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Biomolecular Coarse-Graining with Latent Variables
Get PDFMolecular Dynamics (MD) is a computational microscope which enables the quantitative assessment of thermodynamic and dynamical behavior of chemical and biological systems. However, the spatiotemporal scales reachable via conventional MD render atomistic MD largely unable to appropriately probe biologically pertinent events computationally. Coarse-grained (CG) modeling expands these spatiotemporal scales through systematic elimination of atomistic degrees of freedom in favor of a CG molecular representation. Bottom-up CG modeling aims to develop an effective Hamiltonian which accurately recapitulates the statistical behavior of the CG degrees of freedom. In this work, bottom-up CG methods are developed and applied in a systematic manner to capture various aspects of lipid phase behavior. First, a general protocol for the development of CG lipid models which exhibit self-assembling behavior, the defining characteristic of amphiphiles, is developed. Second, we build upon this work to develop the first bottom-up CG models of simple lipid domains, i.e., ternary mixtures of bilayers in which cholesterol-induced phase separation is observed. We demonstrate a greater sampling efficiency for bottom-up CG models in comparison to top-down CG models. Third, we develop a machine-learning based virtual particle theory for CGing and demonstrate its utility in capturing solvent-mediated behavior, namely the membrane bending modulus, in implicit solvent models of lipid bilayers. Fourth, we develop an entropy-based approach for the variational optimization of ultra coarse-grained (UCG) ‘internal states’ as well as a relative entropy approach to UCG modeling. We apply these methods in tandem to develop a UCG model of a liquid-vapor interface as well as in capturing phase-coexistence in a ripple-phase bilayer. Lastly, we expand the bottom-up CG formalism to include bosonic and fermionic systems and establish the quantum analogue to the relative entropy principle of CGing and its semiclassical expansion
The Academic Priors Project
No full textThis is the repository for the Academic Priors Project, a research project aiming to understand whether cognitive biases or individual differences in cognitive style can influence academics' beliefs about controversial topics in their fields
You’ve Got a Friend in Me: Social Support and Opioid Treatment Disclosure in a National Sample
No full textResearch has shown social relationships play a central role in recovery from opioid use disorder (OUD), yet little is known about how perceived relational dynamics influence willingness to disclose OUD treatment. Although stigma is a well-documented barrier, less is known about the interpersonal conditions that promote openness about treatment experiences. This study investigates how attitudes towards relational support, a stigma-related belief, and recovery status are associated with willingness to disclose OUD treatment to friends and family. Data were drawn from a nationally representative sample of U.S. adults (N = 6,522) via the AmeriSpeak panel. Survey-weighted linear regression models tested whether confidence in supporting others, desire for a friend to share their treatment, and encouragement of others’ treatment predicted disclosure attitudes. Guided by the Disclosure Processes Model (DPM) and Minority Stress Theory (MST), disclosure was conceptualized as a relational act shaped by social context. Results showed that greater perceived relational engagement and higher perceived personal risk of developing OUD were positively associated with willingness to disclose. In contrast, individuals currently in recovery were less willing to disclose. Neither the stigma-related belief nor sociodemographic variables were significantly associated with disclosure. These findings highlight the importance of relationship-based approaches to fostering openness during recovery
Buddhaghosa and Meister Eckhart on the Problem of the Self: A Case Study in Comparative Theology after Religion
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There I Will Give You My Desire: An Apologetic for a Christian Congregation in Face of the Anthropocene
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The Story of Christian Faith: Developing Principles of Religious Education in Conversation with Narrative Theology
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