Nonequilibrium Time Reversibility with Maps and Walks

Time-reversible dynamical simulations of nonequilibrium systems exemplify both Loschmidt’s and Zermélo’s paradoxes. That is, computational time-reversible simulations invariably produce solutions consistent with the irreversible Second Law of Thermodynamics (Loschmidt’s) as well as periodic in the time (Zermélo’s, illustrating Poincaré recurrence). Understanding these paradoxical aspects of time-reversible systems is enhanced here by studying the simplest pair of such model systems. The first is time-reversible, but nevertheless dissipative and periodic, the piecewise-linear compressible Baker Map. The fractal properties of that two-dimensional map are mirrored by an even simpler example, the one-dimensional random walk, confined to the unit interval. As a further puzzle the two models yield ambiguities in determining the fractals’ information dimensions. These puzzles, including the classical paradoxes, are reviewed and explored here.

Emulation of baryonic effects on the matter power spectrum and constraints from galaxy cluster data

Baryonic feedback effects consist of a major systematic for upcoming weak-lensing and galaxy-clustering surveys. In this paper, we present an emulator for the baryonic suppression of the matter power spectrum. The emulator is based on the baryonification model, containing seven free parameters that are connected to the gas profiles and stellar abundances in haloes. We show that with the baryonic emulator, we can not only recover the power spectra of hydro-dynamical simulations at sub-percent precision, but also establish a connection between the baryonic suppression of the power spectrum and the gas and stellar fractions in haloes. This connection allows us to predict the expected deviation from a dark-matter-only power spectrum using measured X-ray gas fractions of galaxy groups and clusters. With these measurements, we constrain the suppression to exceed the percent-level at k=0.1-0.4 h/Mpc and to reach a maximum of 20-28 percent at around k∼ 7 h/Mpc (68 percent confidence level). As a further step, we also perform a detailed parameter study and we present a minimum set of four baryonic parameters that are required to recover the scale and redshift dependence observed in hydro-dynamical simulations. The baryonic emulator can be found at https://github.com/sambit-giri/BCemu.

Chromatin network retards nucleoli coalescence

Nuclear bodies are membraneless condensates that may form via liquid-liquid phase separation. The viscoelastic chromatin network could impact their stability and may hold the key for understanding experimental observations that defy predictions of classical theories. However, quantitative studies on the role of the chromatin network in phase separation have remained challenging. Using a diploid human genome model parameterized with chromosome conformation capture (Hi-C) data, we study the thermodynamics and kinetics of nucleoli formation. Dynamical simulations predict the formation of multiple droplets for nucleolar particles that experience specific interactions with nucleolus-associated domains (NADs). Coarsening dynamics, surface tension, and coalescence kinetics of the simulated droplets are all in quantitative agreement with experimental measurements for nucleoli. Free energy calculations further support that a two-droplet state, often observed for nucleoli in somatic cells, is metastable and separated from the single-droplet state with an entropic barrier. Our study suggests that nucleoli-chromatin interactions facilitate droplets’ nucleation but hinder their coarsening due to the coupled motion between droplets and the chromatin network: as droplets coalesce, the chromatin network becomes increasingly constrained. Therefore, the chromatin network supports a nucleation and arrest mechanism to stabilize the multi-droplet state for nucleoli and possibly for other nuclear bodies.

Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis

We demonstrate the application of the transition manifold framework to the late-stage fibrillation process of the NFGAILS peptide, a amyloidogenic fragment of the human islet amyloid polypeptide (hIAPP). This framework formulates machine learning methods for the analysis of multi-scale stochastic systems from short, massively parallel molecular dynamical simulations. We identify key intermediate states and dominant pathways of the process. Furthermore, we identify the optimally timescale-preserving reaction coordinate for the dock-lock process to a fixed pre-formed fibril and show that it exhibits strong correlation with the mean native hydrogen-bond distance. These results pave the way for a comprehensive model reduction and multi-scale analysis of amyloid fibrillation processes. Graphic Abstract

Comet fragmentation as a source of the zodiacal cloud

<p>Models of the thermal emission of the zodiacal cloud and sporadic meteoroids suggest that the dominant source of interplanetary dust is Jupiter-family comets (JFCs). However, comet sublimation is insufficient to sustain the quantity of dust presently in the inner solar system. It has therefore been suggested that spontaneous disruptions of JFCs may supply the zodiacal cloud.</p> <p>We present a model for the dust produced in comet fragmentations and its evolution, comparing with the present day zodiacal cloud. Using results from dynamical simulations we follow individual JFCs as they evolve and undergo recurrent splitting events. The dust produced by these events is followed with a kinetic model which takes into account the effects of collisional evolution, Poynting-Robertson drag, and radiation pressure. This allows us to model both the size distribution and radial profile of dust resulting from comet fragmentation. Our model suggests that JFC fragmentations can produce enough dust to sustain the zodiacal cloud. We also discuss the feasibility of comet fragmentation producing the spatial and size distribution of dust seen in the zodiacal cloud.</p> <p>By modelling individual comets we are also able to explore the variability of cometary input to the zodiacal cloud. Comets are drawn from a size distribution based on the Kuiper belt and fragment randomly. We show that large comets should be scattered into the inner solar system stochastically, leading to large variations in the historical brightness of the zodiacal light.</p>

