Davide Cassi - Academia.edu (original) (raw)

Papers by Davide Cassi

WORLD SCIENTIFIC eBooks, Mar 20, 2014

arXiv (Cornell University), Jun 19, 2003

We present an analysis of the role of global topology on the structural stability of folded prote... more We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian Network Model (GNM) and we determine the spectral dimension, a parameter describing the low frequency behaviour of the density of modes. We find a surprisingly strong correlation between the spectral dimension and the number of aminoacids of the protein. Considering that the larger the spectral dimension, the more topologically compact is the folded state, our results indicate that for a given temperature and length of the protein, the folded structure corresponds to the less compact folding compatible with thermodynamic stability.

arXiv (Cornell University), Jun 15, 2008

We introduce an alternative thermal diffusive dynamics for the spin-S Ising ferromagnet realized ... more We introduce an alternative thermal diffusive dynamics for the spin-S Ising ferromagnet realized by means of a random walker. The latter hops across the sites of the lattice and flips the relevant spins according to a probability depending on both the local magnetic arrangement and the temperature. The random walker, intended to model a diffusing excitation, interacts with the lattice so that it is biased towards those sites where it can achieve an energy gain. In order to adapt our algorithm to systems made up of arbitrary spins, some non trivial generalizations are implied. In particular, we will apply the new dynamics to two-dimensional spin-1/2 and spin-1 systems analyzing their relaxation and critical behavior. Some interesting differences with respect to canonical results are found; moreover, by comparing the outcomes from the examined cases, we will point out their main features, possibly extending the results to spin-S systems.

arXiv (Cornell University), Apr 28, 2009

An important assumption lying behind innovation diffusion models and word-of-mouth processes is t... more An important assumption lying behind innovation diffusion models and word-of-mouth processes is that of homogeneous mixing: at any time, the individuals making up the market are uniformly distributed in space. When the geographical parameters of the market, such as its area extension, become important, the movement of individuals must be explicitly taken into account. The authors introduce a model for a "micro-level" process for the diffusion of an innovative product, based on a word-of-mouth mechanism, and they explicitly consider the inhomogeneity of markets and the spatial advertising is absent. The authors find an unexpected general failure of the word-of-mouth mechanism for high market densities and they obtain quantitative results for the optimal sampling policy. By introducing a threshold to discriminate between individuals who will purchase and those who will not purchase according to their individual goodwill, they calculate the length of the pre-launch campaign and the final goodwill as a function of the firm's expenditure. These results are applied to a set of major US urban areas.

Physical Review Letters, Jun 13, 2006

We study phase ordering on networks and we establish a relation between the exponent aχ of the ag... more We study phase ordering on networks and we establish a relation between the exponent aχ of the aging part of the integrated autoresponse function χag and the topology of the underlying structures. We show that aχ > 0 in full generality on networks which are above the lower critical dimension dL, i.e. where the corresponding statistical model has a phase transition at finite temperature. For discrete symmetry models on finite ramified structures with Tc = 0, which are at the lower critical dimension dL, we show that aχ is expected to vanish. We provide numerical results for the physically interesting case of the 2−d percolation cluster at or above the percolation threshold, i.e. at or above dL, and for other networks, showing that the value of aχ changes according to our hypothesis. For O(N) models we find that the same picture holds in the large-N limit and that aχ only depends on the spectral dimension of the network.

arXiv (Cornell University), Mar 11, 2022

Measurements indicating that planar networks of superconductive islands connected by Josephson ju... more Measurements indicating that planar networks of superconductive islands connected by Josephson junctions display long range quantum coherence are reported. The networks consist of superconducting islands connected by Josephson junctions and have a tree-like topological structure containing no loops. Enhancements of superconductive gap over specific branches of the networks and sharp increases of pair currents are the main signatures of the coherent states and, in order to unambiguously attribute the observed effects to branches being embedded in the networks, comparisons with geometrically equivalent, but isolated, counterparts are reported. Tuning the Josephson coupling energy by an external magnetic field generates increases of the Josephson currents, along the above mentioned specific branches, which follow a functional dependence typical of phase transitions. Results are presented for double comb and star geometry networks and in both cases the observed effects provide positive quantitative evidence of the predictions of existing theoretical models.

