Target search by active agents in rugged energy landscapes has remained a challenge because standard enhanced sampling methods do not apply to irreversible dynamics. We overcome this non-equilibrium rare-event problem by developing an algorithm generalizing transition-path sampling to active Brownian dynamics. This method is exemplified and benchmarked for a paradigmatic two-dimensional potential with a high barrier. We find that even in such a simple landscape the structure and kinetics of the ensemble of transition paths change drastically in the presence of activity. Indeed, active Brownian particles reach the target more frequently than passive Brownian particles, following longer and counterintuitive search patterns.
We introduce a generalized Langevin model system for different non-Markovian effects in the well and barrier regions of a potential, and use it to numerically study the dependence of the barrier-crossing time. In the appropriate limits, our model interpolates between the theoretical barrier-crossing-time predictions by Grote and Hynes (GH), as well as by Pollak et al., which for a single barrier memory time can differ by several orders of magnitude. Our model furthermore allows to test an analytic rate theory for space-inhomogeneous memory, which disagrees with our numerical results in the lon…
We study the stochastic resonance (SR) of a flexible polymer surmounting a bistable-potential barrier. Due to the flexibility that can enhance crossing rate and change chain conformations at the barrier, the SR behaviors manifest many features of an entropic SR of a new kind, such as the power amplification peaks at optimal chain lengths and elastic constants as well as the optimal noise strengths. The pronounced peaks that emerge depending on the chain lengths and conformation states suggest novel means of manipulating biopolymers, such as efficient separation methods, within undulating chann…
We numerically study the escape kinetics of a self-propelled Janus particle, carrying a cargo, from a meta-stable state. We assume that the cargo is attached to the Janus particle by a flexible harmonic spring. We take into account the effect of velocity field, created in the fluid due to movements of dimer's components, by considering space-dependent diffusion tensor (Oseen tensor). Our simulation results show that the synchronization between barrier crossing events and rotational relaxation process can enhance escape rate to a large extent. Also, the load carrying capability of a Janus parti…
We consider the motion of semiflexible polymers in double-well potentials. We calculate shape, energy, and effective diffusion constant of kink excitations, and in particular their dependence on the bending rigidity of the semiflexible polymer. For symmetric potentials, the kink motion is purely diffusive whereas kink motion becomes directed in the presence of a driving force on the polymer. We determine the average velocity of the semiflexible polymer based on the kink dynamics. The Kramers escape over the potential barriers proceeds by nucleation and diffusive motion of kink-antikink pairs, …
We investigate non-Markovian barrier-crossing kinetics of a massive particle in one dimension in the presence of a memory function that is the sum of two exponentials with different memory times $τ_1$ and $τ_2$. Our Langevin simulations for the special case where both exponentials contribute equally to the total friction show that the barrier crossing time becomes independent of the longer memory time if at least one of the two memory times is larger than the intrinsic diffusion time. When we associate memory effects with coupled degrees of freedom that are orthogonal to a one-dimensional reac…
We investigate the hopping dynamics of a colloidal particle across a potential barrier and within a viscoelastic, i.e., non-Markovian bath, and report two clearly separated time scales in the corresponding waiting time distributions. While the longer time scale exponentially depends on the barrier height, the shorter one is similar to the relaxation time of the fluid. This short time scale is a signature of the storage and release of elastic energy inside the bath, that strongly increases the hopping rate. Our results are in excellent agreement with numerical simulations of a simple Maxwell mo…
We investigate memory effects in barrier-crossing in the overdamped setting. We focus on the scenario where the hidden degrees of freedom relax on exactly the same time scale as the observable. As a prototypical model, we analyze tagged-particle diffusion in a single file confined to a bi-stable potential. We identify the signatures of memory and explain their origin. The emerging memory is a result of the projection of collective many-body eigenmodes onto the motion of a tagged-particle. We are interested in the "confining" (all background particles in front of the tagged-particle) and "pushi…
A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are inferred from ensemble measurements or the position of a transducer (e.g. an AFM cantilever) as a surrogate variable. Direct visualization is highly desirable. Here, we achieve the direct measurement of barrier crossing trajectories by using optical microscopy to observe position and orientation changes of pairs of Ag nanoparticles in an optical ring trap, i.…
We show that the injection of polymer chains into nanochannels becomes easier as the channel becomes narrower. This counter intuitive result arises because of a decrease in the diffusive time scale of the chains with increasing confinement. The results are obtained by extending the de Gennes blob model of confined polymers, and confirmed by hybrid molecular dynamics - lattice-Boltzmann simulations.
