arXiv subjects

Dino Osmanovic

Publications and source records attributed to Dino Osmanovic.

13 recordsLinked to original sources

arXiv2024

Generating forces in confinement via polymerization

Understanding how to produce forces using biomolecular building blocks is essential for the development of adaptive synthetic cells and living materials. Here we ask whether a dynamic polymer system can generate deformation forces in soft compartments by pure self-assembly, motivated by the fact that biological polymer networks like the cytoskeleton can exert forces, move objects, and deform membranes by simply growing, even in the absence of molecular motors. We address this question by investigating polymer force generation by varying the release rate, the structure, and the interactions of self-assembling monomers. First, we develop a toy computational model of polymerization in a soft elastic shell that reveals the emergence of spontaneous bundling which enhances shell deformation. We then extend our model to account more explicitly for monomer binding dynamics. We find that the rate at which monomers are released into the interior of the shell is a crucial parameter for achieving deformation through polymer growth. Finally, we demonstrate that the introduction of multivalent particles that can join polymers can either improve or impede polymer performance, depending on the amount and on the structure of the multivalent particles. Our results provide guidance for the experimental realization of polymer systems that can perform work at the nanoscale, for example through rationally designed self-assembling proteins or nucleic acids.

cond-mat.soft↗

arXiv2024

Complex Dynamics in Reaction-Phase Separation Systems

We investigate the emergence of sustained spatio-temporal behaviors in reaction-phase separation systems. We focus on binary systems, in which either one or both species can phase separate, and we discuss the stability of the homogeneous state determining the conditions for the emergence of a Hopf-type bifurcation. We then examine the effects of a specific autocatalytic chemical reaction, and computationally determine the full solutions to the partial differential equations. We find that when both species phase separate, sustained pulsed dynamics arise in one dimension. When considered in two dimensions, the system generates persistent, complex dynamic droplets, which do not generally appear if only one of the species can phase separate. We finally discuss the emergence of dynamics with complex features, which can be understood using the framework of a cellular automata.

nlin.PS↗

arXiv2023

Robust microphase separation through chemical reaction networks

The interaction of phase-separating systems with chemical reactions is of great interest in various contexts, from biology to material science. In biology, phase separation is thought to be the driving force behind the formation of biomolecular condensates, i.e. organelles without a membrane that are associated with cellular metabolism, stress response, and development. RNA, proteins, and small molecules participating in the formation of condensates are also involved in a variety of biochemical reactions: how do the chemical reaction dynamics influence the process of phase separation? Here we are interested in finding chemical reactions that can arrest the growth of condensates, generating stable spatial patterns of finite size (microphase separation), in contrast with the otherwise spontaneous (unstable) growth of condensates. We consider a classical continuum model for phase separation coupled to a chemical reaction network (CRN), and we seek conditions for the emergence of stable oscillations of the solution in space. Given reaction dynamics with uncertain rate constants, but known structure, we derive easily computable conditions to assess whether microphase separation is impossible, possible for some parameter values, or robustly guaranteed for all parameter values within given bounds. Our results establish a framework to evaluate which classes of CRNs favor the emergence of condensates with finite size, a question that is broadly relevant to understanding and engineering life.

cond-mat.soft↗

arXiv2023

Microscopic modifications of equilibrium probabilities due to non-conservative perturbations with applications to anharmonic systems

The standard relationships of statistical mechanics are upended my the presence of active forces. In particular, it is no longer usually possible to simply write down what the stationary probability of a state of such a system will be, as can be done in ordinary statistical mechanics. While exact expressions are possible for harmonic systems, anharmonic systems tend to be much more difficult to treat. In this manuscript, we investigate how the microscopic probability for anharmonic systems is modified in the presence of non-conservative forces. We recount how non-conservative corrections to microscopic probabilities in generic systems can be represented as integrals over Green's function kernels, and that these Green's functions take the form of path integrals. We show how using analytically tractable form of these functions allows us to calculate corrections to the microscopic probability for a generic anharmonic system. These results are compared to active Brownian particles inside a harmonic or anharmonic well. From this it can be shown that accumulation of probability away from its equilibrium minima is a natural effect arising in anharmonic but not harmonic systems. Finally, we extend the microscopic results to study small active polymers with anharmonic backbone potentials. The interplay of the active driving with the anharmonic backbone potential can be used to understand how the end-to-end distance and mode space distributions of anharmonic active polymers scales with active driving. In particular, the polymer modes with the smallest eigenvalues will be affected by non-conservative forces the most.

cond-mat.stat-mech↗

arXiv2022

Chemical reaction motifs driving non-equilibrium behaviors in phase separating materials

Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the behaviors of a phase separating system is difficult to fully predict theoretically. In this paper, we analyze a mean field theory coupling CRNs to phase separating materials and expound on how the properties of the CRNs affect different classes of non-equilibrium behaviors: the emergence of microphase separation or of temporally oscillating patterns. We examine the problem of achieving microphase separated condensates by first considering tractable problems and illustrating the mathematical conditions leading to microphase separation. We then identify CRN motifs that are likely to yield size control by examining randomly generated networks and parameters. By analyzing the probabilities to observe particular states, we define simple design rules of CRNs that lead to desired non-equilibrium behavior. We show that chemical interactions generating negative feedback facilitate microphase separation, moreover, we demonstrate that the parameters important for the emergence of microphase separation differ for systems with two or four components, due to frustration. Our results provide guidance toward the design of self-regulating material CRNs and provide instructions to manage the formation, dissolution, and organization of compartments.

