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Publications (343)
Connecting active and passive monomers to form partially active polymers can lead to directed transport towards regions of high or low chemical concentration.
Epigenetic inheritance during cell division is essential for preserving cell identity by stabilizing the overall chromatin organisation.Heterochromatin,the condensed and transcriptionally silent fraction of chromatin,is marked by specific epigenetic modifications that are diluted during each cell division.Here we build a physical model,based on the...
The transport of molecules for chemical reactions is critically important in various cellular biological processes. Despite thermal diffusion being prevalent in many biochemical processes, it is unreliable for any sort of directed transport or preferential accumulation of molecules. In this paper we propose a strategy for directed motion in which t...
Directed motion up a concentration gradient is crucial for the survival and maintenance of numerous biological systems, such as sperms moving towards an egg during fertilization or ciliates moving towards a food source. In these systems, chirality - manifested as a rotational torque - plays a vital role in facilitating directed motion. While system...
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. The peculiar properties of this system make it an id...
Polymerlike structures are ubiquitous in nature and synthetic materials. Their configurational and migration properties are often affected by crowded environments leading to nonthermal fluctuations. Here, we study an ideal Rouse chain in contact with a nonhomogeneous active bath, characterized by the presence of active self-propelled agents which e...
Olympic gels are an elusive form of soft matter, comprising a three-dimensional network of mechanically interlocked cyclic molecules. In the absence of defined network junctions, the high conformational freedom of the molecules was previously theorized to confer unique mechanical properties to Olympic gels, such as non-linear elasticity and unconve...
Supplementary file to the article "Oscillatory Force Autocorrelations in Equilibrium Odd-Diffusive Systems" Phys. Rev. Lett. 132, 057102 (2024)
Supplementary file to the article "Collisions Enhance Self-Diffusion in Odd Diffusive Systems" Phys. Rev. Lett. 129, 090601 (2022)
The force autocorrelation function (FACF), a concept of fundamental interest in statistical mechanics, encodes the effect of interactions on the dynamics of a tagged particle. In equilibrium, the FACF is believed to decay monotonically in time, which is a signature of slowing down of the dynamics of the tagged particle due to interactions. Here, we...
We use machine learning algorithms to detect the crystalline phase in undercooled melts in molecular dynamics simulations. Our classification method is based on local conformation and environmental fingerprints of individual monomers. In particular, we employ self-supervised auto-encoders to compress the fingerprint information and a Gaussian mixtu...
Polymer brushes, i.e., end-tethered polymer chains on substrates, are sensitive to adaptation, e.g., swelling, adsorption, and reorientation of the surface molecules. This adaptation can originate from a contacting liquid or atmosphere for partially wetted substrates. The macroscopic contact angle of the aqueous drop can depend on both adaptation m...
The probability per unit time for a thermally activated Brownian particle to escape over a potential well is in general well-described by Kramers theory. Kramers showed that the escape time decreases exponentially with increasing barrier height. The dynamics slow down when the particle is charged and subjected to a Lorentz force due to an external...
The Bond Fluctuation Model (BFM) is a highly efficient and versatile method for simulating polymers, membranes and soft matter related materials. Due to its coarse grained nature, the BFM is employed to understand the universal properties of polymers. Solvent effects are often mediated by explicit solvent particles, while implicit solvent models ha...
The probability per unit time for a thermally activated Brownian particle to escape over a potential well is in general well-described by Kramers theory. Kramers showed that the escape time decreases exponentially with increasing barrier height. The dynamics slow down when the particle is charged and subjected to a Lorentz force due to an external...
Despite the fact that the observation of cononsolvency was reported as early as four decades ago, its phase-transition mechanism is still under debate. In this work, we provided a comprehensive study of the phase behaviors of poly(N-isopropylacrylamide) (PNiPAAm) in sulfoxide or sulfone aqueous solutions. We observed a sharp collapse transition of...
We investigate the encapsulation of polymer-tethered nanoparticles (NP) inside block copolymer (BCP) micelles, which turns to the mutual stabilization of BCP micelles and NPs by each other. It has been demonstrated, for the first time, that in the presence of co-solvent, which is selective for the core-forming block, the encapsulation of polymer-te...
We consider polymer brushes in poor solvent that are grafted onto planar substrates and onto the internal and external surfaces of a cylinder using molecular dynamics simulation, self-consistent field (SCF), and mean-field theory. We derive a unified expression for the mean field free energy for the three geometrical classes. While for low grafting...
