arXiv subjects

Igor M. Kulić

Publications and source records attributed to Igor M. Kulić.

16 recordsLinked to original sources

arXiv2025

The Hidden Wheel-Within

There is this old, eternal question: Why don't animals have wheels? In this perspective we show that they actually do. And they do so in a physically extraordinary way -- by combining incompatible elasticity, differential geometry and dissipative self-organization. Nature's wheel -- the ``wheel-within'' -- has been mysteriously concealed in plain sight, yet it spins in virtually every slender-body organism: in falling cats, crocodilians spinning to subdue their prey, rolling fruit-fly larvae, circumnutating plants and even in some of our own body movements. Flying somehow under the radar of our cognition, in recent years the wheel-within also tacitly entered the field of soft robotics, finally opening our eyes for its ubiquitous role in Nature. We here identify its underlying physical ingredients, namely the existence of a neutrally-stable, shape-invariant and actively driven elastic mode. We then reflect on various man-made realizations of the wheel-within and outline where it could be spinning from here.

cond-mat.soft↗

arXiv2024

Reshaping and Enzymatic Activity may allow Viruses to move through the Mucus

Filamentous viruses like influenza and torovirus often display systematic bends and arcs of mysterious physical origin. We propose that such viruses undergo an instability from a cylindrically symmetric to a toroidally curved state. This ``toro-elastic'' state emerges via spontaneous symmetry breaking under prestress due to short range spike protein interactions magnified by %the filament's surface topography. Once surface stresses are sufficiently large, the filament buckles and the curved state constitutes a soft mode that can potentially propagate through the filament's material frame around a mexican-hat-type potential. In the mucus of our airways, which constitutes a soft, porous 3D network, glycan chains are omnipresent and influenza's spike proteins are known to efficiently bind and cut them. We next show that such a non-equilibrium enzymatic reaction can induce spontaneous rotation of the curved state, leading to a whole body reshaping propulsion similar to -- but different from -- eukaryotic flagella and spirochetes.

cond-mat.soft↗

arXiv2022

The Physics of Self-Rolling Viruses

Viruses are right at the interface of inanimate matter and life. However, recent experiments [T. Sakai, et al., J.~Virol.~{\bf 92}, e01522-17 (2018)] have shown that some influenza strains can actively roll on glycan-covered surfaces. In a previous letter [F. Ziebert and I. M. Kulić, Phys. Rev. Lett. {\bf 126}, 218101 (2021)] we suggested this to be a form of viral surface metabolism: a collection of spike proteins that attach to and cut the glycans act as a self-organized mechano-chemical motor. Here we study in more depth the physics of the emergent self-rolling states. We give scaling arguments how the motion arises, substantiated by a detailed analytical theory that yields the full torque-angular velocity relation of the self-organized motor. Stochastic Gillespie simulations are used to validate the theory and to quantify stochastic effects like virus detachment and reversals of its direction. Finally, we also cross-check several approximations made previously and show that the proposed mechanism is very robust. All these results point together to the statistical inevitability of viral rolling in presence of enzymatic activity.

cond-mat.soft↗

arXiv2020

How Influenza's Spike Motor Works

While often believed to be a passive agent that merely exploits its host's metabolism, influenza virus has recently been shown to actively move across glycan-coated surfaces. This form of enzymatically driven surface motility is currently not well understood and has been loosely linked to burnt-bridge Brownian ratchet mechanisms. Starting from known properties of influenza's spike proteins, we develop a physical model that quantitatively describes the observed motility. It predicts a collectively emerging dynamics of spike proteins and surface bound ligands that combined with the virus' geometry give rise to a self-organized rolling propulsion. We show that in contrast to a Brownian ratchet, the rotary spike drive is not fluctuation driven but operates optimally as a macroscopic engine in the deterministic regime. The mechanism also applies to relatives of influenza and to man-made analogues like DNA-monowheels and should give guidelines for their optimization.

