How Local Interactions Impact the Dynamics of an Epidemic.
Ontology highlight
ABSTRACT:
SUBMITTER: Wren L
PROVIDER: S-EPMC8589636 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis.
| S-EPMC4060508 | biostudies-other
Project description:The dynamics of probe molecules is commonly used to investigate the structural dynamics of room-temperature ionic liquids; however, the extent to which this dynamics reflects the dynamics of the ionic liquids or is probe specific has remained debated. Here, we explore to what extent the vibrational and rotational dynamics of the dicyanamide anion, a common ionic liquid anion, correlates with the structural relaxation of ionic liquids. We use polarization-resolved, ultrafast infrared spectroscopy to probe the temperature- and probe-concentration-dependent dynamics of samples with small amounts of 1-ethyl-3-methylimidazolium ([emim]+) dicyanamide ([DCA]-) dissolved in four [emim]+-based ionic liquids with tetrafluoroborate ([BF4]-), bis(trifluoromethylsulfonyl)imide ([NTf2]-), ethylsufate ([EtSO4]-), and triflate ([OTf]-) as anions. The transient spectra after broad-band excitation at 2000-2300 cm-1, resonant with the symmetric and antisymmetric C≡N stretching vibrations, initially contain oscillatory signatures due to the vibrational coherence between both modes. Vibrational population relaxation occurs on two distinct time scales, ∼6-7 and ∼15-20 ps. The vibrational dynamics is rather insensitive to the details of the ionic liquid anion and temperature, except for the slow vibrational relaxation component. The decay of the excitation anisotropy, a measure of the rotational dynamics of [DCA]-, markedly depends on temperature, and the obtained decay time exhibits an activation energy of ∼15-21 kJ/mol. Remarkably, neither the rotation time nor the activation energy can be simply explained by the variation of the macroscopic viscosity. Hence, our results suggest that the dynamics of dicyanamide is only in part representative of the ionic liquid structural dynamics. Rather, the dynamics of the probe anion seems to be determined by the specific interaction of [DCA]- with the ionic liquid's ions for the class of [emim]+-based ionic liquids studied here.
| S-EPMC6398149 | biostudies-literature
Project description:The COVID-19 epidemic was reported in the Hubei province in China in December 2019 and then spread around the world reaching the pandemic stage at the beginning of March 2020. Since then, several countries went into lockdown. Using a mechanistic-statistical formalism, we estimate the effect of the lockdown in France on the contact rate and the effective reproduction number R e of the COVID-19. We obtain a reduction by a factor 7 (R e = 0.47, 95%-CI: 0.45-0.50), compared to the estimates carried out in France at the early stage of the epidemic. We also estimate the fraction of the population that would be infected by the beginning of May, at the official date at which the lockdown should be relaxed. We find a fraction of 3.7% (95%-CI: 3.0-4.8%) of the total French population, without taking into account the number of recovered individuals before April 1st, which is not known. This proportion is seemingly too low to reach herd immunity. Thus, even if the lockdown strongly mitigated the first epidemic wave, keeping a low value of R e is crucial to avoid an uncontrolled second wave (initiated with much more infectious cases than the first wave) and to hence avoid the saturation of hospital facilities.
| S-EPMC7290065 | biostudies-literature
Project description:In animal groups, individual decisions are best characterized by probabilistic rules. Furthermore, animals of many species live in small groups. Probabilistic interactions among small numbers of individuals lead to a so-called intrinsic noise at the group level. Theory predicts that the strength of intrinsic noise is not a constant but often depends on the collective state of the group; hence, it is also called a state-dependent noise or a multiplicative noise. Surprisingly, such noise may produce collective order. However, only a few empirical studies on collective behaviour have paid attention to such effects owing to the lack of methods that enable us to connect data with theory. Here, we demonstrate a method to characterize the role of stochasticity directly from high-resolution time-series data of collective dynamics. We do this by employing two well-studied individual-based toy models of collective behaviour. We argue that the group-level noise may encode important information about the underlying processes at the individual scale. In summary, we describe a method that enables us to establish connections between empirical data of animal (or cellular) collectives and the phenomenon of noise-induced states, a field that is otherwise largely limited to the theoretical literature. This article is part of the theme issue 'Multi-scale analysis and modelling of collective migration in biological systems'.
| S-EPMC7423372 | biostudies-literature
Project description:The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the 'contact number diffusion' model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics.
| S-EPMC3953337 | biostudies-literature
Project description:The impact of variable infection risk by race and ethnicity on the dynamics of SARS-CoV-2 spread is largely unknown. Here, we fit structured compartmental models to seroprevalence data from New York State and analyze how herd immunity thresholds (HITs), final sizes, and epidemic risk change across groups. A simple model where interactions occur proportionally to contact rates reduced the HIT, but more realistic models of preferential mixing within groups increased the threshold toward the value observed in homogeneous populations. Across all models, the burden of infection fell disproportionately on minority populations: in a model fit to Long Island serosurvey and census data, 81% of Hispanics or Latinos were infected when the HIT was reached compared to 34% of non-Hispanic whites. Our findings, which are meant to be illustrative and not best estimates, demonstrate how racial and ethnic disparities can impact epidemic trajectories and result in unequal distributions of SARS-CoV-2 infection. K.C.M. was supported by National Science Foundation GRFP grant DGE1745303. Y.H.G. and M.L. were funded by the Morris-Singer Foundation. M.L. was supported by SeroNet cooperative agreement U01 CA261277.
