https://pmc.polytechnique.fr/pagesperso/dg/cours/biblio/BiophysJ%2087,%203518%20(2004)%20Weiss,%20Elsner,%20Kartberg,%20Nilsson%20[Anomalous%20Subdiffusion%20Is%20a%20Measure%20for%20Cytoplasmic%20Crowding%20in%20Living%20Cells].pdf

Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.

We review in this article the current theoretical understanding of collective and single particle diffusion on surfaces and how it relates to the existing experimental data. We begin with a brief survey of the experimental techniques that have been employed for the measurement of the surface diffusion coefficients. This is followed by a section on the basic concepts involved in this field. In particular, we wish to clarify the relation between jump or exchange motion on microscopic length scales, and the diffusion coefficients which can be defined properly only in the long length and time scales. The central role in this is played by the memory effects. We also discuss the concept of diffusion under nonequilibrium conditions. In the third section, a variety of different theoretical approaches that have been employed in studying surface diffusion such as first principles calculations, transition state theory, the Langevin equation, Monte Carlo and molecular dynamics simulations, and path integral formalism...

Collective and single particle diffusion on surfaces

We review in this article the current theoretical understanding ofcollective and single particle diA usion on surfaces and how it relates to the existing experimental data. We begin with a brief survey of the experimental techniques that have been employed for the measurement of the surface diA usion coeA cients. This is followed by a section on the basic concepts involved in this ®eld. In particular, we wish to clarify the relation between jump or exchange motion on microscopic length scales, and the diA usion coeA cients which can be de®ned properly only in the long length and time scales. The central role in this is played by the memory eA ects. We also discuss the concept of diA usion under nonequilibrium conditions. In the third section, a variety of diA erent theoretical approaches that have been employed in studying surface diA usion such as ®rst principles calculations, transition state theory, the Langevin equation, Monte Carlo and molecular dynamics simulations, and path integral formalism are presented. These ®rst three sections form an introduction to the ®eld of surface diA usion. Section 4 contains subsections that discuss surface diA usion for various systems which have been investigated both experimentally and theoretically. The focus here is not so much on speci®c systems but rather on important issues concerning diA usion meas

Collective and single particle diÄ usion on surfaces

Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent coarse-grained portions of the system under study and allow, therefore, reaching time and length scales that would be otherwise unreachable from microscopic simulations. The method has been conceptually refined since its introduction almost twenty five years ago. This perspective surveys the major conceptual improvements in the original DPD model, along with its microscopic foundation, and discusses outstanding challenges in the field. We summarize some recent advances and suggest avenues for future developments.

Perspective: Dissipative particle dynamics

Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell−cell and cell−substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.

https://www.pnas.org/content/pnas/112/50/15314.full.pdf

Physics of active jamming during collective cellular motion in a monolayer

http://lib.tkk.fi/Diss/2006/isbn9512280590/article4.pdf

How would you integrate the equations of motion in dissipative particle dynamics simulations

Understanding the fundamental properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for topological constraints, i.e., uncrossability of chains, in polymeric liquids using the dissipative particle dynamics (DPD) method. No new length scales or forces are added. To demonstrate that this approach really prevents chain crossings, we study a melt of linear homopolymers. We show that for short chains the model correctly reproduces Rouse-like dynamics whereas for longer chains the dynamics becomes reptational as the chain length is increased---something that is not attainable using standard DPD or other coarse-grained soft potential methods.

/pdf/reptational-dynamics-in-dissipative-particle-dynamics-48fzgmlx4s.pdf

Reptational dynamics in dissipative particle dynamics simulations of polymer melts

Understanding the complex viscoelastic properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for the topological constraints in polymeric liquids using the Dissipative Particle Dynamics (DPD). The same approach is also applicable in other soft potential models. For short chains the model correctly reproduces Rouse-like dynamics whereas for longer chains the dynamics becomes reptational as the chain length is increased - something that is not attainable using standard DPD or other coarse-grained soft potential methods. Importantly, no new length scales or forces need to be added.

In this work we assess the quality and performance of several novel dissipative particle dynamics integration schemes that have not previously been tested independently. Based on a thorough comparison we identify the respective methods of Lowe and Shardlow as particularly promising candidates for future studies of large-scale properties of soft matter systems.

https://arxiv.org/pdf/cond-mat/0302454.pdf

P. Nikunen

Papers

How would you integrate the equations of motion in dissipative particle dynamics simulations

Reptational dynamics in dissipative particle dynamics simulations of polymer melts

Reptational dynamics in dissipative particle dynamics simulations of polymer melts

How would you integrate the equations of motion in dissipative particle dynamics simulations

Non-equilibrium effects in profile evolution measurements of surface diffusion