We explore the impact of hydrodynamic interactions on the conformational and dynamical properties of externally driven active polymers with tangential forces using multiparticle collision dynamics simulations. This model applies to non-force-neutral motile polymers, such as biofilaments in motility …

[Phys. Rev. E 110, 064504] Published Mon Dec 16, 2024

Fibrin polymerization is responsible for the formation of blood clots and is used in many biomedical applications. Considering polymerization as a dynamic phase transition, we constructed a scaling theory of fibrin networks formation. We show that in the transient state, protofibrils and branched cl…

[Phys. Rev. E 110, L062501] Published Thu Dec 12, 2024

We study the viscoelastic relaxation dynamics of scale-free copolymer networks in the generalized Gaussian structures framework. We focus on the real and imaginary components of the complex dynamic modulus $G^{*}\left(\omega \right)$: the storage and loss moduli. Our chosen scale-free network model builds distinct types …

[Phys. Rev. E 110, 064502] Published Mon Dec 09, 2024

Self-avoiding walk (SAW) represents a linear polymer chain on a large scale, neglecting its chemical details and emphasizing the role of its conformational statistics. The role of the latter is important in the formation of agglomerates and complexes involving polymers and organic or inorganic parti…

[Phys. Rev. E 110, 064503] Published Mon Dec 09, 2024

A model is proposed for mesoscopic dynamics of a magnetoactive elastomer (MAE). The elementary cell comprises two spherical linearly magnetizing particles embedded in an elastoviscous medium of the Kelvin type. The forced oscillations of this system induced by an ac field are studied. Under a static…

[Phys. Rev. E 110, 064501] Published Mon Dec 02, 2024

An ex-situ solid-state nuclear magnetic resonance (NMR) method employing localized magnetic field gradients generated by a needlelike ferromagnet is described. The depth profiling of a multilayer polymeric film using the proposed method and spin density imaging is successfully acquired. The imaging …

[Phys. Rev. E 110, 054503] Published Mon Nov 18, 2024

The need for effective multibody interactions is asserted in understanding the entropically driven phase separation of diblock copolymers, arising from disparity in self cohesion and association between dissimilar components. Through Landau analysis combined with a molecular equation of state to des…

[Phys. Rev. E 110, 054502] Published Thu Nov 14, 2024

We investigate the effects of quenched elastic disorder on the nature of the crumpling-to-flat transition of $D$-dimensional polymerized membranes using a two-loop computation near the upper critical dimension $D_c=4$. While the pure system undergoes fluctuation-induced first-order transitions below $D_c$ a…

[Phys. Rev. E 110, 054501] Published Tue Nov 05, 2024

Dielectric elastomer actuators (DEAs) are an emerging type of soft actuators based on intelligent electroactive polymers. Compared with conventional rigid actuators, DEAs can adapt to extreme hydrostatic pressures without any bulky protective vessels and, therefore, have demonstrated great promises …

[Phys. Rev. E 110, L052501] Published Mon Nov 04, 2024

The formation of tetra-PEG gels, a model network with a well-defined structure, was investigated using particle-tracking microrheology. The dynamic scaling and critical relaxation exponents in the sol-gel transition were determined by applying the time-cure superposition method. Some values of the e…

[Phys. Rev. E 110, 044503] Published Tue Oct 15, 2024

Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the underlying free-energy landscape. In this study we use computer simu…

[Phys. Rev. E 110, 044501] Published Tue Oct 01, 2024

Capturing protracted binding kinetics of polymers onto the surface of nanoobjects is crucial for the rational design of multifunctional nanostructures, such as patchy nanoparticles and nanodrug carriers. Recently, we developed a method—integral of first-passage times (IFS)—to successfully predict no…

[Phys. Rev. E 110, 044502] Published Tue Oct 01, 2024

We study the phase separation kinetics of miktoarm star polymer (MSP) melts/blends with diverse architectures using dissipative particle dynamics simulation. Our study focuses on symmetric and asymmetric miktoarm star polymer (SMSP/AMSP) mixtures based on arm composition and number. For a fixed MSP …

[Phys. Rev. E 110, 034504] Published Wed Sep 25, 2024

Nanoparticles (NPs) that are forcefully driven through a brush-decorated nanochannel form a nonequilibrium system with a rich physical behavior, including a dynamical phase transition between two modes of propagation that correspond to either separate clusters of NPs or a continuous flow channel. Th…

