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Rontani M.,CNR Institute of Neuroscience
Nature Materials | Year: 2011

A study was conducted to demonstrate that tunneling and capacitance spectroscopies were able to image the wavefunctions of electrons in atom-like solid-state systems as they were shaped by an external magnetic field. The tunneling and capacitance spectroscopies probed the electron probability density with energy and space selectivity. The researchers engaged in the study were able to identify two regimes dominated by Coulomb and magnetic confinement. The researchers also investigated the shaping effect of the field on two orbitals of the quantum-dot p-shell. Investigations also revealed that one orbital had x-like symmetry and the other y-like symmetry at zero field, reflecting the elliptical anisotropy of the dot potential.

Trotta E.,CNR Institute of Neuroscience
Nucleic Acids Research | Year: 2013

Codons that code for the same amino acid are often used with unequal frequencies. This phenomenon is termed codon bias. Here, we report a computational analysis of codon bias in yeast using experimental and theoretical genome-wide data. We show that the most used codons in highly expressed genes can be predicted by mRNA structural data and that the codon choice at each synonymous site within an mRNA is not random with respect to the local secondary structure. Because we also found that the folding stability of intron sequences is strongly correlated with codon bias and mRNA level, our results suggest that codon bias is linked to mRNA folding structure through a mechanism that, at least partially, operates before pre-mRNA splicing. Consistent with this, we report evidence supporting the adaptation of the tRNA pool to the codon profile of the most expressed genes rather than vice versa. We show that the correlation of codon usage with the gene expression level also includes the stop codons that are normally not decoded by aminoacyl-tRNAs. The results reported here are consistent with a role for transcriptional forces in driving codon usage bias via a mechanism that improves gene expression by optimizing mRNA folding structures. © The Author(s) 2013. Published by Oxford University Press.

Tozzini V.,CNR Institute of Neuroscience
Accounts of Chemical Research | Year: 2010

(Figure Presented) The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarsegrained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virusspecific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was recently confirmed by the assignment of two of the Nobel prizes in 2008: in chemistry for the discovery of GFP and in medicine for the discovery of HIV. Accordingly, these proteins were studied with essentially all of the available modeling techniques, making them ideal examples for studying the details of multiscale approaches in protein modeling. © 2010 American Chemical Society.

Tozzini V.,CNR Institute of Neuroscience
Quarterly Reviews of Biophysics | Year: 2010

The last decade has witnessed a renewed interest in the coarse-grained (CG) models for biopolymers, also stimulated by the needs of modern molecular biology, dealing with nano- to micro-sized bio-molecular systems and larger than microsecond timescale. This combination of size and timescale is, in fact, hard to access by atomic-based simulations. Coarse graining the system is a route to be followed to overcome these limits, but the ways of practically implementing it are many and different, making the landscape of CG models very vast and complex. In this paper, the CG models are reviewed and their features, applications and performances compared. This analysis, restricted to proteins, focuses on the minimalist models, namely those reducing at minimum the number of degrees of freedom without losing the possibility of explicitly describing the secondary structures. This class includes models using a single or a few interacting centers (beads) for each amino acid. From this analysis several issues emerge. The difficulty in building these models resides in the need for combining transferability/predictive power with the capability of accurately reproducing the structures. It is shown that these aspects could be optimized by accurately choosing the force field (FF) terms and functional forms, and combining different parameterization procedures. In addition, in spite of the variety of the minimalist models, regularities can be found in the parameters values and in FF terms. These are outlined and schematically presented with the aid of a generic phase diagram of the polypeptide in the parameter space and, hopefully, could serve as guidelines for the development of minimalist models incorporating the maximum possible level of predictive power and structural accuracy. © 2010 Cambridge University Press.

Smerzi A.,CNR Institute of Neuroscience
Physical Review Letters | Year: 2012

According to the quantum Zeno effect (QZ), frequent observations of a system can dramatically slow down its dynamical evolution. We show that the QZ is a physical consequence of the statistical indistinguishability of neighboring quantum states. The time scale of the problem is expressed in terms of the Fisher information and we demonstrate that the Zeno dynamics of particle entangled states might require quite smaller measurement intervals than classically correlated states. We propose an interferometric experiment to test the prediction. © 2012 American Physical Society.

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