We study the influence of thermal fluctuations on the buckling behavior of thin elastic capsules with spherical rest shape. Thermal fluctuations affect the buckling instability by two mechanisms. On the one hand, thermal fluctuations can renormalize the capsule's elastic properties and its pressure because of anharmonic couplings between normal displacement modes of different wavelengths. This effectively lowers its critical buckling pressure [Kosmrlj and Nelson, Phys. Rev. X 7, 011002 (2017)]. On the other hand, buckled shapes are energetically favorable already at pressures below the classic…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed. Here, we extend the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately sample the conformational ensemble of a classical system in equilibrium. In analogy to describing different electronic configurations, a surface-hopping scheme couples distinct conformational basins beyond the additivi…
We consider the generalization of the Kramers escape over a barrier problem to the case of a long chain molecule. The problem involves the motion of a chain molecule of $N$ segments across a region where the free energy per segment is higher, so that it has to cross a barrier. We consider the limit where the length of the molecule is much larger than the width of the barrier. The width is taken to be sufficiently wide that a coninuum description is applicable to even to the portion over the barrier. We use the Rouse model and analyze the mechanism of crossing a barrier. There can be two domina…
Ohm's law is one of the most central transport rules stating that the total resistance of sequential single resistances is additive. While this rule is most commonly applied to electronic circuits, it also applies to other transport phenomena such as the flow of colloids or nanoparticles through channels containing multiple obstacles, as long as these obstacles are sufficiently far apart. Here we explore the breakdown of Ohm's law for fluids of repulsive colloids driven over two energetic barriers in a microchannel, using real-space microscopy experiments, particle-resolved simulations, and dy…
Transport of a moving V-shaped barrier exposed to a bath of chiral active particles is investigated in a two-dimensional channel. Due to the chirality of active particles and the transversal asymmetry of the barrier position, active particles can power and steer the directed transport of the barrier in the longitudinal direction. The transport of the barrier is determined by the chirality of active particles. The moving barrier and active particles move in the opposite directions. The average velocity of the barrier is much larger than that of active particles. There exist optimal parameters (…
We report a systematic study of the dynamics of self-propelled particles (SPPs) over a one-dimensional periodic potential landscape, which is fabricated on a microgroove-patterned polydimethylsiloxane (PDMS) substrate. From the measured non-equilibrium probability density function of the SPPs, we find that the escape dynamics of the slow-rotating SPPs across the potential landscape can be described by an effective potential, once the self-propulsion force is included into the potential under the fixed angle approximation. This work demonstrates that the parallel microgrooves provide a versatil…
We theoretically and numerically investigate the transport of active colloids to target regions, delimited by asymmetric energy barriers. We show that it is possible to introduce a generalized effective temperature that is related to the local variance of particle velocities. The stationary probability distributions can be derived from a simple diffusion equation in the presence of an inhomogeneous effective temperature resulting from the action of external force fields. In particular, transitions rates over asymmetric energy barriers can be unbalanced by having different effective temperature…
We study the dynamics of an active Brownian particle with a nonlinear friction function located in a spatial cubic potential. For strong but finite damping, the escape rate of the particle over the spatial potential barrier shows a nonmonotonic dependence on the noise intensity. We relate this behavior to the fact that the active particle escapes from a limit cycle rather than from a fixed point and that a certain amount of noise can stabilize the sojourn of the particle on this limit cycle.
We investigate the crossing of an energy barrier by a self-propelled particle described by a Rayleigh friction term. We reveal the existence of a sharp transition in the external force field whereby the amplitude dramatically increases. This corresponds to a saddle point transition in the velocity flow phase space, as would be expected for any type of repulsive force field. We use this approach to rationalize the results obtained by Eddi \emph{et al.} [\emph{Phys. Rev. Lett.} \textbf{102}, 240401 (2009)] who studied the interaction between a drop propelled by its accompanying wave field and a …
Curvatures in the most probable rupture force ($f^*$) versus log-loading rate ($\log{r_f}$) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple barriers or a single barrier with force-dependent transition state. Here, we provide a criterion to select one scenario over another. If the rupture dynamics occurs by crossing a single barrier in a physical free energy profile describing unbinding, the exponent $ν$, from $(1- f^*/f_c)^{1/ν}\sim(\log r_f)$ with $f_c$ being a critical force in the absence of for…
We study the dynamics of one-dimensional active particles confined in a double-well potential, focusing on the escape properties of the system, such as the mean escape time from a well. We first consider a single-particle both in near and far-from-equilibrium regimes by varying the persistence time of the active force and the swim velocity. A non-monotonic behavior of the mean escape time is observed with the persistence time of the activity, revealing the existence of an optimal choice of the parameters favoring the escape process. For small persistence times, a Kramers-like formula with an e…