[Phys. Rev. E 110, 034503] Published Mon Sep 23, 2024

In this paper, we are concerned with the crossover between strong disorder (SD) and weak disorder (WD) behaviors in three well-known problems that involve minimal paths: directed polymers (directed paths with fixed starting point and length), optimal paths (undirected paths with a fixed end-to-end o…

[Phys. Rev. E 110, 034502] Published Wed Sep 11, 2024

We develop a minimal model to study the stochastic formation of Borromean links within topologically entangled networks without requiring the use of knot invariants. Borromean linkages may form in entangled solutions of open polymer chains or in Olympic gel systems such as kinetoplast DNA, but it is…

[Phys. Rev. E 110, 034501] Published Fri Sep 06, 2024

Amber is a unique example of a fragile glass that has been extensively aged below its glass transition temperature, thus reaching a state that is not accessible under normal experimental conditions. We studied the medium-range order of Baltic amber by x-ray diffraction (XRD) at high pressures. The p…

[Phys. Rev. E 110, 024501] Published Fri Aug 02, 2024

Stretching an elastic material along one axis typically induces contraction along the transverse axes, a phenomenon known as the Poisson effect. From these strains, one can compute the specific volume, which generally either increases or, in the incompressible limit, remains constant as the material…

[Phys. Rev. E 110, 014502] Published Fri Jul 26, 2024

Polymer loop structure commonly appears in biological phenomena, such as DNA looping and DNA denaturation. When a chain forms a loop, its elastic behavior differs from that of an open chain due to the loss of entropy. In the case of reversible loop formation, interesting behavior emerges related to …

[Phys. Rev. E 110, 014501] Published Tue Jul 16, 2024

The effect of shear flows on the thermal conductivity of polymer melts is investigated using a reversed nonequilibrium molecular-dynamics (RNEMD) method. We extended the original RNEMD method to simultaneously produce spatial gradients of temperature and flow velocity in a single direction. This met…

[Phys. Rev. E 109, 064501] Published Mon Jun 03, 2024

Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together wit…

[Phys. Rev. E 109, 044502] Published Tue Apr 09, 2024

The electromechanical response of polymeric soft matter to applied electric fields is of fundamental scientific interest as well as relevant to technologies for sensing and actuation. Several existing theoretical and numerical approaches for polarizable polymers subject to a combined applied electri…

[Phys. Rev. E 109, 044501] Published Wed Apr 03, 2024

Physical networks formed by ionizable polymers with ionic clusters as crosslinks are controlled by coupled dynamics that transcend from ionic clusters through chain motion to macroscopic response. Here, the coupled dynamics, across length scales, from the ionic clusters to the networks in toluene sw…

[Phys. Rev. E 109, 034501] Published Fri Mar 29, 2024

We use molecular dynamics (MD) simulation and nanofluidic experiments to probe the non-equilibrium transient physics of two nanochannel-confined polymers driven against a permeable barrier in a flow field. For chains with a persistence length $P$ smaller than the channel diameter $D$, both simulation an…

[Phys. Rev. E 109, 024501] Published Tue Feb 20, 2024

It is well established that when multivalent counterions or salts are added to a solution of highly charged polyelectrolytes (PEs), correlation effects can cause charge inversion of the PE, leading to electrophoretic mobility (EM) reversal. In this work, we use coarse-grained molecular-dynamics simu…

[Phys. Rev. E 109, 014501] Published Thu Jan 11, 2024

Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these experiments are valuable, and these relations can be obtained throu…

[Phys. Rev. E 108, 064503] Published Tue Dec 26, 2023

Using the recently introduced parsimonious Metropolis Monte Carlo algorithm, bead-stick polymers both with infinite-range Lennard-Jones interaction and with truncation are simulated. The focus lies on determining the Boyle temperature for long chains with thousands of repeat units and on testing for…

[Phys. Rev. E 108, 064502] Published Mon Dec 18, 2023

We present a theoretical model for predicting the phase behavior of polymer solutions in which phase separation competes with oligomerization. Specifically, we consider scenarios in which the assembly of polymer chains into stoichiometric complexes prevents the chains from phase-separating via attra…

[Phys. Rev. E 108, 064501] Published Thu Dec 07, 2023

When a solution of interpenetrating and entangled long flexible polymer chains is cooled to low enough temperatures, the chains crystallize into thin lamellae of nanoscopic thickness and microscopic lateral dimensions. Depending on the nature of the solvent and growth conditions, the lamellae exhibi…

