Metaplasticity and memory in multilevel recurrent feed-forward networks.

Network systems can exhibit memory effects in which the interactions between different pairs of nodes adapt in time, leading to the emergence of preferred connections, patterns, and subnetworks. To a first approximation, this memory can be modeled through a "plastic" Hebbian or homophily mechanism, in which edges get reinforced proportionally to the amount of information flowing through them. However, recent studies on glia-neuron networks have highlighted how memory can evolve due to more complex dynamics, including multilevel network structures and "metaplastic" effects that modulate reinforcement.

Conformation and topology of cyclical star polymers.

We study the conformation and topological properties of cyclical star polymers with f ring arms, each made of n beads. We find that the conformational properties of unlinked cyclical star polymers are compatible with those of linear star polymers with 2f arms made of n/2 beads each. This compatibility vanishes when the topology of the star, measured as the degree of linking between arms, changes.

Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.

The cowpea chlorotic mottle virus (CCMV) has emerged as a model system to assess the balance between electrostatic and topological features of single-stranded RNA viruses, specifically in the context of the viral self-assembly. Yet, despite its biophysical significance, little structural data on the RNA content of the CCMV virion is available. Here, the conformational dynamics of the RNA2 fragment of CCMV was assessed via coarse-grained molecular dynamics simulations, employing the oxRNA2 force field.

EXCOGITO, an Extensible Coarse-Graining Toolbox for the Investigation of Biomolecules by Means of Low-Resolution Representations.

Bottom-up coarse-grained (CG) models proved to be essential to complement and sometimes even replace all-atom representations of soft matter systems and biological macromolecules. The development of low-resolution models takes the moves from the reduction of the degrees of freedom employed, that is, the definition of a between a system's high-resolution description and its simplified counterpart. Even in the absence of an explicit parametrization and simulation of a CG model, the observation of the atomistic system in simpler terms can be informative: this idea is leveraged by the mapping entropy, a measure of the information loss inherent to the process of coarsening.

Quality assessment and community detection methods for anonymized mobility data in the Italian Covid context.

We discuss how to assess the reliability of partial, anonymized mobility data and compare two different methods to identify spatial communities based on movements: Greedy Modularity Clustering (GMC) and the novel Critical Variable Selection (CVS). These capture different aspects of mobility: direct population fluxes (GMC) and the probability for individuals to move between two nodes (CVS). As a test case, we consider movements of Italians before and during the SARS-Cov2 pandemic, using Facebook users' data and publicly available information from the Italian National Institute of Statistics (Istat) to construct daily mobility networks at the interprovincial level.

Thermal properties of knotted block copolymer rings with charged monomers subjected to short-range interactions.

The thermal properties of coarse-grained knotted copolymer rings fluctuating in a highly screening solution are investigated on a simple cubic lattice using the Wang-Landau Monte Carlo algorithm. The rings contain two kinds of monomers A and B with opposite charges that are subjected to short-range interactions. In view of possible applications in medicine and the construction of intelligent materials, it is shown that the behavior of copolymer rings can be tuned by changing both their monomer configuration and topology.

Scaling properties of RNA as a randomly branching polymer.

Formation of base pairs between the nucleotides of a ribonucleic acid (RNA) sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching-for instance, for its spatial compactness or interaction with other biological macromolecules-RNA branching topology remains largely unexplored. Here, we use the theory of randomly branching polymers to explore the scaling properties of RNAs by mapping their secondary structures onto planar tree graphs.

Dynamic and facilitated binding of topoisomerase accelerates topological relaxation.

How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expected of proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc.

Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators.

Recent theoretical studies have demonstrated that the behaviour of molecular knots is a sensitive indicator of polymer structure. Here, we use knots to verify the ability of two state-of-the-art algorithms-configuration assembly and hierarchical backmapping-to equilibrate high-molecular-weight (MW) polymer melts. Specifically, we consider melts with MWs equivalent to several tens of entanglement lengths and various chain flexibilities, generated with both strategies.

