# evol: emergence of single vs. multi-state allostery

      FIG. 1. The elastic network model

<< Allostery, the change of activity of a  macromolecule in response to a perturbation at a distance from its active site, is thought to be a ubiquitous feature of proteins. Initially described in the context of multimeric proteins, it is now understood to underlie the regulation of proteins with diverse structural architectures, from receptors to signaling proteins and metabolic enzymes. >>️

<< Here, (AA) analyze a simplified model of protein allostery under a range of physical and evolutionary constraints. (They) find that a continuum of mechanisms between two archetypes emerges through evolution. In one limit, a single-state mechanism exists where ligand binding induces a displacement along a single normal mode, and in the other limit, a multi-state mechanism exists where ligand binding induces a switch across an energy barrier to a different stable state. Importantly, whenever the two mechanisms are possible, the multi-state mechanism confers a stronger allosteric effect and thus a selective advantage. >>

️

Eric Rouviere, Rama Ranganathan, Olivier Rivoire. Emergence of Single- versus Multi-State Allostery. PRX Life 1, 023004. Nov 9, 2023.

https://journals.aps.org/prxlife/abstract/10.1103/PRXLife.1.023004

Also: allostery in FonT https://flashontrack.blogspot.com/search?q=allostery

Also: allosterico in Notes 

(quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=allosterico

Keywords: gst, allostery, elastic, evolution

# brain: the hypothesis of the genetic link between present moment attention and subjective wellbeing.

<< Considerable evidence supports the role of present-moment attention, a central feature of mindfulness, in subjective wellbeing maintenance and enhancement. >>️

<< Consistent with the “generalist genes hypothesis” and prior evidence, (AA) hypothesized that presence and subjective wellbeing would show a substantial genetic correlation and smaller environmental correlation. >>️

<< This study provides the first evidence known to us showing that present-centered attention, a primary component of mindfulness, has both genetic and environmental overlap with subjective wellbeing. >>️

Kirk Warren Brown, Fazil Aliev, et al. A multivariate twin study of the genetic association between present moment attention and subjective wellbeing. Sci Rep 13, 17456 (2023). doi: 10.1038/ s41598-023-42810-x.

https://www.nature.com/articles/s41598-023-42810-x 

Also: brain, Zen, in https://www.inkgmr.net/kwrds.html 

Keywords: present moment attention, mindfulness, subjective wellbeing, generalist genes hypothesis. 

# astro: black hole portraits will become more frequent

<< This year marks the fifth anniversary of the release of the first-ever image of a black hole, which revealed the glowing doughnut of the supermassive black hole called M87*. The research team that produced the image—the Event Horizon Telescope (EHT) Collaboration—recently released a second image of that same black hole, which lies 55 million light years from Earth (..). This image comes from an updated version of the EHT and confirms key features of the black hole while also revealing changes over time in the pattern of light emanating from the disk surrounding the object. Starting with this release, the collaboration expects to issue increasingly frequent updates in support of the newly developing field of black hole imaging. >>️

<< “Producing the first image of M87* was a herculean effort and involved creating, testing, and verifying many different schemes and approaches to analyzing and interpreting the data,” says Princeton University astrophysicist Andrew Chael, a member of the EHT Collaboration. “Now we are beginning to transition to a point where we understand our instrument and our analysis frameworks really well, so I think we are going to be releasing results a lot more quickly.” >>

️

Katherine Wright. Black Hole Portraits Will Become More Frequent. Physics 17, 43. Mar 15, 2024. 

https://physics.aps.org/articles/v17/43

Kazunori Akiyama, Antxon Alberdi, et al. The persistent shadow of the supermassive black hole of M 87. 