[Phys. Rev. E 108, 054501] Published Wed Nov 22, 2023

Stochastic athermal networks composed of fibers that deform axially and in bending strain stiffen much faster than thermal networks of axial elements, such as elastomers. Here we investigate the physical origin of stiffening in athermal network materials. To this end, we use models of stochastic net…

[Phys. Rev. E 108, 044502] Published Tue Oct 31, 2023

Polymer ejection has been of interest due to its relation to the viral genome ejection. However, the ejection dynamics of a semiflexible polymer from a nanosphere is not yet understood. Here, a theory is developed for the ejection dynamics of a polymer with total length $L_0$ and persistence length $l$ f…

[Phys. Rev. E 108, 044501] Published Mon Oct 30, 2023

We present the (numerically) exact phase diagram of a magnetic polymer on the Sierpińsky gasket embedded in three dimensions using the renormalization group method. We report distinct phases of the magnetic polymer, including paramagnetic swollen, ferromagnetic swollen, paramagnetic collapsed, and f…

[Phys. Rev. E 108, L042502] Published Wed Oct 04, 2023

Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collap…

[Phys. Rev. E 108, L042501] Published Mon Oct 02, 2023

The thermal properties of coarse-grained knotted copolymer rings fluctuating in a highly screening solution are investigated on a simple cubic lattice using the Wang-Landau Monte Carlo algorithm. The rings contain two kinds of monomers A and B with opposite charges that are subjected to short-range …

[Phys. Rev. E 108, 034503] Published Mon Sep 18, 2023

In this article, we simulate the translocation of a semiflexible homopolymer through an extended pore, driven by both a constant and a time-dependent end-pulled force, employing a model introduced in previous studies. The time dependence is simplistically modeled as a cosine function, and we disting…

[Phys. Rev. E 108, 034501] Published Tue Sep 05, 2023

We study conformational properties of diluted dumbbell polymers composed of two rings attached to both ends of a linear spacer segment. Our investigation involves analytical methods of field theory and bead-spring coarse-grained molecular dynamics simulations. We focus on the influence of the relati…

[Phys. Rev. E 108, 034502] Published Tue Sep 05, 2023

The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is…

[Phys. Rev. E 108, 014501] Published Mon Jul 31, 2023

Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance, through imposing a phenomenological incompressibility const…

[Phys. Rev. E 107, 064501] Published Fri Jun 02, 2023

Using the exact enumeration technique, we have studied the force-induced melting of a DNA hairpin on the face centered cubic lattice for two different sequences which differ in terms of loop closing base pairs. The melting profiles obtained from the exact enumeration technique is consistent with the…

[Phys. Rev. E 107, 054501] Published Tue May 23, 2023

We explore the mechanics and damage of slide-ring gels by developing a discrete model for the mechanics of chain-ring polymer systems that accounts for both crosslink motion and internal chain sliding. The proposed framework utilizes an extendable Langevin chain model to describe the constitutive be…

[Phys. Rev. E 107, 044501] Published Fri Apr 21, 2023

Systematic microcanonical inflection-point analysis of precise numerical results obtained in extensive generalized-ensemble Monte Carlo simulations reveals a bifurcation of the coil-globule transition line for polymers with a bending stiffness exceeding a threshold value. The region, enclosed by the…

[Phys. Rev. E 107, L032501] Published Wed Mar 29, 2023

A diffusive trajectory drawn by the generalized Langevin equation (GLE) for a colloidal particle evokes a random fractal of a static polymer configuration. This article proposes a static GLE-like description that enables the generation of a single configuration of a polymer chain with the noise form…

[Phys. Rev. E 107, 034502] Published Thu Mar 23, 2023

Electrophoretic (EP) mobility reversal is commonly observed for strongly charged macromolecules in multivalent salt solutions. This curious effect takes place, e.g., when a charged polymer, such as DNA, adsorbs excess counterions so that the counterion-dressed surface charge reverses its sign, leadi…

[Phys. Rev. E 107, 034503] Published Thu Mar 23, 2023

Molecular dynamics simulations are used to study the effects of different cations on the permeation of charged polymers through flat capillaries with heights below 2 nm. Interestingly, we found that, despite being monovalent, ${\mathrm{Li}}^{+}$, ${\mathrm{Na}}^{+}$, and ${\mathrm{K}}^{+}$ cations have different effects on polymer permeation, whi…

