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Creators/Authors contains: "Snyder, Ryan"

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  1. Free, publicly-accessible full text available June 9, 2026
  2. An experiment designed to teach principles of continuous flow technologies for photocatalysis is 10 described as a part of a two-week summer camp program for high school students. Students learned about green chemistry, photocatalysis, flow chemistry, and the role of 3–D printing for the design and production of custom millifluidic reactors. Students examined reactor designs which differed in terms of residence times and mixing capabilities. Such evaluation was based on the combination of blue and yellow dyes, followed by running a photocatalytic thiol-ene reaction on gram-scale. 
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    Free, publicly-accessible full text available April 11, 2026
  3. Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note. 
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    Free, publicly-accessible full text available July 29, 2026
  4. Abstract In the last several years, there has been a surge in the development of machine learning potential (MLP) models for describing molecular systems. We are interested in a particular area of this field — the training of system‐specific MLPs for reactive systems — with the goal of using these MLPs to accelerate free energy simulations of chemical and enzyme reactions. To help new members in our labs become familiar with the basic techniques, we have put together a self‐guided Colab tutorial (https://cc-ats.github.io/mlp_tutorial/), which we expect to be also useful to other young researchers in the community. Our tutorial begins with the introduction of simple feedforward neural network (FNN) and kernel‐based (using Gaussian process regression, GPR) models by fitting the two‐dimensional Müller‐Brown potential. Subsequently, two simple descriptors are presented for extracting features of molecular systems: symmetry functions (including the ANI variant) and embedding neural networks (such as DeepPot‐SE). Lastly, these features will be fed into FNN and GPR models to reproduce the energies and forces for the molecular configurations in a Claisen rearrangement reaction. 
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  5. Neural network flexibility includes changes in neuronal participation between networks, such as the switching of neurons between single- and dual-network activity. We previously identified a neuron that is recruited to burst in time with an additional network via modulation of its intrinsic membrane properties, instead of being recruited synaptically into the second network. However, the modulated intrinsic properties were not determined. Here, we use small networks in the Jonah crab ( Cancer borealis) stomatogastric nervous system (STNS) to examine modulation of intrinsic properties underlying neuropeptide (Gly 1 -SIFamide)-elicited neuronal switching. The lateral posterior gastric neuron (LPG) switches from exclusive participation in the fast pyloric (∼1 Hz) network, due to electrical coupling, to dual-network activity that includes periodic escapes from the fast rhythm via intrinsically generated oscillations at the slower gastric mill network frequency (∼0.1 Hz). We isolated LPG from both networks by pharmacology and hyperpolarizing current injection. Gly 1 -SIFamide increased LPG intrinsic excitability and rebound from inhibition and decreased spike frequency adaptation, which can all contribute to intrinsic bursting. Using ion substitution and channel blockers, we found that a hyperpolarization-activated current, a persistent sodium current, and calcium or calcium-related current(s) appear to be primary contributors to Gly 1 -SIFamide-elicited LPG intrinsic bursting. However, this intrinsic bursting was more sensitive to blocking currents when LPG received rhythmic electrical coupling input from the fast network than in the isolated condition. Overall, a switch from single- to dual-network activity can involve modulation of multiple intrinsic properties, while synaptic input from a second network can shape the contributions of these properties. NEW & NOTEWORTHY Neuropeptide-elicited intrinsic bursting was recently determined to switch a neuron from single- to dual-network participation. Here we identified multiple intrinsic properties modulated in the dual-network state and candidate ion channels underlying the intrinsic bursting. Bursting at the second network frequency was more sensitive to blocking currents in the dual-network state than when neurons were synaptically isolated from their home network. Thus, synaptic input can shape the contributions of modulated intrinsic properties underlying dual-network activity. 
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  6. null (Ed.)
    Understanding the nucleon spin structure in the regime where the strong interaction becomes truly strong poses a challenge to both experiment and theory. At energy scales below the nucleon mass of about 1 GeV, the intense interaction among the quarks and gluons inside the nucleon makes them highly correlated. Their coherent behaviour causes the emergence of effective degrees of freedom, requiring the application of non-perturbative techniques such as chiral effective field theory. Here we present measurements of the neutron’s generalized spin polarizabilities that quantify the neutron’s spin precession under electromagnetic fields at very low energy-momentum transfer squared down to 0.035 GeV2. In this regime, chiral effective field theory calculations are expected to be applicable. Our data, however, show a strong discrepancy with these predictions, presenting a challenge to the current description of the neutron’s spin properties. 
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