I. Observations, calibration, imaging, and analysis⋆ The Event Horizon Telescope Collaboration. Astron. Astrophys. 681, A79 (2024).

https://www.aanda.org/articles/aa/full_html/2024/01/aa47932-23/aa47932-23.html

Also: astrophysics, black hole, in https://www.inkgmr.net/kwrds.html 

Keywords: astrophysics, black hole

# gst: rearrangements of a jammed 2-D emulsion (during slow compression).

<< As amorphous materials get jammed, both geometric and dynamic heterogeneity are observed. (AA)  investigate the correlation between the local geometric heterogeneity and local rearrangements in a slowly compressed bidisperse quasi-two-dimensional emulsion system. The compression is driven by evaporation of the continuous phase. >>

<< droplets in heterogeneous local regions are more likely to have local rearrangements. These rearrangements are generally T1 events where two droplets converge toward a void, and two droplets move away from the void to make room for the converging droplets. Thus, the presence of the voids tends to orient the T1 events. >>️

<< The presence of a correlation between the structural quantities and the rearrangement dynamics remains qualitatively unchanged over the entire range of packing fractions observed. >>️

Xin Du, Eric R. Weeks. Rearrangements during slow compression of a jammed  two-dimensional emulsion. Phys. Rev. E 109, 034605. Mar 20,  2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.034605

Also: drop, in https://www.inkgmr.net/kwrds.html 

Keywords: drops, droplets, droploids 

# brain: apropos of wars ... VR plus tDCS to reduce symptoms of posttraumatic stress disorder (PTSD) (in military veterans).

<< Key Points. Question. Can therapeutic exposure using virtual reality (VR) be augmented with simultaneously applied transcranial direct current stimulation (tDCS) to reduce symptoms of posttraumatic stress disorder (PTSD)? >>

<< Meaning. These findings suggest that the use of combined VR exposure plus tDCS could be a promising treatment for warzone-related PTSD. >>️️

Mascha van’t Wout-Frank, Amanda R. Arulpragasam, et al. Virtual Reality and Transcranial Direct Current Stimulation for Posttraumatic Stress Disorder. A Randomized Clinical Trial. JAMA Psychiatry. doi: 10.1001/jamapsychiatry.2023.5661. Mar 6, 2024.

https://jamanetwork.com/journals/jamapsychiatry/fullarticle/2815835

Also: brain, in https://www.inkgmr.net/kwrds.html 

Keywords: life, war, brain, VR, tDCS, PTSD, veterans

# gst: near the Hopf boundary, Intermittency and chimera states.

AA << study collective dynamics of networks of mutually coupled identical Lorenz oscillators near a subcritical Hopf bifurcation. Such systems exhibit induced multistable behavior with interesting spatiotemporal dynamics including synchronization, desynchronization, and chimera states. >>️

<< For analysis, (AA) first consider a ring topology with nearest-neighbor coupling and find that the system may exhibit intermittent behavior due to the complex basin structures and dynamical frustration, where temporal dynamics of the oscillators in the ensemble switches between different attractors. Consequently, different oscillators may show a dynamics that is intermittently synchronized (or desynchronized), giving rise to intermittent chimera states. The behavior of the intermittent laminar phases is characterized by the characteristic time spent in the synchronization manifold, which decays as a power law. >>

<< Such intermittent dynamics is quite general and is also observed in an ensemble of a large number of oscillators arranged in variety of network topologies including nonlocal, scale-free, random, and small-world networks. >>️

Anjuman Ara Khatun, Yusra Ahmed Muthanna, et al. Collective dynamics of coupled Lorenz oscillators near the Hopf boundary: Intermittency and chimera states. Phys. Rev. E 109, 034208. March 15, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.034208

Also: transition, intermittency, chaos, chimera, network, in https://www.inkgmr.net/kwrds.html

Keywords: gst, transition, intermittency, chaos, chimera, network

# gst: apropos of random walks, intermittent random walks under stochastic resetting

AA << analyze a one-dimensional intermittent random walk on an unbounded domain in the presence of stochastic resetting. In this process, the walker alternates between local intensive search, diffusion, and rapid ballistic relocations in which it does not react to the target. >>

AA << demonstrate that Poissonian resetting leads to the existence of a non-equilibrium steady state. (They) calculate the distribution of the first arrival time to a target along with its mean and show the existence of an optimal reset rate. In particular, (..) the initial condition of the walker, i.e., either starting diffusely or relocating, can significantly affect the long-time properties of the search process. >>

<< the presence of distinct parameter regimes for the global optimization of the mean first arrival time when ballistic and diffusive movements are in direct competition. >>️

Rosa Flaquer-Galmes, Daniel Campos,  Vicenc Mendez. Intermittent random walks under stochastic resetting. Phys. Rev. E 109, 034103. March 4, 2024. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.034103  