[Phys. Rev. E 107, 034501] Published Fri Mar 17, 2023

The electrical signal associated with a biopolymer translocating through a nanoscale pore depends on the size, topology, and configuration of each molecule. Building upon recent interest in using solid-state nanopores for studying the topology of knotted and supercoiled DNA, we present experimental …

[Phys. Rev. E 107, 024504] Published Mon Feb 27, 2023

In this paper, we present a self-consistent field theory of macroscopic forces in spatially inhomogeneous flexible chain polyelectrolyte solutions. We derive an analytical expression for a stress tensor which consists of three terms: isotropic hydrostatic stress, electrostatic (Maxwell) stress, and …

[Phys. Rev. E 107, 024503] Published Wed Feb 15, 2023

Salt concentration and confinement effects affect the configuration of polyelectrolyte (PE) brushes due to electrostatic interactions. In this work, we develop a new theoretical model to analyze the electrostatics and swelling-shrinking behavior of two opposing PE brushes. By comparing three length …

[Phys. Rev. E 107, 024502] Published Fri Feb 10, 2023

Polymer models play the special role of elucidating the elementary features describing the physics of long molecules and become essential to interpret the measurements of their magnitudes. In this work the end-to-end distance of an extensible discrete wormlike chain polymer as a function of the appl…

[Phys. Rev. E 107, 024501] Published Mon Feb 06, 2023

Deformable nanoparticles (NPs) offer unprecedented opportunities as dynamic building blocks that can spontaneously reconfigure during assembly in response to environmental cues. Designing reconfigurable materials based on deformable NPs hinges on an understanding of the shapes that can be engineered…

[Phys. Rev. E 107, 014502] Published Tue Jan 10, 2023

We study a classical model of thermally fluctuating polymers confined to two dimensions, experiencing a grooved periodic potential, and subject to pulling forces both along and transverse to the grooves. The equilibrium polymer conformations are described by a mapping to a quantum system with a non-…

[Phys. Rev. E 107, 014501] Published Fri Jan 06, 2023

Entropic repulsion between DNA ring polymers under confinement is a key mechanism governing the spatial segregation of bacterial DNA before cell division. Here we establish that “internal” loops within a modified-ring polymer architecture enhance entropic repulsion between two overlapping polymers c…

[Phys. Rev. E 106, 054502] Published Fri Nov 18, 2022

The conformational and dynamical properties of a tethered semiflexible polymer chain under tangential active force ($f_a$) are studied by using the Langevin dynamics simulation method. The head of the polymer is fixed near an infinite flat surface at $z=0$. The polymer is equilibrated first at $f_a=0$ and t…

[Phys. Rev. E 106, 054501] Published Tue Nov 01, 2022

While the propagation of shocks through monoatomic liquids and solids is now well understood, the response of macromolecular systems to shock compression remains far less studied. Here we use molecular dynamics simulations to study the shock compression of diblock copolymers assembled in a lamellae …

[Phys. Rev. E 106, 044502] Published Tue Oct 04, 2022

We provide a Boltzmann-type kinetic description for dilute polymer solutions based on two-fluid theory. This Boltzmann-type description uses a quasiequilibrium based relaxation mechanism to model collisions between a polymer dumbbell and a solvent molecule. The model reproduces the desired macroscop…

[Phys. Rev. E 106, 044501] Published Mon Oct 03, 2022

The adsorption of a single $\mathit{AB}$ random copolymer (RC) chain onto an inhomogeneous $ab$ surface with a regular periodic pattern is studied theoretically. The problem is considered within the simplest model of a partially directed random walk in two dimensions by using the method of generating functions a…

[Phys. Rev. E 106, 034501] Published Wed Sep 21, 2022

Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized single-chain model, such as the freely jointed chain model. T…

[Phys. Rev. E 106, 024502] Published Mon Aug 15, 2022

Computer simulations are used to characterize the entropic force of one or more polymers tethered to the tip of a hard conical object that interact with a nearby hard flat surface. Pruned-enriched Rosenbluth method Monte Carlo simulations are used to calculate the variation of the conformational fre…

[Phys. Rev. E 106, 024501] Published Thu Aug 11, 2022

Synthetic and natural nanomaterials with self-propelling mechanisms continue to be explored to boost chain mobility beyond normal reptation in the crowded environments of entangled chains. Here we employ scaling theory and numerical simulations to demonstrate that activating one chain end of a singu…

