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Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Molecular dynamics simulations are used to investigate the atomic mobility and diffusivity of a generalized Frenkel-Kontorova model which takes into account anharmonic (exponential) interaction of atoms subjected to a three-dimensional…
Molecular diffusion measurements are widely used to probe microstructure in materials and living organisms noninvasively. The precise relation of diffusion metrics to microstructure remains a major challenge: In complex samples, it is often…
Systems under external confinement and constraints often show interesting properties. In this thesis, we study some systems under external confinement. We begin by finding out the probability distribution of end-to-end separation of a Worm…
The hardness of materials plays an important role in material design. There are numerous experimental methods to measure the hardness of materials, but theoretical prediction of hardness is challenging. By investigating the correlation…
We analyze the diffusive transport of Brownian particles in narrow channels with periodically varying cross-section. The geometrical confinements lead to entropic barriers, the particle has to overcome in order to proceed in transport…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
Defects are inevitable during the manufacturing processes of materials. Presence of these defects and their dynamics significantly influence the responses of materials. A thorough understanding of dislocation dynamics of different types of…
To the present day, the Beenakker-Mazur (BM) method is the most comprehensive statistical physics approach to the calculation of short-time transport properties of colloidal suspensions. A revised version of the BM method with an improved…
The encounter of diffusing entities underlies a wide range of natural phenomena. The dynamics of these first-passage dynamics are strongly influenced by confining geometries. Confinement modifies microscopic diffusion through conservative…
Detailed calculations of the transport coefficients of a recently introduced particle-based model for fluid dynamics with a non-ideal equation of state are presented. Excluded volume interactions are modeled by means of biased stochastic…
Local diffusion coefficients in disordered systems such as spin glass systems and living cells are highly heterogeneous and may change over time. Such a time-dependent and spatially heterogeneous environment results in irreproducibility of…
We derive diffusive macroscopic equations for the particle and energy density of a system whose time evolution is described by a kinetic equation for the one particle position and velocity function f(r,v,t) that consists of a part that…
Active matter systems under confinement display persistent surface motion and a strong boundary affinity. However, despite extensive studies of their positional dynamics, much less attention has been given to the corresponding orientational…
Linear particle transport in stochastic media is key to such relevant applications as neutron diffusion in randomly mixed immiscible materials, light propagation through engineered optical materials, and inertial confinement fusion, only to…
Mass transport of impurities immersed in a confined quasi-two-dimensional moderately dense granular gas of inelastic hard spheres is studied. The effect of the confinement on granular particles is modeled through a collisional model (the…
Using a numerical approach based on the coupling of the discrete and finite element methods, we explore the variation of the bulk modulus K of soft particle assemblies undergoing isotropic compression. As the assemblies densify under…
Flowing granular materials segregate due to differences in particle size (driven by percolation) and density (driven by buoyancy). Modelling the segregation of mixtures of large/heavy particles and small/light particles is challenging due…
Particle tracking microrheology (PT-$\mu$r) exploits the thermal motion of embedded particles to probe the local mechanical properties of soft materials. Despite its appealing conceptual simplicity, PT-$\mu$r requires calibration procedures…
The collective diffusion coefficient $D_\mathrm{coll}$ is a key quantity for describing the macroscopic transport properties of soft matter systems. However, measuring $D_\mathrm{coll}$ is a fundamental experimental and numerical challenge,…