCALENDAR