Postdoctoral Researcher in Biophysics

 in the "Theoretical Microbial Ecology" group

of Prof. Rosalind Allen

at the Friedrich-Schiller-University Jena

Research interests

My research focuses mainly on unicellular microorganisms called bacteria. From the single-celled to the ecological scale, I am interested in finding general and fundamental biophysical principles that regulate their physiology, interactions, and community dynamics. My research tools are mathematical modelling and numerical simulations. Whenever possible, I favor simple and coarse models. I pay particular attention to collaboration with the experimentalists and to the data analysis. I believe that any resulting theory must be useful, elegant, and general. 

My main research interests are

• Theoretical Biophysics, complex systems and dynamics

• Mathematical and computational modelling of biological systems

• Theoretical Ecology, bacterial communities

• System and synthetic Biology

• Data analysis and software development

Here you will find an overview of my research

and some slides from my previous works (2020)

My social media

Twitter Theoretical Biophysics

Mastodon Theoretical Biophysics


Theoretical Biophysics webpage


Virtual Population Dynamics Seminars

and the Biotheorist Meetings in Jena

BTMJ - Biotheorist Meeting Jena

Research topics

Resource allocation

To grow, bacteria convert nutrients into biomass via the process of transcription-translation. To initiate transcription, RNA polymerase (RNAP) reversibly binds a sigma factor that directs RNAP to a specific subset of genes. In response to changing environmental conditions, bacteria activate alternative sigma factors, changing the global pattern of expressed genes.  Since RNAPs are finite in the cells, sigma factors compete for binding them.

Sigma factor

We found that sigma factor competition redirects inner resources of the cell by providing a mechanism for an indirect up-regulation of the stress genes (M2014). By competing, sigma factors also creates cross-talk within these genes, a feature that often spoils proper functioning of synthetic circuits. We showed that by careful theoretical design, sigma factors can be ingredients in synthetic circuits that are not only able to work in absence of genetic cross-talk in a single but also in several bacteria species (P2018).

Give a look at a sigma factor competition talk and poster

Check the presentation on the timer circuits

Synthetic community

Competition for limiting nutrients and exchange of molecules determine the complex dynamics of bacterial communities. Mathematical modeling is a useful tool to assess the coexistence of microbial species and the associated enhancement of bioproduction. We focused on a synthetic community where one strain of bacteria harnesses the toxic byproduct of another strain, which in turn produces a compound. We found that their coexistence leads to an advantage in optimizing the production of the compound by exploiting the detoxifying effect.  (M2020).

Read a presentation and a poster on this topic

Marine communities

Marine phytoplankton is composed of unicellular algae and their associated bacteria. These algal communities are highly variable in species composition, but their patterns tend to recur seasonally. To clarify the role of the bacterial community in the phytoplankton, we monitored the growth dynamics of several bacterial species and microalgae in community. Supported by Lotka-Volterra models, we found that interactions between bacteria and algae are highly species-specific and depend on algal fitness, bacterial metabolism, and community composition. 

A poster and a presentation, a talk (INI Cambridge) and a talk (ICTP Trieste) on this topic

LUX deconvolution

Many biological studies rely on luminescence reporters. These have a high signal-to-noise ratio, but as a disadvantage, constant light emission leads to unwanted crosstalk between adjacent wells on a microplate where bacteria are placed for measurements, thus falsifying the measurements. We have developed a new computational method to correct for luminescence crosstalk and estimate the actual luminescence activity in a microplate (M2019).

Find here a poster and a presentation on our deconvolution process

Membrane proteins

The cytoplasmic bacterial membrane has a remarkably intricate temporal and spatial organization that is critical for the maintenance of fundamental biological processes. We focused on the theoretical study of the diffusion of single proteins on a curved bacterial membrane, pointing out that the vast majority of membrane proteins assemble in clusters and follow, unexpectedly, Brownian dynamics (L2018).

Find here a poster on this topic

AMR of PG layer

In bacteria, the peptidoglycan (PG) layer maintains cell shape by counteracting turgor pressure. During growth, new material is incorporated into the existing layer through the interaction of several enzymes. We theoretically study the dynamics of incorporation of a new material into the PG layer via a coarse-grained mechanical (biophysical) model to assess its stability and understand the evolution of antimicrobial resistance (AMR).

Ion transport in biopiles

In E. coli, the NhaA antiporters anchored in the lipid bilayer membrane are responsible for creating a pH gradient by exchanging sodium for protons. Theoretically, this gradient can be exploited to create a difference of potential between the opposite sides of the membrane, which can serves as a biopile. We created synthetic micelles with NhaAs to study such proton flow, which we described by a mathematical model. In this way, we established a rational design for biopile based on antiporters, useful for medical applications (pending patent).

High energy physics

During my Master's in Theoretical Physics, I worked on High Energy Physics studying the "Transverse Momentum Distribution of a Top-Antitop pair in QCD". 

Thesis and presentation (in Italian)