Francesco Mambretti

University of Milan

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Luca Casiraghi

University of Milan

Tommaso Bellini

University of Milan

Elvezia Maria Paraboschi

Humanitas University

Samir Suweis

University of Padua

Anna Tovo

Humanitas University

D. E. Galli

University of Milan

Davide Pini

University of Milan

R. E. Grisenti

GSI Helmholtz Centre for Heavy Ion Research

Anton Kalinin

GSI Helmholtz Centre for Heavy Ion Research

E. Tentori

University of Padua

Cooperative Institutions

University of Milan

Deutsches Elektronen-Synchrotron DESY

European X-Ray Free-Electron Laser

Goethe University Frankfurt

University of Padua

Universität Hamburg

The University of Tokyo

Istituti di Ricovero e Cura a Carattere Scientifico

École Polytechnique Fédérale de Lausanne

Center for Free-Electron Laser Science

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Synthetic Eco-Evolutionary Dynamics in Simple Molecular Environment

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Luca Casiraghi Francesco Mambretti Anna Tovo Elvezia Maria Paraboschi Samir Suweis

Abstract The understanding of eco-evolutionary dynamics, and in particular the mechanism of coexistence of species, is still fragmentary and in need of test bench model systems. To this aim we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 10 15 single-strand DNA oligonucleotide ‘individuals’. We begin with a seed of random sequences which we select via affinity capture from ∼ 10 12 DNA oligomers of fixed sequence (‘resources’) over which they compete. At each cycle (‘generation’), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences (‘species’) drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource binding dominates the selection in the first generations, while inter and intra-individual interactions become important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.

Evolutionary Dynamics

Dynamics

10.1101/2023.07.21.549992

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Reviewer #1 (Public Review): Synthetic Eco-Evolutionary Dynamics in Simple Molecular Environment

Luca Casiraghi Francesco Mambretti Anna Tovo Elvezia Maria Paraboschi Samir Suweis

The understanding of eco-evolutionary dynamics, and in particular the mechanism of emergence of species, is still fragmentary and in need of test bench model systems. To this aim we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 1015 single-strand DNA oligonucleotide ‘individuals’. We begin with a seed of random sequences which we select via affinity capture from ∼ 1012 DNA oligomers of fixed sequence (‘resources’) over which they compete. At each cycle (‘generation’), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences (‘species’) drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource binding dominates the selection in the first generations, while inter and intra-individual interactions becomes important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.

Evolutionary Dynamics

Dynamics

10.7554/elife.90156.1.sa2

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Low-temperature ordering of the dimer phase of a two-dimensional model of core-softened particles

Physical review. E (2021)

Francesco Mambretti Michela Martinelli F. Civillini M. Bertoletti Sephira Riva

Purely pairwise interactions of the core-softened type, i.e., featuring a soft repulsion followed by a hard-core interaction at shorter distance, give rise to nontrivial equilibrium structures entirely different from the standard close packing of spheres. In particular, in a suitable low-temperature region of their phase diagram, such interactions are well known to favor a transition from a fluid to a cluster crystal. The residual mutual interaction between individual clusters can lead to the formation of patterns of their reciprocal orientations. In this work, we investigate two examples of such models in two dimensions, at the density most appropriate to the dimer phase, whereby clusters consist of just two particles, studying them with optimization techniques and Monte Carlo simulations. We focus on the dimer crystal, and unveil a second phase transition at extremely low temperature. This transition leads from a triangular dimer lattice with randomly disordered dimer orientations at high temperature to a reduced-symmetry ground state with nematic orientational order and a slightly distorted structure characterized by a centered-rectangular lattice at low temperature.