| S-EPMC8221808 | biostudies-literature
Project description:As infectious disease outbreaks emerge, public health agencies often enact vaccination and social distancing measures to slow transmission. Their success depends on not only strategies and resources, but also public adherence. Individual willingness to take precautions may be influenced by global factors, such as news media, or local factors, such as infected family members or friends. Here, we compare three modes of epidemiological decision-making in the midst of a growing outbreak using network-based mathematical models that capture plausible heterogeneity in human contact patterns. Individuals decide whether to adopt a recommended intervention based on overall disease prevalence, the proportion of social contacts infected, or the number of social contacts infected. While all strategies can substantially mitigate transmission, vaccinating (or self isolating) based on the number of infected acquaintances is expected to prevent the most infections while requiring the fewest intervention resources. Unlike the other strategies, it has a substantial herd effect, providing indirect protection to a large fraction of the population.
| S-EPMC6890219 | biostudies-literature
Project description:We exploited the high temporal and spatial resolution of neutron spin echo spectroscopy to investigate the large-scale dynamics of semiflexible conjugated polymer chains in solutions. We used a generalized approach of the well-established Zimm model of flexible polymers to describe the relaxation mode spectra of locally stiff polythiophene chains. The Zimm mode analysis confirms the existence of beads with a finite length that corresponds to a reduced number of segmental modes in semiflexible chains. Irrespective of the temperature and the molecular weight of the conjugated polymer, we witness a universal behavior of the local chain stiffness and invariability of the bead length. Our experimental findings indicate possibly minor role of the change in ?-electron conjugation length (and therefore conjugated backbone planar to non-planar conformational transition) in the observed thermochromic behavior of polythiophene but instead point on the major role of chain dynamics in this phenomenon. We also obtained the first experimental evidence of an existence of a single-chain glass state in conjugated polymers.
| S-EPMC7305133 | biostudies-literature
Project description:In the intracellular environment, motor-driven cargo must navigate a dense cytoskeletal network among abundant organelles.We investigated the effects of the crowded intracellular environment on early endosomal trafficking. Live-cell imaging of an endosomal cargo (endocytosed epidermal growth factor-conjugated quantum dots) combined with high-resolution tracking was used to analyze the heterogeneous motion of individual endosomes. The motile population of endosomes moved toward the perinuclear region in directed bursts of microtubule-based, dynein-dependent transport interrupted by longer periods of diffusive motion. Actin network density did not affect motile endosomes during directed runs or diffusive interruptions. Simultaneous two-color imaging was used to correlate changes in endosomal movement with potential obstacles to directed runs. Termination of directed runs spatially correlated with microtubule-dense regions, encounters with other endosomes, and interactions with the endoplasmic reticulum. During a subset of run terminations, we also observed merging and splitting of endosomes, deformation of the endoplasmic reticulum, and directional reversals at speeds up to 10-fold greater than characteristic in vitro motor velocities. These observations suggest that endosomal membrane tension is high during directed run termination.Our results indicate that the crowded cellular environment significantly impacts the motor-driven motility of organelles. Rather than simply acting as impediments to movement, interactions of trafficking cargos with intracellular obstacles may facilitate communication between membrane-bound compartments or contribute to the generation of membrane tension necessary for fusion and fission of endosomal membranes or remodeling of the endoplasmic reticulum.
| S-EPMC3738301 | biostudies-literature
Project description:We present a comprehensive micro- and macrorheological study of the effect of weak depletion attraction (Ψdep ≈ 1-10 kBT) on dense colloidal suspensions stabilized by short-range repulsive interactions. We used aqueous polymer dispersions as model system and demonstrated the unique capabilities of multiple particle tracking (MPT) to disclose structural changes in such technically important systems exhibiting many characteristic features of hard sphere systems. Below the hard sphere freezing point ϕc, viscosity increases monotonically with increasing Ψdep due to the transition from a fluid to a fluid/crystalline and finally to a gel state. Above ϕc, increasing attraction strength first results in a viscosity reduction corresponding to the formation of large, permeable crystals and then in a viscosity increase when a network of dense, small crystals forms. The fraction of the fluid and crystal phase, particle concentration in each phase as well as the modulus of the micro-crystals are obtained, the latter decreases with Ψdep. Above the colloidal glass transition strong heterogeneities and different local particle mobility in the repulsive and attractive arrested states are found. Particles are trapped in the cage of neighboring particles rather than in an attractive potential well. The intermediate ergodic state exhibits uniform tracer diffusivity.
| S-EPMC5031965 | biostudies-literature