Brownian Dynamics - Science topic

Attractive colloids diffuse and aggregate to form gels, solid-like particle networks suspended in a fluid. Gravity is known to strongly impact the stability of gels once they are formed. However, its effect on the process of gel formation has seldom been studied. Here, we simulate the effect of gravity on gelation using both Brownian dynamics and a...

When a ferrofluid is magnetized in a strong magnetic field, and then the field is switched off, the magnetization decays from its saturation value to zero. The dynamics of this process are controlled by the rotations of the constituent magnetic nanoparticles, and for the Brownian mechanism, the respective rotation times are strongly influenced by t...

Perception-reaction delays have experimentally been found to cause a spontaneous circling of microswimmers around a targeted center. Here we investigate the many-body version of this experiment with Brownian-dynamics simulations of active particles in a plane. For short delays, the soft spherical discs form a hexagonal colloidal crystallite around...

Active matter systems provide fascinating examples of pattern formation and collective motility without counterpart in equilibrium systems. Here, we employ Brownian dynamics simulations to study the collective motion and self-organization in systems of self-propelled semiflexible filaments, inspired by the gliding motility of filamentous Cyanobacte...

Motion of a driven particle in a two-dimensional (2D) periodic potential of square symmetry is studied by means of Brownian dynamics simulations. The average drift velocity and long time diffusion coefficients are obtained as a function of driving force and temperature. For driving forces above the critical depinning force, a reduction of drift vel...

Many motile microorganisms communicate with each other and their environments via chemical signaling which leads to long-range interactions mediated by self-generated chemical gradients. However, consequences of the interplay between crowding and chemotactic interactions on their collective behavior remain poorly understood. In this work, we use Br...

Solutions of polymer chains are modelled using non-equilibrium Brownian dynamics simulations, with physically associative beads which form reversible crosslinks to establish a system-spanning physical gel network. Rheological properties such as zero-shear viscosity and relaxation modulus are investigated systematically as functions of polymer conce...

One of the most remarkable observations in dense active matter systems is the appearance of long-range velocity correlations without any explicit aligning interaction (of e.g.\ Vicsek type). Here we show that this kind of long range velocity correlation can also be generated in a dense athermal passive system by the inclusion of a very small fracti...

DNA nanostructures are increasingly used for the realization of mechanically active nanodevices and DNA-based nanorobots. A fundamental challenge in this context is the design of molecular machine elements that connect the rigid structural components and are powered in an effective way. Here we investigate a pivot joint that enables rotational moti...

We consider a system of non-interacting particles on a line with initial positions distributed uniformly with density $\rho$ on the negative half-line. We consider two different models: (i) each particle performs independent Brownian motion with stochastic resetting to its initial position with rate $r$ and (ii) each particle performs run and tumbl...

Lipid mesophases are being intensively studied as potential candidates for drug-delivery purposes. Extensive experimental characterization has unveiled a wide palette of release features depending on the nature of the host lipids and of the guest molecule, as well as on the environmental conditions. However, only a few simulation works have address...

The transport of particles through channels is of paramount importance in physics, chemistry, and surface science due to its broad real world applications. Much insight can be gained by observing the transition paths of a particle through a channel and collecting statistics on the lifetimes in the channel or the escape probabilities from the channe...

We investigate the stationary flow of a colloidal gel under an inhomogeneous external shear force using adaptive Brownian dynamics simulations. The interparticle forces are derived from the Stillinger–Weber potential, where the three-body term is tuned to enable network formation and gelation in equilibrium. When subjected to the shear force field,...

We investigate the sedimentation dynamics of a binary mixture, the species of which differ by their Stokes coefficients but are identical otherwise. We analyze the sedimentation dynamics and the morphology of the final deposits using Brownian dynamics simulations for mixtures with a range of sedimentation velocities of both species. In addition, we...

The genomic DNA of bacteria occupies only a fraction of the cell called the nucleoid, although it is not bounded by any membrane and would occupy a volume hundreds of times larger than the cell in the absence of constraints. The two most important contributions to the compaction of the DNA coil are the cross-linking of the DNA by nucleoid proteins...

X-ray Photon Correlation Spectroscopy (XPCS) probes the spontaneous fluctuation in spatial configurations of mixed phases, which can significantly impact the material properties of complex fluid. Tailored material design, however, requires navigation through massive multi-dimensional parameter space which is beyond the bandwidth of current XPCS bea...

