Physics
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Item Ultracold Gases in a Two-Frequency Breathing Lattice(2024) Dewan, Aftaab; Rolston, Steven L; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Driven systems have been of particular interest in the field of ultracold atomic gases. Theprecise control and relative purity allows for construction of many novel Hamiltonians. One such system is the ‘breathing’ lattice, where both the frequency and amplitude is modulated in time, much like an accordion. We present the results of a phenomenological investigation of a proposed experiment, one where we apply a two-frequency breathing lattice to an atomic system. The results are surprising, as they indicate the possibility of a phase-dependent transition between nearest-neighbour and beyond nearest-neighbour interactions.Item A UNITED-ATOM REPRESENTATION FOR SPHINGOLIPIDS IN THE CHARMM MOLECULAR DYNAMICS FORCE FIELD(2023) Lucker, Joshua; Klauda, Jeffery B; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The development of the CHARMM force field (FF) in the late 1970’s and early 1980’s was groundbreaking at the time. For the first time, a computer program was created that could simulate biological systems on a macromolecular scale. Starting with the simulation of simple proteins, CHARMM has since expanded to include such macromolecules as nucleic acids and lipids, now being able to model complex biological systems and processes. Force fields like CHARMM can be represented in different ways. For example, force fields can be represented through an all-atom representation, in which all atoms in a system are modeled as distinct interaction units. This representation can be simplified into a united-atom representation, which shall be the primary focus of this thesis. A united atom FF has no explicit interaction sites for hydrogen. Instead, the hydrogens are lumped onto the atoms they are connected to, termed ‘heavy atoms’ as these atoms have a greater atomic weight than hydrogen. The CHARMM FF originally had a united-atom representation for proteins, which was abandoned to focus on all-atom representations. However, in certain cases, such as lipid tails, united-atom representations are often useful in certain situations; as compared to all-atom representations, united-atom models often speed up simulation times, which is useful in the simulation of large enough systems of molecules. Although there are currently united-atom representations for many types of biomolecules in the CHARMM FF, including multiple types of membrane lipids, there has yet to be a united-atom model for sphingolipids, a type of membrane lipid most commonly found in the myelin sheath of neurons, although its presence has been noted in many types of eukaryotic cells. The goal of this thesis is thus to develop such a model and implement it in the CHARMM FF.Item Optical and quantum interferences in strong field ionization and optimal control(2017) Foote, David B.; Hill, Wendell T.; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)For decades, ultrafast laser pulses have been used to probe and control strong-field molecular dynamics, including in optimal control experiments. While these experiments successfully recover the optimal control pulses (OCPs), they have a limitation -- it is generally unknown how the OCP guides the target system to its final state. This thesis is concerned with "unpacking" OCPs to explain how they achieve their control goals. The OCPs that inspired this work consisted of pulse trains; a twin-peaked pulse (TPP) is the simplest example. Consequently, TPPs with variable interpeak delay and relative phase were employed in this work to study ionization, the first step in many control experiments. Two types of interference influence ionization from a TPP: optical interference (OI) between the electric fields of the two peaks, and quantum interference (QuI) between the electron wavepackets produced by the two peaks. Two sets of experiments were performed to determine what roles OI and QuI play in controlling ionization from a TPP and how they in turn influence subsequent molecular dynamics. The first set of experiments measured the total ionization yield induced by the TPPs. It was found that OI was principally responsible for changing the ion yield; QuI-induced oscillations were not observed. Small imperfections in the shape of the TPP (i.e., pedestals and subordinate peaks) were found to have a surprisingly large influence in the OI, highlighting the need for researchers in molecular control experiments to characterize the temporal profile of their pulses accurately. A time-dependent perturbation theory simulation showed that the signatures of QuI in the ionic continuum vanish when measuring {\it total} electron yield, but appear in {\it energy-resolved} electron yields. The second set of experiments measured photoelectron energy distributions from a TPP with a velocity map imager to search for QuI. The experiments were performed at high intensities (~10^14 W/cm^2) where the ponderomotive energy tends to wash out the fine energy structures of QuI. The thesis ends by proposing a modified, low-intensity experiment that will allow for the first unambiguous observation of QuI in non-resonant, multiphoton ionization.Item UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS(2017) Goldtzvik, Yonathan Yitshak; Thirumalai, Devarajan; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Molecular motors are indispensable machines that are in charge of transporting cargoes within living cells. Despite recent advances in the study of these molecules, there is much that we still do not understand regarding the underlying mechanisms that allow them to efficiently move cargoes along polar cellular filaments. In this thesis, I report my investigation on two motor proteins superfamilies, dyneins and kinesins. Using theoretical modeling, we provide fundamental insight into their function. Dynein is a large motor that transports cargo along microtubules towards their negative pole. Unlike other motors, such as conventional kinesin, the motility of dynein is highly stochastic. We developed a novel theoretical approach, which reproduces a wide variety of its properties, including the unique step size distribution observed in experiments. Furthermore, our