cond-mat.soft↗

arXiv2018

The Helical Superstructure of Intermediate Filaments

Intermediate filaments are the least explored among the large cytoskeletal elements. We show here that they display conformational anomalies in narrow microfluidic channels. Their unusual behavior can be understood as the consequence of a previously undetected, large scale helically curved superstructure. Confinement in a channel orders the otherwise soft, strongly fluctuating helical filaments and enhances their structural correlations, giving rise to experimentally detectable, strongly oscillating tangent correlation functions. We propose an explanation for the detected intrinsic curving phenomenon - an elastic shape instability that we call autocoiling. The mechanism involves self-induced filament buckling via a surface stress located at the outside of the cross-section. The results agree with ultrastructural findings and rationalize for the commonly observed looped intermediate filament shapes.

cond-mat.soft↗

arXiv2017

Magnetic Merry Go Round - Resonant Reshaping of Colloidal Clusters on a Current Carrying Wire

We describe a simple physical method for trapping and transforming magnetic colloid clusters on a current carrying wire. We use the wire's field as a mould to form colloidal rings and helices on its surface. To transform the initially amorphous, kinetically trapped, bulky clusters we induce a low frequency magnetic modulation wave that spins around the wire axis, effectively eliminates defects from the clusters and stretches them into slender rings and helical structures. A qualitative theoretical model of the underlying resonant transformations is developed and the practical potential of the wire as a magnetic micro-assembler is discussed.

cond-mat.soft↗

arXiv2016

Squeezed Helical Elastica

We theoretically study the conformations of a helical semi-flexible filament confined to a flat surface. This squeezed helix exhibits a variety of unexpected shapes resembling circles, waves or spirals depending on the material parameters. We explore the conformation space in detail and show that the shapes can be understood as the mutual elastic interaction of conformational quasi-particles. Our theoretical results are potentially useful to determine the material parameters of such helical filaments in an experimental setting.

physics.bio-ph↗

arXiv2014

Crunching Biofilament Rings

We discuss a curious example for the collective mechanical behavior of coupled non-linear monomer units entrapped in a circular filament. Within a simple model we elucidate how multistability of monomer units and exponentially large degeneracy of the filament's ground state emerge as a collective feature of the closed filament. Surprisingly, increasing the monomer frustration, i.e., the bending prestrain within the circular filament, leads to a conformational softening of the system. The phenomenon, that we term polymorphic crunching, is discussed and applied to a possible scenario for membrane tube deformation by switchable dynamin or FtsZ filaments. We find an important role of cooperative inter-unit interaction for efficient ring induced membrane fission.

cond-mat.soft↗

arXiv2014

Why Microtubules run in Circles - Mechanical Hysteresis of the Tubulin Lattice

The fate of every eukaryotic cell subtly relies on the exceptional mechanical properties of microtubules. Despite significant efforts, understanding their unusual mechanics remains elusive. One persistent, unresolved mystery is the formation of long-lived arcs and rings, e.g. in kinesin-driven gliding assays. To elucidate their physical origin we develop a model of the inner workings of the microtubule's lattice, based on recent experimental evidence for a conformational switch of the tubulin dimer. We show that the microtubule lattice itself coexists in discrete polymorphic states. Curved states can be induced via a mechanical hysteresis involving torques and forces typical of few molecular motors acting in unison. This lattice switch renders microtubules not only virtually unbreakable under typical cellular forces, but moreover provides them with a tunable response integrating mechanical and chemical stimuli.

cond-mat.soft↗

arXiv2013

Confotronic Dynamics of Tubular Lattices

Tubular lattices are ubiquitous in nature and technology. Microtubules and nanotubes of all kinds act as important pillars of biological cells and the man-made nano-world. We show that when prestress is introduced in such structures, localized conformational quasiparticles emerge and govern the collective shape dynamics of the lattice. When coupled via cooperative interactions these quasiparticles form larger-scale quasipolymer superstructures exhibiting collective dynamic modes and giving rise to a hallmark behavior radically different from semiflexible beams.

cond-mat.soft↗

arXiv2012

Helices at Interfaces

Helically coiled filaments are a frequent motif in nature. In situations commonly encountered in experiments coiled helices are squeezed flat onto two dimensional surfaces. Under such 2-D confinement helices form "squeelices" - peculiar squeezed conformations often resembling looped waves, spirals or circles. Using theory and Monte-Carlo simulations we illuminate here the mechanics and the unusual statistical mechanics of confined helices and show that their fluctuations can be understood in terms of moving and interacting discrete particle-like entities - the "twist-kinks". We show that confined filaments can thermally switch between discrete topological twist quantized states, with some of the states exhibiting dramatically enhanced circularization probability while others displaying surprising hyperflexibility.

