Topography, Spike Dynamics, and Nanomechanics of Individual Native SARS-CoV-2 Virions

We establish a general linear response relation for spiking neuronal networks, based on chains with unbounded memory. This relation allow us to predict the influence of a weak amplitude time dependent external stimuli on spatio-temporal spike correlations, from the spontaneous statistics (without stimulus) in a general context where the memory in spike dynamics can extend arbitrarily far in the past. Using this approach, we show how the linear response is explicitly related to the collective effect of the stimuli, intrinsic neuronal dynamics, and network connectivity on spike train statistics. We illustrate our results with numerical simulations performed over a discrete time integrate and fire model.

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SARS-CoV-2 Spike Affinity and Dynamics Exclude the Strict Requirement of an Intermediate Host

10.1101/2021.08.11.455960 ◽

2021 ◽

Author(s):

Matteo Castelli ◽

Luigi Scietti ◽

Nicola Clementi ◽

Mattia Cavallaro ◽

Silvia Faravelli ◽

...

Keyword(s):

Intermediate Host ◽

Receptor Binding ◽

Animal Species ◽

Evolutionary Process ◽

Evolutionary Model ◽

Model Based ◽

Rhinolophus Affinis ◽

Strict Requirement ◽

Spike Dynamics

SARS-CoV-2 proximal origin is still unclear, limiting the possibility of foreseeing other spillover events with pandemic potential. Here we propose an evolutionary model based on the thorough dissection of SARS-CoV-2 and RaTG13 - the closest bat ancestor - spike dynamics, kinetics and binding to ACE2. Our results indicate that both spikes share nearly identical, high affinities for Rhinolophus affinis bat and human ACE2, pointing out to negligible species barriers directly related to receptor binding. Also, SARS-CoV-2 spike shows a higher degree of dynamics and kinetics optimization that favors ACE2 engagement. Therefore, we devise an affinity-independent evolutionary process that likely took place in R. affinis bats and limits the eventual involvement of other animal species in initiating the pandemic to the role of vector.

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Dopamine modulation of spike dynamics in bursting neurons

European Journal of Neuroscience ◽

10.1111/j.1460-9568.2005.03894.x ◽

2005 ◽

Vol 21 (3) ◽

pp. 763-772 ◽

Cited By ~ 24

Author(s):

Attila Szücs ◽

Henry D. I. Abarbanel ◽

Michail I. Rabinovich ◽

Allen I. Selverston

Keyword(s):

Bursting Neurons ◽

Spike Dynamics ◽

Dopamine Modulation

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Structures and function of locked conformations of SARS-CoV-2 spike

10.1101/2021.03.10.434733 ◽

2021 ◽

Author(s):

Kun Qu ◽

Xiaoli Xiong ◽

Katarzyna A. Ciazynska ◽

Andrew P. Carter ◽

John A. G. Briggs

Keyword(s):

Receptor Binding ◽

Functional Characterization ◽

Protein S ◽

Binding Domain ◽

Receptor Binding Domain ◽

Neutral Ph ◽

And Function ◽

Cellular Compartments ◽

Domain Dynamics ◽

Spike Dynamics

AbstractThe spike protein (S) of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the locked conformation was not previously observed for SARS-CoV-1 S and its function remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct “S-R/x3” to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures revealing two distinct locked states, with or without the D614G substitution that has become fixed in the globally circulating SARS-CoV-2 strains. The D614G mutation induces a structural change in domain D from locked-1 to locked-2 conformation to alter spike dynamics, promoting transition into the closed conformation from which opening of the receptor binding domain is permitted. The transition from locked to closed conformations is additionally promoted by a change from low to neutral pH. We propose that the locked conformations of S are present in the acidic cellular compartments where virus is assembled and egresses. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed form which itself can stochastically transition into the open form. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.

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Spike Dynamics in the Presence of Noise

SIAM Journal on Applied Dynamical Systems ◽

10.1137/20m1312319 ◽

2020 ◽

Vol 19 (4) ◽

pp. 2783-2802

Author(s):

Chunyi Gai ◽

David Iron ◽

Theodore Kolokolnikov ◽

John Rumsey

Keyword(s):

Spike Dynamics

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Spatio-temporal spike dynamics predict surgical outcome in adult focal epilepsy

Clinical Neurophysiology ◽

10.1016/j.clinph.2021.10.023 ◽

2021 ◽

Author(s):

Petr Klimes ◽

Laure Peter-Derex ◽

Jeff Hall ◽

François Dubeau ◽

Birgit Frauscher

Keyword(s):

Surgical Outcome ◽

Focal Epilepsy ◽

Spatio Temporal ◽

Spike Dynamics

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Управляемая нейроморфная динамика систем фазовой синхронизации

Письма в журнал технической физики ◽

10.21883/pjtf.2021.21.51629.18891 ◽

2021 ◽

Vol 47 (21) ◽

pp. 43

Author(s):

Л.А. Цырульникова ◽

А.Р. Сафин

Keyword(s):

Phase Modulation ◽

Phase Locked Loop ◽

Frequency Stability ◽

Gain Factor ◽

Phase Locked Loops ◽

Reference Oscillator ◽

Common Control ◽

Three Phase ◽

Single Spike ◽

Spike Dynamics

We consider the neuromorphic dynamics of a filter-free phase locked loop with a phase modulation of a reference oscillator. The transition from pulsed single-spike dynamics to the bursting dynamics can be easily controlled by changing the depth and frequency of phase modulation, as well as the gain factor along the ring of the phase locked loop. The possibility of implementing neuromorphic calculations of the "OR" type in the scheme of three phase locked loops mutually coupled through a common control circuit is shown. The presented results can be used in the design of hardware-implemented neuromorphic networks with increased frequency stability, resistant to noise influences.

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