arXiv subjects

Carlo Guardiani

Publications and source records attributed to Carlo Guardiani.

7 recordsLinked to original sources

arXiv2023

Bubbles enable volumetric negative compressibility in metastable elastocapillary systems

Although coveted in applications, few materials expand when subject to compression or contract under decompression, i.e., exhibit the negative compressibility phenomenon. A key step to achieve such counterintuitive behaviour is the destabilisations of (meta)stable equilibria of the constituents. Here, we propose a simple strategy to obtain negative compressibility exploiting capillary forces both to precompress the elastic material and to release such precompression by a threshold phenomenon -- the reversible formation of a bubble in a lyophobic flexible cavity. We demonstrate that the solid part of such metastable elastocapillary systems displays negative compressibility across different scales: hydrophobic microporous materials, proteins, and millimetre-sized laminae. This concept is applicable to fields such as porous materials, biomolecules, sensors and may be easily extended to create unexpected material susceptibilities.

cond-mat.soft↗

arXiv2014

Coarse-grained modeling of protein unspecifically bound to DNA

There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in solution (jumps), 1D-diffusion along DNA (sliding), and small jumps (hopping) achieving association rates higher than for 3D-diffusion only. We investigate the FD phenomenology through Molecular Dynamics simulations in the framework of coarse-grained modeling. Despite the crude approximations, we show that the model generates, upon varying equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, by focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix leading to a coupling of translation along the DNA-axis with rotation around it. The 1D-diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument able to quantitatively reproduce the measured values.

q-bio.BM↗

arXiv2007

Computational analysis of folding and mutation properties of C5 domain from Myosin binding protein C

Thermal folding Molecular Dynamics simulations of the domain C5 from Myosin Binding Protein C were performed using a native-centric model to study the role of three mutations related to Familial Hypertrophic Cardiomyopathy. Mutation of Asn755 causes the largest shift of the folding temperature, and the residue is located in the CFGA' beta-sheet featuring the highest Phi-values. The mutation thus appears to reduce the thermodynamic stability in agreement with experimental data. The mutations on Arg654 and Arg668, conversely, cause a little change in the folding temperature and they reside in the low Phi-value BDE beta-sheet, so that their pathologic role cannot be related to impairment of the folding process but possibly to the binding with target molecules. As the typical signature of Domain C5 is the presence of a longer and destabilizing CD-loop with respect to the other Ig-like domains we completed the work with a bioinformatic analysis of this loop showing a high density of negative charge and low hydrophobicity. This indicates the CD-loop as a natively unfolded sequence with a likely coupling between folding and ligand binding.

q-bio.GN↗

arXiv2006

A toy model of polymer stretching

We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the cantilever) and long-range interactions terms inside each domain. Exact equilibrium computations and Monte Carlo simulations qualitatively reproduce the experimental saw-tooth pattern of force-extension profiles, corresponding (in our model) to first-order phase transitions. We study the influence of the coupling induced by the cantilever and the pulling speed on the relative heights of the force peaks. The results suggest that the increasing height of the critical force for subsequent unfolding events is an out-of-equilibrium effect due to a finite pulling speed. The dependence of the average unfolding force on the pulling speed is shown to reproduce the experimental logarithmic law.

q-bio.BM↗

arXiv2006

Testing simplified protein models of the hPin1 WW domain

The WW domain of the human Pin1 protein for its simple topology and the large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of the present work is to compare the reliability of the chemically-based Sorenson/Head-Gordon (SHG) model and a standard native centric model in reproducing through molecular dynamics simulations some of the well known features of the folding transition of this small domain. Our results show that the Gō model correctly reproduces the cooperative, two-state, folding mechanism of the WW-domain, while the SHG model predicts a transition occurring in two stages: a collapse followed by a structural rearrangement. The lack of a cooperative folding in the SHG simulations appears to be related to the non-funnel shape of the energy landscape featuring a partitioning of the native valley in sub-basins corresponding to different chain chiralities. However the SHG approach remains more reliable in estimating the $Φ$-values with respect to Gō-like description. This may suggest that the WW-domain folding process is stirred by energetic and topological factors as well, and it highlights the better suitability of chemically-based models in simulating mutations.

cond-mat.stat-mech↗

arXiv2004

A microscopic model of evolution of recombination

We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not related to the population itself, and a dynamic one that accounts for interactions between organisms e.g. competition. We focus on the dynamics of colonization of an empty niche. As competition is a function of the population, selection pressure rapidly changes in time. The simulations show that both in the case of flat and steep static fitness landscapes, recombination provides a high velocity of movement in the phenotypic space thus allowing recombinants to colonize the highest fitness regions earlier than non recombinants that are often driven to extinction. The stabilizing effects of competition and assortativity are also discussed. Finally, the analysis of phase diagrams shows that competition is the key factor for the evolution of recombination, while assortativity plays a significant role only in small populations.

q-bio.PE↗

arXiv2004

A model of sympatric speciation through assortative mating

A microscopic model is developed, within the frame of the theory of quantitative traits, to study both numerically and analytically the combined effect of competition and assortativity on the sympatric speciation process, i.e. speciation in the absence of geographical barriers. Two components of fitness are considered: a static one that describes adaptation to environmental factors not related to the population itself, and a dynamic one that accounts for interactions between organisms, e.g. competition. The effects of finiteness of population size on survival of coexisting species are also accounted for. The simulations show that both in the case of flat and ripid static fitness landscapes, competition and assortativity do exert a synergistic effect on speciation. We also show that competition acts as a stabilizing force against extinction due to random sampling in a finite population. Finally, evidence is shown that speciation can be seen as a phase transition.

q-bio.PE↗