arXiv subjects

Igor M. Kulic

Publications and source records attributed to Igor M. Kulic.

12 recordsLinked to original sources

arXiv2020

Dynamics of Fiberboids

Fiberboids are active filaments trapped at the interface of two phases, able of harnessing energy (and matter) fluxes across the interface in order to produce a rolling-like self-propulsion. We discuss several table-top examples and develop the physical framework for understanding their complex dynamics. In spite of some specific features in the examples studied we conclude that the phenomenon of fiberboids is highly generic and robust across different materials, types of fluxes and timescales. Fiberboid motility should play a role from the macroscopic realm down to the micro scale and, as recently hypothesized, possibly as a means of biological self-propulsion that has escaped previous attention.

cond-mat.soft↗

arXiv2014

Theory of Coherent Van der Waals Matter

We explain in depth the previously proposed theory of the coherent Van der Waals(cVdW) interaction - the counterpart of Van der Waals (VdW) force - emerging in spatially coherently fluctuating electromagnetic fields. We show that cVdW driven matter is dominated by many body interactions, which are significantly stronger than those found in standard Van der Waals (VdW) systems. Remarkably, the leading 2- and 3-body interactions are of the same order with respect to the distance $(\propto R^{-6})$, in contrast to the usually weak VdW 3-body effects ($\propto R^{-9}$). From a microscopic theory we show that the anisotropic cVdW many body interactions drive the formation of low-dimensional structures such as chains, membranes and vesicles with very unusual, non-local properties. In particular, cVdW chains display a logarithmically growing stiffness with the chain length, while cVdW membranes have a bending modulus growing linearly with their size. We argue that the cVdW anisotropic many body forces cause local cohesion but also a negative effective "surface tension". We conclude by deriving the equation of state for cVdW materials and propose new experiments to test the theory, in particular the unusual 3-body nature of cVdW.

cond-mat.soft↗

arXiv2013

Self-Assembly of Colloidal Superstructures in Coherently Fluctuating Fields

From microscopic fluid clusters to macroscopic droplets, the structure of fluids is governed by the Van der Waals force, a force that acts between polarizable objects. In this Letter, we derive a general theory that describes the non-equilibrium counterpart to the Van der Waals force, which emerges in spatially coherently fluctuating electromagnetic fields. We describe the formation of a novel and complex hierarchy of self-organized morphologies in magnetic and dielectric colloid systems. Most striking among these morphologies are dipolar foams - colloidal superstructures that swell against gravity and display a high sensitivity to the applied field. We discuss the dominance of many body forces and derive the equation of state for a material formed by the coherent Van der Waals force. Our theory is applied to recent experiments in paramagnetic colloidal systems and a new experiment is suggested to test the theory.

cond-mat.soft↗

arXiv2010

Polymorphic Dynamics of Microtubules

Starting from the hypothesis that the tubulin dimer is a conformationally bistable molecule - fluctuating between a curved and a straight configuration at room temperature - we develop a model for polymorphic dynamics of the microtubule lattice. We show that tubulin bistability consistently explains unusual dynamic fluctuations, the apparent length-stiffness relation of grafted microtubules and the curved-helical appearance of microtubules in general. Analyzing experimental data we conclude that taxol stabilized microtubules exist in highly cooperative yet strongly fluctuating helical states. When clamped by the end the microtubule undergoes an unusual zero energy motion - in its effect reminiscent of a limited rotational hinge.

q-bio.BM↗

arXiv2007

Brownian dynamics of a microswimmer

We report on dynamic properties of a simple model microswimmer composed of three spheres and propelling itself in a viscous fluid by spinning motion of the spheres under zero net torque constraint. At a fixed temperature and increasing the spinning frequency, the swimmer demonstrates a transition from dissipation-dominated to a pumping-dominated motion regime characterized by negative effective friction coefficient. In the limit of high frequencies, the diffusion of the swimmer can be described by a model of an active particle with constant velocity.

physics.flu-dyn↗

arXiv2007

Motor driven microtubule shape fluctuations - force from within the lattice

We develop a general theory of microtubule (MT) deformations by molecular motors generating internal force doublets within the MT lattice. We describe two basic internal excitations, the S and V shape, and compare them with experimental observations from literature. We explain the special role of tubulin vacancies and the dramatic deformation amplifying effect observed for katanin acting at positions of defects. Experimentally observed shapes are used to determine the ratio of MT shear and stretch moduli ($\approx 6\times10^{-5}$) and to estimate the forces induced in the MT lattice by katanin (10's of pN). For many motors acting on a single MT we derive expressions for the end-to-end distance reduction and provide criteria for dominance of this new effect over thermal fluctuations. We conclude that molecular motors if acting cooperatively can ''animate'' MTs from within the lattice and induce slack even without cross-bridging to other structures, a scenario very much reminiscent of the motor driven axoneme.

