Modeling and engineering gene expression based on a computational approach: methodology and applications 

Gene expression is a process intrinsic to all life, whereby information encoded in the genetic material is used to build proteins that drive the functioning of living organisms. Gene expression is a multi-step process mediated by millions of intracellular biological machines (e.g. RNA polymerases, transcription factors, ribosomes, tRNAs, miRNAs), with complex interactions among them. Deciphering, modelling, and engineering the process of gene expression is therefore an extremely challenging undertaking, but one with enormous potential to impact any biomedical field.

In our lab, we develop various computational models and algorithms that are used in conjunction with state-of-the-art approaches for genome editing to understand and engineer this process. Our pipeline is based among others on biophysical simulations, machine learning, tools from electrical engineering, computer science, and computational molecular evolution.

In recent years these models have been used in various applications such as generating vaccines and oncolytic viruses, producing therapeutic proteins and green energy, generating cheap food ingredients, designing efficient biosensors, and developing novel diagnosis tools based on cancer genomes.

The aim of this seminar is to provide an introduction to the field and to the approaches developed in our lab for mastering gene expression, and to demonstrate the applications of our tools. The talk will be self-contained and will not require prior knowledge.

אבסטרקט

In a moving acoustic medium, sound waves travel differently with and against the fluid flow. This well-established acoustic effect is backed by the intuition that the fluid velocity-bias imparts momentum on the propagating acoustic waves, thus violating reciprocity. Based on this conception, fluid flow that is transverse to the wave direction of propagation will not break reciprocity. In this work we contrast this common wisdom and theoretically show that the interplay between transverse mean flow and transverse structural gliding-asymmetry can yield strong nonreciprocity and even, surprisingly, one-way acoustic waveguiding. To demonstrate that, we analyze a waveguide that comprises of a few adjacent acoustic sub-diffraction chains, each consists of acoustic scatterers with monopolar or dipolar response. The structure is embedded in a fluid with mean flow velocity transverse to the waveguide axis. We find the symmetry breaking conditions under which nonreciprocity is obtained, and we show how under transverse mean flow, with Mach numbers as low as 0.02, one-way propagation of the acoustic wave is obtained on a sub-wavelength-thick acoustic waveguide.

As opposed to the case when the flow is transverse to the waveguide axis, nonreciprocity in a waveguide in longitudinal fluid flow is of no surprise. However, one-way guiding in this regime is not trivial. In the second part of this work we demonstrate this effect in a single sub-diffraction chain of dipoles, embedded in a medium with longitudinal mean flow with Mach number of 0.1.

Our results may open another venue for the design of nonreciprocal acoustic wave devices for various applications.

.