Two-dimensional colloidal crystals are of considerable fundamental and practical importance. However, their quality is often low due to the widespread presence of domain walls and defects. In this work, we explored the annealing process undergone by monolayers of superparamagnetic colloids adsorbed onto fluid interfaces in the presence of magnetic...

Within each human cell, different kinds of RNA polymerases and a panoply of transcription factors bind chromatin to simultaneously determine 3D chromosome structure and transcriptional programme. Experiments show that, in some cases, different proteins segregate to form specialised transcription factories; in others they mix together, binding promi...

The self-assembly behavior of diblock copolymer/homopolymer/nanorods hybrid system under oscillation field is performed by using Cell Dynamics Scheme (CDS) and Brownian Dynamics (BD). The effects of the amplitude and frequency of the oscillation field on the formation and evolution of the mixture morphology are investigated systematically. It is fo...

Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules in box-like cavities with strong confinement in one direction and with square and elliptical cross sections in...

A bstract Von Willebrand factor (VWF) is a giant extracellular glycoprotein that carries out a key adhesive function during primary hemostasis. Upon vascular injury and triggered by the shear of flowing blood, VWF establishes specific interactions with several molecular partners in order to anchor platelets to collagen on the exposed sub-endothelia...

Transport of rodlike particles in macromolecular networks is critical for many important biological processes and technological applications. Here, we report that speeding-up dynamics occurs once the rod length L reaches around integral multiple of the network mesh size ax. We find that such a fast diffusion follows the sliding dynamics and demonst...

The motion of ions through pores formed in the inner and outer plasma membranes of Escherichia coli cells during electroporation is simulated in 3-D space using a Brownian dynamics model, which is mostly deterministic following Newtonian mechanics, but has some stochastic properties to account for elastic ionic scattering in water. The pore’s condu...

Emergent non-reciprocal interactions violating Newton's third law are widespread in out-of-equilibrium systems. It has been demonstrated recently that phase separating mixtures with such non-reciprocal interactions between components exhibit travelling states that have no equilibrium counterpart. Using extensive Brownian dynamics simulations, we in...

We re-examine results obtained with the recently proposed density functional theory framework based on forces (force-DFT) [Tschopp et al., Phys. Rev. E 106, 014115 (2022)]. We compare inhomogeneous density profiles for hard sphere fluids to results from both standard density functional theory (DFT) and from computer simulations. Test situations inc...

The package performs molecular-dynamics-like agent-based simulations for models of aligning self-propelled particles in two dimensions such as e.g. the seminal Vicsek model or variants of it. In one class of the covered models, the microscopic dynamics is determined by certain time discrete interaction rules. Thus, it is no Hamiltonian dynamics and...

A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the p...

For classical many-body systems subject to Brownian dynamics we develop a superadiabatic dynamical density functional theory (DDFT) for the description of inhomogeneous fluids out-of-equilibrium. By explicitly incorporating the dynamics of the inhomogeneous two-body correlation functions we obtain superadiabatic forces directly from the microscopic...

The protein SAS-6 forms dimers, which then self-assemble into rings that are critical for the nine-fold symmetry of the centriole organelle. It has recently been shown experimentally that the self-assembly of SAS-6 rings is strongly facilitated on a surface, shifting the reaction equilibrium by four orders of magnitude compared to the bulk. Moreove...

Hydrodynamic interactions play an important role in the dynamics of colloidal systems. In this work, we investigate these interactions in systems with two and three collinear Brownian particles that are moving near a wall. Using the holographic optical tweezers and position tracking techniques, the auto and cross correlation functions were determin...

Advective dispersion of solutes in long thin axisymmetric channels is important to the analysis and design of a wide range of devices, including chemical separations systems and microfluidic chips. Despite extensive analysis of Taylor dispersion in various scenarios, all previous analyses have not been able to provide a simple prediction of the lon...

Transport of particles through channels is of paramount importance in physics, chemistry and surface science due to its broad real world applications. Much insights can be gained by observing the transition paths of a particle through a channel and collecting statistics on the lifetimes in the channel or the escape probabilities from the channel. I...

