Thesis advisor: Udayan Mohanty / The conformational dynamics plays a significant role in a wide range of biological systems, from small RNA molecules to the large-scale ribonucleoprotein assemblies, in which ions are found critical and have notable structural and functional impacts. In the glass-forming liquids, the structural dynamics also calls for further investigations and deeper understandings. To this end, using four distinct chapters, this dissertation discusses the ion-related conformational dynamics in various scales of biomolecular systems, as well as the fluctuation effects in the glass-forming liquids. In chapter 1, we investigate the dynamics of ions and water molecules in the outer solvation sphere of a widely studied 58-nucleotide rRNA fragment. Molecular dynamics (MD) simulations with explicit solvent molecules and atomic details are performed for the RNA fragment in ionic solution. We determine all of the association sites and spatial distributions of residence times for Mg2+, K+, and water molecules in those sites. In accordance to the analysis of the dynamics of the RNA fragment, we provide insights into how the dynamics of ions and water molecules are intricately linked with the kinetics of the RNA fragment. In addition, the long-lived sites for Mg2+ ions identified from the simulation agree with the metal ion locations determined in the X-ray structure. The excess ion atmosphere around the RNA fragment is calculated and compared with the experimental measures. The results from this study indicate that the 58-mer rRNA fragment in ionic solution forms a complex polymer that is encased by a fluctuating network of ions and water. In chapter 2, the conformational dynamics of a large-scale ribonucleoprotein assembly, ribosome, is studied with molecular dynamics simulations with a newly developed model that accounts for electrostatic and ionic effects on the biomolecules. In this study, an all-atom structure based model is constructed with explicit representations of non-hydrogen atoms from biomolecules and diffuse ions. Implicit treatment is applied to the solvent molecules with the solvation effect associated with diffuse ions described by effective potentials. Parameters in this model are refined against explicit solvent simulations and experimental measures. This model with refined parameters is able to capture the excess Mg2+ ions for prototypical RNA systems and their dependence on the Mg2+ concentrations. Motivated by this, we apply the model to a bacterial ribosome and find that the position of the extended L1 stalk region can be controlled by the diffuse ions. This simulation also indicated ion-induced long-range interactions between L1 stalk and tRNA, which provides insights into the impact of ions on the functional rearrangements of ribosome. In chapter 3, we focus on the dynamics of the glass-forming liquids. In this study, we generalized the Adam-Gibbs model of relaxation in glass-forming liquids and take into account the fluctuations in the number of molecules inside the cooperative rearranging region. We obtain the expressions of configurational fractions at the glass-transition temperature with and without the fluctuation effect in Adam-Gibbs model, and determine the configurational fraction for several glass-forming liquids at glass-transition temperature in the absence of fluctuation effects. A connection between the β Kohlrausch-Williams-Watts parameters and the configurational fraction at the glass-transition temperature is also reported in this study. In chapter 4, we apply the model developed in chapter 2 to a ribosome structure to investigate the effects of diffuse ions on the aminoacyl-tRNA (aa-tRNA) accommodation process. The aa-tRNA accommodation is a critical step in the tRNA selection process which serves the purpose of protein synthesis in the ribosome. Experimental and computational efforts were made to reveal the mechanism and the energetic properties of the accommodation process, while the effects from diffuse ions on this process remain elusive. To this end, we design and perform MD simulations of ribosome structure with different treatment of electrostatics and diffuse ions in the system. Simulations with various ionic concentrations are also performed to study the concentration effects. The simulation trajectories indicate that diffuse ions can facilitate the aa-tRNA accommodation process and stabilize the accommodated configurations. In addition, we observe that Mg2+ ions play critical roles in stabilizing the accommodated configurations and a few millimolar change of Mg2+ concentration can alter the tendency of the tRNA configurational change during the accommodation process. This result shed light on the investigations of suitable ionic environment for the tRNA selection in the ribosome. It will be fruitful to extend this strategy into the investigations of other conformational rearrangements in the ribosome, such as tRNA translocation and subunit rotation, which will provide us with deeper understanding about the functional mechanism of the ribosome. / Thesis (PhD) — Boston College, 2021. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

abstract: Broadband dielectric spectroscopy is a powerful technique for understanding the dynamics in supercooled liquids. It generates information about the timescale of the orientational motions of molecular dipoles within the liquid. However, dynamics of liquids measured in the non-linear response regime has recently become an area of significant interest, because additional information can be obtained compared with linear response measurements. The first part of this thesis describes nonlinear dielectric relaxation experiments performed on various molecular glass forming-liquids, with an emphasis on the response at high frequencies (excess wing). A significant nonlinear dielectric effect (NDE) was found to persist in these modes, and the magnitude of this NDE traces the temperature dependence of the activation energy. A time resolved measurement technique monitoring the dielectric loss revealed that