Seminars

[Google Meet Link]: meet.google.com/yxv-fpmw-fmq [Download title and abstract of the talk]: https://www.imsc.res.in/~asamal/seminar/Pan-JunKim_Oct27_2020.pdf [Abstract]: A primary challenge in biology is to explain how complex phenotypes arise from individual molecules encoded in genes. Molecular interaction networks offer a key to understand how genotypes are translated into phenotypes. For example, sleep/wake cycles in animals are generated by molecular circuits of interacting genes and gene products, called circadian clocks. Circadian clocks are important for both animal and plant life as well. I will discuss how the molecular interactions for rhythmic protein turnover are related to a presumable driving force of the circadian clock machinery—the biosynthetic cost reduction. However, considering only genes in a given organism and its own molecular interactions may not be enough to understand the holistic picture of the organism’s phenotypes. For example, our resident gut microbial community, or gut microbiome, provides us with a variety of biochemical capabilities not encoded in our genes. This human gut microbiome is linked not only to our health, but also to various disorders such as obesity, cancer, and diabetes. We constructed the literature-curated global interaction network of the human gut microbiome mediated by various chemicals. Our network framework shows promise for investigating complex microbe-microbe and host-microbe chemical cross-talk, and identifying disease-associated features.

Stopping a process in its midst -- only to start it all over again -- may prolong, leave unchanged, or even shorten the time taken for its completion. Among these three possibilities the latter is particularly interesting as it suggests that restart can be used to expedite the completion of complex processes which otherwise would hinder. I will introduce the problem of first passage under restart using the example of simple diffusion, but will then explain why many unknowns compel us to generalize to arbitrary first passage processes and restart mechanisms. Finally, I will demonstrate how the framework developed herein can serve as a platform to understand bio-chemical reactions and generic search processes. Google Meet link: meet.google.com/kuk-yhsw-yep

TBA

[Google Meet Link]: meet.google.com/bmk-gpxy-uyd [Download title and abstract of the talk]: https://www.imsc.res.in/~asamal/seminar/AndreaDeMartino_Oct29_2020.pdf [Abstract]: The growth performance of microbial populations can be studied by an information theoretic approach relating the mean single-cell growth yield (`fitness') to the entropy ofthe growth-yield distribution (‘information'). Within Mass-Balance models, one finds that,for any value of the information, the achievable fitness is strictly bounded, leading to atheoretical “rate-distortion curve” in the (information, fitness) plane. Next, values of fitnessand information for E. coli populations can be inferred from experimental massspectrometry data probing growth in different conditions. For a large number ofexperimental datasets, inferred points robustly approach the theoretical bound as thequality of the growth medium improves. Besides giving insight into the interplay betweenmetabolism and gene expression, this approach can yield information that is currentlyinaccessible by other methods, both in silico and experimental.

We study the transcendence of the limit $h(A)$ of the sequence \[A, A^A, A^{A^A},\ldots.\] In 2010, Sondow and Marques studied the case that $A$ is rational numbers or algebraic numbers satisfying some special conditions. In this talk, we extend their results and give an asymptotic formula for the number of algebraic numbers $A$ such that $h(A)$ is algebraic. This is the joint work with Hirotaka Kobayashi and Kota Saito. Google meet link for this talk is meet.google.com/yvz-yngc-nif