Lectures
“The Multi-scale phenomena in the mammalian cortex: General observations and the role of Acetylcholine” Klaus M. Stiefel
The nervous system has strong multi-scale characteristics. In my presentation, I will first outline some general thoughts about its multi-scale properties, and their consequences for neural functioning.
Different scales of organization are the consequences of different temporal and spatial scales, different physical forces, and limited information transfer between scales. The neural multi-scale architecture has significant advantages for the parallelization of computations.
In the second part I will outline the effects of the neuromodulator acetylcholine on multiple levels of the mammalian cortex. Acetylcholine acts on different types of receptor proteins, and changes many of the electrophysiological properties of cortical neurons, like input resistance, membrane potential, synaptic potential size and potassium current conductance. These changes in at the single-cell levels lead to changes in the oscillatory properties at the network level. I will present an approach to simulate a detailed model of a single neuron embedded in a more abstract model of a cortical network. This approach allows the study of biologically detailed models of neurons in a realistic dynamical environment, and the effect of acetylcholine on both.
Bjorn Engquist Coming soon......... “Coupling the Micro and the Macro: n-Bauplan and The Complexity of Biology at large” Diego Rasskin-Gutman Biological organization is modular and hierarchical. As a consequence, exclusive emphasis in the small parts (molecules) downplays the big picture. Conversely, excessive emphasis on the big parts (organisms) downplays the underlying processes that shape the individual. Coupling spatiotemporal scales is fundamental to start grasping the complexities at which biological processes operate. Concepts such as “archetypes,” “types,” or “Baupläne” have been used to address the similarities and differences of organizational features in morphology--sometimes structure--all along the history of biology. To be sure, these terms appeared in pre-molecular biology times, when morphological data was used to group tax and generate evolutionary hypotheses about relationships. It is obvious for today’s status of biological knowledge that all of these concepts are too general as well as largely outdated. However, it is also obvious that statements such as “living organisms are organized” are tautological; biology cannot be disorganized at any level (the very etymology of the therm “organism” denotes this). This truly warrants an effort to bring Baupläne back into the new modern biology, incorporating what molecular biology has to offer, i.e, not viewing the concept as a strictly morphological one, but as a multilayered definition encompassing all levels of biological organization in a metanework of relations. “Time-scale challenges in molecular dynamics simulations” Maddalena Venturoli In recent years, molecular dynamics (MD) simulations have become a tool of choice in chemistry, material sciences and molecular biology. MD allows one to simulate the motion of the individuals atoms of complex systems involved in complicated processes and thereby obtain a detailed information about the dynamics of these systems. MD can be used to analyze from first principles chemical processes such as allosteric transitions of biomolecules, nucleation events during phase transformation, fracture and crack propagation in solids, defect dynamics in crystals, etc. in a way which is potentially more precise and less expensive than by doing actual experiments and without having to rely on effective macroscopic models. To achieve its full potential, however, MD must be integrated as a part in multiscale algorithms. This is the only possibility to be able to tackle problems involving systems of realistic size made of an enormously large number of atoms, and to simulate their dynamics on very long time-scales of actual interest. In my talk, I will discuss challenges related to this second issue and show how to access time-scales which are much too long for direct simulations but on which rare but important reactive events arise. In particular, I will discuss two main aspects related to the modeling and simulation of rare events: free energy calculations and transition pathways identification. “MULTI-SCALE PHENOMENA IN BIOLOGY AND SCIENTIFIC PERSPECTIVISM”
Multi-scaling has not been investigated systematically yet from the perspective of a naturalistic philosophy of science, according to which philosophy is continuous with science. Scientific perspectivism has roots in William James's pragmatist philosophy. In my talk I will first argue that useful resources for a philosophical account of multi-scaling are provided in Ronald N. Giere's Scientific Perspectivism (University of Chicago Press, 2006), William C. Wimsatt's Re-engineering Philosophy for Limited Beings: Piecewise Approximations to Reality (Harvard University Press, 2007), and in work by James R. Griesemer (University of California Davis), and then discuss some methodological and epistemological issues that are particular to multi-scaling in light of the scientific-perspectivist view. “Multi-scale Simulations on the ES and its impacts” Keiko Takahashi Earth Simulator enables us to simulate various phenomena with ultra high resolution with new physical schemes. We are now going to develop Multi-Scale Simulator for the Geoenvironment (MSSG) to perform seamless simulation between weather and climate. I will introduce outline and characteristics of the MSSG and ultra high resolution simulations results with MSSG will be also introduced in my presentation. In addition, latest results of simulations on ES in biology, which were performed by our collaborators, will be also introduced. I would like to show future possibility including our grand challenge in high performance simulations.