While the behavior of active colloidal molecules is well studied by now for a constant activity, the effect of activity gradients is much less understood. Here we explore one of the simplest molecules in activity gradients, namely active chiral dimers composed of two particles with opposite active torques of the same magnitude. We show analytically...
It is generally believed that collisions of particles reduce the self-diffusion coefficient. Here we show that in odd-diffusive systems, which are characterized by diffusion tensors with antisymmetric elements, collisions surprisingly can enhance the self-diffusion. In these systems, due to an inherent curving effect, the motion of particles is fac...
We propose a mesoscopic Brownian magneto heat pump made of a single charged Brownian particle that is steered by an external magnetic field. The particle is subjected to two thermal noises from two different heat sources. When confined, the particle performs gyrating motion around a potential energy minimum. We show that such a magneto-gyrator can...
We consider a rigid assembly of two active Brownian particles, forming an active colloidal dimer, in a gradient of activity. We show analytically that depending on the relative orientation of the two particles the active dimer accumulates in regions of either high or low activity, corresponding to, respectively, chemotaxis and antichemotaxis. Certa...
The chain walking (CW) polymerization technique has the unique property of a movable catalyst synthesizing its own path by creating branch-on-branch structures. By successive attachment of monomers, the resulting architecture ranges from dendritic to linear growth depending on the walking rate, which is defined by the ratio of walking steps and rea...
Thermally activated escape of a Brownian particle over a potential barrier is well understood within Kramers theory. When subjected to an external magnetic field, the Lorentz force slows down the escape dynamics via a rescaling of the diffusion coefficient without affecting the exponential dependence on the barrier height. Here, we study the escape...
In molecular dynamics simulations we investigate the self-organized formation of droplets from a continuous flow of incoming nanoparticles. This transformation is facilitated by a cylindrical channel that is decorated with a polymer brush in a marginally poor solvent. We analyze droplet formation and propagation by means of simple scaling arguments...
We propose a mesoscopic Brownian magneto heat pump made of a single charged Brownian particle that is steered by an external magnetic field. The particle is subjected to two thermal noises from two different heat sources. When confined, the particle performs gyrating motion around a potential energy minimum. We show that such a magneto-gyrator can...
While the behavior of active colloidal molecules is well studied by now for a constant activity, the effect of activity gradients is much less understood. Here we explore one of the simplest molecules in activity gradients, namely active chiral dimers composed of two particles with opposite active torques of the same magnitude. We show analytically...
It is generally believed that collisions of particles reduce the self-diffusion coefficient. Here we show that in odd-diffusive systems, which are characterized by diffusion tensors with antisymmetric elements, collisions surprisingly can enhance the self-diffusion. In these systems, due to an inherent curving effect, the motion of particles is fac...
We consider the formation of droplets from a 2-component liquid mixture induced by a large polymer chain that has preferential attraction to one of the components. We assume that the liquid mixture is in a fully miscible state, but far above the critical interaction limit of the two species. We show that the polymer coil acts as a chemical potentia...
We consider a rigid assembly of two active Brownian particles, forming an active colloidal dimer, in a gradient of activity. We show analytically that depending on the relative orientation of the two particles the active dimer accumulates in regions of either high or low activity, corresponding to, respectively, chemotaxis and antichemotaxis. Certa...
Thermally activated escape of a Brownian particle over a potential barrier is well understood within Kramers theory. When subjected to an external magnetic field, the Lorentz force slows down the escape dynamics via a rescaling of the diffusion coefficient without affecting the exponential dependence on the barrier height. Here, we study the escape...
Polymer brushes, consisting of densely end-tethered polymers to a surface, can exhibit rapid and sharp conformational transitions due to specific stimuli, which offer intriguing possibilities for surface-based sensing of the stimuli. The key toward unlocking these possibilities is the development of methods to readily transduce signals from polymer...
We consider the formation of droplets from a 2-component liquid mixture induced by a large polymer chain that has preferential solubility with one of the components. We assume that the liquid mixture is in a fully miscible state, but far above the critical interaction limit of the two species. We show that the polymer coil acts as a chemical potent...
A Brownian particle performs gyrating motion around a potential energy minimum when subjected to thermal noises from two different heat baths. Here, we propose a magneto-gyrator made of a single charged Brownian particle that is steered by an external magnetic field. Key properties, such as the direction of gyration, the torque exerted by the engin...
We simulated the crystallization and melting behavior of entangled polymer melts using molecular dynamics where each chain is subject to a force dipole acting on its ends. This mimics the deformation of chains in a flow field but represents a well-defined equilibrium system in the melt state. Under weak extension within the linear response of the c...