Lattice (music)

Hexagonal Lattice

10.1103/physreve.104.044602

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Citations (6)

How Does Structural Disorder Impact Heterogeneous Catalysts? The Case of Ammonia Decomposition on Non-Stoichiometric Lithium Imide

Francesco Mambretti Umberto Raucci Manyi Yang Michele Parrinello

Among the many catalysts suggested for ammonia decomposition, Li2NH has been shown to be quite promising. In the recent past, we have performed extensive \textit{ab-initio}-quality simulations to explain the workings of this unusual catalyst. In the complex scenario that has emerged, surface dynamics and structural disorder enhanced by the interaction with the reacting ammonia molecules played a crucial role. Non-stoichiometric lithium imide Li(2-x)(NH2)x(NH)(1-x) has been reported to have better catalytic performances than pure lithium imide. Stimulated by these findings, we follow up our first study simulating the ammonia decomposition on such non-stoichiometric compound. We attribute the enhanced reactivity to the fact that the compositional disorder further enhances the fluctuations in the topmost layers of the catalyst, strengthening our dynamical picture of this catalytic process.

Stoichiometry

Imide

Reactivity

10.26434/chemrxiv-2023-79p32

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Citations (2)

Dynamical stochastic simulation of complex electrical behavior in neuromorphic networks of metallic nanojunctions

Scientific Reports (2022)

Francesco Mambretti Matteo Mirigliano E. Tentori Nicolò Pedrani Gianluca Martini

Nanostructured Au films fabricated by the assembling of nanoparticles produced in the gas phase have shown properties suitable for neuromorphic computing applications: they are characterized by a non-linear and non-local electrical behavior, featuring switches of the electric resistance whose activation is typically triggered by an applied voltage over a certain threshold. These systems can be considered as complex networks of metallic nanojunctions where thermal effects at the nanoscale cause the continuous rearrangement of regions with low and high electrical resistance. In order to gain a deeper understanding of the electrical properties of this nano granular system, we developed a model based on a large three dimensional regular resistor network with non-linear conduction mechanisms and stochastic updates of conductances. Remarkably, by increasing enough the number of nodes in the network, the features experimentally observed in the electrical conduction properties of nanostructured gold films are qualitatively reproduced in the dynamical behavior of the system. In the activated non-linear conduction regime, our model reproduces also the growing trend, as a function of the subsystem size, of quantities like Mutual and Integrated Information, which have been extracted from the experimental resistance series data via an information theoretic analysis. This indicates that nanostructured Au films (and our model) possess a certain degree of activated interconnection among different areas which, in principle, could be exploited for neuromorphic computing applications.

Neuromorphic engineering

Electrical network

10.1038/s41598-022-15996-9

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Citations (5)

Synthetic Eco-Evolutionary Dynamics in Simple Molecular Environment

Luca Casiraghi Francesco Mambretti Anna Tovo Elvezia Maria Paraboschi Samir Suweis

The understanding of eco-evolutionary dynamics, and in particular the mechanism of coexistence of species, is still fragmentary and in need of test bench model systems. To this aim we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 10 15 single-strand DNA oligonucleotide ‘individuals’. We begin with a seed of random sequences which we select via affinity capture from ∼ 10 12 DNA oligomers of fixed sequence (‘resources’) over which they compete. At each cycle (‘generation’), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences (‘species’) drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource binding dominates the selection in the first generations, while inter and intra-individual interactions become important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.

Evolutionary Dynamics

Dynamics

10.7554/elife.90156.2

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Citations (0)

How Does Structural Disorder Impact Heterogeneous Catalysts? The Case of Ammonia Decomposition on Non-stoichiometric Lithium Imide

ACS Catalysis (2024)

Francesco Mambretti Umberto Raucci Manyi Yang Michele Parrinello

Among the many catalysts suggested for ammonia decomposition, Li2NH has been shown to be quite promising. In the recent past, we have performed extensive ab initio-quality simulations to explain the workings of this unusual catalyst. In the complex scenario that has emerged, surface dynamics and structural disorder enhanced by the interaction with the reacting ammonia molecules have played crucial roles. Non-stoichiometric lithium imide (Li2–x(NH2)x(NH)1–x) has been reported to have better catalytic performances than pure lithium imide. Stimulated by these findings, we follow up our previous study simulating the ammonia decomposition on such non-stoichiometric compounds. We attribute the enhanced reactivity to the fact that the compositional disorder further enhances the fluctuations in the topmost layers of the catalyst, strengthening our dynamic picture of this catalytic process.