cond-mat.soft↗

arXiv2011

Cooperative Lattice Dynamics and Anomalous Fluctuations of Microtubules

Microtubules have been in biophysical focus for several decades. Yet the confusing and mutually contradicting results regarding their elasticity and fluctuations have shed some doubts on their present understanding. In this paper we expose the empirical evidence for the existence of discrete GDP-tubulin fluctuations between a curved and a straight configuration at room temperature as well as for conformational tubulin cooperativity. Guided by a number of experimental findings, we build the case for a novel microtubule model, with the principal result that microtubules can spontaneously form micron size cooperative helical states with unique elastic and dynamic features. The polymorphic dynamics of the microtubule lattice resulting from the tubulin bistability quantitatively explains several experimental puzzles including anomalous scaling of dynamic fluctuations of grafted microtubules, their apparent length-stiffness relation and their remarkably curved-helical appearance in general. We point out that tubulin dimers's multistability and its cooperative switching could participate in important cellular processes, and could in particular lead to efficient mechanochemical signalling along single microtubules.

cond-mat.soft↗

arXiv2011

A Solvable Model for Polymorphic Dynamics of Biofilaments

We investigate an analytically tractable toy model for thermally induced polymorphic dynamics of cooperatively rearranging biofilaments - like microtubules. The proposed 4 -block model, which can be seen as a coarse-grained approximation of the full polymorphic tube model, permits a complete analytical treatment of all thermodynamic properties including correlation functions and angular fourier mode distributions. Due to its mathematical tractability the model straightforwardly leads to some physical insights in recently discussed phenomena like the "length dependent persistence length". We show that a polymorphic filament can disguise itself as a classical worm like chain on small and on large scales and yet display distinct anomalous tell-tale features indicating an inner switching dynamics on intermediate length scales.

cond-mat.soft↗

arXiv2008

The role of microtubule movement in bidirectional organelle transport

We study the role of microtubule movement in bidirectional organelle transport in Drosophila S2 cells and show that EGFP-tagged peroxisomes in cells serve as sensitive probes of motor induced, noisy cytoskeletal motions. Multiple peroxisomes move in unison over large time windows and show correlations with microtubule tip positions, indicating rapid microtubule fluctuations in the longitudinal direction. We report the first high-resolution measurement of longitudinal microtubule fluctuations performed by tracing such pairs of co-moving peroxisomes. The resulting picture shows that motor-dependent longitudinal microtubule oscillations contribute significantly to cargo movement along microtubules. Thus, contrary to the conventional view, organelle transport cannot be described solely in terms of cargo movement along stationary microtubule tracks, but instead includes a strong contribution from the movement of the tracks.

physics.bio-ph↗

arXiv2007

Semi-classical buckling of stiff polymers

A quantitative theory of the buckling of a worm like chain based on a semi-classical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows to go beyond the classical Euler buckling is derived in the linear and non-linear regime as well. It is shown that the thermal fluctuations in the nonlinear buckling regime increase the end-to-end distance of the semiflexible rod if it is confined to 2 dimensions as opposed to the 3 dimensional case. Our approach allows a complete physical understanding of buckling in D=2 and in D=3 below and above the Euler transition.

cond-mat.soft↗

arXiv2006

Hitchhiking Through the Cytoplasm

We propose an alternative mechanism for intracellular cargo transport which results from motor induced longitudinal fluctuations of cytoskeletal microtubules (MT). The longitudinal fluctuations combined with transient cargo binding to the MTs lead to long range transport even for cargos and vesicles having no molecular motors on them. The proposed transport mechanism, which we call ``hitchhiking'', provides a consistent explanation for the broadly observed yet still mysterious phenomenon of bidirectional transport along MTs. We show that cells exploiting the hitchhiking mechanism can effectively up- and down-regulate the transport of different vesicles by tuning their binding kinetics to characteristic MT oscillation frequencies.

cond-mat.soft↗