Abstract:
We present and compare different versions of a simple particle pump-model that describes average directed current of repulsively interacting particles in a narrow channel, due to time-varying local potentials. We analyze the model on discrete lattice with particle exclusion, using three choices of potential-dependent hopping rates that obey microscopic reversibility. Treating the strength of the external potential as a small parameter with respect to thermal energy, we present a perturbative calculation to obtain the expression for average directed current. This depends on driving frequency, phase, and particle density. The directed current vanishes as density goes to zero or close packing. For two choices of hopping rates, it reaches maximum at intermediate densities, while for a third choice, it shows a curious current reversal with increasing density. This can be interpreted in terms of a particle-hole symmetry. Stochastic simulations of the model show good agreement with our analytic predictions.

Abstract:
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 Like Chain (WLC) polymer whose ends are positionally (and orientationally) constrained. We use Monte-Carlo simulations (MC) and a theoretical mapping of the WLC to a quantum particle moving on the surface of an unit sphere to find multimodality in Helmholtz ensemble as a generic signature of semi-flexibility. Secondly, we study Laser Induced Freezing using a Kosterlitz-Thouless type renormalization group calculation and a restricted MC simulation to obtain phase diagrams for Hard Disk, Soft Disk and DLVO potentials. They show very good agreement with phase diagrams simulated by other groups. Lastly, we study the strain response and failure mechanism of a two-dimensional solid confined within a hard wall channel using MC and molecular dynamics simulations. We find a reversible plastic failure through solid-smectic coexistence and observe layering transitions. Mean field calculations can capture some of these features. We study the heat transport in this system thorugh nonequilibrium molecular dynamics simulations and find strong signatures of the transitions. We propose a simple free volume calculation that reproduces some qualitative features of the strain response of heat current for small strains.

Abstract:
We show that the mechanical properties of a worm-like-chain (WLC) polymer, of contour length $L$ and persistence length $\l$ such that $t=L/\l\sim{\cal O}(1)$, depend both on the ensemble and the constraint on end-orientations. In the Helmholtz ensemble, multiple minima in free energy near $t=4$ persists for all kinds of orientational boundary conditions. The qualitative features of projected probability distribution of end to end vector depend crucially on the embedding dimensions. A mapping of the WLC model, to a quantum particle moving on the surface of an unit sphere, is used to obtain the statistical and mechanical properties of the polymer under various boundary conditions and ensembles. The results show excellent agreement with Monte-Carlo simulations.

Abstract:
Within the Rayleigh-Helmholtz model of active Brownian particles activity is due to a non-linear velocity dependent force. In the presence of an external trapping potential or a constant force, the steady state of the system breaks detailed balance producing a net entropy. Using molecular dynamics simulations, we obtain the probability distributions of entropy production in these steady states. The distribution functions obey detailed fluctuation theorem for entropy production. Using simulation results, we further show that the steady state response function obeys a modified fluctuation-dissipation relation.

Abstract:
Starting from the pioneering work of G. S. Agarwal [Zeitschrift f\"ur Physik 252, 25 (1972)], we present a unified derivation of a number of modified fluctuation-dissipation relations (MFDR) that relate response to small perturbations around non-equilibrium steady states to steady-state correlations. Using this formalism we show the equivalence of velocity forms of MFDR derived using continuum Langevin and discrete master equation dynamics. The resulting additive correction to the Einstein relation is exemplified using a flashing ratchet model of molecular motors.

Abstract:
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the filament. The stochastic binding-unbinding of the motor proteins and their ability to move along the polymer, generates active forces. As the pulling force reaches a threshold value, the polymer eventually desorbs from the substrate. Performing molecular dynamics simulations of the polymer in presence of a Langevin heat bath, and stochastic motor activity, we obtain desorption phase diagrams. The correlation time for fluctuations in desorbed fraction increases as one approaches complete desorption, captured quantitatively by a power law spectral density. We present theoretical analysis of the phase diagram using mean field approximations in the weakly bending limit of the polymer and performing linear stability analysis. This predicts increase in the desorption force with the polymer bending rigidity, active velocity and processivity of the motor proteins to capture the main features of the simulation results.

Abstract:
We show using computer simulations and mean field theory that a system of particles in two dimensions, when confined laterally by a pair of parallel hard walls within a quasi one dimensional channel, possesses several anomalous structural and mechanical properties not observed in the bulk. Depending on the density $\rho$ and the distance between the walls $L_y$, the system shows structural characteristics analogous to a weakly modulated liquid, a strongly modulated smectic, a triangular solid or a buckled phase. At fixed $\rho$, a change in $L_y$ leads to many reentrant discontinuous transitions involving changes in the number of layers parallel to the confining walls depending crucially on the commensurability of inter-layer spacing with $L_y$. The solid shows resistance to elongation but not to shear. When strained beyond the elastic limit it fails undergoing plastic deformation but surprisingly, as the strain is reversed, the material recovers completely and returns to its original undeformed state. We obtain the phase diagram from mean field theory and finite size simulations and discuss the effect of fluctuations.

Abstract:
We study the phenomenon of laser induced freezing, within a numerical renormalization scheme which allows explicit comparison with a recent defect mediated melting theory. Precise values for the `bare' dislocation fugacities and elastic moduli of the 2-d hard disk system are obtained from a constrained Monte Carlo simulation sampling only configurations {\em without} dislocations. These are used as inputs to appropriate renormalization flow equations to obtain the equilibrium phase diagram which shows excellent agreement with earlier simulation results. We show that the flow equations need to be correct at least up to third order in defect fugacity to reproduce meaningful results.

Abstract:
Starting from a commensurate triangular thin solid strip, confined within two hard structureless walls, a stretch along its length introduces a rectangular distortion. Beyond a critical strain the solid fails through nucleation of "smectic"-like bands. We show using computer simulations and simple density functional based arguments, how a solid-smectic transition mediates the failure. Further, we show that the critical strain introducing failure is {\em inversely} proportional to the channel width i.e. thinner strips are stronger!

Abstract:
We investigate by direct numerical solution of appropriate renormalization flow equations, the validity of a recent dislocation unbinding theory for laser induced freezing/melting in two dimensions. The bare elastic moduli and dislocation fugacities which are inputs to the flow equations are obtained for three different 2-d systems (hard disk, inverse $12^{th}$ power and the Derjaguin-Landau-Verwey-Overbeek potentials) from a restricted Monte Carlo simulation sampling only configurations {\em without} dislocations. We conclude that (a) the flow equations need to be correct at least up to third order in defect fugacity to reproduce meaningful results, (b) there is excellent quantitative agreement between our results and earlier conventional Monte Carlo simulations for the hard disk system and (c) while the qualitative form of the phase diagram is reproduced for systems with soft potentials there is some quantitative discrepancy which we explain.