Amrita Goswami

• Doctor of Philosophy
• Postdoctoral researcher at University of Iceland

d-SEAMS is an open-source, community supported engine for the analysis of molecular dynamics trajectories. Our framework is built around the usage of deterministic cryptographic hashes for the dependency build graph via the nix expression functional syntax. Furthermore the various workflows supported by our engine are exposed to the user via intuit...

We develop intuitive metrics for quantifying complex nucleating systems under confinement. These are shown to arise naturally from the analysis of the topological ring network, and are amenable for use as order parameters for such systems. Drawing inspiration from qualitative visual inspection, we introduce a general topological criterion for eluci...

Inspired by the discovery of high-pressure ice inclusions in diamond, we investigate the rich structural diversity of high-pressure phases of quasi-two-dimensional water constrained by diamond matrices, using molecular dynamics simulations. Monolayer ices formed are structurally similar to monolayer ices constrained by graphene. We report new bilay...

We present a family of general topological criteria, for the determination of structures of quasi-one-dimensional and quasi-two-dimensional ices. Confined systems are characterized by a plethora of diverse ordered structures and interesting hydrogen-bond-networks (HBNs), distinct from those formed in the bulk. Our methodology has no a-priori assump...

Hydrodynamic flow can have complex and far-reaching consequences on the rate of homogeneous nucleation. We present a general formalism for calculating the nucleation rates of simply sheared systems. We have derived an extension to the conventional Classical Nucleation Theory, explicitly embodying the shear rate. Seeded molecular dynamics simulation...

High performance computing (HPC) clusters are typically managed in arestrictive manner; the large user base makes cluster administrators unwillingto allow privilege escalation. Here we discuss existing methods of packagemanagement, including those which have been developed with scalability in mind,and enumerate the drawbacks and advantages of each...

Lava emplacement is a complex physical phenomenon, affected by several factors. These include, but are not limited to features of the terrain, the lava settling process, the effusion rate or total erupted volume, and the probability of effusion from different locations. One method, which has been successfully employed to predict lava flow emplaceme...

The structure of the solvation shell of aqueous Fe+3 ion has been a subject of controversy due to discrepancies between experiments and different levels of theory. We address this issue by performing simulations for a wide range of ion concentrations, using various potential energy functions, supplemented by density functional theory calculations o...

Any optimization algorithm programming interface can be seen as a black-box function with additional free parameters. In this spirit, simulated annealing (SA) can be implemented in pseudo-code within the dimensions of a single slide with free parameters relating to the annealing schedule. Such an implementation, however, necessarily neglects much o...

Any optimization alogrithm programming interface can be seen as a black-box function with additional free parameters. In this spirit, simulated annealing (SA) can be implemented in pseudo-code within the dimensions of single slide with free parameters relating to the annealing schedule. Such an implementation however, neglects necessarily much of t...

One of the most ubiquitous and technologically important phenomena in nature is the nucleation of homogeneous flowing systems. The microscopic effects of shear on a nucleating system are still imperfectly understood, although in recent years a consistent picture has emerged. The opposing effects of shear can be split into two major contributions fo...

One of the most ubiquitous and technologically important phenomena in nature is the nucleation of homogeneous flowing systems. The microscopic effects of shear on a nucleating system are still imperfectly understood, although in recent years a consistent picture has emerged. The opposing effects of shear can be split into two major contributions fo...

Using molecular simulations and a modified classical nucleation theory, we study the nucleation, under flow, of a variety of liquids: different water models, Lennard-Jones, and hard sphere colloids. Our approach enables us to analyze a wide range of shear rates inaccessible to brute-force simulations. Our results reveal that the variation of the nu...

Properties of crystalline and amorphous materials are characterized by the underlying long-range and local crystalline order. Deformations and defects are structural hallmarks of plasticity, ice formation, and crystal growth mechanisms. Partitioning topological networks into constituent crystal building blocks, which is the basis of topological ide...

Spatiotemporal control aspects of pulsed laser experiments rely on the ability to modulate the shape of the generated pulses efficiently. Drawing from current state-of-the-art theoretical aspects of computational simulations to reduce the sim-to-real bottlenecks, we devise a novel schematic for the generation of on-the-fly calibrated pulse trains w...

The study of shear-affected nucleation is a burgeoning field, with far-reaching implications for industry and several branches of science. In this work, we combine a modified CNT approach with equilibrium and non-equilibrium simulations to describe the shear-dependent nucleation behaviour of the TIP4P/2005, TIP4P/Ice, mW water models, and a Lennard...

Hydrodynamic flow can have complex and far-reaching consequences on the rate of homogenous nucleation. We present a general formalism for calculating the nucleation rates of simply sheared systems. We have derived an extension to the conventional Classical Nucleation Theory, explicitly embodying the shear rate. Seeded Molecular Dynamics simulations...

Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, d...

We develop intuitive metrics for quantifying complex nucleating systems under confinement. These are shown to arise naturally from the analysis of the topological ring network, and are amenable for use as order parameters for such systems. Drawing inspiration from qualitative visual inspection, we introduce a general topological criterion for eluci...

d-SEAMS is an open-source, community supported engine for the analysis of molecular dynamics trajectories. Our framework is built around the usage of deterministic cryptographic hashes for the dependency build graph via the nix expression functional syntax. Furthermore the various workflows supported by our engine are exposed to the user via intuit...