Bending elasticity of macromolecules: analytic predictions from the wormlike chain model

We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our results go beyond the Hookean regime and explore the nonlinear elastic behaviour of a single molecule. We present analytical formulae for the bend angle distribution and for the moment-angle relation. Our analytical study is compared against numerical Monte Carlo simulations. The functional forms derived here can be applied to fluorescence microscopic studies on actin and DNA. Our results are relevant to recent studies in "kinks" and cyclization in short and intermediate length DNA strands.Comment: 4 page

Testing WWγWW\gamma vertex in radiative muon decay

Large numbers of muons will be produced at facilities developed to probe lepton flavor violating process $\mu\to e\gamma$. We show that by constructing a suitable asymmetry, radiative muon decay $\mu\to e \gamma\nu_\mu\bar{\nu}_e$ can also be used to test the $WW\gamma$ vertex at such facilities. The process has two missing neutrinos in the final state and on integrating their momenta, the partial differential decay rate shows no radiation-amplitude-zero. We establish, however, that an easily separable part of the normalized differential decay rate, odd under the exchange of photon and electron energies, does have a zero in the case of standard model (SM). This "new type of zero" has hitherto not been studied in literature. A suitably constructed asymmetry using this fact, enables a sensitive probe for the $WW\gamma$ vertex beyond the SM. With a simplistic analysis, we find that the $C$ and $P$ conserving dimension four $WW\gamma$ vertex can be probed at ${\cal O}(10^{-2})$ with satisfactory significance level.Comment: 9 pages, 4 figure

Temporal Variability in Ocean Mesoscale and Submesoscale Turbulence

Turbulence in the Ocean is characterized by a highly nonlinear interaction of waves, eddies and jets drawing energy from instabilities of the large-scale flow and spans a wide range of scales. Turbulent mesoscale eddies are well known as the dominant reservoir of kinetic energy in the ocean and are suspected to contribute significantly to the transport of heat, momentum, and chemical tracers, thereby playing an important role in the global climate system. The intermediate-scale flow structures (i.e. the submesoscale), often manifest as fronts, filaments, wakes and coherent vortices and pose considerable theoretical challenges due to the breakdown of balanced dynamics and the overlapping of scales with inertia-gravity waves. The full role of these submesoscale motions in transport and mixing, therefore remains unknown. This thesis is divided into three chapters focusing on different aspects of turbulence in the mesoscale and submesoscale range. In Chapter 1, we develop an analytical framework for understanding the time dependent mesoscale eddy equilibration process in the Southern Ocean using theory and idealized numerical simulations. In the Southern Ocean, conventional wisdom dictates that the equilibrium stratification is determined by a competition between westerly-wind-driven Ekman upwelling and baroclinic eddy restratification. The transient picture however, is not well established. To study the time dependent response of the stratification in the Southern Ocean to changing winds, we derive a simple theoretical framework describing the energetic pathways between wind input, available potential energy (APE), eddy kinetic energy (EKE), and dissipation. By characterizing the phase and amplitude of the APE and EKE response to oscillating wind stress, with a transfer function, we show that the transient ocean response lies between - a high frequency (Ekman) limit, characterized by the isopycnal slopes responding directly to wind stress, and a low frequency ("eddy saturation") limit, wherein a large fraction of the anomalous wind work goes into mesoscale eddies. Both the phase and amplitude responses of EKE and APE predicted by the linear theory agrees with results from numerical simulations using an eddy resolving isopycnal-coordinate model. Furthermore, this theory can be used to explain certain features, like the lagged EKE response to winds, observed in previous modeling studies and observations. In Chapter 2, we investigate the role of submesoscale flows and inertia-gravity waves (IGW) on lateral transport, and lagrangian coherence, using velocity fields and particle trajectories from a high resolution ocean general circulation model (MITgcm llc4320). We use a temporal filter to partially filter the fast timescale processes, which results in a largely rotational/geostrophic flow, with a rapid drop off in energy at scales away from the mesoscales. We calculate and compare various Lagrangian diagnostics from particle advection simulations with these filtered/unfiltered velocities.At large length/time scales, dispersion by filtered and unfiltered velocities is comparable, while at short scales, unfiltered velocities disperse particles much faster. For the temporally filtered velocity fields, we observe strong material coherence similar to previous studies with altimetry derived velocities. When temporal filtering is reduced/removed, this material coherence breaks down with the particles experiencing enhanced vertical motion, which indicates that vertical advection is mainly associated with small scale, high frequency motions embedded within the larger scale flows. This study suggests that Lagrangian diagnostics based on satellite-derived surface geostrophic velocity fields, even with improved spatial resolution, as in the upcoming SWOT mission, may overestimate the presence of coherent structures and underestimate small scale dispersion. These high-frequency unbalanced motions are likely to alias the estimation of surface currents from low temporal resolution satellite altimetry, and the high-wavenumber sea surface height (SSH) variability may represent a dynamically different ageostrophic regime, where geostrophy might not be the best route to infer velocities. In Chapter 3, we explore statistical models based on machine learning (ML) algorithms, as an alternate route to infer surface currents from satellite observable quantities like SSH, wind and temperature. Our model is simply a regression problem with sea surface height, sea surface temperature, windstress (quantities that are directly observable by satellites) as input (regressors) and the surface currents (which are typically inferred by physical models like geostrophy, Ekman etc.) as the output (regressands). To help the model learn physical principles like geostrophy (which relies on taking spatial gradients), we also provide the spatial coordinates and information in the neighboring gridpoints as additional features. Using output from an ocean general circulation model (CESM POP) simulation as data, we first train a linear rigression model on small domains and show that linear models only work up to a certain extent in small localized regions far from the equator (no large variation in the Coriolis parameter f). We then train a deep neural network on the whole globe for a relatively short period of time and use it to make predictions. Even with a short training period, the NN can make fairly accurate predictions of surface currents over most of the global ocean just as well as the physical models themselves. At its present state the NN fails to pick up on some mesoscale and submesoscale turbulent flow features. We discuss some possible ways to address these present problems in future studies

