Biological transport webs, such as the blood circulatory system in the brain and other animal organs, or the slime mold Physarum polycephalum, are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function. In…

We have recently demonstrated a technology using sequential hybridization and single molecule FISH to multiplex a large number of mRNA molecules directly in single cells in complex tissue samples. mRNAs in cells are barcoded by sequential rounds of hybridization, imaging, and probe stripping. The number of barcodes available with this approach…

We have recently demonstrated a technology using sequential hybridization and single molecule FISH to multiplex a large number of mRNA molecules directly in single cells in complex tissue samples. mRNAs in cells are barcoded by sequential rounds of hybridization, imaging, and probe stripping. The number of barcodes available with this approach…

Lunch@ 11:45, Seminar 12-1:00

Lunch @ 11:45, seminar 12-1:00

Lunch@ 11:45, Seminar 12-1:00

Lunch@ 11:45, Seminar 12-1:30

A central question in biology is how complex, spatial-temporal cellular behaviors arise from biochemical networks. Much work has led to the identification and cataloguing of various network architectures, and the explication of how static network motifs can give rise to dynamic response characteristics, including ultrasensitive, switch-like, and…

Medicine as well as biology increasingly rely on the use of cutting‐edge physics and engineering, in order to pursue the next generation nanomedical applications and to address fundamental questions in the life sciences. Central to this task is the study of micro- and nano systems, focusing on how engineered systems combined with natural ones can…

Spontaneous activity is ubiquitous in cortex, but its role in the assembly and maintenance of cortical circuits is unclear at present. Novel chronic recording techniques enable following neural population activity over long periods of time. Combined with adequate statistical analysis techniques this could shed new light on how patterns of…

Cell proliferation requires timely and reliable DNA replication. Genetic and biochemical evidence reveals that the replication process is subject to a variety of conflict mechanisms, including DNA damage, concurrent DNA transcription, and DNA-bound protein complexes which can all act to stall the replication process. Without a mechanism for rapid…

Lunch@ 11:45, Seminar 12-1:00

"Balancing on an edge: dynamical criticality as a biological strategy for flexibility and integration. A number of biological systems organize themselves so as to be perpetually at the fulcrum between large, opposing forces. Simultaneously rapid synthesis and degradation of mRNA or proteins, ion channels open while ion pumps go at full blast,…

One of the most critical aspects of protein functioning in cells is the ability of protein molecules to quickly find and recognize specific targets on DNA. Kinetic measurements indicate that in many cases the corresponding association rates are surprisingly large. For some proteins they might be even larger than maximal allowed 3D diffusion rates…

Cilia and flagella are slender cellular appendages that have motile, sensory and regulatory roles. They drive the movement of cells through fluids, thereby powering the swimming of spermatozoa and ciliated microorganisms, and they drive the movement of fluid past cells, thereby generating fluid and mucus flows in the airways, reproductive tracts…

Lunch @ 11:45, talk @ 12pm.

Lunch @ 11:45, talk @ 12pm.

Much of complex biology results from interactions among a large number of individually simpler elements. Blood regeneration is no different. About 100 billion new blood cells are made everyday from a much smaller yet a large population of diverse stem cell population. I will present a phenomenological model of blood regeneration, which provides…

The big challenge in modern biology is to understand and control the mechanisms by which living organisms organize, maintain, remodel, and restore their shape. Some creatures are able to regenerate whole limbs or eyes, and many examples of adaptive pattern regulation tell us that understanding cell differentiation is not enough; large-scale shape…

In recent years, through parallel advances in microscopy, fluorescent probe development, and computational modeling, it has become possible to describe gene expression in a fundamentally different way: one can now directly observe single molecules of RNA in living and fixed cells using the fluorescence microscope. In this talk, I will describe…