32 research outputs found
Modeling real world phenomena using molecular dynamics and continuum simulations
No full textIn the first part of this work, MD trajectory simulations of ice-like argon and amorphous silica aggregates have been performed on the HOPG and crystalline quartz surface. The ice-like argon aggregate showed tendency to deform and fragment upon contact with the surface while the more rigid amorphous SiO 2 aggregate retained its structure and gained rotational energy upon contact with the smoother HOPG surface and got accommodated or stuck when incident on the rougher quartz surface. It was observed that the final total kinetic energy retained by the aggregates decreased as the incident velocity was increased. Fragmentation was observed only from the ice-like argon aggregates. The time of emission of the fragmented Ar atoms was shorter when the ice-like argon was incident on the quartz surface compared to that obtained when the aggregate was incident on the HOPG surface. Also, more number of Ar atoms were emitted when the aggregate was incident on the quartz surface compared to that from the HOPG surface. It was observed that the sticking probability of ice-like argon aggregate is higher than that of the amorphous SiO 2 aggregate when incident on the HOPG surface. The sticking probability of SiO 2 is significantly higher than that of the ice-like argon aggregate at 1.5 km/s on the quartz surface. Dr. Levin was the supervisor for this portion of the thesis only.
In the second part of this work, two types of experimental systems have been modeled, with an aim to replicate the results of experiments and study the dynamics of the respective systems in a more detailed manner. Firstly, continuum simulations have been performed to understand a recently developed method which can potentially reduce the time required to diagnose a bacterial infection by weeks. Secondly, molecular dynamics and ab-initio molecular dynamics simulations have been performed to validate molecular-sieving of organic molecules like cyclohexane and n-hexane through carbon nanotubes. This can potentially lead to a process which can separate liquids which are otherwise very hard to separate.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01The student, Archith Rayabharam, accepted the attached license on 2019-04-22 at 15:10.The student, Archith Rayabharam, submitted this Thesis for approval on 2019-04-22 at 15:42.This Thesis was approved for publication on 2019-04-23 at 15:58.DSpace SAF Submission Ingestion Package generated from Vireo submission #13826 on 2019-08-22 at 16:23:36Made available in DSpace on 2019-08-23T20:48:23Z (GMT). No. of bitstreams: 2
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Previous issue date: 2019-04-23Embargo set by: Seth Robbins for item 112367
Lift date: 2021-08-23T20:48:32Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemLimited Restriction Lifted for Item 112367 on 2021-08-24T09:15:11Z
Transport and selectivity studies of protons across 2D membranes and molecules through angstrom-sized nanopores
No full textSubmission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-12-01The student, Archith Rayabharam, accepted the attached license on 2023-09-04 at 16:15.The student, Archith Rayabharam, submitted this Dissertation for approval on 2023-09-04 at 16:17.This Dissertation was approved for publication on 2023-09-25 at 09:57.DSpace SAF Submission Ingestion Package generated from Vireo submission #19812 on 2024-03-01 at 13:47:40Transport of molecules and ions across membranes has been a widely researched subject over the past few years due to its wide applications ranging from desalination, separation of molecules to batteries and energy storage. My research consists of three such topics, namely, understanding ion transport across 2D membranes with intrinsic defects and their potential application to desalination; and studying the selectivity of hard-to-separate liquids through precise control of the size of angstrom-sized nanopores and sequencing proteins using solid-state nanopores. These studies are performed using computational tools which include classical, ab-initio Molecular Dynamics(MD) and Density Functional Theory (DFT). Ab-initio MD makes use of Density Functional Theory (DFT) to calculate the electron charge distribution, after which the forces and energies are calculated from the resulting charge distribution. In the study of proton transport through 2D membranes, we show that water can dissociate on the surface due to the catalytic activity of 2D cubic Ti2 C membrane. The dissociated protons move into the interstitials present in the membrane and are able to transport across the membrane. We make use of this phenomena to demonstrate quantum desalination in a system where we have a nanopore in the membrane. We show that the pore facilitates the transport of OH− ions across the membrane and combining this with the interstitial transport of protons, we are able to generate water by transporting hydroxide ions and protons through two separate pathways. In addition to interstitial transport of protons, we also study the experimentally observed phenomenon of proton tunneling through hexagonal boron nitride (hBN), where the energy barriers of proton transport through pristine and defective hBN are evaluated. These energy barriers are used to estimate tunneling probabilities and fluxes of protons through the material, and the temperature dependence of these properties are studied. The second study consists of making use of angstrom-sized nanopores of precise diameter to sieve hard-to-separate liquids which have similar properties, for instance hexane and cyclohexane, and water and ethanol. In addition to MD (classical and ab-initio), time-dependent density functional theory (TD-DFT) simulations are used to show that ethanol is indeed excluded from the narrow pores chosen. We identify the diameter of the nanotube required for sieving water from ethanol-water mixtures through Potential of Mean Force (PMF) simulations and calculated the free energy barriers for water and ethanol filling the nanotubes. In the third study, we analyze the sequence of the β-amyloid protein through MD simulations, where we impel the amino acids through a sub-nm silica nanopore under the effect of an electric field. The effects of current, charge, number of water molecules, and radii of gyration of amino acids are leveraged to construct the sequence of β-amyloid
Structural and Dynamical Properties of H<sub>2</sub>O and D<sub>2</sub>O under Confinement
No full textWater (H2O) is of great
