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Ivan Tanasijevic

Publications and source records attributed to Ivan Tanasijevic.

2 recordsLinked to original sources

Recycle only when you have to!

AlphaFold 3-like models (e.g., Boltz, Protenix, etc.) have pushed the frontier of protein binder design. This architecture is used both for the generation of binder candidates (e.g., by hallucination or converting these models into backbone or full atom generative models) as well as for the screening of these candidates for valid binders. In this paper, we start from the observation that AlphaFold 3's confidence metrics (ipSAE, ipTM) as well as structural consistency metrics can be predicted directly from the trunk even at early recycling. Because our proposed predictor is cheap, differentiable, and available at every cycle, it can be used in two distinct ways: as a decision signal to wisely spend the recycling budget for screening and as an objective for hallucination-based design. We show that both applications lead to increased performance at significantly reduced computational cost.

q-bio.QM↗

Microswimmers in vortices: Dynamics and trapping

Biological and artificial microswimmers often self-propel in external flows of vortical nature; relevant examples include algae in small-scale ocean eddies, spermatozoa in uterine peristaltic flows and bacteria in microfluidic devices. A recent experiment has shown that swimming bacteria in model vortices are expelled from the vortex all the way to a well-defined depletion zone (Sokolov and Aranson (2016) "Rapid expulsion of microswimmers by a vortical flow." Nature Comm. 7, 11114). In this paper, we propose a theoretical model to investigate the dynamics of elongated microswimmers in elementary vortices, namely active particles in two- and three-dimensional rotlets. A deterministic model first reveals the existence of bounded orbits near the centre of the vortex and unbounded orbits elsewhere. We further discover a conserved quantity of motion that allows us to map the phase space according to the type of the orbit (bounded vs unbounded). We next introduce translational and rotational noise into the system. Using a Fokker--Planck formalism, we quantify the quality of trapping near the centre of the vortex by examining the probability of escape and the mean time of escape from the region of deterministically bounded orbits. We finally show how to use these findings to formulate a prediction for the radius of the depletion zone, which compares favourably with the experiments of Sokolov and Aranson (2016).

physics.bio-ph↗