Polymer brush surfaces that alter their physical properties in response to chemical stimuli have the capacity to be used as new surface‐based sensing materials. For such surfaces, detecting the polymer conformation is key to their sensing capabilities. Herein, we report on FRET‐integrated ultrathin (<70 nm) polymer brush surfaces that exhibit stimu...
Different methods for creating Olympic gels are analyzed using computer simulations. First ideal reference samples are obtained from freely interpenetrating semi-dilute solutions and melts of cyclic polymers. The distribution of pairwise concatenations per cyclic molecule is given by a Poisson-distribution and can be used to describe the elastic st...
We study the changes in the conformations of brushes upon the addition of crosslinks between the chains using the bond fluctuation model. The Flory-Rehner model applied to uni-axially swollen networks predicts a collapse for large degrees of crosslinking $q$ proportional to $q^{-1/3}$ in disagreement with our simulation data. We show that the heigh...
Active particles with their characteristic feature of self-propulsion are regarded as the simplest models for motility in living systems. The accumulation of active particles in low activity regions has led to the general belief that chemotaxis requires additional features and at least a minimal ability to process information and to control motion....
FRET chemistry was integrated within stimuli-responsive polymer brush layers on planar substrates for spatial sensing of changing polymer conformations. Sensing was demonstrated for a variety of liquid mixture compositions, including high-resolution observation of lateral differences in polymer conformation at immiscible liquid interfaces (see pict...
Stimulus response of polymer-decorated nanopores/nanochannels is a fascinating topic both in polymer science and modern nanotechnology; however, it is still challenging for standard analytical methods to characterize these switchable nanopores/nanochannels. In this study, based on the physics of polymer translocation, we developed an analytical met...
Densely packed polymer chains grafted to a substrate, especially polymer brushes, have been studied intensively. Of special interest are systems that react to changes in external conditions or”remember” previous conditions. With this focus, we explore the properties of PNiPAAm brushes and relate published work to own results. The co-nonsolvency eff...
The bond fluctuation method is used to simulate both non-concatenated entangled and interpenetrating melts of ring polymers. We find that the swelling of interpenetrating rings upon dilution follows the same laws as for linear chains. Knotting and linking probabilities of ring polymers in semi-dilute solution are analyzed using the HOMFLY polynomia...
Using the bond fluctuation model we study polymer networks obtained by endlinking of symmetric 4-arm star polymers. We consider two types of systems. Solutions of one type (A) of star polymers and solution of two types (A,B) of star polymer where A-type polymers can only crosslink with B-type polymers. We find that network defects in $A$ networks a...
A mean field rate theory description of the homo- and co-polymerization of $f$-functional molecules is developed, which contains the formation of short cyclic structures inside the network. The predictions of this model are compared with Monte-Carlo simulations of cross-linking of star polymers in solution. We find that homo-polymerizations are wel...
The swelling equilibrium of Olympic gels, which are composed of entangled cyclic polymers, is studied by Monte Carlo Simulations. In contrast to chemically crosslinked polymer networks, we observe that Olympic gels made of chains with a \emph{larger} degree of polymerization, $N$, exhibit a \emph{smaller} equilibrium swelling degree, $Q\propto N^{-...
Concatenation and equilibrium swelling of Olympic gels, which are composed of entangled cyclic polymers, is studied by Monte Carlo Simulations. The average number of concatenated molecules per cyclic polymers, $f_n$, is found to depend on the degree of polymerization, $N$, and polymer volume fraction at network preparation, ${\phi}_0$, as $f_n ~ {\...
In this paper, we elucidate a generic mechanism behind strain-induced phase transition in aqueous solutions of silk-inspired biomimetics by atomistic molecular dynamics simulations. We show the results of modeling of homopeptides polyglycine Gly30 and polyalanine Ala30 and a heteropeptide (Gly-Ala-Gly-Ala-Gly-Ser)5, i.e., the simplest and yet relev...
Native cellulose is insoluble in water, despite the high number of hydrogen bonding sites per chain, as molecules preferably hydrogen bond to each other, preventing its use in industrial applications. The modification of cellulose has received considerable recent attention, motivated by the move away from conventional petroleum-based, water-soluble...
Active particles with their characteristic feature of self-propulsion are regarded as the simplest models for motility in living systems. The accumulation of active particles in low activity regions has led to the general belief that chemotaxis requires additional features and at least a minimal ability to process information and to control motion....
Recently, we have shown that a tensile stress applied to chains of polyethylene oxide (PEO) in water reduces the solubility and leads to a phase separation of PEO chains from water with the formation of a two phase region. In this work, we further elucidate the generic mechanism behind strain-induced phase transitions in aqueous PEO solutions with...
