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1. Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?

   https://doi.org/10.3390/membranes13070629  

   Chaisson, Emily H. ; Heberle, Frederick A. ; Doktorova, Milka ( July 2023 , Membranes)

   The compositional asymmetry of biological membranes has attracted significant attention over the last decade. Harboring more differences from symmetric membranes than previously appreciated, asymmetric bilayers have proven quite challenging to study with familiar concepts and techniques, leaving many unanswered questions about the reach of the asymmetry effects. One particular area of active research is the computational investigation of composition- and number-asymmetric lipid bilayers with molecular dynamics (MD) simulations. Offering a high level of detail into the organization and properties of the simulated systems, MD has emerged as an indispensable tool in the study of membrane asymmetry. However, the realization that results depend heavily on the protocol used for constructing the asymmetric bilayer models has sparked an ongoing debate about how to choose the most appropriate approach. Here we discuss the underlying source of the discrepant results and review the existing methods for creating asymmetric bilayers for MD simulations. Considering the available data, we argue that each method is well suited for specific applications and hence there is no single best approach. Instead, the choice of a construction protocol—and consequently, its perceived accuracy—must be based primarily on the scientific question that the simulations are designed to address.

    

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2. Dynamics of an unusual cone-building trachyte eruption at Pu‘u Wa‘awa‘a, Hualālai volcano, Hawai‘i

   https://doi.org/10.1007/s00445-017-1106-z  

   Shea, Thomas ; Leonhardi, Tanis ; Giachetti, Thomas ; Lindoo, Amanda ; Larsen, Jessica ; Sinton, John ; Parsons, Elliott ( April 2017 , Bulletin of Volcanology)
3. Identification of Network Dynamics and Disturbance for a Multizone Building

   https://doi.org/10.1109/TCST.2019.2949546  

   Zeng, Tingting ; Barooah, Prabir ( June 2020 , IEEE Transactions on Control Systems Technology)
4. Gas-phase formation of silicon monoxide via non-adiabatic reaction dynamics and its role as a building block of interstellar silicates

   https://doi.org/10.1039/D2CP02188A  

   He, Chao ; Luo, Yuheng ; Doddipatla, Srinivas ; Yang, Zhenghai ; Millar, Tom J. ; Sun, Rui ; Kaiser, Ralf I. ( August 2022 , Physical Chemistry Chemical Physics)

   Silicon monoxide (SiO) is classified as a key precursor and fundamental molecular building block to interstellar silicate nanoparticles, which play an essential role in the synthesis of molecular building blocks connected to the Origins of Life. In the cold interstellar medium, silicon monoxide is of critical importance in initiating a series of elementary chemical reactions leading to larger silicon oxides and eventually to silicates. To date, the fundamental formation mechanisms and chemical dynamics leading to gas phase silicon monoxide have remained largely elusive. Here, through a concerted effort between crossed molecular beam experiments and electronic structure calculations, it is revealed that instead of forming highly-stable silicon dioxide (SiO 2 ), silicon monoxide can be formed via a barrierless, exoergic, single-collision event between ground state molecular oxygen and atomic silicon involving non-adiabatic reaction dynamics through various intersystem crossings. Our research affords persuasive evidence for a likely source of highly rovibrationally excited silicon monoxide in cold molecular clouds thus initiating the complex chain of exoergic reactions leading ultimately to a population of silicates at low temperatures in our Galaxy. 

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5. Nonadiabatic reaction dynamics to silicon monosulfide (SiS): A key molecular building block to sulfur-rich interstellar grains

   https://doi.org/10.1126/sciadv.abg7003  

   Doddipatla, Srinivas ; He, Chao ; Goettl, Shane J. ; Kaiser, Ralf I. ; Galvão, Breno R. ; Millar, Tom J. ( June 2021 , Science Advances)

   Sulfur- and silicon-containing molecules are omnipresent in interstellar and circumstellar environments, but their elementary formation mechanisms have been obscure. These routes are of vital significance in starting a chain of chemical reactions ultimately forming (organo) sulfur molecules—among them precursors to sulfur-bearing amino acids and grains. Here, we expose via laboratory experiments, computations, and astrochemical modeling that the silicon-sulfur chemistry can be initiated through the gas-phase reaction of atomic silicon with hydrogen sulfide leading to silicon monosulfide (SiS) via nonadiabatic reaction dynamics. The facile pathway to the simplest silicon and sulfur diatomic provides compelling evidence for the origin of silicon monosulfide in star-forming regions and aids our understanding of the nonadiabatic reaction dynamics, which control the outcome of the gas-phase formation in deep space, thus expanding our view about the life cycle of sulfur in the galaxy. 

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