Modern Physics Letters B, Oct 30, 1994

Starting from some recent rigorous results about correlation functions of statistical model on tr... more Starting from some recent rigorous results about correlation functions of statistical model on tree structures, we analyze the nature of phase transitions occurring on Bethe lattices, showing the lack of long range order and the purely geometrical origin of the thermodynamic singularities. This approach gives a very simple formula for the critical temperature for any model with compact symmetry group and immediately leads to the value 1 for the critical exponent γ. The “geometrical” critical behavior only partially coincides with the mean field solution and violates the usual scaling relations.

Modern Physics Letters B, Dec 20, 1992

We study by analytical techniques the dynamical phase transition between recursive and transient ... more We study by analytical techniques the dynamical phase transition between recursive and transient regime induced on comb lattices by a topological bias. The critical exponents are expressed as functions of the intrinsic dimensions of these structures. In particular we show that, unlike what happens on Bethe lattices, it takes in general two different exponents to characterize the approach to the critical point from the recursive phase and from the transient one. These exponents depend respectively on the connectivity and on the spectral dimension.

Physical review, 1992

By mapping the harmonic-oscillations equations onto the random-walk equations, we calculate analy... more By mapping the harmonic-oscillations equations onto the random-walk equations, we calculate analytically the low-frequency vibrational spectrum of a Bethe lattice and show that it has a gap between zero frequency and a critical frequency. Using these results, we then obtain a low-temperature asymptotic expression for the vibrational specific heat and find that it goes exponentially to zero as T~O.

Mathematics

In this study, we investigate the effect of weight thresholding (WT) on the robustness of real-wo... more In this study, we investigate the effect of weight thresholding (WT) on the robustness of real-world complex networks. Here, we assess the robustness of networks after WT against various node attack strategies. We perform WT by removing a fixed fraction of weak links. The size of the largest connected component indicates the network’s robustness. We find that real-world networks subjected to WT hold a robust connectivity structure to node attack even for higher WT values. In addition, we analyze the change in the top 30% of central nodes with WT and find a positive correlation in the ranking of central nodes for weighted node centralities. Differently, binary node centralities show a lower correlation when networks are subjected to WT. This result indicates that weighted node centralities are more stable indicators of node importance in real-world networks subjected to link sparsification.

Complexity

Computing the robustness of a network, i.e., the capacity of a network holding its main functiona... more Computing the robustness of a network, i.e., the capacity of a network holding its main functionality when a proportion of its nodes/edges are damaged, is useful in many real applications. The Monte Carlo numerical simulation is the commonly used method to compute network robustness. However, it has a very high computational cost, especially for large networks. Here, we propose a methodology such that the robustness of large real-world social networks can be predicted using machine learning models, which are pretrained using existing datasets. We demonstrate this approach by simulating two effective node attack strategies, i.e., the recalculated degree (RD) and initial betweenness (IB) node attack strategies, and predicting network robustness by using two machine learning models, multiple linear regression (MLR) and the random forest (RF) algorithm. We use the classic network robustness metric R as a model response and 8 network structural indicators (NSI) as predictor variables and...

We compared seven node vaccination strategies in twelve real-world complex networks. The node vac... more We compared seven node vaccination strategies in twelve real-world complex networks. The node vaccination strategies are modeled as node removal on networks. We performed node vaccination strategies both removing nodes according to the initial network structure, i.e., non-adaptive approach, and performing partial node rank recalculation after node removal, i.e., semi-adaptive approach. To quantify the efficacy of each vaccination strategy, we used three epidemic spread indicators: the size of the largest connected component, the total number of infected at the end of the epidemic, and the maximum number of simultaneously infected individuals. We show that the best vaccination strategies in the non-adaptive and semi-adaptive approaches are different and that the best strategy also depends on the number of available vaccines. Furthermore, a partial recalculation of the node centrality increases the efficacy of the vaccination strategies up to 80%.