Quantifying Eulerian Eddy Leakiness in an Idealized Model

An idealized eddy‐resolving ocean basin, closely resembling the North Pacific Ocean, is simulated using MITgcm. We identify rotationally coherent Lagrangian vortices (RCLVs) and sea surface height (SSH) eddies based on the Lagrangian and Eulerian framework, respectively. General statistical results show that RCLVs have a much smaller coherent core than SSH eddies with the ratio of radius is about 0.5. RCLVs are often enclosed by SSH anomaly contours, but SSH eddy identification method fails to detect more than half of RCLVs. Based on their locations, two types of eddies are classified into three categories: overlapping RCLVs and SSH eddies, nonoverlapping SSH eddies, and nonoverlapping RCLVs. Using Lagrangian particles, we examine the processes of leakage and intrusion around SSH eddies. For overlapping SSH eddies, over the lifetime, the material coherent core only accounts for about 25% and about 50% of initial water leak from eddy interior. The remaining 25% of water can still remain inside the boundary, but only in the form of filaments outside the coherent core. For nonoverlapping SSH eddies, more water leakage (about 60%) occurs at a faster rate. Guided by the number and radius of SSH eddies, fixed circles and moving circles are randomly selected to diagnose the material flux around these circles. We find that the leakage and intrusion trends of moving circles are quite similar to that of nonoverlapping SSH eddies, suggesting that the material coherence properties of nonoverlapping SSH eddies are not significantly different from random pieces of ocean with the same size

Using time-dependent indirect CPCP asymmetries to measure TT and CPTCPT violation in B0B^0-Bˉ0{\bar B}^0 mixing

Quantum field theory, which is the basis for all of particle physics, requires that all processes respect $CPT$ invariance. It is therefore of paramount importance to test the validity of $CPT$ conservation. In this Letter, we show that the time-dependent, indirect $CP$ asymmetries involving $B$ decays to a $CP$ eigenstate contain enough information to measure $T$ and $CPT$ violation in $B^0$-${\bar B}^0$ mixing, in addition to the standard $CP$-violating weak phases. Entangled $B^0{\bar B}^0$ states are not required (so that this analysis can be carried out at LHCb, as well as at the $B$ factories), penguin pollution need not be neglected, and the measurements can be made even if the $B^0$-${\bar B}^0$ width difference vanishes.Comment: 10 pages, no figures, changes: removed almost all discussion of what can and cannot be done with the method of entangled states; explained that CPT- and T-violating parameters also contribute to CP-violating effects; reorganized the presentation of the paper; added footnotes and reference

Koopman Operator–Based Knowledge-Guided Reinforcement Learning for Safe Human–Robot Interaction

We developed a novel framework for deep reinforcement learning (DRL) algorithms in task constrained path generation problems of robotic manipulators leveraging human demonstrated trajectories. The main contribution of this article is to design a reward function that can be used with generic reinforcement learning algorithms by utilizing the Koopman operator theory to build a human intent model from the human demonstrated trajectories. In order to ensure that the developed reward function produces the correct reward, the demonstrated trajectories are further used to create a trust domain within which the Koopman operator–based human intent prediction is considered. Otherwise, the proposed algorithm asks for human feedback to receive rewards. The designed reward function is incorporated inside the deep Q-learning (DQN) framework, which results in a modified DQN algorithm. The effectiveness of the proposed learning algorithm is demonstrated using a simulated robotic arm to learn the paths for constrained end-effector motion and considering the safety of the human in the surroundings of the robot

Quantifying Eulerian Eddy Leakiness in an Idealized Model

An idealized eddy‐resolving ocean basin, closely resembling the North Pacific Ocean, is simulated using MITgcm. We identify rotationally coherent Lagrangian vortices (RCLVs) and sea surface height (SSH) eddies based on the Lagrangian and Eulerian framework, respectively. General statistical results show that RCLVs have a much smaller coherent core than SSH eddies with the ratio of radius is about 0.5. RCLVs are often enclosed by SSH anomaly contours, but SSH eddy identification method fails to detect more than half of RCLVs. Based on their locations, two types of eddies are classified into three categories: overlapping RCLVs and SSH eddies, nonoverlapping SSH eddies, and nonoverlapping RCLVs. Using Lagrangian particles, we examine the processes of leakage and intrusion around SSH eddies. For overlapping SSH eddies, over the lifetime, the material coherent core only accounts for about 25% and about 50% of initial water leak from eddy interior. The remaining 25% of water can still remain inside the boundary, but only in the form of filaments outside the coherent core. For nonoverlapping SSH eddies, more water leakage (about 60%) occurs at a faster rate. Guided by the number and radius of SSH eddies, fixed circles and moving circles are randomly selected to diagnose the material flux around these circles. We find that the leakage and intrusion trends of moving circles are quite similar to that of nonoverlapping SSH eddies, suggesting that the material coherence properties of nonoverlapping SSH eddies are not significantly different from random pieces of ocean with the same size