Imide

Stoichiometry

Reactivity

10.1021/acscatal.3c05376

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Citations (7)

Crystal Nucleation in Supercooled Atomic Liquids

Physical Review Letters (2024)

Johannes Möller Alexander Schottelius Michele Caresana Ulrike Boesenberg Chan Kim

The liquid-to-solid phase transition is a complex process that is difficult to investigate experimentally with sufficient spatial and temporal resolution. A key aspect of the transition is the formation of a critical seed of the crystalline phase in a supercooled liquid, that is, a liquid in a metastable state below the melting temperature. This stochastic process is commonly described within the framework of classical nucleation theory, but accurate tests of the theory in atomic and molecular liquids are challenging. Here, we employ femtosecond x-ray diffraction from microscopic liquid jets to study crystal nucleation in supercooled liquids of the rare gases argon and krypton. Our results provide stringent limits to the validity of classical nucleation theory in atomic liquids, and offer the long-sought possibility of testing nonclassical extensions of the theory.

Supercooling

Metastability

Classical nucleation theory

Crystal (programming language)

Krypton

10.1103/physrevlett.132.206102

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Citations (6)

Structural transition, orientational order, and anomalous specific heat in a two-dimensional dimer crystal of core-softened particles

Physical review. E (2024)

Davide Pini T. Rovelli Francesco Mambretti D. E. Galli

Systems featuring hard-core--soft-shell repulsive pair potentials can form ordered phases, where particles organize themselves in aggregates with nontrivial geometries. The dimer crystal formed by one such potential, namely, the hard-core plus generalized exponential model of order 4, has been recently investigated, revealing a low-temperature structural phase transition, with the onset of nematic ordering of the dimers. In the present work, we aim to characterize this phase transition via a mean-field theory, by which a detailed analysis of the low-temperature properties of the system is carried out under quadrupole approximation. We determine the transition temperature and identify its order parameter, highlighting the link between the structural transition and the nematic ordering of the system. The first-order character of the transition is established and supported by the Landau expansion of the free energy in powers of the order parameter. The theory is subsequently generalized to take into account lattice vibrations and dimer length fluctuations. Finally, we provide an explanation for the anomalous behavior displayed by the specific heat in the vanishing-temperature limit, which is also supported by Monte Carlo simulations.

Crystal (programming language)

Specific heat

10.1103/physreve.109.034128

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Citations (1)

Emergence of an Ising critical regime in the clustering of one-dimensional soft matter revealed through string variables

Physical review. E (2020)

Francesco Mambretti S. Molinelli Davide Pini Gianluca Bertaina D. E. Galli

Soft matter systems are renowned for being able to display complex emerging phenomena such as clustering phases. Recently, a surprising quantum phase transition has been revealed in a one-dimensional (1D) system composed of bosons interacting via a pairwise soft potential in the continuum. It was shown that the spatial coordinates undergoing two-particle clustering could be mapped into quantum spin variables of a 1D transverse Ising model. In this work we investigate the manifestation of an analogous critical phenomenon in 1D classical fluids of soft particles in the continuum. In particular, we study the low-temperature behavior of three different classical models of 1D soft matter, whose interparticle interactions allow for clustering. The same string variables highlight that, at the commensurate density for the two-particle cluster phase, the peculiar pairing of neighboring soft particles can be nontrivially mapped onto a 1D discrete classical Ising model. We also observe a related phenomenon, namely the presence of an anomalous peak in the low-temperature specific heat, thus indicating the emergence of Schottky phenomenology in a nonmagnetic fluid.

Soft matter

10.1103/physreve.102.042134

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Citations (6)