We study the motion of a Brownian particle subjected to Lorentz force
due to an external magnetic field. Each spatial degree of freedom of the particle is coupled to a different thermostat. We show that the magnetic field results in correlation between different velocity components in the stationary state. Integrating the velocity
autocorrelation m...
We study the motion of a Brownian particle subjected to Lorentz force due to an external magnetic field. Each spatial degree of freedom of the particle is coupled to a different thermostat. We show that the magnetic field results in correlation between different velocity components in the stationary state. Integrating the velocity autocorrelation m...
Structural forces within aqueous water at a solid interface can significantly change surface reactivity and the affinity of solutes towards it. We show by molecular dynamics simulation how hydrophilic and hydrophobic quartz surfaces perturb the orientational structure of aqueous water, ultimately strengthening dipolar forces between molecules in pr...
In systems with overdamped dynamics, the Lorentz force reduces the diffusivity of a Brownian particle in the plane perpendicular to the magnetic field. The anisotropy in diffusion implies that the Fokker-Planck equation for the probability distribution of the particle acquires a tensorial coefficient. The tensor, however, is not a typical diffusion...
We investigate the self-assembly of cylinder-forming polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) block copolymers (BCP) mixed with metal nanoparticles (NP) coated with short-chain polystyrene (PS) ligands. The NP formed hierarchical superstructures under confinement of cylindrical PS domains of PS-b-P4VP BCP. The complexity of NP superstruc...
In systems with overdamped dynamics, the Lorentz force reduces the diffusivity of a Brownian particle in the plane perpendicular to the magnetic field. The anisotropy in diffusion implies that the Fokker-Planck equation for the probabiliy distribution of the particle acquires a tensorial coefficient. The tensor, however, is not a typical diffusion...
Active Brownian particles (ABPs) are physical models for motility in simple life forms and easily studied in simulations. An open question is to what extent an increase of activity by a gradient of fuel, or food in living systems, results in an evolutionary advantage of actively moving systems such as ABPs over non-motile systems, which rely on the...
We consider the dynamics of a charged active Brownian particle in three dimensions subjected to an external magnetic field. We show that, in the presence of a field gradient, a macroscopic flux emerges from a flux-free system and the density distribution becomes inhomogeneous. The flux is induced by the gradient of the magnetic field only and does...
The Fokker-Planck equation provides a complete statistical description of a particle undergoing random motion in a solvent. In the presence of Lorentz force due to an external magnetic field, the Fokker-Planck equation picks up a tensorial coefficient, which reflects the anisotropy of the particle's motion. This tensor, however, cannot be interpret...
Interaction of single-chain nanoparticles
(SCNPs) with lipid membranes is studied theoretically
based on Monte Carlo simulations using the bond fluctuation
model. SCNPs with a tunable elasticity represent an
intermediate between rigid nanoparticles and flexible polymers. The degree of cross-linking between monomers of the
precursor polymer is the k...
Using Brownian dynamics simulations, the motion of active Brownian particles (ABPs) in the presence of fuel (or 'food') sources is studied. It is an established fact that within confined stationary systems, the activity of ABPs generates density profiles that are enhanced in regions of low activity, which is generally referred to as 'anti-chemotaxi...
Recently developed chain walking (CW) catalysis is an elegant approach to produce materials with controllable structure and properties. However, there is still a lack in understanding, how the reaction mechanism influences the macromolecular structures. In this study, series of dendritic polyethylenes (PE) synthesized by Pd- α –diimine-complex thro...
Co-nonsolvency occurs if a mixture of two good solvents causes the collapse or demixing of polymers into a polymer-rich phase in a certain range of compositions of these two solvents. In this work, we systematically study the co-nonsolvency behavior of poly(N-isopropylacrylamide) brushes of different grafting densities in a series of alcohol–water...
The Fokker-Planck equation provides complete statistical description of a particle undergoing random motion in a solvent. In the presence of Lorentz force due to an external magnetic field, the Fokker-Planck equation picks up a tensorial coefficient, which reflects the anisotropy of the particle's motion. This tensor, however, can not be interprete...
We consider the nonequilibrium dynamics of a charged active Brownian particle in the presence of a space dependent magnetic field. It has recently been shown that the Lorentz force induces a particle flux perpendicular to density gradients, thus preventing a diffusive description of the dynamics. Whereas a passive system will eventually relax to an...
