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Scientific Report 2007-2009<br />
Condensed matter physics and biophysics<br />
emergent self-organization. There is no leader to guide individuals towards the common patterns.<br />
Rather, collective behaviour arises spontaneously as a consequence of the local interactions between<br />
individuals, much as it happens in ordering phenomena in condensed matter systems. A<br />
crucial issue is therefore to understand how self-organization emerges in animal aggregations and<br />
how behavior rules at the individual level regulate collective efficiency and group function. Bird<br />
flocking is a striking example of collective animal behaviour which is currently under investigation<br />
in our Department (C13).<br />
Statistical mechanics is also exploited to address fundamental biological problems in which the<br />
complexity of the living matter is relevant. Genes expressions, protein folding, metabolic pathways<br />
require understanding the connections and the interactions between a large number of components.<br />
For example, in a model system like the bacterium E.Coli, the estimated number of reactions<br />
composing the metabolic cycle is about 1100. Understanding the global organization of uxes at<br />
the cellular level, is thus fundamental both to predict responses to environmental perturbations,<br />
drugs, or gene knockouts, and to infer the critical epistatic interactions between metabolic genes<br />
(C14).<br />
As a last example of offspring of statistical mechanics, we mention the ongoing research on<br />
dynamical chaotic systems (C15,C16,C17). Macroscopic systems are dynamical systems with a<br />
very large number of degrees of freedom and many characteristic times (e.g. application to climate<br />
and turbulence). In these cases, the usual indicators (Lyapunov exponents and Kolmogorov-Sinai<br />
entropy) are not very relevant. The innovative approach followed in Rome considers chaos a crucial<br />
requirement to develop a statistical approach to macroscopic dynamical systems (C16,C17). An<br />
application of stochastic processes to deep see convection processes is also currently investigated<br />
(C18).<br />
Strongly connected to statistical mechanics is the numerical investigation (via molecular dynamics<br />
or Monte Carlo methods) of systems of different level of complexity, from the ab-inito<br />
quantum mechanics calculations, to atomistic studies of hard, soft and bio-matter, (including<br />
hydrated proteins (C19)), to coarse-grained methods (C20) for bridging the gap from the Å-fs<br />
space-time scales to hydrodynamic behavior. Currently, we are working on a specific kind of<br />
mixed quantum-classical dynamics, the so-called non-adiabatic dynamics. In non-adiabatic situations,<br />
the coupling between nuclear (the bath) and electronic (quantum subsystem) motions in<br />
a molecular system, or the interactions with the environment, can induce transitions among the<br />
eigenstates of the electronic Hamiltonian that affects the (photo)chemistry and physics of nonadiabatic<br />
systems. Our work on developing efficient and rigorous MD algorithms for non-adiabatic<br />
simulations aims at controlling a number of interesting processes by understanding and modifying<br />
these transitions, for example via coupling to a control environment or via an appropriate pattern<br />
of excitations (C21). In the context of classical statistical mechanics, we are also active in<br />
the development of optimal methodologies for investigating rare events, i.e. events characterized<br />
by time-scales not accessible by brute force MD (e.g. chemical reactions, phase transformations,<br />
conformational changes related to the functionality of proteins), and the physics of systems out of<br />
equilibrium (C22). Rare events describe transitions over barriers higher than the thermal energy<br />
of the system, among metastable states of the free energy landscape and as such are characterized<br />
by time-scales much longer than those accessible by brute force MD. Chemical reactions, phase<br />
transformations, nucleation processes, and conformational changes related to the functionality of<br />
proteins are just a few examples of these events.<br />
Next we move to the soft and bio matter studies. Here again, we build upon the developments<br />
which took place at the end of last century in the physics of simple and complex liquids and in<br />
the physics of disordered systems. Soft and bio matter have a twofold interest: one one side we<br />
need to understand the microscopic origin to the self-organization and the build up of structures<br />
at mesoscopic length scales. On the other side, we need to learn how to engineer nano and micro<br />
<strong>Sapienza</strong> Università di Roma 49 Dipartimento di Fisica