### Dr Andrea Rocco

### Biography

I graduated in Physics at the University of Pisa (Italy) in 1994, discussing a thesis in quantum field theory. In 1998 I obtained my PhD in Physics from the University of North Texas (USA), where I focused on the role of stochastic processes in classical and quantum mechanical systems.

Between 1998 and 2007 I held postdoctoral positions at the University of Barcelona (Spain), the University of Rome "La Sapienza" (Italy), CWI (The Netherlands), and the University of Oxford (UK). During this period of time, I made a gradual transition from the general fields of statistical mechanics and pattern formation towards the modelling of biological systems. In 2007 I obtained a Lectureship in Applied Mathematics at the University of Bath (UK), where I taught mathematical biology modules at both MSc and undergraduate levels.

In 2009 I joined the University of Surrey (UK) as Research Fellow in Systems Biology, and was appointed Lecturer in Mathematical Biology in 2012.

### Research Activity

As a theoretical physicist, my research focus has primarily been within the general fields of statistical mechanics, nonlinear dynamics, and pattern formation. In recent years, I have made a transition towards the study of biological systems, for which I adopt a variety of theoretical methodologies borrowed from physics and mathematics, such as dynamical systems theory and the theory of stochastic processes. In my group, the emphasis is not on building high complexity models, but rather on uncovering general and fundamental mechanisms in biological systems.

I am always happy to consider **applications for PhD positions**. Interested candidates are welcome to enquire by email to discuss suitable topics. Given the theoretical aspects involved, a solid mathematical or theoretical physics background is required in all projects. I don't have **openings at the postdoctoral level** at the moment, but a number of grant applications are currently under evaluation, and openings may appear in the close future.

### Group Members

**Gerardo Aquino**, Postdoctoral Research Fellow, The role of stochastic fluctuations in stem cell differentiation**Nick Werren**, PhD candidate, Memory effects in open quantum systems, (co-supervised with Jim Al-Khalili and Johnjoe McFadden)**Winifred Nyinoh**, PhD candidate, Molecular investigation of drug synergy in*mycobacteria,*(First supervisor: Johnjoe McFadden)**Ethan Wyke**, MSc Student in Physics, Quantum Tunnelling through a Stochastically Fluctuating Barrier, (co-supervised with Jim Al-Khalili)

### Former Group Members

**Finn Gubay**, Postdoctoral Research Fellow**Hossein Nili**, Postdoctoral Research Fellow. Now at IPM, Institute for Research in Fundamental Sciences, Iran**Noah Mesfin**, MSc student in Systems Biology. Now PhD candidate at Oxford Brookes University, UK.

### Research Collaborations

- Robert Kelsh (University of Bath, UK)
- Johnjoe McFadden (University of Surrey, UK)
- Jim Al-Khalili (University of Surrey, UK)

### Editorial and Review Activity

- Editorial Board Member of Nature journal Scientific Reports, Biological Physics Area
- Review Editor for Frontiers in Bioinformatics and Computational Biology
- Reviewer for Physical Review E, Physical Review Letters, European Physical Journal B, Bulletin of Mathematical Biology, PLOS Computational Biology, PLOS ONE, Journal of the Royal Society Interface, Nucleic Acid Research, Fluctuations and Noise Letters, Physica A.

### Research

### Research interests

My current research focuses on noise propagation across molecular networks, critical phenomena in living systems, stochastic dynamics in cell differentiation, and noise effects in open quantum systems. In general, my research questions regard understanding the noise-induced transitions in gene networks, stochastic off-equilibrium dynamics and non-ergodic behaviours, and the balance between biological variability and individual robustness. The ultimate goal is to construct a theoretical framework in which fluctuations can be understood in general terms, and their role in shaping the organism dynamics elucidated.

### Research projects

*et*

*al*, in “Systems Biology of Tuberculosis”, Springer (2013)]. Consideration of these effects has led me to introduce the concept of stochastic control in metabolic networks [Rocco, Phys. Biol. (2009)], where noise itself is proven to be able to act as a control mechanism that tunes metabolic concentrations and fluxes. I am now interested in the principles underpinning noise propagation across different layers of regulation in gene networks.