cond-mat.soft↗

arXiv2005

Apparent Persistence Length Renormalization of Bent DNA

We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in quantum mechanical tunneling problems. The results reveal a remarkable feature of sliding loops - an apparent strong reduction of the persistence length. We generalize these results to several other experimentally interesting situations ranging from rigid DNA-protein loops to the problem of anchoring deflections in AFM stretching of semiflexible polymers. Expressions relating the force-extension measurements to the underlying loop/boundary deflection geometry are provided and applied to the case of the GalR-loop complex. The theoretical predictions are complemented and quantitatively confirmed by MD simulations.

cond-mat.soft↗

arXiv2004

Twirling DNA Rings - Swimming Nanomotors Ready for a Kickstart

We propose a rotary DNA nanomachine that shows a continuous rotation with a frequency of 10^2 -10^4 Hz. This motor consists of a DNA ring whose elastic features are tuned such that it can be externally driven via a periodic temperature change. As a result the ring propels itself through the fluid with a speed up to microns per second.

cond-mat.soft↗

arXiv2004

Theory of Nucleosome Corkscrew Sliding in the Presence of Synthetic DNA Ligands

Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong through one-basepair twist defects and through ten-basepair bulge defects. A recent experiment demonstrated that the repositioning is strongly suppressed in the presence of minor-groove binding DNA ligands. In the present study we give a quantitative theory for nucleosome repositioning in the presence of such ligands. We show that the experimentally observed octamer mobilities are consistent with the picture of bound ligands blocking the passage of twist defects through the nucleosome. This strongly supports the model of twist defects inducing a corkscrew motion of the nucleosome as the underlying mechanism of nucleosome sliding. We provide a theoretical estimate of the nucleosomal mobility without adjustable parameters, as a function of ligand concentration, binding affinity, binding site orientiation, temperature and DNA anisotropy. Having this mobility at hand we speculate about the interaction between a nucleosome and a transcribing RNA polymerase and suggest a novel mechanism that might account for polymerase induced nucleosome repositioning.

q-bio.SC↗

arXiv2003

Twist-bend instability for toroidal DNA condensates

We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second structural transition to a twisted entangled state, in which individual filaments lower their bending energy by additionally orbiting around the mean path along which they wind. This ``topological ripening'' is consistent with known simulations and experimental results. It connects and rationalizes various experimental observations ranging from strong DNA entanglement in viral capsids to the unusually short pitch of the cholesteric phase of DNA in sperm-heads. We propose that topological ripening of DNA toroids could improve the efficiency and stability of gene delivery.

cond-mat.soft↗

arXiv2002

High-T_{c} Superconductors with AF Order: Limitations on Spin-Fluctuation Pairing Mechanism

The very intriguing antagonistic interplay of antiferromagnetism (AF) and superconductivity (SC), recently discovered in high-temperature superconductors, is studied in the framework of a microscopic theory. We explain the surprisingly large increase of the magnetic Bragg peak intensity $I_{Q}$ at $Q\sim (π,π)$ in the magnetic field $H\ll H_{c2}$ at low temperatures $0<T\ll T_{c},T_{AF}$ in $La_{2-x}Sr_{x}CuO_{4}$. Good agreement with experimental results is found. The theory predicts large anisotropy of the relative intensity $R_{Q}(H)=(I_{Q}(H)-I_{Q}(0))/I_{Q}(0)$%, i.e. $R_{Q}(H\parallel c-axis)\gg R_{Q}(H\perp c-axis)$. The quantum (T=0) phase diagram at H=0 is constructed. The theory also predicts: (i) the magnetic field induced AF order in the SC state; (ii) small value for the spin-fluctuation coupling constant $g<(0.025-0.05)$ $eV$. The latter gives very small SC critical temperature $T_{c}(\ll 40$ $K)$, thus questioning the spin-fluctuation mechanism of pairing in HTS oxides.

cond-mat.supr-con↗

arXiv2000

Josephson Effect in Magnetic Superconductors with Spiral Magnetic Order

It is shown that in magnetic superconductors with spiral magnetic order the Josephson current has an additional contribution which depends: (i) on the relative orientation (magnetic phase) $θ=θ_{L}-θ_{R}$ of magnetizations on the left ($L$) and right ($R$) banks of the contact, (ii) on the junction helicity $χ=χ_{L}χ_{R}$, (with spiral helicity $χ_{L(R)}=\pm 1$), i.e. $J=[J_{c}-J_χ\cos θ]\sin ϕ$ with $ϕ=ϕ_{L}-ϕ_{R}$. The ratio $R_χ\equiv J_χ/J_{c}$ is calculated as a function of the superconducting order parameter $Δ$, the exchange field energy $h$ and the wave vector $Q$ of the spiral magnetic structure. The $π$-Josephson contact can be realized in such a system in some region of parameters. Some possible consequences of this new phase relation is also analyzed.

cond-mat.str-el↗