The role of local structure in dynamical arrest

Amorphous solids, or glasses, are distinguished from crystalline solids by their lack of long-range structural order. At the level of two-body structural correlations, glassformers show no qualitative change upon vitrifying from a supercooled liquid. Nonetheless the dynamical properties of a glass are so much slower that it appears to take on the properties of a solid. While many theories of the glass transition focus on dynamical quantities, a solid's resistance to flow is often viewed as a consequence of its structure. Here we address the viewpoint that this remains the case for a glass. Recent developments using higher-order measures show a clear emergence of structure upon dynamical arrest in a variety of glass formers and offer the tantalising hope of a structural mechanism for arrest. However a rigorous fundamental identification of such a causal link between structure and arrest remains elusive. We undertake a critical survey of this work in experiments, computer simulation and theory and discuss what might strengthen the link between structure and dynamical arrest. We move on to highlight the relationship between crystallisation and glass-forming ability made possible by this deeper understanding of the structure of the liquid state, and emphasize the potential to design materials with optimal glassforming and crystallisation ability, for applications such as phase-change memory. We then consider aspects of the phenomenology of glassy systems where structural measures have yet to make a large impact, such as polyamorphism (the existence of multiple liquid states), aging (the time-evolution of non-equilibrium materials below their glass transition) and the response of glassy materials to external fields such as shear.Comment: 70 page

Coupling Lattice Boltzmann and Molecular Dynamics models for dense fluids

We propose a hybrid model, coupling Lattice Boltzmann and Molecular Dynamics models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.Comment: 14 pages, 5 figure

Equations for Stochastic Macromolecular Mechanics of Single Proteins: Equilibrium Fluctuations, Transient Kinetics and Nonequilibrium Steady-State

A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement are stochastic; the former is represented by a master equation for a set of discrete states, and the latter is described by a continuous Smoluchowski equation. Combining these two equations into one, a comprehensive theory for the Brownian dynamics and statistical thermodynamics of single macromolecules arises. This approach is shown to have wide applications. It is applied to protein-ligand dissociation under external force, unfolding of polyglobular proteins under extension, movement along linear tracks of motor proteins against load, and enzyme catalysis by single fluctuating proteins. As a generalization of the classic polymer theory, the dynamic equation is capable of characterizing a single macromolecule in aqueous solution, in probabilistic terms, (1) its thermodynamic equilibrium with fluctuations, (2) transient relaxation kinetics, and most importantly and novel (3) nonequilibrium steady-state with heat dissipation. A reversibility condition which guarantees an equilibrium solution and its thermodynamic stability is established, an H-theorem like inequality for irreversibility is obtained, and a rule for thermodynamic consistency in chemically pumped nonequilibrium steady-state is given.Comment: 23 pages, 4 figure

Molecular dynamics simulations and microscopic hydrodynamics of nanoscale liquid structures

In this thesis, issues pertaining to the dynamics of nanoscale liquid systems, such as nanojets and nanobridges, in vacuum as well as in ambient gaseous conditions, are explored using both extensive molecular dynamics simulations and theoretical analyses. The simulation results serve as ``theoretical experimental data' (together with laboratory experiments when available) for the formulation, implementation, and testing of modified hydrodynamic formulations, including stochastic hydrodynamics. These investigations aim at extending hydrodynamic formulations to the nanoscale regime. In particular, the instability, and breakup of liquid nanobridges and nanojets are addressed in details. As an application of the microscopic hydrodynamics, a heated-nozzle technique to generate and control nanojets is proposed. Both simulations and microscopic hydrodynamic modeling reveal the formation of a ``virtual convergent nozzle', which consists of a narrowing convergent liquid core within a growing evaporative sheath, by the nanojet itself inside the real nozzle. The diameter of the resulting ejected nanojet is much smaller than the diameter of the nozzle. By adjusting the temperature distribution of the real nozzle, the size and shape of the virtual nozzle are changed, which in turn changes the diameter and the direction of the ejected nanojet.Ph.D.Committee Chair: Landman, Uzi; Committee Member: Chou, Mei-Yin; Committee Member: Gao, Jianping; Committee Member: Glezer, Ari; Committee Member: Luedtke, W. D