Protein design under competing conditions for the availability of amino acids.

Isolating the properties of proteins that allow them to convert sequence into the structure is a long-lasting biophysical problem. In particular, studies focused extensively on the effect of a reduced alphabet size on the folding properties. However, the natural alphabet is a compromise between versatility and optimisation of the available resources.

Identification of Protein Functional Regions.

Protein sequence stores the information relative to both functionality and stability, thus making it difficult to disentangle the two contributions. However, the identification of critical residues for function and stability has important implications for the mapping of the proteome interactions, as well as for many pharmaceutical applications, e. g.

Design of Protein-Protein Binding Sites Suggests a Rationale for Naturally Occurring Contact Areas.

Molecular recognition is a critical process for many biological functions and consists in noncovalent binding of different molecules, such as protein-protein, antigen-antibody, and many others. The host-guest molecules involved often show a shape complementarity, and one of the leading specifications for molecular recognition is that the interaction should ideally be specific, i.e.

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.

The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g.

Author Correction: The role of directional interactions in the designability of generalized heteropolymers.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Compactness of viral genomes: effect of disperse and localized random mutations.

Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation.

The role of directional interactions in the designability of generalized heteropolymers.

Heteropolymers are important examples of self-assembling systems. However, in the design of artificial heteropolymers the control over the single chain self-assembling properties does not reach that of the natural bio-polymers, and in particular proteins. Here, we introduce a sufficiency criterion to identify polymers that can be designed to adopt a predetermined structure and show that it is fulfilled by polymers made of monomers interacting through directional (anisotropic) interactions.

Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers.

Knots appear frequently in semiflexible (bio)polymers, including double-stranded DNA, and their presence can affect the polymer's physical and functional properties. In particular, it is possible and indeed often the case that multiple knots appear on a single chain, with effects which have only come under scrutiny in the last few years. In this manuscript, we study the interaction of two knots on a stretched semiflexible polymer, expanding some recent results on the topic.

Discretized knot motion on a tensioned fiber induced by transverse waves.

Topological entanglement is a ubiquitous feature of many biological as well as artificial polymers and fibers. While the equilibrium properties of entangled chains have been the subject of several studies, little is known about their out-of-equilibrium behavior. Here, we address the problem of a stretched knotted fiber driven by a periodic force applied to one of its termini.

Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses.

Recent studies have shown that single-stranded (ss) viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison, it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. To further explore the compactness selection hypothesis, we systematically compare the predicted sizes of >100 wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints.

Computational study on the progressive factorization of composite polymer knots into separated prime components.

Using Monte Carlo simulations and advanced knot localization methods, we analyze the length and distribution of prime components in composite knots tied on freely jointed rings. For increasing contour length, we observe the progressive factorization of composite knots into separated prime components. However, we observe that a complete factorization, equivalent to the "decorated ring" picture, is not obtained even for rings of contour lengths N ≃ 3 N(0), about tens of times the most probable length of the prime knots tied on the rings.

Driving knots on DNA with AC/DC electric fields: topological friction and memory effects.

The dynamical properties of entangled polyelectrolytes are investigated theoretically and computationally for a proposed novel micromanipulation setup. Specifically, we investigate the effects of DC and AC electric fields acting longitudinally on knotted DNA chains, modelled as semiflexible chains of charged beads, under mechanical tension. We consider various experimentally accessible values of the field amplitude and frequency as well as several of the simplest knot types.

Multiscale entanglement in ring polymers under spherical confinement.

The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated by using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length l(k) depends on the ring contour length L(c) and the radius of the confining sphere R(c). In the no- and strong-confinement cases, we observe weak knot localization and complete knot delocalization, respectively.

DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting.

Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids is both highly knotted and neatly structured. What is the physical basis of this organization? Here we show evidence from stochastic simulation techniques that suggests that a key element is the tendency of contacting DNA strands to order, as in cholesteric liquid crystals. This interaction favors their preferential juxtaposition at a small twist angle, thus promoting an approximately nematic (and apolar) local order.