The long, rich history of topology in mathematics has provenextremely useful for the study of DNA. DNA, the geneticblueprint for life, undergoes tremendous flux as it ispackaged, replicated, segregated, transcribed, recombined andrepaired. Extremely long and skinny, DNA is prone toentanglement. Every time it is copied, the two resulting'daughter...
Creator:
Zechiedrich, Lynn (Baylor College of Medicine)
Created:
2010-04-09
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
DNA double helix should experience local breaks under sufficient bending or/and unwinding torsional stress. Local distortions of DNA under negative torsional stress have been studied in details, but until now very little has been known about distortions by bending stress. We addressed this question in the current study by probing the structure o...
Creator:
Vologodskii, Alexander (New York University)
Created:
2007-09-17
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Let G be a graph of density p on n vertices. Erdös, Luczak and Spencer defined a subgraph H of G to be full if H has m vertices and every vertex of H has degree at least p(m - 1) in H. Let f(G) denote the largest number of vertices in a full subgraph of G and let fp(n) denote the smallest value of f(G) over all graphs G of density p with n verti...
Creator:
Verstraete, Jacques (University of California, San Diego)
Created:
2014-09-11
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Cancer is a disease that is driven by somatic mutations that accumulate in the genome during an individual's lifetime. Recent advances in DNA sequencing technology are enabling genome-wide measurements of these mutations in numerous cancers. A major challenge in analyzing this data is to distinguish functional mutations that drive cancer progres...
Creator:
Vandin, Fabio (Brown University)
Created:
2012-02-29
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
In both bacteria and eukaryotes, maintaining DNA compaction isa sine qua non of chromatin function. At the same timeaccessibility to transcribing, replicating and recombiningenzymes must be maintained. I will argue that these twinrequirements can be viewed in the context of the overalltopology of, for bacteria, the DNA itself, and of, foreukaryo...
Creator:
Travers, Andrew (MRC Laboratory of Molecular Biology)
Created:
2007-09-20
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
DNA twist step-parameters are in common use in thecommunity of structural biologists. If, for a molecule with aclosed axial curve, the writhing number, a measure of thechiral distortion of the axial curve of the molecule fromplanarity, is added to the sum over all steps of such twists,the result has no particular significance. This is in markedc...
Creator:
Tobias, Irwin (Rutgers, The State University Of New Jersey)
Created:
2007-09-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Worm-like chain model, ring closure, J factor Statistical mechanics of DNA supercoiling Monte Carlo simulations of DNA DNA stretching Extraction of sequence-dependent parameters from statisticalensembles DNA denaturation, effect of topological constraints, role intranscription regulation Probability of knotting and catenation, removal ofknots/ca...
Creator:
Swigon, David (University of Pittsburgh)
Created:
2007-09-15
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recover...
Creator:
Shental, Noam (Open University of Israel)
Created:
2012-02-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Part 1: In this part of the talk we will discuss the coil-stretch hysteresis in dilute polymer solutions for extension dominated flows, including three-dimensional mixed flows. We will then turn to entangled systems and discuss the role of slip-link simulations in elucidating the extensional behavior in concentrated solutions and melts.Part 2: P...
Creator:
Shaqfeh, Eric S. G. (Stanford University)
Created:
2009-09-14
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Single chromatin fibers were reconstituted in vitroby salt dialysis from purified histone octamers and 2×18 tandemrepeats of the 5S DNA positioning sequence. The fibers wereflanked by naked ˆ¼600 bp DNA spacers and ˆ¼500 bp DNA stickersmodified with digoxigenin and biotin destined to be linkedrespectively to the coated bottom of the flow cell a...
Creator:
Prunell, Ariel (Institut Jacques Monod)
Created:
2007-09-18
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
In experiments where DNA is pulled at constant force and twisted, a mixedstate of extended twisted DNA and plectonemically supercoiled DNA iseasily obtained. I will review the thermodynamics of this 'statecoexistence' phenomenon. A particularly elegant use ofplectoneme-extended DNA coexistence is as a source of constant torque forsingle-DNA expe...
Creator:
Marko, John F. (Northwestern University)
Created:
2007-09-18
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Duplex DNA, the genetic material in living cells, is an unusually inflexible biopolymer. The persistence length of duplex DNA corresponds to 150 base pairs under physiological conditions. Surprisingly, the physical origin of this DNA stiffness is unknown. In particular, the contribution of the high negative charge density of DNA to its stiffness...
Creator:
Maher, James (Mayo Clinic)
Created:
2007-09-20
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Genetic recombination is important in the repair of double strand DNA breaks, the processing of stalled replication forks and in the generation of genetic diversity in evolution. During this process, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction. The junction adopts a folded structure in the pres...
Creator:
Lilley, David M.J. (University of Dundee)
Created:
2007-09-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The formation of DNA loops by proteins bound at distant sites along a singlemolecule is an essential mechanistic aspect of many biological processesincluding gene regulation, DNA replication, and recombination. Thebiological importance of DNA loop formation is underscored by an abundanceof architectural proteins in cells such as HU, IHF, and HMG...
Creator:
Levene, Stephen D. (University of Texas at Dallas)
Created:
2007-09-17
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
DNA can easily be deformed by external factors including molecular interactions and applied forces. We haveused molecular modeling and simulation to investigate the structural and energetic nature of these deformationsboth in generic terms and, more finely, to understand their sequence dependence and therefore to decode theirrole in recognition ...
Creator:
Lavery, Richard (Centre National de la Recherche Scientifique (CNRS))
Created:
2007-09-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The higher order structure of chromatin depends crucially on the local geometry of the DNA on the nucleosome. Fluorescence resonance energy transfer (FRET) is a very convenient method to measure intramolecular distances in such large biomolecules and thereby obtain information on the DNA geometry. Varying label positions, DNA fragment length, hi...
One of the more interesting of recent combinatorial directionshas been the attempt to understand the extent to whichvarious classical facts remain true in a random setting.The present talk will mostly discuss what we know about this questionwhen the 'classical fact' is the Erdos-Ko-Rado Theorem.(Joint with Arran Hamm.)
Creator:
Kahn, Jeff N. (Rutgers, The State University of New Jersey)
Created:
2014-09-10
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
DNA looping allows protein transcription factors to act at a distance along DNA. Looping is also a test bed for theories on DNA and protein structure and flexibility. However, most natural DNA loops are not stable enough for structural studies. We have designed and constructed bent DNA molecules that form hyperstable DNA loops anchored by the La...
Creator:
Kahn, Jason D. (University of Maryland)
Created:
2007-09-20
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Finding rare genetic variations in large cohorts requires tedious preparation of large numbers of specimens for sequencing. We are developing a solution, called DNA Sudoku, to reduce prep time and increase the throughput of samples. By using a combinatorial pooling approach, we multiplex specimens and then barcode the pools, rather than individu...
Creator:
Esposito, Dina (Whitehead Institute for Biomedical Research)
Created:
2012-02-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
In the past few years, we have experienced a paradigm shift in human genetics. Accumulating lines of evidence have highlighted the pivotal role of rare genetic variations in a wide variety of traits and diseases. Studying rare variations is a needle in a haystack problem, as large cohorts have to be assayed in order to trap the variations and ga...
Creator:
Erlich, Yaniv (Whitehead Institute for Biomedical Research)
Created:
2012-02-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