Atomistically-informed continuum modeling and isogeometric analysis of 2D materials over holey substrates

This work develops, discretizes, and validates a continuum model of a molybdenum disulfide (MoS$_2$) monolayer interacting with a periodic holey silicon nitride substrate via van der Waals (vdW) forces. The MoS$_2$ layer is modeled as a geometrically nonlinear Kirchhoff-Love shell, and vdW forces are modeled by a Lennard-Jones potential, simplified using approximations for a smooth substrate topography. The material parameters of the shell model are calibrated by comparing small-strain tensile and bending tests with atomistic simulations. This model is efficiently discretized using isogeometric analysis (IGA) for the shell structure and a pseudo-time continuation method for energy minimization. The IGA shell model is validated against fully-atomistic calculations for several benchmark problems with different substrate geometries. The continuum simulations reproduce deflections, strains and curvatures predicted by atomistic simulations, which are known to strongly affect the electronic properties of MoS$_2$, with deviations well below the modeling errors suggested by differences between the widely-used reactive empirical bond order and Stillinger-Weber interatomic potentials. Agreement with atomistic results depends on geometric nonlinearity in some cases, but a simple isotropic St. Venant-Kirchhoff model is found to be sufficient to represent material behavior. We find that the IGA discretization of the continuum model has a much lower computational cost than atomistic simulations, and expect that it will enable efficient design space exploration in strain engineering applications. This is demonstrated by studying the dependence of strain and curvature in MoS$_2$ over a holey substrate as a function of the hole spacing on scales inaccessible to atomistic calculations. The results show an unexpected qualitative change in the deformation pattern below a critical hole separation

MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION

Micellar structures have been proposed for potential application in hydrotropy, biomimetics, dispersion and emulsification, enhanced oil recovery, detergency, templating, drug delivery, personal care products, drag reduction, nanoscale reaction vessels, therapeutic gene delivery, bio-catalysis and so on. Though several studies exist, there still remains a gap in the current knowledge on structural response of single micelles in solution to uniaxial extensional flow deformation. These knowledge gaps are possibly due to the inability of traditional experimental studies to investigate micellar properties at the time- and length-scale pertinent to self-assembly and micellar dynamics. To this end, this work aims to utilise coarse-grained molecular dynamics simulations to investigate the dynamics and structural response of various infinitely dilute micellar solutions under the influence of uniaxial extensional flow. Spherical vesicles formed from hexacosanoate anion and octyltrimethylammonium cation; rod-like and worm-like micelles formed from hexacosanoate and palmitate anions; and branched worm-like micelles formed from cetyltrimethylammonium cation and sodium salicylate anion have been parametrised according to the Martini force field formalism. These structures were simulated in equilibrium; under uniaxial extensional flow; and in cessation of uniaxialextensional flow. Changes in micellar structure in uniaxial extensional flow and subsequent stress responses are presented for each micellar system at varying deformation rates. It is observed that structural changes and stress response are dependent on micellar stress relaxation ability whilst undergoing uniaxial deformation. The nature and varying influence of stress relaxation as a function of deformation rate is studied for each structure. Deformation of these structures in a direction normal to their principal orientation is also investigated. It is shown that orientation has a short-term effect on the dynamics and structural evolution of non-isotropic micellar structures. Finally, structural and stress responses following cessation of uniaxial extensional flow are presented

The effective temperature

This review presents the effective temperature notion as defined from the deviations from the equilibrium fluctuation-dissipation theorem in out of equilibrium systems with slow dynamics. The thermodynamic meaning of this quantity is discussed in detail. Analytic, numeric and experimental measurements are surveyed. Open issues are mentioned.Comment: 58 page