arXiv subjects

Tsvi Tlusty

Publications and source records attributed to Tsvi Tlusty.

At least 37 records · Page 2Linked to original sources

arXiv2022

Quasiparticles, Flat Bands, and the Melting of Hydrodynamic Matter

The concept of quasiparticles -- long-lived low-energy particle-like excitations -- has become a keystone of condensed quantum matter, where it explains a variety of emergent many-body phenomena, such as superfluidity and superconductivity. Here, we use quasiparticles to explain the collective behavior of a classical system of hydrodynamically interacting particles in two dimensions. In the disordered phase of this matter, measurements reveal a sub-population of long-lived particle pairs. Modeling and simulation of the ordered crystalline phase identify the pairs as quasiparticles, emerging at the Dirac cones of the spectrum. The quasiparticles stimulate supersonic pairing avalanches, bringing about the melting of the crystal. In hexagonal crystals, where the intrinsic threefold symmetry of the hydrodynamic interaction matches that of the crystal, the spectrum forms a flat band dense with ultra-slow, low-frequency phonons whose collective interactions induce a much sharper melting transition. Altogether, these findings demonstrate the usefulness of concepts from quantum matter theory in understanding many-body physics in classical dissipative settings.

cond-mat.soft↗

arXiv2022

Acceleration of enzymatic catalysis by active hydrodynamic fluctuations

The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed active noise. Essential elements of this circuitry are enzymes, catalysts that speed up the rate of metabolic reactions by orders of magnitude, thereby making life possible. Here, we examine the possibility that active noise in the cell, or in vitro, affects enzymatic catalytic rate by accelerating or decelerating the crossing rate of energy barriers during the reaction. Considering hydrodynamic perturbations induced by biochemical activity as a source of active noise, we evaluate their impact on the enzymatic cycle using a combination of analytic and numerical methods. Our estimates show that the fast component of the active noise spectrum enhances the rate of enzymes, while reactions remain practically unaffected by the slow noise spectrum. Revisiting the physics of barrier crossing under the influence of active hydrodynamic fluctuations suggests that the biochemical activity of macromolecules such as enzymes is coupled to active noise. Thus, we propose that enzymatic catalysis is a collective, many-body process in which enzymes may affect each other's activity via long-range hydrodynamic interaction, with potential impact on biochemical networks in living and artificial systems alike.

physics.bio-ph↗

arXiv2021

de novo gene birth as an inevitable consequence of adaptive evolution

Phylostratigraphy suggests that new genes are continually born de novo from non-genic sequences, and the genes that persist found new lineages, contributing to the adaptive evolution of organisms. While recent evidence supports the view that de novo gene birth is frequent and widespread, the mechanisms underlying this process are yet to be discovered. Here we hypothesize and examine a potential general mechanism of gene birth driven by the accumulation of beneficial mutations at non-genic loci. To demonstrate this possibility, we model this mechanism within the boundaries set by current knowledge on mutation effects. Estimates from this analysis are in line with observations of recurrent and extensive gene birth in genomics studies. Thus, we propose that, rather than being inactive and silent, non-genic regions are likely to be dynamic storehouses of potential genes.

q-bio.PE↗

arXiv2021

Exotic Topology in Ordinary Soft Matter

Hydrodynamics is shown to induce non-Hermitian topological phenomena in ordinary, passive soft matter. This is demonstrated for the first time by subjecting a 2D elastic lattice to a low-Reynolds viscous flow. The interplay of hydrodynamics and elasticity splits Dirac cones into bulk Fermi arcs, pairing exceptional points with opposite half-integer topological charges. The bulk Fermi arc is a generic hallmark of the system exhibited in all lattice and flow symmetries. Analytic model and simulations explain how the emergent singularities shape the spectral bands and give rise to a web of van Hove singularity lines in the density of states. The present findings suggest that non-Hermitian physics can be explored in a broad class of ordinary soft matter, living and artificial alike, opening avenues for topology-based technology in this regime.