for the steady state NDE to develop it would take a very large number of high amplitude alternating current (ac) field cycles. High frequency modes were found to be ‘slaved’ to the average structural relaxation time, contrary to the standard picture of heterogeneity. Nonlinear measurements were also performed on the Johari-Goldstein β-relaxation process. High ac fields were found to modify the amplitudes of these secondary modes. The nonlinear features of this secondary process are reminiscent of those found for the excess wing regime, suggesting that these two contributions to dynamics have common origins. The second part of this thesis describes the nonlinear effects observed from the application of high direct current (dc) bias fields superposed with a small amplitude sinusoidal ac field. For several molecular glass formers, the application of a dc field was found to slow down the system via reduction in configurational entropy (Adam-Gibbs relation). Time resolved measurements indicated that the rise of the non-linear effect is slower than its decay, as observed in the electro-optical Kerr effect. A model was discussed which quantitatively captures the observed magnitudes and time dependencies of the NDE. Asymmetry in these rise and decay times was demonstrated as a consequence of the quadratic field dependence of the entropy change. It was demonstrated that the high bias field modifies the polarization response to the field, even including the zero field limit. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

The work presented in this doctoral thesis employs colloidal suspensions to explore key open problems in condensed matter physics. Colloidal suspensions, along with gels, polymers, emulsions and liquid crystals belong to a family of materials that are collectively labelled as soft matter. Compositionally, colloidal suspensions consist of particles whose size ranges from a few nanometers to a few microns, dispersed in a solvent. A hallmark feature of these systems is that they exhibit Brownian motion, which makes them suitable for investigating statistical mechanical phenomena. Over the last fifteen years or so, colloids have been used extensively as model systems to shed light on a wide array of such phenomena typically observed in atomic systems. The chief reason why colloids are good mimics of atomic systems is their large size and slow dynamics. Unlike atomic systems, the dynamics of colloids can be probed in real time with single-particle resolution, which allows one to establish the link between macroscopic behavior and the microscopic processes that give rise to it. Yet another important feature is that colloidal systems exhibit various phases of matter such as crystals, liquids and glasses, which makes them versatile model systems that can probe a broad class of condensed matter physics problems. The work described in this thesis takes advantage of these lucrative features of colloidal suspensions to gain deeper insights into the physics of glass formation as well as shear-induced anisotropic grain growth in polycrystalline materials. The thesis is organized into two preliminary chapters, four work chapters and a concluding chapter, as follows. Chapter 1 provides an introduction to colloidal suspensions and reviews the chief theo-retical concepts regarding glass formation and grain boundary dynamics that form an integral part of subsequent chapters. Chapter 2 describes the experimental methods used for performing the work presented in the thesis and consists of two parts. The first part describes the protocols followed for synthesizing the size-tunable poly (N-isoprolypacrylamide) (PNIPAm) particles used in our study of shear-induced grain growth. The second part describes the instrumentation and techniques, such as holographic optical tweezers, confocal microscopy, rheology and Bragg diffraction microscopy, used to perform the measurements described in the thesis. Chapter 3 deals with our work on the dynamical facilitation (DF) theory of glass forma-tion. Despite decades of research, it remains to be established whether the transformation of a liquid into a glass is fundamentally thermodynamic or dynamic in origin. While obser-vations of growing length scales are consistent with thermodynamic perspectives, the purely dynamic approach of the DF theory has thus far lacked experimental support. Further, for glass transitions induced by randomly freezing a subset of particles in the liquid phase, theory and simulations support the existence of an underlying thermodynamic phase transi-tion, whereas the DF theory remains unexplored. In Chapter 3, using video microscopy and holographic optical tweezers, we show that dynamical facilitation in a colloidal glass-forming liquid grows with density as well as the fraction of pinned particles. In addition, we observe that heterogeneous dynamics in the form of string-like cooperative motion, which is consid-ered to be consistent with thermodynamic theories, can also emerge naturally within the framework of facilitation. These findings suggest that a deeper understanding of the glass transition necessitates an amalgamation of existing theoretical approaches. In Chapter 4, we further explore the question of whether glass formation is an intrinsi-cally thermodynamic or dynamic phenomenon. A major obstacle in answering this question lies in determining whether relaxation close to the glass transition is dominated by activated hopping, as espoused by various thermodynamic theories, or by the correlated motion of localized excitations, as proposed in the Dynamical Facilitation (DF) approach. In Chapter 4, we surmount this central challenge by developing a scheme based on real space micro-scopic analysis of particle dynamics and applying it to ascertain the relative importance of hopping and facilitation in a colloidal glass-former. By analysing the spatial organization of excitations within cooperatively rearranging regions (CRRs) and examining their parti-tioning into shell-like and core-like regions, we establish the existence of a crossover