We present a Brownian dynamics study of a 2D bath of active particles interacting among each other through usual steric interactions and, additionally, via non-reciprocal avoidant orientational interactions. We motivate them by the fact that the two flagella of the alga Chlamydomonas interact sterically with nearby surfaces such that a torque acts...

An easy access to clean water pivots function and development of a modern society. However, it remains arduous to develop energy-efficient, facile, and portable water treatment systems for point-of-use (POU) applications, which is particularly imperative for the safety and resilience of a society during extreme weathers and critical events. Here, w...

In this Brownian dynamics simulation study on the formation of aggregates made of spherical particles, we build on the well-established diffusion-limited cluster aggregation (DLCA) model. We include rotational effects, allow diffusivities to be size-dependent as is physically relevant, and incorporate settling under gravity. We numerically characte...

Magnetic nanoparticles in suspensions provide fascinating model systems to study field-induced effects. Their response to external fields also opens up promising new applications, e.g., in hyperthermia. Despite significant research efforts, several basic questions regarding the influence of external fields on the magnetization dynamics are still op...

We propose a microscopic picture for understanding the nonlinear rheology of supercooled liquids with soft repulsive potentials. Based on Brownian dynamics simulations of supercooled charge-stabilized colloidal suspensions, our analysis shows that the shear thinning of viscosity (η) at large enough shear rates (γ[over ˙]), expressed as η∼γ[over ˙]^...

We investigate the stationary flow of a colloidal gel under an inhomogeneous external shear force using adaptive Brownian dynamics simulations. The interparticle forces are derived from the Stillinger-Weber potential, where the three-body term is tuned to enable network formation and gelation in equilibrium. When subjected to the shear force field,...

The self-assembly of two-dimensional dodecagonal quasicrystals (DDQCs) from patchy particles is investigated by Brownian dynamics simulations. The patchy particle has a five-fold rotational symmetry pattern described by the spherical harmonics Y55. From the formation of the DDQC obtained by an annealing process, we find the following mechanism. The...

Brownian dynamics of a mobile impurity in a bath is affected by spin-orbit coupling~(SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and analyze quantum simulators of this dynamics in cold Bose gases. In particular, we derive a master equation and explore it in a one-dimensional setting. To validate the standard ass...

Single-molecule experiments have now achieved a time resolution allowing observation of transition paths, the brief trajectory segments where the molecule undergoing an unfolding or folding transition enters the energetically or entropically unfavorable barrier region from the folded/unfolded side and exits to the unfolded/folded side, thereby comp...

In the two-dimensional (2D) melting transition of colloidal systems, the hexatic-isotropic (H-I) transition can be either first-order or continuous. However, how particle dynamics differs at a single particle level during these two different melting transitions remains to be disclosed. In this work, by Brownian dynamics (BD) simulations, we have sy...

Eukaryotic chromosomes compact during mitosis and meiosis into elongated cylinders - and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here, we present Brownian-dynamics simulations involving two types of such proteins. The first anchors topologically-stable...

Experiment, theory, and simulation are employed to understand the dispersion of colloidal particles in a periodic array of oscillating harmonic traps generated by optical tweezers. In the presence of trap oscillation, a non-monotonic and anisotropic dispersion is observed. Surprisingly, the stiffest traps produce the largest dispersion at a critica...

For classical many-body systems subject to Brownian dynamics we develop a superadiabatic dynamical density functional theory (DDFT) for the description of inhomogeneous fluids out-of-equilibrium. By explicitly incorporating the dynamics of the inhomogeneous two-body correlation functions we obtain superadiabatic forces directly from the microscopic...

In the last decade, Python-powered physics simulations ecosystem has been growing steadily, allowing greater interoperability, and becoming an important tool in numerical exploration of physical phenomena, particularly in soft matter systems. Driven by the need for fast and precise numerical integration in colloidal dynamics, here we formulate the...

The overdamped Brownian dynamics of a harmonic oscillator is a paradigmatic system in non-equilibrium statistical mechanics, which reliably models relevant stochastic systems such as colloidal particles submitted to optical confinement. In this work, optimal thermal protocols are tailored to minimise the connection time between equilibrium states o...

Crowded environments are known to affect the diffusion of macromolecules, but their effects on the diffusion of small molecules are largely uncharacterized. We investigate how three protein crowders, bovine serum albumin, hen egg-white lysozyme and myoglobin, influence the diffusion rates and interactions of four small molecules: fluorescein, and t...