[Phys. Rev. E 106, L022501] Published Tue Aug 09, 2022

A theoretical picture describing the tensile strength ${\sigma }_T$ of elastomers is developed. ${\sigma }_T$ is composed of three factors: (1) the tensile strength of individual polymer load-bearing chains (LBCs) according to Eyring's theory, (2) an occupation number of LBC states using Fermi statistics, and (3) an excl…

[Phys. Rev. E 106, 014505] Published Fri Jul 29, 2022

The glass transition temperature ($T_g$) is one of the most fundamental properties of polymers. $T_g$ is predicted by some theories as a sudden change in a “macroscopic” quantity (e.g., compressibility). However, for systems with “soft” glass transitions where the change is gradual it becomes hard to pinp…

[Phys. Rev. E 106, 014506] Published Fri Jul 29, 2022

Inspired by how the shape deformations in active organisms help them to migrate through disordered porous environments, we simulate active ring polymers in two-dimensional random porous media. Flexible and inextensible active ring polymers navigate smoothly through the disordered media. In contrast,…

[Phys. Rev. E 106, 014504] Published Thu Jul 28, 2022

We devise a deep learning solver inspired by physics-informed neural networks (PINNs) to tackle the polymer self-consistent field theory (SCFT) equations for one-dimensional AB-diblock copolymers. The PINNs framework comprises two parallel feedforward neural networks that separately represent the se…

[Phys. Rev. E 106, 014503] Published Mon Jul 25, 2022

The self-correlation function and corresponding self-intermediate scattering function in Fourier space are important quantities for describing the molecular motions of liquids. This work draws attention to a largely overlooked issue concerning the analysis of these space-time density-density correla…

[Phys. Rev. E 106, 014502] Published Mon Jul 11, 2022

Indentation is a common experimental technique to study the mechanics of polymeric materials. The main advantage of using indentation is this provides a direct correlation between the microstructure and the small-scale mechanical response, which is otherwise difficult within the standard tensile tes…

[Phys. Rev. E 106, 014501] Published Wed Jul 06, 2022

Employing Langevin dynamics simulations, we investigated the kinetics of the collapse transition for a polymer of length $N$ when a particular monomer at a position $1\le X\le N$ is pinned. The results are compared with the kinetics of a free polymer. The equilibrium $\theta$-point separating the coil from the globu…

[Phys. Rev. E 105, 064505] Published Mon Jun 27, 2022

We have studied the structure of complexes of the cationic surfactant dodecyltrimethylammonium bromide (DTAB) with DNA as a function of surfactant to DNA base molar ratio ($R$) and salt concentration. Small-angle x-ray scattering data show the formation of nematic gels at lower and higher salt concent…

[Phys. Rev. E 105, 064504] Published Fri Jun 24, 2022

The conformational and dynamical properties of isolated semiflexible active polar ring polymers are investigated analytically. A ring is modeled as a continuous Gaussian polymer exposed to tangential active forces. The analytical solution of the linear non-Hermitian equation of motion in terms of an…

[Phys. Rev. E 105, L062501] Published Wed Jun 15, 2022

Dynamic instability—the growth, catastrophe, and shrinkage of quasi-one-dimensional filaments—has been observed in multiple biopolymers. Scientists have long understood the catastrophic cessation of growth and subsequent depolymerization as arising from the interplay of hydrolysis and polymerization…

[Phys. Rev. E 105, 064503] Published Wed Jun 08, 2022

A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination of tension and torque involves, in the framework of this met…

[Phys. Rev. E 105, 064502] Published Fri Jun 03, 2022

We use molecular dynamics simulation to probe the nonequilibrium physics of single nanochannel-confined semiflexible polymers in a homogeneous flow field. The flow field compresses the polymer against the end of the nanochannel, simulating an experiment of a nanochannel confined chain compressed aga…

[Phys. Rev. E 105, 064501] Published Wed Jun 01, 2022

Flow of viscoelastic polymer solutions in curved channels exhibits instability caused by the elastic nature of polymers even at low Reynolds numbers. However, scaling of the onset of this purely elastic instability in semidilute polymer solutions has not been previously reported. Here we experimenta…

[Phys. Rev. E 105, L052501] Published Mon May 23, 2022

We have applied zero-time-averaged alternating electric fields to DNA molecules in a cross-shaped nanofluidic slit. We observed a net drift of DNA molecules, the magnitude of which depends on the square of the electric field amplitude. From the rate of accumulation of DNA at the center of the device…

