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