societal importance,
and there
has been a significant amount of research on its fundamental properties
and related physical phenomena. Deuterium dioxide (D2O),
known as heavy water, also draws much interest as an important medium
for medical imaging, nuclear reactors, etc. Although many experimental
studies on the fundamental properties of H2O and D2O have been conducted, they have been primarily limited to
understanding the differences between H2O and D2O in the bulk state. In this paper, using path integral molecular
dynamics simulations, the structural and dynamical properties of H2O and D2O in bulk and under nanoscale confinement
in a (14,0) carbon nanotube are studied. We find that in bulk, structural
properties such as bond angle and bond length of D2O are
slightly smaller than those of H2O while D2O
is slightly more structured than H2O. The dipole moment
of D2O tends to be 4% higher than that of H2O, and the hydrogen bonding of D2O is also stronger than
that of H2O. Under nanoscale confinement in a (14,0) carbon
nanotube, H2O and D2O exhibit a smaller bond
length and bond angle. The hydrogen bond number decreases, which demonstrates
a weakened hydrogen bond interaction. Moreover, confinement results
in a lower libration frequency and a higher OH(OD) bond stretching
frequency with an almost unchanged HOH(DOD) bending frequency. The
D2O-filled (14,0) carbon nanotube is found to have a smaller
radial breathing mode than the H2O-filled (14,0) carbon
nanotube
Regret Analysis of Learning-Based Linear Quadratic Gaussian Control with Additive Exploration
No full textThis thesis addresses the Learning-Based Control (LBC) of unknown partially observable systems in the Linear Quadratic (LQ) paradigm. In this setting of learning-based LQ control, the control action influences not only the control performance but also the rate at which the system is being learnt, causing a conflict between learning and control (exploration and exploitation), which is particularly challenging to address. This thesis aims to develop a novel LBC algorithm for unknown partially observable systems in the LQG setting that is computationally efficient and can guarantee an optimal exploration-exploitation trade-off, quantified by a metric called regret. The regret quantifies the cumulative performance gap between the LBC policy and the ideal controller having full knowledge of the true system dynamics. The contributions in this thesis involve a novel LBC algorithm deployed in a two-phase structure. The first phase involves injecting Gaussian input signals to obtain an initial system model. The subsequent second phase deploys the proposed LBC strategy in an episodic setting, where the model is updated for each episode, and the resulting updated LQG controller is applied with additive Gaussian signals for exploration. In addition, the thesis establishes strong theoretical guarantees on optimal regret growth.Mechanical Engineering | Systems and Contro
Prospects for sub-nanometer scale imaging of optical phenomena using electron microscopy
No full textAnomalous interfacial dynamics of single proton charges in binary aqueous solutions
No full textOur understanding of the dynamics of charge transfer between solid surfaces and liquid electrolytes has been hampered by the difficulties in obtaining interface, charge, and solvent-specific information at both high spatial and temporal resolution. Here, we measure at the single charge scale the dynamics of protons at the interface between an hBN crystal and binary mixtures of water and organic amphiphilic solvents (alcohols and acetone), evidencing a marked influence of solvation on interfacial dynamics. Applying single-molecule localization microscopy to emissive crystal defects, we observe correlated activation between adjacent ionizable surface defects, mediated by the transport of single excess protons along the solid/liquid interface. Solvent content has a nontrivial effect on interfacial dynamics, leading at intermediate water fraction to an increased surface diffusivity, as well as an increased affinity of the proton charges to the solid surface. Our measurements evidence the notable role of solvation on interfacial proton charge transport.LBE
Anomalous interfacial dynamics of single proton charges in binary aqueous solutions
No full textInternational audienceOur understanding of the dynamics of charge transfer between solid surfaces and liquid electrolytes has been hampered by the difficulties in obtaining interface, charge, and solvent-specific information at both high spatial and temporal resolution. Here, we measure at the single charge scale the dynamics of protons at the interface between an hBN crystal and binary mixtures of water and organic amphiphilic solvents (alcohols and acetone), evidencing a marked influence of solvation on interfacial dynamics. Applying single-molecule localization microscopy to emissive crystal defects, we observe correlated activation between adjacent ionizable surface defects, mediated by the transport of single excess protons along the solid/liquid interface. Solvent content has a nontrivial effect on interfacial dynamics, leading at intermediate water fraction to an increased surface diffusivity, as well as an increased affinity of the proton charges to the solid surface. Our measurements evidence the notable role of solvation on interfacial proton charge transport
Selective filling of n-hexane in a tight nanopore
No full textPartial funding for Open Access provided by the UMD Libraries' Open Access Publishing Fund.Molecular sieving may occur when two molecules compete for a nanopore. In nearly all known examples, the nanopore is larger than the molecule that selectively enters the pore. Here, we experimentally demonstrate the ability of single-wall carbon nanotubes with a van der Waals pore size of 0.42 nm to separate n-hexane from cyclohexane—despite the fact that both molecules have kinetic diameters larger than the rigid nanopore. This unexpected finding challenges our current understanding of nanopore selectivity and how molecules may enter a tight channel. Ab initio molecular dynamics simulations reveal that n-hexane molecules stretch by nearly 11.2% inside the nanotube pore. Although at a relatively low probability (28.5% overall), the stretched state of n-hexane does exist in the bulk solution, allowing the molecule to enter the tight pore even at room temperature. These insights open up opportunities to engineer nanopore selectivity based on the molecular degrees of freedom.https://doi.org/10.1038/s41467-020-20587-