Recent studies have demonstrated the efficiency of Variational Autoencoders (VAE) to compress high-dimensional implied volatility surfaces. The encoder part of the VAE plays the role of a calibration operation which maps the vol surface into a low dimensional latent space representing the most relevant implicit model parameters. The decoder part of...

von Willebrand factor (VWF) is a multimeric blood protein that acts as a mechanical probe, responding to changes in flow to initiate platelet plug formation. Previously, our labs had shown using single-molecule imaging that shear stress can extend surface-tethered VWF, but paradoxically we found that the required shear stress was higher than report...

We propose a simulation method for Brownian dynamics of hard spheres in one dimension for arbitrary continuous external force fields. It is an event-driven procedure based on the fragmentation and mergers of clusters formed by particles in contact. It allows one to treat particle interactions in addition to the hard-sphere exclusion as long as the...

Nanofibrous networks are the foundation and natural building strategy for all life forms on our planet. Apart from providing structural integrity to cells and tissues, they also provide a porous scaffold allowing transport of substances, where the resulting properties rely on the nanoscale network structure. Recently, there has been a great deal of...

The theory of nuclear spin relaxation in a liquid permeating a solid structure of irregular geometry is examined. The effects of restricted diffusion and the demagnetizing field generated by an inhomogeneous distribution of magnetic susceptibility in the system are explored. A framework comprising Brownian Dynamics, average Hamiltonian theory, and...

We investigate the structural relaxation of a soft-sphere liquid quenched isochorically ($\phi=0.7$) and instantaneously to different temperatures $T_f$ above and below the glass transition. For this, we combine extensive Brownian dynamics simulations and theoretical calculations based on the non-equilibrium self-consistent generalized Langevin equ...

Confinement of biopolymers inside volumes with micro- or nanoscale lateral dimensions is ubiquitous in nature. Investigating the behavior of biopolymers in a confined environment is essential to improve our basic understanding in life sciences. In this work, we present a nanopore gated sub-attoliter silicon nanocavity device, which allows DNA compa...

For suspensions with electromagnetic particles exposed to an external field, we examine the effect of the solidification of the suspending medium on the formation of particle structures, representative of the curing of a photo-reactive resin during stereolithography. To that end, Brownian Dynamics (BD) simulations are examined in which the solidifi...

Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this feat, here we engineer and study DNA-bas...

Modern particle technology is strongly focused on particle and nanoparticle systems with various applications, such as printable electronics or biomedical sensors. In product design, the physical properties of the particles, i.e. particle size, density or composition and in particular interparticle interactions define final macroscopic quantities o...

We revisit a model of semiflexible Gaussian chains proposed by Winkler \textit{et al}, solve the dynamics of the discrete description of the model and derive exact algebraic expressions for some of the most relevant dynamical observables, such as the mean-square displacement of individual monomers, the dynamic structure factor, the end-to-end vecto...

Being motivated by recent progress in nanopore sensing, we develop a theory of the effect of large analytes, or blockers, trapped within the nanopore confines, on diffusion flow of small solutes. The focus is on the nanopore diffusion resistance which is the ratio of the solute concentration difference in the reservoirs connected by the nanopore to...

Diffusion in a macromolecularly crowded environment is essential for many intracellular processes, from metabolism and catalysis to gene transcription and translation. So far, theoretical and experimental work has focused on anomalous subdiffusion, and the effects of interactions, shapes, and composition, while the compactness or softness of macrom...

Compactly, this thesis encompasses two major parts to examine mechanical responses of polymer compounds and two dimensional materials: 1- Molecular dynamics approach is investigated to study transverse impact behavior of polymers, polymer compounds and two dimensional materials. 2- Large deflection of circular and rectangular membranes is examined...

We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asy...

Metastasis is the process by which cancer cells acquire the capability to leave the primary tumor and travel to distant sites. Recent experiments have suggested that the epithelial-mesenchymal transition can regulate invasion and metastasis. Another possible scenario is the collective motion of cells. Recent studies have also proposed a jamming-unj...

Electrostatics is an important part of virus life. Understanding the detailed distribution of charges over the surface of a virus is important to predict its interactions with host cells, antibodies, drugs, and different materials. Using a coarse-grained model of the entire viral envelope developed by D. Korkin and S.-J. Marrink's scientific groups...