Physics-Biology interface seminar

Held every second Wednesday at 11am in the moyen amphi at LPS (not LPTMS!) in Orsay, this seminar series aims to be a central forum for the Physics/Biology interface in the south of Paris.

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Other seminars and conferences you might be interested in:

Paris-Saclay Biomechanics seminar - last Thu. of the month in Palaiseau (subscribe to their announcements)
Seminar of the Physical Chemistry Laboratory - in Orsay

Informations for speakers
Past seminars
Contact the organizer

Developing and applying fast constant pH methods in biological systems: From biomaterials to virus

Fernando Luis Barroso Da Silva (University of São Paulo, Brazil)


pH is a key parameter for biological and technological processes. Different numerical schemes were developed during the last years for such simulations ranging from Poisson-Boltzmann approaches to explicit solvent based methods. Ideally, the proton equilibria should correctly describe the experimental system without hampering the calculation time. A fast proton titration scheme (FPTS), rooted in the Kirkwood model of impenetrable spheres, where salt is treated at the Debye-Huckel level, was specially developed for proteins and nucleic acids. This method has now been coupled with OPEP5 force field for constant pH molecular dynamics simulations. A benchmark study will be presented. Despite our approximations, both the robustness and its ability to proper describe the system physics by these numerical methods can be confirmed. FPTS was also applied to quantify protein stability and biomolecular interactions. In this talk, I will present results for some protein systems with importance in different applied fields from biomaterials to public health.

Location: Moyen Amphi, Building 510, Université Paris-Sud Orsay

Formation of intracellular amorphous carbonates by bacteria

Karim Benzerara (Sorbonne Universités, Paris)

Living cells can sustain out-of-equilibrium states in a given environment by consuming free energy. The formation of some intracellular mineral phases provides some examples of this. Here I will review some of the work we have performed in the last years to describe and understand how some cyanobacteria, which are abundant photosynthesizing bacteria appeared several billions years ago at the surface of the Earth, manage to form intracellular amorphous carbonates. I will show the environmental conditions under which they catalyze this process, detail the methodologies (including cryo-TEM and spectroscopies) we used to characterize these phases and finally address the involved (bio)molecular mechanisms. The question of the selective advantage(s) provided by this process, if any, will be asked. The implications for basic and applied research will also be addressed. Overall, this talk should convince you that a highly interdisciplinary work is crucially needed to globally understand this intracellular biomineralization process.

Location: Moyen Amphi, Building 510, Université Paris-Sud Orsay

Stefan Karpitschka (MPI Göttingen)

Location: Moyen Amphi, Building 510, Université Paris-Sud Orsay

Intelligence, a recipe

Matthew Turner (Warwick University, UK)

We study information-processing (artificial), or “intelligent” (living), agents. These agents seek maximal control of their environment via future state maximisation (FSM), a principle that we argue may relate to intelligent behaviour more generally. Here we study moving, re-oreintable agents that seek to maximise their space of accessible (visual) environments, out to some time horizon. The action of each agent is (re)established by exhaustive enumeration of its future decision tree at each time step - each agent chooses the branch of its tree leading from the present to the richest future state space. Remarkably, cohesive swarm-like motion emerges that is similar to that observed in animal systems, such as bird flocks. We develop heuristics that mimic computationally intensive FSM but that could also operate in real time under animal cognition. Finally, we show that iterative application of these heuristics as the model for the behaviour of others, when determining the dynamics of self under full FSM, can lead to a form of closure for the problem. I will argue that this offers a philosophically attractive, bottom-up mechanism for the emergence of swarming.

Location: Moyen Amphi, Building 510, Université Paris-Sud Orsay