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Please use this identifier to cite or link to this item: http://arks.princeton.edu/ark:/88435/dsp0176537414b
 Title: Computer-Aided Understanding of Perturbations in Soft Matter Systems Authors: Uralcan, Betul Advisors: Debenedetti, Pablo G. Contributors: Chemical and Biological Engineering Department Keywords: CapacitanceMolecular simulationProtein FoldingRoom temperature ionic liquidswater Subjects: Chemical engineeringBiophysicsEnergy Issue Date: 2019 Publisher: Princeton, NJ : Princeton University Abstract: This dissertation aims to advance the fundamental knowledge on the structure and dynamics of condensed matter, focusing on systems relevant to emerging problems in biotechnology and energy. We aim to do this using tools and techniques derived from statistical mechanics with the aid of computer simulations, and when appropriate, combined with principles from experimental science. In the ﬁrst part, we study the eﬀects of solution composition on the electrochemical response of a double layer capacitor using electrical impedance spectroscopy measurements and molecular dynamics simulations in a constant potential ensemble. We ﬁnd that capacitance ﬁrst increases with ion concentration following its expected ideal solution behavior but decreases upon approaching the pure ionic liquid limit. In the second part, we use atomistic replica-exchange molecular dynamics simulations and thermodynamic analysis to investigate the eﬀects of ionic liquid-induced perturbations on the folding/unfolding thermodynamics of the Trp-cage miniprotein, and compare our ﬁndings to circular dichroism measurements. We ﬁnd that ionic liquid-induced denaturation resembles cold unfolding, where unfolded states are populated by compact, partially folded structures in which elements of the secondary structure are conserved, while the tertiary structure is disrupted. In the third part, we perform a fully atomistic computational study of Trp-cage in explicit water, and construct the complete stability diagram in the (P,T) plane. At ambient temperature, we ﬁnd that application of pressure shifts the equilibrium of conformational states towards denaturation. Below 250K, the stability of the native fold depends non-monotonically upon pressure. Our simulations also show while cold unfolding and thermal denaturation mechanisms diﬀer signiﬁcantly at ambient pressure, they exhibit progressive similarity at elevated pressures. In the ﬁnal part, we consider three commonly used molecular water models (ST2, TIP4P/2005, and TIP5P) that support the existence of the metastable liquid-liquid transition. We demonstrate that a corresponding-states-like rescaling of pressure and temperature results in a signiﬁcant degree of universality in the pattern of thermodynamic response function extrema. We also report an intriguing correlation between the location of the liquid-liquid critical point, the density extrema locus, and the liquid-vapor stability limit, and demonstrate a similar correlation for two theoretical models. URI: http://arks.princeton.edu/ark:/88435/dsp0176537414b Alternate format: The Mudd Manuscript Library retains one bound copy of each dissertation. Search for these copies in the library's main catalog: catalog.princeton.edu Type of Material: Academic dissertations (Ph.D.) Language: en Appears in Collections: Chemical and Biological Engineering

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