from a facilitation-dominated regime at low area fractions to a hopping-dominated one close to the glass transition. Remarkably, this crossover coincides with the change in morphology of CRRs predicted by the Random First-Order Transition theory (RFOT), a prominent ther-modynamic framework. Further, we analyse the variation of the concentration of excitations with distance from an amorphous wall and find that the evolution of these concentration profiles with area fraction is consistent with the presence of a crossover in the relaxation mechanism. By identifying regimes dominated by distinct dynamical processes, our study offers microscopic insights into the nature of structural relaxation close to the glass transi-tion. In Chapter 5, we extend our investigation of the glass transition to systems composed of anisotropic particles. The primary motivation for this is to bridge a long-standing di-vide between theories and simulations on one hand, and experiments on molecular liquids on the other. In particular, theories and simulations predominantly focus on simple glass-formers composed of spherical particles interacting via isotropic interactions. Indeed, even the prominent theory of Dynamical Facilitation has not even been formulated to account for anisotropic shapes or interactions. On the other hand, an overwhelming majority of liquids possess considerable anisotropy, both in particle shape as well as interactions. In Chapter 5, we mitigate this situation by developing the DF theory further and applying it to systems with orientational degrees of freedom as well as anisotropic attractive interactions. By analyzing data from experiments on colloidal ellipsoids, we show that facilitation plays a pivotal role in translational as well as orientational relaxation. Further, we demonstrate that the introduction of attractive interactions leads to spatial decoupling of translational and rotational facilitation, which subsequently results in the decoupling of dynamical het-erogeneities. Most strikingly, the DF theory can predict the existence of reentrant glass transitions based on the statistics of localized dynamical events, called excitations, whose duration is substantially smaller than the structural relaxation time. Our findings pave the way for systematically testing the DF approach in complex glass-formers and also establish the significance of facilitation in governing structural relaxation in supercooled liquids. In Chapter 6, we turn our attention away from the glass transition and address the problem of grain growth in sheared polycrystalline materials. The fabrication of functional materials via grain growth engineering implicitly relies on altering the mobilities of grain boundaries (GBs) by applying external fields. While computer simulations have alluded to kinetic roughening as a potential mechanism for modifying GB mobilities, its implications for grain growth have remained largely unexplored owing to difficulties in bridging the disparate length and time scales involved. In Chapter 6, by imaging GB particle dynamics as well as grain network evolution under shear, we present direct evidence for kinetic roughening of GBs and unravel its connection to grain growth in driven colloidal polycrystals. The capillary fluctuation method allows us to quantitatively extract shear-dependent effective mobilities. Remarkably, our experiments reveal that for sufficiently large strains, GBs with normals parallel to shear undergo preferential kinetic roughening resulting in anisotropic enhancement of effective mobilities and hence directional grain growth. Single-particle level analysis shows that the anisotropy in mobility emerges from strain-induced directional enhancement of activated particle hops normal to the GB plane. Finally, in Chapter 7, we present our conclusions and discuss possible future directions.

An increase in the co-operativity in the motion of particles and a growth of a suitably defined dynamical correlation length seem to be generic features exhibited by all liquids upon supercooling. These features have been observed both in experiments and in numerical simulations of glass-forming liquids. Specially designed NMR experiments have estimated that the rough magnitude of this correlation length is of the order of a few nanometers near the glass transition. Simulations also predict that there are regions in the system which are more liquid-like than other regions. A complete theoretical understanding of this behaviour is not available at present. In recent calculations, Berthier, Biroli and coworkers [1, 2] extended the simple mode coupling theory (MCT) to incorporate the effects of dynamic heterogeneity and predicted the existence of a growing dynamical correlation length associated with the cooperativity of the dynamics. MCT also predicts a power law divergence of different dynamical quantities at the mode coupling temperature and at temperatures somewhat higher than the mode coupling temperature, these predictions are found to be consistent with experimental and simulation results. The system size dependence of these quantities should exhibit finite size scaling (FSS) similar to that observed near a continuous phase transition in the temperature range where they show power law growth. Hence we have used the method of finite size scaling in the context of the dynamics of supercooled liquids. In chapter 2, we present the results of extensive molecular dynamics simulations of a model glass forming liquid and extract a dynamical correlation length ξ associated with dynamic heterogeneity by performing a detailed finite size scaling analysis of a four-point dynamic susceptibility χ4(t) [3] and the associated Binder cumulant. We find that although these quantities show the “normal” finite size scaling behaviour expected for a system with a growing correlation length, the relaxation time τ does not. Thus glassy dynamics can not be fully understood in terms of “standard” critical phenomena. Inspired by the success of the empirical Adam-Gibbs relation [4] which relates dynamics with the