[Phys. Rev. E 105, 054503] Published Wed May 11, 2022

Chirality is a design feature of a number of biomolecules (e.g., collagen). In these molecules, cholesteric (chiral-nematic) behavior emerges from a combination of the tendency for the biopolymers to align (nematic interactions) and for the alignment direction to change with position, rotating aroun…

[Phys. Rev. E 105, 054501] Published Mon May 09, 2022

Polymerized ionic liquids (PILs) are typically single-ion conductors, where one kind of ionic species is either placed as the pendant group to the chain (pendant PILs) or directly incorporated into the polymeric backbone (backbone PILs). This paper compares the thermodynamics, ionic dynamics, and me…

[Phys. Rev. E 105, 054502] Published Mon May 09, 2022

The article presents a comprehensive study of counterion dynamics around a generic linear polyelectrolyte chain with the help of coarse-grained computer simulations. The ion-chain coupling is discussed in the form of binding time, mean-square displacement (MSD) relative to the chain, local ion trans…

[Phys. Rev. E 105, 044501] Published Fri Apr 01, 2022

Surface creasing is a common occurrence in gels under strong enough compression. The transition from smooth to creased surface has been well studied in equilibrium conditions and applied to achieve stimuli-responsive properties. Classical predictions of the creased state, assuming the gel is at equi…

[Phys. Rev. E 105, 034504] Published Thu Mar 31, 2022

The characterization of the interactions between two fully flexible self-avoiding polymers is one of the classic and most important problems in polymer physics. In this paper we measure these interactions in the presence of active fluctuations. We introduce activity into the problem using two of the…

[Phys. Rev. E 105, 034503] Published Thu Mar 24, 2022

Molecular dynamics simulations were employed to investigate the impact of interactions between dendritic polyeclectrolytes and amphiphilic surfactants on the supramolecular complex formation. We recognize two crucial parameters that govern association of surfactants within dendrimers: surfactant hyd…

[Phys. Rev. E 105, 034501] Published Tue Mar 08, 2022

We study the influence of arm architecture on the conformational properties of hybrid star-shaped macromolecules called rosette polymers containing linear and ring grafts connected to a central branching point in a good solvent regime. We utilize analytical methods and molecular dynamics simulations…

[Phys. Rev. E 105, 034502] Published Tue Mar 08, 2022

The natural configuration of an intrinsically curved and twisted filament is uniquely a helix so that it can be referred to as a helical filament. We find that confining a helical filament on a cylinder can create a bistable state. When $c_{0}R=0.5$, where $c_0$ is the intrinsic curvature of filament and $R$ …

[Phys. Rev. E 105, 024502] Published Mon Feb 14, 2022

Knots can spontaneously form in DNA, proteins, and other polymers and affect their properties. These knots often experience spatial confinement in biological systems and experiments. While confinement dramatically affects the knot behavior, the physical mechanisms underlying the confinement effects …

[Phys. Rev. E 105, 024501] Published Wed Feb 09, 2022

We investigate the local elastic properties of polystyrene doped with ${\mathrm{SiO}}_2$ nanoparticles by analyzing the local density fluctuations. The density fluctuations were established from coarse-grained molecular dynamics simulations performed with the MARTINI force field. A significant increase in polysty…

[Phys. Rev. E 105, L012501] Published Tue Jan 11, 2022

We investigate modifications of a stochastic polymer picture through a shift in the boundary between the system and an external environment. A conventional bead-and-spring model serving as the coarse-graining model is given by the Langevin equation for all the monomers subject to white noise. Howeve…

[Phys. Rev. E 105, 014501] Published Mon Jan 03, 2022

This article focuses on a preaveraging description of polymer nonequilibrium stretching, where a single polymer undergoes a transient process from equilibrium to nonequilibrium steady state by pulling one chain end. The preaveraging method combined with mode analysis reduces the original Langevin eq…

[Phys. Rev. E 105, 014502] Published Mon Jan 03, 2022

We demonstrate that size fluctuations close to polymers critical point originate the non-Gaussian diffusion of their center of mass. Static universal exponents $\gamma$ and $\nu$—depending on the polymer topology, on the dimension of the embedding space, and on equilibrium phase—concur to determine the potenti…