Also: walk, walking, random, in https://www.inkgmr.net/kwrds.html

Keywords: gst, walk, intermittent random walk, stochasticity, stochastic resetting

# gst: multi-component droplets may exhibit self-lubricating effects

<< Over the past decade, there has been a growing interest in the study of multicomponent drops. These drops exhibit unique phenomena, as the interplay between hydrodynamics and the evolving physicochemical properties of the mixture gives rise to distinct and often unregulated behaviors. >>

<< Of particular interest is the complex dynamic behavior of the drop contact line, which can display self-lubrication effect. The presence of a slipping contact line in self-lubricating multicomponent drops can suppress the coffee-stain effect, conferring valuable technological applications. >>

Huanshu Tan, Detlef Lohse, Xuehua Zhang. Self-Lubricating Drops. arXiv: 2403.01207v1 [physics.flu-dyn]. Mar 2, 2024

https://arxiv.org/abs/2403.01207

Also: drop droplet droploid, in https://www.inkgmr.net/kwrds.html

Keywords: drop, droplet, droploid, multicomponent drops, drop contact line, self-lubrication

# brain: apropos of mandering minds, the 'default mode' network.

<< When your mind is wandering, your brain’s “default mode” network is active. Its discovery 20 years ago inspired a raft of research into networks of brain regions and how they interact with each other. >>

<< The default mode was one of the first brain networks characterized by science. It consists of a handful of brain regions, including a few at the front of the brain, like the dorsal and ventral medial prefrontal cortices, and others scattered throughout the organ, like the posterior cingulate cortex, the precuneus and the angular gyrus. These regions are associated with memory, experience replay, prediction, action consideration, reward/ punishment and information integration. >> ️

<< The default mode is clearly up to something complicated; it’s involved in many different processes that can’t be neatly described. >>

<< “It’s kind of silly to think that we’re ever going to be like, ‘This one brain region or one brain network does one thing,’” (..). “I don’t think that’s how it works.” (..) “Network interactions are more elucidating to study in some ways than just a network in isolation because they do work together and then come apart and then change what they’re doing over time”. >> Lucina Uddin.️

Lucina Uddin << is particularly interested in how the default mode network interacts with the ️salience network, which seems to help us identify the most relevant piece of information at any given time. Her work suggests that the salience network detects when something is important to pay attention to and then acts as an off switch for the default mode network. >>

Vinod Menon << has developed what he calls️ ️the triple network theory. It posits that abnormal interactions between the default mode network, the salience network and a third one called the frontoparietal network could contribute to mental health disorders. >>️

Nora Bradford. What Your Brain Is Doing When You’re Not Doing Anything.  quantamagazine.org. Feb 5, 2024. 

https://www.quantamagazine.org/what-your-brain-is-doing-when-youre-not-doing-anything-20240205/

FonT: the cat when it is in a contemplative state ... Who knows in what forms and with what results an artificial intelligence (AI) will be able to structure itself in networks of this type.

Also: brain, brain default mode network, in  https://pubmed.ncbi.nlm.nih.gov/?term=brain+default+mode+network

Also: brain, salience network, in https://pubmed.ncbi.nlm.nih.gov/?term=brain+salience+network

Also: brain, triple network theory, in https://pubmed.ncbi.nlm.nih.gov/?term=brain+triple+network+theory

Also: brain, ai (artificial intell), analogy,  in https://www.inkgmr.net/kwrds.html

Keywords: brain, mind, default mode network, salience network, triple network theory, AI

# gst: self-trapped nonlinear waves with multiple phase singularities.

AA << investigate the existence of self-trapped nonlinear waves with multiple phase singularities. >>️

They << focus on configurations with an antivortex surrounded by a triangular arrangement of vortices within a hosting soliton. (AA) find stationary patterns that can be interpreted as stable self-trapped vortex crystals, constituting the first example of a configuration of this sort with space-independent potentials. Their stability is linked to their norm, transitioning from unstable to stable as their size increases, with an intermediate region where the structure is marginally unstable, undergoing a remarkable and puzzling self-reconstruction during its evolution. >>️

Angel Paredes and Humberto Michinel. Self-trapping of vortex crystals via competing nonlinearities.  Phys. Rev. E 109, 024216. Feb 22, 2024. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.024216

Also: waves, soliton, vortex, in https://www.inkgmr.net/kwrds.html

Keywords: gst, waves, soliton, self-trapping, vortex 

# life: apropos of 1or2achoos (from Wuhan (?)) ; CD8+ T cell and early mucosal IgA responses seem strongly associated with viral (SARS-CoV-2) control.