*et al*, PLoS Genetics (2011)]. By using a combination of mathematical analysis and simulations, we could predict mathematically and validate experimentally several new features of this network. More recently we have refined that core network, to include an analysis of the role played by Wnt signaling in melanocyte differentiation [Vibert

*et al*, Pigment Cell & Melanoma Research (2017)]. We are now interested in assessing the role played by noise, both intrinsic and extrinsic, in the dynamics of the differentiation process. More details in our dedicated website Systems Biology of Stem Cell Differentiation. We acknowledge the UK Biotechnology and Biological Sciences Research Council (BBSRC) for funding.

*et al*, PLoS ONE (2013)]. The proposed mechanism is currently under experimental validation.

*et al*, Plasma Sources Sci. Technol. (2006) for a review]. I also studied the effect of extrinsic noise on the propagation of reaction-diffusion fronts. In the case of the so-called Fisher Equation (FKPP), I contributed to identifying the anomalous sub-diffusive behaviour characterizing the front position [Rocco

*et al*, Phys. Rev. E (2000)], and to generalize it through the definition of a new roughness universality class for travelling waves in 2 bulk dimensions [Tripathy

*et al,*Phys. Rev. Lett. (2001)]. In the context of off-equilibrium statistical mechanics, I also addressed fundamental issues on complexity reduction in models for glasses [Crisanti

*et al*, J. Chem. Phys. (2000)]. During my PhD, I developed fractional calculus techniques to study fractal phenomena in both space and time [Rocco & West, Physica (1999); Grigolini

*et al*, Phys. Rev. E (1999)].

### Research Networks and Metrics

### My teaching

**Introduction to Mathematical Biology (Level 3 - Module Organizer, ***Module Descriptor***)**

This module aims at providing students with the problem-solving skills required to construct and solve simple mathematical models of molecular networks. Dynamical modelling, in terms of ordinary differential equations, is introduced, using gene regulatory networks as case studies (regulatory cascades, feedback loops, logic gates). The students are provided with the general techniques to analyse such models, and compute the solution numerically with the aid of dedicated software. Derivation of qualitative features, relating to steady states analysis, multistability, and oscillatory behaviours, is also discussed.

**Systems Biology (Level 3, ***Module Descriptor***)**

### My publications

### Publications

L. Vibert, G. Aquino, I. Gehring, T. Subkankulova, T.F. Schilling, **A. Rocco**, R.N. Kelsh,
*An ongoing role for Wnt signaling in differentiating melanocytes in vivo, *Pigment cell & melanoma research 30 (2), 219-232 (2017)

Y. Hu, S. Wang, N. Ma, S.M. Hingley-Wilson, **A. Rocco**, J. McFadden, H. Tang,
*Trajectory energy minimization for cell growth tracking and genealogy analysis,*
Royal Society Open Science 4 (5), UNSP 170207 (2017)

A.A. Mannan, Y. Toya, K. Shimizu, J. McFadden, A.M. Kierzek, **A. Rocco,**
*Integrating kinetic model of E. coli with genome scale metabolic fluxes overcomes its open system problem and reveals bistability in central metabolism,*
PloS one 10 (10), e0139507 (2015)

**A. Rocco**, A. Kierzek, J. McFadden,
*Slow protein fluctuations explain the emergence of growth phenotypes and persistence in clonal bacterial populations,*
PloS one 8 (1), e54272 (2013)

**A. Rocco**, A. Kierzek, J. McFadden,
*Stochastic Effects in Metabolic Networks,*
Encyclopedia of Systems Biology, 1991-1993, Springer (2013)

**A. Rocco**, A. Kierzek, J. McFadden,
*Stochastic gene expression in bacterial pathogens: A mechanism for persistence?*
Systems Biology of Tuberculosis, 157-177, Springer (2013)

E.R. Greenhill, **A. Rocco**, L. Vibert, M. Nikaido, R.N. Kelsh,
*An iterative genetic and dynamical modelling approach identifies novel features of the gene regulatory network underlying melanocyte development,*
PLoS genetics 7 (9), e1002265 (2011) [see also modelling supplementary material]