[Phys. Rev. E 104, L062501] Published Thu Dec 30, 2021

Living polymers composed of noncovalently bonded building blocks with weak backbone flexibility may self-assemble into thermoresponsive lyotropic liquid crystals. We demonstrate that the reversible polymer assembly and phase behavior can be controlled by the addition of (nonadsorbing) rigid colloida…

[Phys. Rev. E 104, 054505] Published Mon Nov 29, 2021

The globular-stretch transition of a collapsed polymer in low strain rate elongational flow is studied using polymeric protrusion kinetics scaling laws and numerical simulation. Results demonstrate the influence of fluid flow on the occurrence probability of long-length thermally nucleated polymeric…

[Phys. Rev. E 104, 054504] Published Mon Nov 22, 2021

We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on a fcc lattice which explicitly takes into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer strands may cross through each other. By applying the method …

[Phys. Rev. E 104, 054503] Published Thu Nov 18, 2021

In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effec…

[Phys. Rev. E 104, 054502] Published Mon Nov 08, 2021

We study a lattice model of a single magnetic polymer chain, where Ising spins are located on the sites of a lattice self-avoiding walk in $d=2$. We consider the regime where both conformations and magnetic degrees of freedom are dynamic, thus the Ising model is defined on a dynamic lattice and confor…

[Phys. Rev. E 104, 054501] Published Fri Nov 05, 2021

Polymer chains undergoing adsorption are expected to show universal critical behavior which may be investigated using partition function zeros. The focus of this work is the adsorption transition for a continuum chain, allowing for investigation of a continuous range of the attractive interaction an…

[Phys. Rev. E 104, 034502] Published Mon Sep 27, 2021

A fundamental paradigm in polymer physics is that macromolecular conformations in equilibrium can be described by universal scaling laws, being key for structure, dynamics, and function of soft (biological) matter and in the materials sciences. Here we reveal that during diffusion-influenced, nonequ…

[Phys. Rev. E 104, 034501] Published Thu Sep 16, 2021

The spatial correlations of entangled polymer dynamics are examined by molecular dynamics simulations and neutron spin-echo spectroscopy. Due to the soft nature of topological constraints, the initial spatial decays of intermediate scattering functions of entangled chains are, to the first approxima…

[Phys. Rev. E 104, 024503] Published Thu Aug 26, 2021

We present an exact solution for the height distribution of the KPZ equation at any time $t$ in a half space with flat initial condition. This is equivalent to obtaining the free-energy distribution of a polymer of length $t$ pinned at a wall at a single point. In the large $t$ limit a binding transition …

[Phys. Rev. E 104, 024502] Published Fri Aug 13, 2021

We employ a recently derived semirealistic set of coarse-grained interactions to simulate polymer brushes of cis-1,4-polybutadiene grafted on a cuprous-oxide surface within the framework of dissipative particle dynamics. We consider two types of brushes, I and Y, that differ in the way they are conn…

[Phys. Rev. E 104, 024501] Published Wed Aug 11, 2021

We investigate the solution landscapes of the confined diblock copolymer and homopolymer in two-dimensional domain by using the extended Ohta–Kawasaki model. The projection saddle dynamics method is developed to compute the saddle points with mass conservation and construct the solution landscape by…

[Phys. Rev. E 104, 014505] Published Thu Jul 29, 2021

We present the results of a quantitative study of the phase behavior of a model polymer chain with side spheres using two independent computer simulation techniques. We find that the mere addition of side spheres results in key modifications of standard polymer behavior. One obtains a marginally com…

[Phys. Rev. E 104, L012501] Published Mon Jul 26, 2021

We derive exact results for displacement fields that develop as a response to external pinning forces in two-dimensional athermal networks. For a triangular lattice arrangement of particles interacting through soft potentials, we develop a Green's function formalism which we use to derive exact resu…

[Phys. Rev. E 104, 014503] Published Mon Jul 19, 2021

The conformations of biological polyelectrolytes (PEs), such as polysaccharides, proteins, and nucleic acids, affect how they behave and interact with other biomolecules. Relative to neutral polymers, PEs in solution are more locally rigid due to intrachain electrostatic repulsion, the magnitude of …

[Phys. Rev. E 104, 014504] Published Mon Jul 19, 2021

We propose a model of strain-induced crystallization in elastomers, combining Flory's original work with a description of crystallization adopted from the theory of micellar solutions. The experimentally observed hysteresis appears in the model due to a continuous, unidirectional change of the free …

[Phys. Rev. E 104, 014502] Published Wed Jul 14, 2021