Exploiting the transit timing capabilities of Ariel

The Transit Timing Variation (TTV) technique is a powerful dynamical tool to measure exoplanetary masses by analysing transit light curves. We assessed the transit timing performances of the Ariel Fine Guidance Sensors (FGS1/2) based on the simulated light curve of a bright, 55 Cnc, and faint, K2-24, planet-hosting star. We estimated through a Markov-Chain Monte-Carlo analysis the transit time uncertainty at the nominal cadence of 1 second and, as a comparison, at a 30 and 60-s cadence. We found that at the nominal cadence Ariel will be able to measure the transit time with a precision of about 12s and 34s, for a star as bright as 55 Cnc and K2-24, respectively. We then ran dynamical simulations, also including the Ariel timing errors, and we found an improvement on the measurement of planetary masses of about 20-30% in a K2-24-like planetary system through TTVs. We also simulated the conditions that allow us to detect the TTV signal induced by an hypothetical external perturber within the mass range between Earth and Neptune using 10 transit light curves by Ariel.

A search for a fifth planet around HR 8799 using the star-hopping RDI technique at VLT/SPHERE

Context. Direct imaging of extrasolar giant planets demands the highest possible contrasts (ΔH ≳ 10 mag) at the smallest angular separations (∼0.1″) from the star. We present an adaptive optics observing method, called star-hopping, recently offered as standard queue observing (service mode) for the SPHERE instrument at the VLT. The method uses reference difference imaging (RDI) but, unlike earlier RDI applications, images of a reference star for PSF subtraction are obtained within minutes of observing the target star. Aims. We aim to significantly gain in contrast beyond the conventional angular differencing imaging (ADI) method to search for a fifth planet at separations less than 10 au, interior to the four giant planets of the HR 8799 system. The most likely semimajor axes allowed for this hypothetical planet, which were estimated via dynamical simulations in earlier works, were 7.5 au and 9.7 au within a mass range of 1–8 MJup. Methods. We obtained 4.5 h of simultaneous low-resolution integral field spectroscopy (R ∼ 30, Y − H band with IFS) and dual-band imaging (K1 and K2 bands with IRDIS) of the HR 8799 system, interspersed with observations of a reference star. The reference star was observed for about one-third of the total time and generally needs to be of similar brightness (ΔR ≲ 1 mag) and separated on sky by ≲1–2°. The hops between stars were made every 6–10 min, with only 1 min gaps in on-sky integration per hop. Results. We did not detect the hypothetical fifth planet at the most plausible separations, 7.5 and 9.7 au, down to mass limits of 3.6 MJup and 2.8 MJup, respectively, but attained an unprecedented contrast limit of 11.2 magnitudes at 0.1″. We detected all four planets with high signal-to-noise ratios. The YJH spectra for planets c, d were detected with redder H-band spectral slopes than found in earlier studies. As noted in previous works, the planet spectra are matched very closely by some red field dwarfs. Finally, comparing the current locations of the planets to orbital solutions, we found that planets e and c are most consistent with coplanar and resonant orbits. We also demonstrated that with star-hopping RDI, the contrast improvement at 0.1″ separation can be up to 2 mag. Conclusions. Since ADI, meridian transit and the concomitant sky rotation are not needed, the time of observation can be chosen from within a window that is two to three times larger. In general, star-hopping can be used for stars fainter than R = 4 magnitudes, since for these a reference star of suitable brightness and separation is usually available.

Systems-level network modeling deciphers the master regulators of phenotypic plasticity and heterogeneity in melanoma

Phenotypic (i.e. non-genetic) heterogeneity in melanoma drives dedifferentiation, recalcitrance to targeted therapy and immunotherapy, and consequent tumor relapse and metastasis. Various markers or regulators associated with distinct phenotypes in melanoma have been identified, but, how does a network of interactions among these regulators give rise to multiple “attractor” states and phenotypic switching remains elusive. Here, we inferred a network of transcription factors (TFs) that act as master regulators for gene signatures of diverse cell-states in melanoma. Dynamical simulations of this network predicted how this network can settle into different “attractors” (TF expression patterns), suggesting that TF network dynamics drives the emergence of phenotypic heterogeneity. These simulations can recapitulate major phenotypes observed in melanoma and explain de-differentiation trajectory observed upon BRAF inhibition. Our systems-level modeling framework offers a platform to understand trajectories of phenotypic transitions in the landscape of a regulatory TF network and identify novel therapeutic strategies targeting melanoma plasticity.