“Sporadic dispersal in the marine environment: implications for feeding, reproduction, recruitment, and the evolution of life histories” Robert
Warner In marine systems, water conveys information, food, gametes, and young, on scales from millimeters to thousands of kilometers. Turbulence at all of these scales leads to very different patterns of transport than that predicted by simple advection-diffusion models, because particles can be accumulated over time and space, held together, and delivered in dense pulses. This talk explores the implications of highly stochastic transport in marine systems at a wide range of scales. At the smallest scales, turbulence acts to disrupt any smooth gradients of concentration emanating from a source, complicating chemical communication and food finding. Equally, organisms that depend on water movement to deliver food can find themselves in feast-or-famine situations. Where fertilization depends on a minimum sperm concentration reaching the eggs, the effective fertilization distance can be larger than predicted by simple diffusion. At larger scales, recruitment of pelagic larvae into coastal habitats appears to be intermittent and heterogeneous on annual time scales, driven by advection in turbulent coastal circulation. Local rates of larval settlement may be largely decoupled from local stock abundances, even if self-recruitment is substantial. This provides an unexplored source of uncertainty in stock-recruitment relationships. On the other hand, the pulsed aspect of recruitment, even at long distances from a source, may alleviate the Allee effects that limit the success of long-distance colonization. High variation in recruitment, especially occasional large pulses of recruitment, may enhance the contribution of the storage effect on species persistence and coexistence. Finally, the stochastic nature of connectivity may make it difficult to assess the effects of spatial fisheries management policies, because it is likely to take long periods of sampling in order to detect recruitment responses to a management change. On evolutionary time scales, models suggest that the stochastic nature of successful recruitment could exert strong selection on life histories, leading to extreme iteroparity and fine partitioning of reproductive effort. Thus the long lives and high fecundity of many marine organisms may be an evolutionary response to coastal ocean circulation. “Multiscale Analysis in Biology - Paradigms and Problems” Hans G. Othmer New techniques in cell and molecular biology have produced huge advances in our understanding of signal transduction and cellular response in many systems, and this has led to better cell-level models for problems ranging from biofilm formation to embryonic development. However, many problems involve very large numbers of cells, and detailed cell-based descriptions are computationally prohibitive at present. Thus rational techniques for incorporating cell-level knowledge into macroscopic equations are needed for these problems. In this talk we discuss several examples that arise in the context of cell motility and pattern formation. We will discuss systems in which the micro-to-macro transition can be made more or less completely, and also describe other systems that will require new insights and techniques. Anthony Bell Coming soon.........
Walter R. Tschinkel Because they are social insects, ants operate both as individuals and as members of a superorganism (the colony). In addition to the transitions from scale to scale seen in ordinary organisms, ants thus present the transition from the scale of the individual ant to the scale of the superorganism. Natural selection acts primarily at the superorganism level, with modifications at lower levels resulting from effects on colony and individual development. I will present three cases that could benefit from an understanding of how phenomena at one scale translate into phenomena at a larger scale. These will include (1) the nest architecture of subterranean ant nests and its creation by groups of workers; (2) the establishment and maintenance of territory through the interactions of individual workers, and the regulation of ant biomass on a landscape scale through territorial behavior; (3) In the Namib Desert of Namibia, a mysterious local phenomenon results in a landscape patterned by regularly dispersed bare circle 4-20 m in diameter in the grassland. While the cause of these patterns in not known, it clearly cuts across scales.
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