cond-mat.soft↗

arXiv2020

Spatial distributions of non-conservatively interacting particles

Certain types of active systems can be treated as an equilibrium system with excess non-conservative forces driving some of the microscopic degrees of freedom. We derive results for how many particles interacting with each other with both conservative and non-conservative forces will behave. Treating non-conservative forces perturbatevily, we show how the probability distribution of the microscopic degrees of freedom is modified from the Boltzmann distribution. We compare the perturbative expansion to an exactly solvable non-conservative system. We then derive approximate forms of this distribution through analyzing the nature of our perturbations. Finally, we consider how the approximate forms for the microscopic distributions we have derived lead to different macroscopic states when coarse grained, and compare it qualitatively to simulation of non-conservatively interacting particles. In particular we note by introducing non-conservative interactions between particles we modify densities through extra terms which couple to surfaces

cond-mat.stat-mech↗

arXiv2019

Chemically Active Nanodroplets in a Multi-Component Fluid

We introduce a model of chemically active particles of a multi-component fluid that can change their interactions with other particles depending on their state. Since such switching of interactions can only be maintained by the input of chemical energy, the system is inherently non-equilibrium. Focusing on a scenario where the equilibrium interactions would lead to condensation into a liquid droplet, and despite the relative simplicity of the interaction rules, these systems display a wealth of interesting and novel behaviors such as oscillations of droplet size and molecular sorting, and raise the possibility of spatio-temporal control of chemical reactions on the nanoscale

cond-mat.soft↗

arXiv2017

Effect of Grafting on Aggregation of Intrinsically Disordered Proteins

A significant part of the proteome is composed of intrinsically-disordered proteins (IDPs). These proteins do not fold into a well-defined structure and behave like ordinary polymers. In this work we consider IDPs which have the tendency to aggregate, model them as heteropolymers that contain a small number of associating monomers and use computer simulations in order to compare the aggregation of such IDPs that are grafted to a surface or free in solution. We then discuss how such grafting may affect the analysis of in-vitro experiments and could also be used to suppress harmful aggregation.

physics.bio-ph↗

arXiv2016

Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Current models of animal evolution focus on selection of individuals, ignoring the much faster selection of symbiotic bacteria. Here we take host-symbiont interactions into account by introducing a Population Genetics-like model of holobionts exposed to toxic stress. The stress can be alleviated by selection of resistant individuals (host and bacteria) and by secretion of a detoxification agent ("detox"). By defining a new measure, termed the Lamarckian, we show that selection of resistant bacteria over one generation of hosts leads to stress-dependent increase in the tolerance of the host's offspring. This benefit is mediated by co-alleviation of toxic and physiologic stress. Prolonged exposure leads to further adaptation by 'group selection' of bacterial communities with higher detox per bacterium. These findings show that Lamarckian adaptation can arise via interactions between two levels of Darwinian selection within a holobiont system. The conclusions and modelling framework are applicable to diverse types of holobiont systems.

q-bio.PE↗

arXiv2016

Dynamics of Active Rouse Chains

We consider how active forces modeled as non-thermal random noise affect the average dynamical properties of a Rouse polymer. As the power spectrum of the noise is not known we keep the analytical treatment as generic as possible and then present results for a few examples of active noise. We discuss the connection between our results and recent experimental studies of dynamics of labeled DNA telomeres in living cells, and propose new chromatin tracking experiments that will allow one to determine the statistical properties of the active forces associated with chromatin remodeling processes.

cond-mat.stat-mech↗

arXiv2016

Effect of non-specific interactions on formation and stability of specific complexes

We introduce a simple model to describe the interplay between specific and non-specific interactions. We study the influence of various physical factors on the static and dynamic properties of the specific interactions of our model and show that contrary to intuitive expectations, non-specific interactions can assist in the formation of specific complexes and increase their stability. We then discuss the relevance of these results for biological systems.

cond-mat.soft↗

arXiv2015

Universal Protein Distributions in a Model of Cell Growth and Division

Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal measurements of protein content, showing accumulation and division across generations. Here we present a stochastic growth-and-division model with feedback which captures these observed properties. The limiting copy number distribution is calculated exactly, and a single parameter is found to determine the distribution shape and the variance-to-mean relation. Estimating this parameter from bacterial temporal data reproduces the measured distribution shape with high accuracy, and leads to predictions for future experiments.

physics.bio-ph↗

arXiv2012

Bistable collective behavior of polymers tethered in a nanopore

Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along its central axis. The relative stability of these two phases depends on the interpolymer interactions. The existence of the two phases suggests a transport mechanism in which marginal changes in these interactions, possibly induced by nuclear transport receptors, cause the pore to transform between open and closed configurations.

cond-mat.soft↗