Complex networks are the preferential framework to model spreading dynamics in several real-world... more Complex networks are the preferential framework to model spreading dynamics in several real-world complex systems. Complex networks can describe the contacts between infectious individuals, responsible for disease spreading in real-world systems. Understanding how the network structure affects an epidemic outbreak is therefore of great importance to evaluate the vulnerability of a network and optimize the disease control. Here we argue that the best network structure indexes (NSIs) to predict the disease spreading extent in real-world networks are based on the notion of network node distance rather than on network connectivity as commonly believed. We numerically simulated, via a type-SIR model, epidemic outbreaks spreading on 50 real-world networks. We then tested which NSIs, among 40, could a priori better predict the disease fate. We found that the “average normalized node closeness” and the “average node distance” are the best predictors of the initial spreading pace, whereas in...

arXiv: Physics and Society, 2020

In this work we introduce a new nodes attack strategy removing nodes with highest conditional wei... more In this work we introduce a new nodes attack strategy removing nodes with highest conditional weighted betweenness centrality (CondWBet). We compare its efficacy with well-known attack strategies from literature over five real-world complex weighted networks. We use the network weighted efficiency (WEFF) like a measure encompassing the weighted structure of the network in addition to the commonly used binary-topological measure, the largest connected cluster (LCC). We find that the recently proposed conditional betweenness strategy (CondBet) (Nguyen et al. 2019) is the best to fragment the LCC in all cases. Further, we find that the introduced CondWBet strategy is the best to decrease the network efficiency (WEFF) in 3 out of 5 cases. Last, CondWBet is be the most effective strategy to reduce WEFF at the beginning of the removal process whereas the Strength that removes nodes with highest link weights first, shows the highest efficacy in the final phase of the removal process when t...

Scientific Reports, 2020

We report on phenomena observed in planar integrated networks obtained connecting superconducting... more We report on phenomena observed in planar integrated networks obtained connecting superconducting island by Josephson tunnel junctions. These networks, identifiable as tree-like graphs, have branches consisting of series arrays of Josephson junctions which can be individually current biased and characterized. Both Josephson supercurrents and gap parameters of the arrays embedded in the graph structures display properties significantly different from those of “reference” arrays fabricated on the same chips and having identical geometrical shape. The temperature and magnetic field dependencies of the Josephson current of the embedded arrays both show a singular behavior when a critical value is reached by the Josephson characteristic energy. The gap parameter of the junctions generating the embedded arrays is higher than that of the junctions forming the reference geometrical arrays.

In this paper we model the excitation energy transfer (EET) of the photosynthetic system I (PSI) ... more In this paper we model the excitation energy transfer (EET) of the photosynthetic system I (PSI) of the common pea plant Pisum Sativum as complex interacting network. The magnitude of the link energy transfer between nodes-chromophores is computed by Forster Resonant Energy Transfer (FRET) using the pairwise physical distances between chromophores from the PDB (Protein Data Bank). We measure the global PSI network EET efficiency adopting well-known network theory indicators: the network efficiency (Eff) and the largest connected component (LCC). We find that when progressively removing the weak links of lower EET, the network efficiency (Eff) decreases while the EET paths integrity (LCC) is still preserved. This finding would show that the PSI is a resilient system owning a large window of functioning feasibility and it is completely impaired only when removing most of the network links. Furthermore, we perform nodes removal simulations to understand how the nodes-chromophores malfu...

Physical Review E, 2016

Encounters between walkers performing a random motion on an appropriate structure can describe a ... more Encounters between walkers performing a random motion on an appropriate structure can describe a wide variety of natural phenomena ranging from pharmacokinetics to foraging. On homogeneous structures the asymptotic encounter probability between two walkers is (qualitatively) independent of whether both walkers are moving or one is kept fixed. On infinite comb-like structures this is no longer the case and here we deepen the mechanisms underlying the emergence of a finite probability that two random walkers will never meet, while one single random walker is certain to visit any site. In particular, we introduce an analytical approach to address this problem and even more general problems such as the case of two walkers with different diffusivity, particles walking on a finite comb and on arbitrary bundled structures, possibly in the presence of loops. Our investigations are both analytical and numerical and highlight that, in general, the outcome of a reaction involving two reactants on a comb-like architecture can be strongly different according to whether both reactants are moving (no matter their relative diffusivities) or only one, and according to the density of shortcuts among the branches.

$Research paper thumbnail of T c enhancement in inhomogeneous superconductors and fractal dynamics$

Il Nuovo Cimento D, 1989

Summary In this letter we propose a possible general mechanism ofT c enhancement in nonhomogeneo... more Summary In this letter we propose a possible general mechanism ofT c enhancement in nonhomogeneous superconductors in terms of the anomalies of electron-phonon dynamics in fractal systems. The high-T c superconductivity in oxyde ceramics is interpreted within such framework.

Series on Advances in Statistical Mechanics, 2023

Proteins: Structure, Function, and Bioinformatics, 2004