Using molecular dynamics simulations, we study the response of a polymer brush exposed to co-nonsolvent (CNS), which acts as a preferential solvent for the polymer. We investigate a broad range of attractions between CNS and monomers and of grafting densities over the full range of cosolvent volume fractions. We compare our simulation results with...
We consider tendomers, which are formed by pairs of rotaxane molecules where each one consists of a linear chain with $N$ Kuhn segments that are threaded through $m+1$ small rings....
We study dendrimers embedded in a solution of linear chains with various degrees of polymerization and concentrations. We distinguish the term “crowding”, addressing the impact of the polymer environment on the dendrimer, from the term “semidilute”, which refers to the state of the polymer environment only. Depending on the length of linear chains,...
We investigate the consequences of lipid peroxidation on the permeation properties of membranes comprising unsaturated lipid molecules, by means of coarse-grained molecular simulations. After discussion of the impact of peroxidation on the properties of lipid bilayer such as stretching modulus, area per lipid, water permeation, and the distribution...
We reconsider the isothermal equation of state (EOS) for linear homopolymers in good solvents, p=p(c,T), which relates the osmotic pressure p of polymers with the bulk concentration c and the temperature T. The classical scaling theory predicts the EOS in dilute and semidilute regimes. We suggest a generalized EOS that extends the universal behavio...
Alternating block copolymers consisting of diketopyrrolopyrrole and benzothiadiazole electron acceptor units linked together via aromatic five-membered donor heterocycles are studied using a combination of computer simulation techniques and experiments. Four copolymers are modeled starting from their monomers to stacked macromolecules: with two dif...
We use the bond fluctuation model to study the contraction process of two polymer loops with N segments that are connected each to the bottom and top parts of a Feringa engine. The change in the size of the molecules as well as the folding of the two strands follows approximately scaling predictions that are derived by assuming that the strands are...
Diketopyrrolopyrrole (DPP) derivatives are promising compounds for application in organic electronics. Here, we investigate several symmetrical N‐unsubstituted and N‐methyl substituted DPPs which differ in the heteroatom in the aromatic flanks. The conformational, electronic, and optical properties are characterized for single molecules in vacuum o...
Using coarse grained molecular dynamics simulations, we study how functionalized binary brushes may be used to create surfaces whose functionality can be tuned. Our model brushes consist of a mixture of nonresponsive polymers with functionalized responsive polymers. The functional groups switch from an exposed to a hidden state when the conformatio...
Bio-engineered surfaces that aim to induce normal cell behaviour in vitro need to ‘mimic’ the extracellular matrix in a way that allows cell adhesion. In this computational work, several model cell-binding peptides with a minimal cell-adhesive Arg–Gly–Asp sequence are investigated in the bulk as well as immobilised on a soft surface. For this reaso...
Using molecular dynamics simulations and scaling theory, we present a systematic study of the function of cylindrical nanopores which are decorated with polymer brushes. Our focus is on the regimes in which these systems are able to function as switchable gates for bulky nanoparticles. The process of switching is triggered through the addition of a...
Liquid-liquid phase separation leads to the formation of condensed phases that coexist with a fluid. Here we investigate how the positions of a condensed phase can be controlled by using concentration gradients of a regulator that influences phase separation. We consider a mean field model of a ternary mixture where a concentration gradient of a re...
In this study, the cononsolvency transition of poly(N-isopropylacrylamide) (PNiPAAm) brushes in aqueous ethanol mixtures was studied by using Vis-spectroscopic ellipsometry (SE) discussed in conjunction with the adsorption-attraction model. We proved that the cononsolvency transition of PNiPAAm brushes showed features of a volume phase transition,...
Modifying material properties in simple macromolecules like polyethylene (PE) is achieved by different connection modes of ethylene monomers resulting in a plurality of possible topologies - from highly linear to dendritic species. However, the challenge still lies in the experimental identification of the topology and conformation of the isolated...
We study dynamical properties of confined, self-propelled Brownian particles in an inhomogeneous activity profile. Using Brownian dynamics simulations, we calculate the probability to reach a fixed target and the mean first passage time to the target of an active particle. We show that both these quantities are strongly influenced by the inhomogene...
A theoretical concept for phase segregation of polymers in the presence of multicomponent selective solvents is presented. Phase separation is caused by nonspecific attractive interactions between the polymers and a smaller component in the solution instead of repulsion between monomers and solvent molecules. We call the component that adsorbs on t...
Synthetic polymers, nanoparticles, and carbon-based materials have great potential in applications including drug delivery, gene transfection, in vitro and in vivo imaging, and the alteration of biological function. Nature and humans use different design strategies to create nanomaterials: biological objects have emerged from billions of years of e...