configurational entropy, we have calculated the configurational entropy for different system sizes and temperatures to explain the nontrivial scaling behaviour of the relaxation time. We find that the behaviour of the relaxation time τ can be explained in terms of the Adam-Gibbs relation [4] for all temperatures and system sizes. This observation raises serious questions about the validity of the mode coupling theory which does not include the effects of the potential energy (or free energy) landscape on the dynamics. On the other hand, in the “random first order transition” theory (RFOT), introduced by Wolynes and coworkers [5], the configurational entropy plays a central role in determining the dynamics. So we also tried to explain our simulation results in terms of RFOT. However, this interpretation has the drawback that the value of one of the exponents of this theory extracted from our numerical results does not satisfy an expected physical bound, and there is no clear explanation for the obtained values of other exponents. Thus we find puzzling values for the exponents relevant to the applicability of RFOT, which are in need of explanation. This can be due to the fact that RFOT focuses only near the glass transition, while all our simulation results are for temperatures far above the glass transition temperature (actually, above the mode coupling temperature). Interestingly, results similar to ours were obtained in a recent analysis [6] of experimental data near the laboratory glass transition, on a large class of glass-forming materials. Thus right now we do not have any theory which can explain our simulation data consistently from all perspectives. There have been some attempts to extend the RFOT analysis to temperatures above the mode coupling temperature [7, 8] and to estimate a length scale associated with the configurational entropy at such temperatures. We compare our results with the predictions arising from these analyses. In chapter 3, we present simulation results that suggest that finite size scaling analysis is probably the only feasible method for obtaining reliable estimates of the dynamical correlation length for supercooled liquids. As mentioned before, although there exists a growing correlation length, the behaviour of all measured quantities (specifically, the relaxation time) is not in accordance with the behaviour expected in “standard” critical phenomena. So one might suspect the results for the correlation length extracted from the scaling analysis. To find out whether the results obtained by doing finite size scaling are correct, we have done simulations of very large system sizes for the same model glass forming liquid. In earlier studies, the correlation length has been extracted from the wave vector dependence of the dynamic susceptibility in the limit of zero wave vector, but to estimate the correlation length with reasonable accuracy one needs data in the small wave vector range. This implies that one needs to simulate very large systems. But as far as we know, in all previous studies typical system sizes of the order of 10, 000 particles have been used to do this analysis. In this chapter we show by comparing results for systems of 28, 000 and 350, 000 particles that these previous estimates are not reliable. We also show that one needs to simulate systems with at least a million particles to estimate the correlation length correctly near the mode coupling temperature and this size increases with decreasing temperature. We compare the correlation length obtained by analyzing the wave vector dependence of the dynamic susceptibility for a 350, 000particle system with the results obtained from the finite size scaling analysis. We were only able to compare the results in the high temperature range due to obvious reasons. However the agreement in the high temperature range shows that the finite size scaling analysis is robust and also establishes the fact that finite size scaling is the only practical method to extract reliable correlation lengths in supercooled liquids. In chapter 4, we present a free energy landscape analysis of dynamic heterogeneity for a monodisperse hard sphere system. The importance of the potential energy landscape for particles interacting with soft potentials is well known in the glass community from the work of Sastry et al. [9] and others, but the hard sphere system which does not have any well defined potential energy landscape also exhibits similar slow dynamics in the high density limit. Thus it is not clear how to treat the hard sphere systems within the same energy landscape formalism. Dasgupta et al. [10, 11, 12, 13, 14, 15] showed that one can explain the slow dynamics of these hard core systems in term of a free energy landscape picture. They and other researchers showed that these system have many aperiodic local minima in its free energy landscape, with free energy lower than that of the liquid. Using the Ramkrishnan-Yussouff free energy functional, we have performed multi parameter variational minimizations to map out the detailed density distribution of glassy free energy minima. We found that the distribution of the widths of local density peaks at glassy minima is spatially heterogeneous. By performing hard sphere event driven molecular dynamics simulation, we show that there exists strong correlation between these density inhomogeneity and the local Debye-Waller factor which provides a measure of the dynamic heterogeneity observed in simulations. This result unifies the system of hard core particles with the other soft core particles in terms of a landscapebased description of dynamic heterogeneity. In chapter 5, we extend the same free energy analysis to a polydisperse system and show that there is a critical polydispersity beyond which the crystal state is not stable and glassy states are thermodynamically stable. We also found a reentrant behaviour in the liquid-solid phase transition within this free-energy based formalism. These results are in qualitative agreement with experimental observations for colloidal systems.