cond-mat.soft↗

arXiv2021

A topological look into the evolution of developmental programs

Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and inventing new cell types. A hurdle to understanding developmental evolution is the difficulty of even describing the intertwined network of spatiotemporal processes underlying the development of complex multicellular organisms. Nonetheless, an overview of developmental trajectories can be obtained from cell type lineage maps. Here, we propose that these lineage maps can also reveal how developmental programs evolve: the modes of evolving new cell types in an organism should be visible in its developmental trajectories, and therefore in the geometry of its cell type lineage map. This idea is demonstrated using a parsimonious generative model of developmental programs, which allows us to reliably survey the universe of all possible programs and examine their topological features. We find that, contrary to belief, tree-like lineage maps are rare and lineage maps of complex multicellular organisms are likely to be directed acyclic graphs where multiple developmental routes can converge on the same cell type. While cell type evolution prescribes what developmental programs come into existence, natural selection prunes those programs which produce low-functioning organisms. Our model indicates that additionally, lineage map topologies are correlated with such a functional property: the ability of organisms to regenerate.

q-bio.MN↗

arXiv2021

Dimensional Reduction in Complex Living Systems: Where, Why, and How

The unprecedented prowess of measurement techniques provides a detailed, multi-scale look into the depths of living systems. Understanding these avalanches of high-dimensional data -- by distilling underlying principles and mechanisms -- necessitates dimensional reduction. We propose that living systems achieve exquisite dimensional reduction, originating from their capacity to learn, through evolution and phenotypic plasticity, the relevant aspects of a non-random, smooth physical reality. We explain how geometric insights by mathematicians allow one to identify these genuine hallmarks of life and distinguish them from universal properties of generic data sets. We illustrate these principles in a concrete example of protein evolution, suggesting a simple general recipe that can be applied to understand other biological systems.

q-bio.OT↗

arXiv2021

Positional information as a universal predictor of freezing

Variation of positional information, measured by the two-body excess entropy $\mathsf{S}_\mathrm{2}$, is studied across the liquid-solid equilibrium transition in a simple two-dimensional system. Analysis reveals a master relation between $\mathsf{S}_\mathrm{2}$ and the freezing temperature $T_{\mathrm{f}}$, from which a scaling law is extracted: $-\mathsf{S}_\mathrm{2}\sim |T_{\mathrm{f}} - T| ^{-1/3}$. Theoretical and practical implications of the observed universality are discussed.

cond-mat.stat-mech↗

arXiv2021

Structural asymmetry along protein sequences and co-translational folding

Proteins are translated from the N- to the C-terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the protein data bank (PDB). We find remarkable enrichment of $α$-helices at the C terminus and $β$-strands at the N terminus. Furthermore, this $α$-$β$ asymmetry correlates with sequence length and contact order, both determinants of folding rate, hinting at possible links to co-translational folding (CTF). Hence, we propose the 'slowest-first' scheme, whereby protein sequences evolved structural asymmetry to accelerate CTF: the slowest of the cooperatively-folding segments are positioned near the N terminus so they have more time to fold during translation. A phenomenological model predicts that CTF can be accelerated by asymmetry, up to double the rate, when folding time is commensurate with translation time; analysis of the PDB reveals that structural asymmetry is indeed maximal in this regime. This correspondence is greater in prokaryotes, which generally require faster protein production. Altogether, this indicates that accelerating CTF is a substantial evolutionary force whose interplay with stability and functionality is encoded in sequence asymmetry.

q-bio.BM↗

arXiv2021

Inverse Design of Non-Equilibrium Steady-States: A Large Deviation Approach

The design of small scale non-equilibrium steady states (NESS) is a challenging, open ended question. While similar equilibrium problems are tractable using standard thermodynamics, a generalized description for non-equilibrium systems is lacking, making the design problem particularly difficult. Here we show we can exploit the large deviation behavior of a Brownian particle and design a variety of geometrically complex steady-state density distributions and flux field flows. We achieve this design target from direct knowledge of the joint large deviation functional for the empirical density and flow, and a "relaxation" algorithm on the desired target states via adjustable force field parameters. We validate the method by replicating analytical results, and demonstrate its capacity to yield complex prescribed targets, such as rose-curve or polygonal shapes on the plane. We consider this dynamical fluctuation approach a first step towards the design of more complex NESS where general frameworks are otherwise still lacking.

cond-mat.stat-mech↗

arXiv2020

Walking droplets, swimming microbes: on memory in physics and life

Whirling and swerving, a bacterium is swimming in a test tube, foraging for food. On the surface of a vibrating bath, a droplet starts walking. A certain similarity, but mostly dissimilarity, between the physical memory that emerges in Couder's droplet experiments and the biological memory of the bacterium is noted. It serves as a starting point for a short perspective and speculation on the multilevel, loopy memory of living matter.