<< the earliest stages of SARS-CoV-2 infection remain poorly characterized. Wagstaffe et al. conducted a human SARS-CoV-2 infection challenge study, enabling analysis of the innate and adaptive immune responses during the early postexposure period. (..) Modeling of the immune response identified CD8+ T cell and early mucosal IgA responses as strongly associated with viral control, >> Claire Olingy.  ️

Helen R. Wagstaffe, Ryan S. Thwaites, et al. Mucosal and systemic immune correlates of viral control after SARS-CoV-2 infection challenge in seronegative adults. Sci Immunol. Vol 9, Issue 92. doi: 10.1126/ sciimmunol.adj9285. Feb 9, 2024. 

https://www.science.org/doi/10.1126/sciimmunol.adj9285   

Also: aproposito di '1or2achoos' (da Wuhan (?)). FonT.  jul 13, 2022. 

https://flashontrack.blogspot.com/2022/07/life-aproposito-di-1or2achoos-da-wuhan.html 

Also: sars, covid, 1or2achoos, virus, in  https://www.inkgmr.net/kwrds.html

Keywords:  sars, covid, 1or2achoos, virus, mucosa, early viral control 

# life: Hollywood movies revisited, you'll have to be very careful, a cycle of panic and neglect (e.g. about an 'Entity X') is beginning to repeat.

<< Your Highnesses, Your Excellencies,

Dear colleagues and friends, (..).

I thank Your Highnesses for your hospitality, for your steadfast support for the World Health Organization and global health, and for the opportunity to address you today.  >>️

<< On the 12th of February 2018 – exactly six years ago – I stood on this stage and said the world was not prepared for a pandemic, and expressed my concern at that time that a pandemic could happen anytime. >>️

<< As you remember, less than two years later, in December 2019, the COVID-19 pandemic struck, and indeed, the world was not prepared. >>️

<< Today I stand before you, in the aftermath of COVID-19,

With millions of people dead,

With social, economic and political shocks that reverberate to this day, >>️

<< The cycle of panic and neglect is beginning to repeat. >>️

<< It may be caused by an influenza virus, or a new coronavirus, or it may be caused by a new pathogen we don’t even know about yet – what we call Disease X. >>️

WHO Director-General's speech at the World Governments Summit – 12 Feb 2024.️ WHO. 

https://www.who.int/director-general/speeches/detail/who-director-general-s-speech-at-the-world-governments-summit---12-february-2024   

Also: sars, covid, 1or2achoos, virus, in https://www.inkgmr.net/kwrds.html

Keywords: sars, covid, 1or2achoos, virus, disease X

# behav: ADHD may have been a feature of nomadic exploration among hunter-gatherer societies

<< All mobile organisms forage for resources, choosing how and when to search for new opportunities by comparing current returns with the average for the environment. In humans, nomadic lifestyles favouring exploration have been associated with genetic mutations implicated in attention deficit hyperactivity disorder (ADHD), inviting the hypothesis that this condition may impact foraging decisions in the general population. >>️

David L. Barack, Vera U. Ludwig, et al. 

Attention deficits linked with proclivity to explore while foraging. Proc Royal Society B.  doi: 10.1098/ rspb.2022.2584. Feb 21, 2024. 

https://doi.org/10.1098/rspb.2022.2584     

<< Is it a legacy of the hunter-gatherer world? >> Arjun Ramakrishnan

Chen Ly. ADHD may have evolved to help foragers know when to cut their losses. newscientist.com Feb 21,2024.

https://www.newscientist.com/article/2418114-adhd-may-have-evolved-to-help-foragers-know-when-to-cut-their-losses

Also: nomads, bushmen, behav, uncertainty, curiosity, in https://www.inkgmr.net/kwrds.html

Keywords: adhd, nomads, hunter-gatherers, behavior, behaviour