model enables us to derive several simple expressions that can be fitted to experiment, thus providing a physical interpretation. A less understood aspect of dynein is the complex set of allosteric transitions in response to ATP binding and hydrolysis, and microtubule binding. The resulting conformational transitions propel the motor forward to the minus end of the microtubule. Furthermore, its activity is regulated by external strain. Using coarse grained Brownian dynamics simulations, we show that a couple of insert loops in the AAA2, a sub domain in the AAA+ ring in the motor domain, play an important role in several of the alllosteric pathways. Kinesins are highly processive motor proteins that transport cargo along microtubules toward their positive poles. Experiments show that the kinesin motor domains propel the motor forward by passing each other in a hand-over-hand motion. However, there is a debate as to whether the motor domains do so in a symmetrical manner or an asymmetrical motion. Using coarse grained Brownian dynamics simulations of the kinesin dimer, we show that the kinesin stepping mechanism is influenced by the size of its cargo. Furthermore, we find that stepping occurs by a combinations of both the symmetric and asymmetric mechanisms. The results I present in this thesis are a testimony that theoretical approaches are invaluable to the study of molecular motors.Item COLLISION DYNAMICS OF HIGHLY ORIENTED SUPER ROTOR MOLECULES FROM AN OPTICAL CENTRIFUGE(2017) Murray, Matthew J.; Mullin, Amy S; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Sophisticated optical methods provide some of the most promising tools for complete control of a molecule’s energy and orientation, which enables a more complete understanding of chemical reactivity and structure. This dissertation investigates the collision dynamics of molecular super rotors with oriented angular momentum prepared in an optical centrifuge. Molecules with anisotropic polarizabilities are trapped in the electric field of linearly polarized light and then angularly accelerated from 0 to 35 THz over the duration of the optical pulse. This process drives molecules to extreme rotational states and the ensemble of molecules has a unidirectional sense of rotation determined by the propagation of the optical field. High resolution transient IR absorption spectroscopy of the super rotor molecules reveals the dynamics of collisional energy transfer. These studies show that high energy CO2 and CO rotors release large amounts of translational energy through impulsive collisions. Time-evolution of the translational energy distribution of the CO2 J=0-100 state shows that depletion from low J states involves molecules with sub-thermal velocities. Polarization-dependent Doppler profiles of CO rotors show anisotropic kinetic energy release and reveal a majority population of molecular rotors in the initial plane of rotation. Experimental modifications improved signal to noise levels by a factor of 10, enabling new transient studies in the low-pressure, single-collision regime. Polarization-dependent studies show that CO2 rotors in the J=54-100 states retain their initial angular momentum orientation, and that this effect increases as a function of rotational angular momentum. These studies show that rotating molecules behave like classical gyroscopes. Polarization-dependent measurements of CO2 rotors in the presence of He and Ar buffer gases show that CO2 super rotors are more strongly relaxed by He collisions, demonstrating the importance of rotational adiabaticity in the relaxation process. Quantum scattering calculations of the He-CO2 and Ar-CO2 collision systems were performed to interpret the qualitative features of the experimental results. This work provides a detailed mechanistic understanding of the unique collisional dynamics of super rotor molecules.Item From Structure to Thermodynamics with Local Molecular Field Theory(2013) Remsing, Richard Charles; Weeks, John D; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A fundamental goal of statistical mechanics is to connect a description of the intermolecular interactions and the accompanying microscopic structural details of a molecular system to its macroscopic thermodynamic properties. When the interactions between molecular components are treated with sufficient simplicity, as in an ideal gas or a hard sphere fluid for example, the link between structure and thermodynamics can be apparent. In contrast, when both local and non-local interactions are present in the system, competition between the various short and long ranged forces can lead to surprising thermodynamic behaviors as exemplified by the complexities of liquid water. Local molecular field (LMF) theory provides a physically motivated formalism for systematically decomposing the structure and thermodynamics of molecular systems into portions arising from local and non-local interactions. In this thesis, LMF theory is employed to examine the structure and thermodynamics of molecular systems, with a focus on aqueous solutions. LMF-motivated truncations of classical water models are first developed as analysis tools to explore the roles of the local hydrogen bond network, dispersion interactions, and long ranged multipolar interactions in the determination of sev- eral anomalous thermodynamic properties of bulk water. This type of analysis is then extended to the study the relative importance of hydrogen bonding and inter- facial unbalancing potentials in hydrophobic effects. The underlying ideas of LMF theory are then utilized to study local and non-local interactions in ion solvation. Modifications to classical dielectric continuum theories are explored with a focus on determining the electrostatic potentials inside ionic cores. LMF ideas are then used to develop the concept of a Gaussian test charge. We then argue that this type of test charge is the appropriate generalization of a classical point test charge to probe the dielectric response of molecularly detailed systems and develop an accurate for- malism for the description of the dielectric response to such probes. Finally, a LMF theoretic foundation for performing free energy calculations is developed and tested before concluding the thesis with a discussion of future work involving LMF theory.