q-bio.PE↗

arXiv2020

Master curve of boosted diffusion for ten catalytic enzymes

Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity couples to molecular motion contrasts with generations of accumulated knowledge about diffusion at equilibrium. To test the limits of this idea, a critical testbed is mobility of catalytically active enzymes. Sentiment is divided about reality of enhanced enzyme diffusion with evidence for and against. Here a master curve shows that enzyme diffusion coefficient increases in proportion to the energy release rate, the product of Michaelis-Menten reaction rate and Gibbs free energy change with the highly satisfactory correlation coefficient of 0.97. For ten catalytic enzymes (urease, acetylcholinesterase, seven enzymes from the glucose cascade cycle, and another), our measurements span from roughly 40% enhanced diffusion coefficient at high turnover rate and negative Gibbs free energy to no enhancement at slow turnover rate and positive Gibbs free energy. Moreover, two independent measures of mobility show consistency, provided that one avoids undesirable fluorescence photophysics. The master curve presented here quantifies the limits of both ideas, that enzymes display enhanced diffusion and that they do not within instrumental resolution, and has possible implications for understanding enzyme mobility in cellular environments. The striking linear dependence for the exergonic enzymes (negative Gibbs free energy) together with the vanishing effect for endergonic enzyme (positive Gibbs free energy) are consistent with a physical picture where the mechanism boosting the diffusion is an active one, utilizing the available work from the chemical reaction.

cond-mat.soft↗

arXiv2020

$αβ$ DCA method identifies unspecific binding but specific disruption of the group I intron by the StpA chaperone

Chaperone protein - the most disordered among all protein groups - help RNAs fold into their functional structure by destabilizing misfolded configurations or stabilizing the functional ones. But disentangling the mechanism underlying RNA chaperoning is challenging, mostly due to inherent disorder of the chaperones and the transient nature of their interactions with RNA. In particular, it is unclear how specific the interactions are and what role is played by amino acid charge and polarity patterns. Here, we address these questions in the RNA chaperone StpA. We adapted direct coupling analysis (DCA) into the $αβ$DCA method that can treat in tandem sequences written in two alphabets, nucleotides and amino acids. With $αβ$DCA, we could analyze StpA-RNA interactions and show consistency with a previously proposed two-pronged mechanism: StpA disrupts specific positions in the group I intron while globally and loosely binding to the entire structure. Moreover, the interactions are strongly associated with the charge pattern: negatively charged regions in the destabilizing StpA N-terminal affect a few specific positions in the RNA, located in stems and in the pseudoknot. In contrast, positive regions in the C-terminal contain strongly coupled amino acids that promote non-specific or weakly-specific binding to the RNA. The present study opens new avenues to examine the functions of disordered proteins and to design disruptive proteins based on their charge patterns.

q-bio.BM↗

arXiv2020

Reaching and violating thermodynamic uncertainty bounds in information engines

Thermodynamic uncertainty relations (TURs) set fundamental bounds on the fluctuation and dissipation of stochastic systems. Here, we examine these bounds, in experiment and theory, by exploring the entire phase space of a cyclic information engine operating in a non-equilibrium steady state. Close to its maximal efficiency, we find that the engine violates the original TUR. This first experimental demonstration of TUR violation agrees with recently proposed softer bounds: The engine satisfies two generalized TUR bounds derived from the detailed fluctuation theorem with feedback control and another bound linking fluctuation and dissipation to mutual information and Renyi divergence. We examine how the interplay of work fluctuation and dissipation shapes the information conversion efficiency of the engine, and find that dissipation is minimal at a finite noise level, where the original TUR is violated.

cond-mat.stat-mech↗

arXiv2020

Cross-cultural data shows musical scales evolved to maximise imperfect fifths

Musical scales are used throughout the world, but the question of how they evolved remains open. Some suggest that scales based on the harmonic series are inherently pleasant, while others propose that scales are chosen that are easy to communicate. However, testing these theories has been hindered by the sparseness of empirical evidence. Here, we assimilate data from diverse ethnomusicological sources into a cross-cultural database of scales. We generate populations of scales based on multiple theories and assess their similarity to empirical distributions from the database. Most scales tend to include intervals which are close in size to perfect fifths (``imperfect fifths''), and packing arguments explain the salient features of the distributions. Scales are also preferred if their intervals are compressible, which may facilitate efficient communication and memory of melodies. While scales appear to evolve according to various selection pressures, the simplest h imperfect-fifths packing model best fits the empirical data.