E. Greenhill, **A. Rocco**, M. Nikaido, R.N. Kelsh,
*Melanocytes, modeling and maths-do we really understand differentiation?*
Pigment Cell & Melanoma Research 5 (22), 21-21 (2009)

L. Vibert, **A. Rocco**, M. Nikkaido, E.R. Greenhill, R.N. Kelsh,
*Testing in vivo the genetic regulatory network underlying melanocyte differentiation,*
Mechanisms of Development 126, S316-S317 (2009)

**A. Rocco**,
*Stochastic control of metabolic pathways,*
Phys. Biol. **6**, 016002 (2009)

G. Lunter, **A. Rocco**, N. Mimouni, A. Heger, A. Caldeira, J. Hein,
*Uncertainty in Homology Inferences: Assessing and Improving Genomic Sequence Alignment,*
Genome Res. **18**, 298 (2008) [see also commentary paper]

U. Ebert, C. Montijn, T.M.P. Briels, W. Hundsdorfer, B. Meulenbroek, **A. Rocco**, E.M. van Veldhuizen,
*The multiscale nature of streamers,*
Plasma Sources Sci. Technol. **15**, S118 (2006)

B. Meulenbroek, **A. Rocco**, U. Ebert,
*Streamer branching rationalized by conformal mapping techniques, *
Phys Rev. E **69**, 067402 (2004)

B. Coluzzi, A. Crisanti, E. Marinari, F. Ritort, **A. Rocco**,
*A New Method to Compute the Configurational Entropy in Spin Glasses,*
Eur. Phys. J. B **32**, 495 (2003)

**A. Rocco**, U. Ebert and W. Hundsdorfer,
*Branching of Negative Streamers in free flight,*
Phys. Rev. E **66**, 035102 (2002)

A. Crisanti, F. Ritort, **A. Rocco**, and M. Sellitto,
*Is the Stillinger and Weber decomposition relevant for coarsening models?*
J. Phys.: Condens. Matter **14**, 1523 (2002)

**A. Rocco**, L. Ramírez-Piscina, J. Casademunt,
*Kinematic reduction of reaction-diffusion fronts with multiplicative noise: Derivation of stochastic sharp-interface equations,*
Phys. Rev. E **65**, 056116 (2002)

A. Torcini, A. Vulpiani, **A. Rocco,**
*Front propagation in chaotic and noisy reaction diffusion systems: A discrete-time map approach,*
Eur. Phys. J. B **25**, 333 (2002)

**A. Rocco**, J. Casademunt, U. Ebert, and W. van Saarloos,
*Diffusion coefficient of propagating fronts with multiplicative noise,*
Phys. Rev. E **65**, 012102 (2002)

G. Tripathy, **A. Rocco**, J. Casademunt, and W. van Saarloos,
*Universality class of fluctuating pulled fronts,*
Phys. Rev. Lett. **86**, 5215 (2001)

A. Crisanti, F. Ritort, **A. Rocco**, and M. Sellitto,
*Inherent Structures and non-equilibrium dynamics of 1D constrained kinetic models: A comparison study,*
J. Chem. Phys. **113**, 10615 (2000)

F.X. Magdaleno, **A. Rocco**, J. Casademunt,
*Interface dynamics in Hele-Shaw flows with centrifugal forces: Preventing cusp singularities with rotation,*
Phys. Rev. E **62**, R5887 (2000)

**A. Rocco**, U. Ebert, and W. van Saarloos,
*Subdiffusive fluctuations of "pulled" fronts with multiplicative noise,*
Phys. Rev. E **62**, R13 (2000)

P. Grigolini, **A. Rocco** and B.J. West,
*Fractional Calculus as a Macroscopic Manifestation of Randomness,*
Phys. Rev. E **59** 2603 (1999)

**A. Rocco** and B.J. West,
*Fractional Calculus and the Evolution of Fractal Phenomena,*
Physica A **265**, 535 (1999)

**A. Rocco** and P. Grigolini,
*The Markov approximation revisited: Inconsistency of the standard quantum Brownian motion model,*
Phys. Lett. A **252**, 115 (1999)

P. Allegrini, P. Grigolini, **A. Rocco,**
*Slow motion as a thermal gradient effect,*
Phys. Lett. A **233**, 309 (1997)