Biology occurs in concentrated mixtures of ions that are far from ideal. Solutions are remarkably concentrated where they are most important. Multi-molar solutions (often >10M) are found in and near DNA & RNA, proteins, active sites of enzymes, transporters, and ion channels, as well as electrodes of batteries. Poisson Boltzmann treatments fail ...
Creator:
Eisenberg, Robert S. (Rush University)
Created:
2015-07-21
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Cellular information processing is carried out by complex biomolecular networksthat are able to function reliably despite environmental noise and genetic mutations.The robustness and evolvability of biological systems is supported in part by neutralnetworks and neutral spaces that allow for the preservation of phenotype despite underlyinggenotyp...
Creator:
Myers, Christopher R. (Cornell University)
Created:
2008-04-24
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Recently, numerous engineers have demonstrated that genetic circuits canbe effectively modeled and analyzed utilizing methods originallydeveloped for electrical circuits leading to new understanding of theirbehavior. If this is possible, then it may also be possible to designsynthetic genetic circuits that behave like particular electricalcircui...
Creator:
Myers, Chris J. (The University of Utah)
Created:
2008-04-24
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The evolution of communication provides one of the fewexamples in evolutionary biology where principles of physicalacoustics, interacting with developmental constraints onphysiology and motor control, have clear and predictableeffects on evolutionary outcomes. I will provide two clearexample of this, relating to basic physiological constraintson...
Creator:
Fitch, W. Tecumseh (University of St. Andrews)
Created:
2008-04-23
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Implicit-solvent models commonly decompose the molecular solvation free energy into a sum of electrostatic and non-polar terms, with separate theoretical and numerical procedures employed for each component. In this talk I will describe a new method for estimating the electrostatic free energy of solvation, called BIBEE (boundary-integral-based ...
Creator:
Bardhan, Jaydeep P. (Argonne National Laboratory)
Created:
2008-12-11
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
This talk will discuss recent developments in one-electron model Hamiltonians for the hydrated electron, and their application to both anionic water clusters and bulk aqueous electrons. Our group has recently developed a new hydrated-electron model that combines the polarizable AMOEBA water model with a 'static exchange' treatment of the electro...
Creator:
Herbert, John M. (The Ohio State University)
Created:
2009-01-12
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
A perusal of the contemporary biological literature involving high-throughput data sets reveals the generation of a vast amount of data and an enormous number of models (classifiers, clusters, networks) derived from this data via a plethora of algorithms. There tends to be four interrelated characteristics common to these publications: (1) no ex...
Creator:
Dougherty, Edward R. (Texas A & M University)
Created:
2011-11-14
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Most infections are the result of a surface-attached communityofbacteria that displays many unique characteristics. Ourunderstandingis still limited, however, with respect to how pathogens arecolonizing surfaces to begin infection. It is known that thearrivalof bacteria to host tissues is often aided by self-generatedmotilityof the organism.Path...
Creator:
Alber, Mark S. (University of Notre Dame)
Created:
2010-09-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The nascent field of synthetic biology offers the promise of engineered genenetworks with novel biological phenotypes. Numerous synthetic gene circuitshave been created in the past decade, including bistable switches,oscillators, and logic gates. Despite a booming field and although recentlydeveloped designs of regulatable gene networks are inge...
Creator:
Kaznessis, Yiannis N. (University of Minnesota, Twin Cities)
Created:
2008-05-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Many neurological diseases, such as epilepsy and Parkinson's disease, present symptoms of pathological neuronal activity. Large bursts of neuronal activity or large scale synchronous oscillations may arise from changes in the dynamics of the neurons and/or how they are connected. How changes in network topology result in these pathological behav...
Creator:
Netoff, Theoden (University of Minnesota, Twin Cities)
Created:
2012-09-05
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Joint work with Bastiaan J. Braams and Yimin Wang (Department of Chemistry and Cherry L. Emerson Center for Scientific Computation,Emory University, Atlanta, GA 30322).The currently exists a variety of methods to representpotential energy surfaces for high dimensional systems, andthese will be reviewed after a short, selective, historicalintrodu...
Creator:
Bowman, Joel M. (Emory University)
Created:
2009-01-12
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The concept of function has a tainted history in science and philosophy, having been mated to teleology and harnessed to pull various discredited theories. This presentation begins with a short history designed to give a sense of what made the concept of function problematic. Current philosophical attention to the problem revolves ellipse-like a...
Creator:
Cummins, Robert (University of Illinois at Urbana-Champaign)
Created:
2008-04-23
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Homology on semimodule-valued sheaves naturally generalizes network flows from the setting of numerical capacity constraints to other sorts of constraints (e.g. stochastic, multicommodity). In this talk, we present new work relating the algebraic structure of flows with local network properties and algebraic properties of the ground semiring. Fo...
Creator:
Krishnan, Sanjeevi (University of Pennsylvania)
Created:
2014-03-03
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
A large variety of complex systems, from the brain to the weather networks and complex infrastructures, are formed by several networks that coexist, interact and coevolve forming a 'network of networks'. Modeling such multilayer structures and characterizing the rich interplay between their structure and their dynamical behavior is crucial in or...
Creator:
Bianconi, Ginestra (Queen Mary University of London)
Created:
2014-05-01
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Figure 1. Segmentation of the internal carotid artery (left).Vessel tree with the common, internal and external carotidarteries (right).Accurate vessel segmentation is required in many clinicalapplications, such as identifying the degree of stenosis(narrowing) of a vessel to assess if blood flow to an organ issufficient, quantification of plaque...
Creator:
Atev, Stefan E. (ViTAL Images, Inc.)
Created:
2011-08-03
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Driven by rapid advances in many fields including Biology, Finance and Web Services, applications involving millions or even billions of data items such as documents, user records, reviews, images or videos are not that uncommon. Given a query from a user, fast and accurate retrieval of relevant items from such massive data sets is of critical i...
Creator:
Kumar, Sanjiv (Google Inc.)
Created:
2011-08-03
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Biofilms form when microbes grow attached to a surface and become encased in a self-produced extracellular matrix. The fact that biofilm growth has been observed in most bacteria studied to date suggests that this form of growth is important in the ecology and physiology of most, if not all, bacteria. Biofilms have profound impact on human healt...
Creator:
Sanabria-Valentàn, Edgardo Luis (Harvard Medical School)
Created:
2010-09-13
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Multiplicative updates multiply the parameters bynonnegative factors. These updates are motivated bya Maximum Entropy Principle and they are prevalent in evolutionaryprocesses where the parameters are for exampleconcentrations of species and the factors are survival rates.The simplest such update is Bayes rule and we givean in vitro selection al...
Creator:
Warmuth, Manfred K (University of California, Santa Cruz)
Created:
2012-03-27
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Action potentials are the packets of communication in the nervous system. The voltage dependent sodium and potassium channels are the crucial players in the initiation and propagation of the action potential. Voltage sensing in these channels is mediated by the movement of intrinsic charges of the channel proteins in response to changes in the e...
Creator:
Bezanilla, Francisco (University of Chicago)
Created:
2015-07-21
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.