The dielectric response of non-interacting dipoles is discussed in the framework of the classical model of stochastic reorientations in an asymmetric double well potential (ADWP). In the nonlinear regime, this model exhibits some pecularities in the static response. We find that the saturation behavior of the symmetric double well potential model does not follow the Langevin function and only in the linear regime the standard results are recovered. If a finite asymmetry is assumed, the nonlinear susceptibilities are found to change the sign at a number of characteristic temperatures that depen…
We study non-equilibrium analogues of surface phase transitions in a minimal model of active particles in contact with a purely repulsive potential barrier that mimics a thin porous membrane. Under conditions of bulk motility-induced phase separation, the interaction strength $\varepsilon_w$ of the barrier controls the affinity of the dense phase for the barrier region. We uncover clear signatures of a wetting phase transition as $\varepsilon_w$ is varied. In common with its equilibrium counterpart, the character of this transition depends on the system dimensionality: a continuous transition …
The glassy dynamics of soft harmonic spheres is often mapped onto the dynamics of hard spheres by considering an effective diameter for the soft particles and therefore an effective packing fraction. While in this approach the thermal fluctuations within valleys of the energy landscape are covered, the crossing of energy barriers from one valley into another usually is neglected. Here we argue - motivated by studies of the glass transition based on explorations of the energy landscape - that the crossing of energy barriers can be attributed by an effective decrease of the glass transition pack…
We formulate the theory for steering an active particle with optimal travel time between two locations and apply it to the Mexican hat potential without brim. For small heights the particle can cross the potential barrier, while for large heights it has to move around it. Thermal fluctuations in the orientation strongly affect the path over the barrier. Then we consider a smart active particle and apply reinforcement learning. We show how the active particle learns in repeating episodes to move optimally. The optimal steering is stored in the optimized action-value function, which is able to r…
Active particles (living or synthetic) often move through inhomogeneous environments, such as gradients in light, heat or nutrient concentration, that can lead to directed motion (or taxis). Recent research has explored inhomogeneity in the rheological properties of a suspending fluid, in particular viscosity, as a mechanical (rather than biological) mechanism for taxis. Theoretical and experimental studies have shown that gradients in viscosity can lead to reorientation due to asymmetric viscous forces. In particular, recent experiments with Chlamydomonas reinhardtii algae swimming across sha…
The dynamics of binary colloidal mixture subjected to an external potential barrier is investigated using molecular dynamics simulations. The depletion interactions between the potential barrier and larger components of the mixture alters the dynamics of the system significantly. The larger particles undergo sub-Arrhenius diffusion while smaller particles obey normal Arrhenius diffusion. These results show that quantum phenomena such as tunneling is not required to have sub-Arrhenius diffusion, in contrast to the general agreement in the literature. The depletion interactions between the exter…
Non-equilibrium critical phenomena generally exist in many dynamic systems, like chemical reactions and some driven-dissipative {reactive} particle systems. Here, by using computer simulation and theoretical analysis, we demonstrate the crucial role of the activation barrier on the criticality of dynamic phase transitions in a minimal reactive hard-sphere model. We find that at zero thermal noise, with increasing the activation barrier, the type of transition changes from a continuous conserved directed percolation into a discontinuous dynamic transition by crossing a \emph{tricritical} point.…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but these events are extremely rare if the barrier is much larger than thermal energy. To speed up the slow rate processes in computer simulations, we extend the recently proposed path integral hyperdynamics method to the cases of polymers. We consider the cases where the polymers' radii of gyration are comparable to the distance between the well bottom and the…
The persistent motion of bacteria produces clusters with a stationary cluster size distribution (CSD). Here we develop a minimal model for bacteria in a narrow channel to assess the relative importance of motility diversity (i.e. polydispersity in motility parameters) and confinement. A mixture of run-and-tumble particles with a distribution of tumbling rates (denoted generically by $α$) is considered on a 1D lattice. Particles facing each other cross at constant rate, rendering the lattice quasi-1D. To isolate the role of diversity, the global average $α$ stays fixed. For a binary mixture wit…
Activity significantly enhances the escape rate of a Brownian particle over a potential barrier. Whereas constant activity has been extensively studied in the past, little is known about the effect of time-dependent activity on the escape rate of the particle. In this paper we study the escape problem for a Brownian particle that is transiently active; the activity decreases rapidly during the escape process. Using the effective equilibrium approach we analytically calculate the escape rate, under the assumption that the particle is either completely passive or fully active when crossing the b…
The escape rate of a Brownian particle over a potential barrier is accurately described by the Kramers theory. A quantitative theory explicitly taking the activity of Brownian particles into account has been lacking due to the inherently out-of-equilibrium nature of these particles. Using an effective equilibrium approach [Farage et al., Phys. Rev. E 91, 042310 (2015)] we study the escape rate of active particles over a potential barrier and compare our analytical results with data from direct numerical simulation of the colored noise Langevin equation. The effective equilibrium approach gener…
