arXiv subjects
Publications and source records attributed to Cecilia Clementi.
We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct description of all essential thermodynamic and structural properties of liquid water.
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of observables numerically computed along dynamical trajectories are found to reproduce results given by the statistical mechanics of homopolymer models. The dynamical treatment, however, indicates a nontrivial transition between regimes of slow and fast phase space mixing. Such a transition is inaccessible to a statistical mechanical treatment and reflects a bimodality in the relaxation of time averages to corresponding ensemble averages. It is also found that a change in the energy dependence of the largest Lyapunov exponent indicates the theta-transition between filamentary and globular polymer configurations, clearly detecting the transition even for a finite number of particles.
Integrability, one of the classic issues in galactic dynamics and in general in celestial mechanics, is here revisited in a Riemannian geometric framework, where newtonian motions are seen as geodesics of suitable ``mechanical'' manifolds. The existence of constants of motion that entail integrability is associated with the existence of Killing tensor fields on the mechanical manifolds. Such tensor fields correspond to hidden symmetries of non-Noetherian kind. Explicit expressions for Killing tensor fields are given for the N=2 Toda model, and for a modified Henon-Heiles model, recovering the already known analytic expressions of the second conserved quantity besides energy for each model respectively.
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the topological control of the folding process, we study the folding of simplified models of five small globular proteins constructed using a Go-like potential in order to retain the information about the native structures but drastically reduce the energetic frustration and energetic heterogeneity among residue-residue native interactions. By comparing the structure of the transition state ensemble experimentally determined by Phi-values and of the intermediates with the ones obtained using our models, we show that these energetically unfrustrated models can reproduce the global experimentally known features of the transition state ensembles and "on-route" intermediates, at least for the analyzed proteins. This result clearly indicates that, as long as the protein sequence is sufficiently minimally frustrated, topology plays a central role in determining the folding mechanism.
The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The predictive power of these models suggest that, even for these very large proteins with completely different folding mechanisms and functions, real protein sequences are sufficiently well designed and much of the structural heterogeneity observed in the intermediates and the transition state ensembles is determined by topological effects.
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer interactions revealed by atomic force experiments. Force curves during association and dissociation are characterized by sudden jumps followed by smooth behavior and form hysteresis loops. Furthermore, the process is reversible in a finite range of temperature stabilizing the dimer. It is shown that in the interface between the two monomeric subunits the design procedure naturally favors those amino acids whose mutual interaction is stronger. Furthermore it is shown that the width of the hysteresis loop increases as the design procedure improves, i.e. stabilizes more the dimer.
We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like heteropolymer sequences, whose lowest energy (native) conformations were then identified by Molecular Dynamics. Then we turned to investigate whether one can find a pairwise contact potential, whose ground states are the contact maps associated with these native conformations. We show that such a requirement cannot be satisfied exactly - i.e. no such contact parameters exist. Nevertheless, we found that one can find contact energy parameters for which an energy minimization procedure, acting in the space of contact maps, yields maps whose corresponding structures are close to the native ones. Finally we show that when these structures are used as the initial point of a Molecular Dynamics energy minimization process, the correct native folds are recovered with high probability.
We perform a microcanonical study of classical lattice phi^4 field models in 3 dimensions with O(n) symmetries. The Hamiltonian flows associated to these systems that undergo a second order phase transition in the thermodynamic limit are here investigated. The microscopic Hamiltonian dynamics neatly reveals the presence of a phase transition through the time averages of conventional thermodynamical observables. Moreover, peculiar behaviors of the largest Lyapunov exponents at the transition point are observed. A Riemannian geometrization of Hamiltonian dynamics is then used to introduce other relevant observables, that are measured as functions of both energy density and temperature. On the basis of a simple and abstract geometric model, we suggest that the apparently singular behaviour of these geometric observables might probe a major topological change of the manifolds whose geodesics are the natural motions.
The Hamiltonian dynamics of classical planar Heisenberg model is numerically investigated in two and three dimensions. By considering the dynamics as a geodesic flow on a suitable Riemannian manifold, it is possible to analytically estimate the largest Lyapunov exponent in terms of some curvature fluctuations. The agreement between numerical and analytical values for Lyapunov exponents is very good in a wide range of temperatures. Moreover, in the three dimensional case, in correspondence with the second order phase transition, the curvature fluctuations exibit a singular behaviour which is reproduced in an abstract geometric model suggesting that the phase transition might correspond to a change in the topology of the manifold whose geodesics are the motions of the system.
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective potential between the amino acids from the knowledge of the native states of the designed sequences.
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also uncovers the shortcomings of any optimization procedure. The strategy can be applied on any data set of native structures such as those available from the Protein Data Bank (PDB). In this work, however, we explain and test our approach on simple lattice models, where the true interactions are known a priori. Excellent agreement is obtained between the extracted and the true potentials even for modest numbers of protein structures in the PDB. Comparisons with other methods are also discussed.
This paper deals with the problem of analytically computing the largest Lyapunov exponent for many degrees of freedom Hamiltonian systems. This aim is succesfully reached within a theoretical framework that makes use of a geometrization of newtonian dynamics in the language of Riemannian geometry. A new point of view about the origin of chaos in these systems is obtained independently of homoclinic intersections. Chaos is here related to curvature fluctuations of the manifolds whose geodesics are natural motions and is described by means of Jacobi equation for geodesic spread. Under general conditions ane effective stability equation is derived; an analytic formula for the growth-rate of its solutions is worked out and applied to the Fermi-Pasta-Ulam beta model and to a chain of coupled rotators. An excellent agreement is found the theoretical prediction and the values of the Lyapunov exponent obtained by numerical simulations for both models.