cs.SD↗

arXiv2020

Kinetic Proofreading and the Limits of Thermodynamic Uncertainty

To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively-studied KPR circuits, DNA replication by the T7 DNA polymerase and translation by the E. coli ribosome. Using experimental data, we analyze the performance of these two vital systems in light of the fundamental bounds set by the recently-discovered thermodynamic uncertainty relation (TUR), which places an inherent trade-off between the precision of a desirable output and the amount of energy dissipation required. We show that the DNA polymerase operates close to the TUR lower bound, while the ribosome operates $\sim5$ times farther from this bound. This difference originates from the enhanced binding discrimination of the polymerase which allows it to operate effectively as a reduced reaction cycle prioritizing correct product formation. We show that approaching this limit also decouples the thermodynamic uncertainty factor from speed and error, thereby relaxing the accuracy-speed trade-off of the system. Altogether, our results show that operating near this reduced cycle limit not only minimizes thermodynamic uncertainty, but also results in global performance enhancement of KPR circuits.

physics.bio-ph↗

arXiv2019

Large-Scale Survey of Cell-Differentiation Programs in a Generative Model Reveals Regeneration as an Epiphenomenon of Development

Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity using a generative model. We sample millions of biologically feasible developmental schemes, allowing us to comment on the statistical properties of cell-differentiation trajectories they produce. Our results indicate that, in contrast to common views, cell-type lineage graphs are unlikely to be tree-like. Instead, they are more likely to be directed acyclic graphs, with multiple lineages converging on the same terminal cell-type. Additionally, in line with the hypothesis that whole body regeneration is an epiphenomenon of development, a majority of the `organism' generated by our model can regenerate using pluripotent cells. The generative framework is modular and flexible, and can be adapted to test additional hypotheses about general features of development.

q-bio.MN↗

arXiv2019

Efficiency fluctuations and noise induced refrigerator-to-heater transition in information engines

Understanding noisy information engines is a fundamental problem of non-equilibrium physics, particularly in biomolecular systems agitated by thermal and active fluctuations in the cell. By the generalized second law of thermodynamics, the efficiency of these engines is bounded by the mutual information passing through their noisy feedback loop. Yet, direct measurement of the interplay between mutual information and energy has so far been elusive. To allow such examination, we explore here the entire phase-space of a noisy colloidal information engine, and study efficiency fluctuations due to the stochasticity of the mutual information and extracted work. We find that the average efficiency is maximum for non-zero noise level, at which the distribution of efficiency switches from bimodal to unimodal, and the stochastic efficiency often exceeds unity. We identify a line of anomalous, noise-driven equilibrium states that defines a refrigerator-to-heater transition, and test the generalized integral fluctuation theorem for continuous engines.

cond-mat.stat-mech↗

arXiv2019

Enhanced diffusion and enzyme dissociation

The concept that catalytic enzymes can act as molecular machines transducing chemical activity into motion has conceptual and experimental support, but much of the claimed support comes from experimental conditions where the substrate concentration is higher than biologically relevant and accordingly exceeds kM, the Michaelis-Menten constant. Moreover, many of the enzymes studied experimentally to date are oligomeric. Urease, a hexamer of subunits, has been considered to be the gold standard demonstrating enhanced diffusion. Here we show that urease and certain other oligomeric enzymes of high catalytic activity above kM dissociate into their smaller subunit fragments that diffuse more rapidly, thus providing a simple physical mechanism of enhanced diffusion in this regime of concentrations. Mindful that this conclusion may be controversial, our findings are sup-ported by four independent analytical techniques, static light scattering, dynamic light scattering (DLS), size-exclusion chroma-tography (SEC), and fluorescence correlation spectroscopy (FCS). Data for urease are presented in the main text and the con-clusion is validated for hexokinase and acetylcholinesterase with data presented in supplementary information. For substrate concentration regimes below kM at which these enzymes do not dissociate, our findings from both FCS and DLS validate that enzymatic catalysis does lead to the enhanced diffusion phenomenon. INTRODUCT

cond-mat.soft↗