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Water Dynamics around T0 vs. R4 of Hemoglobin from Local Hydrophobicity Analysis
Seyedeh Maryam Salehi, Marco Pezzella, Adam Willard +2
The local hydration around tetrameric Hb in its T and R conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (…
Tomography of Feshbach Resonance States
Baruch Margulis, Karl P. Horn, Daniel M. Reich +8
Feshbach resonances are fundamental to interparticle interactions and become particularly important in cold collisions with atoms, ions, and molecules. Here we present the detectio…
Local Hydration Control and Functional Implications Through S-Nitrosylation of Proteins: Kirsten rat sarcoma virus (KRAS) and Hemoglobin (Hb)
Haydar Taylan Turan, Markus Meuwly
S-nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification (PTM) that can affect the function of proteins. As…
Interaction at a Distance: Xenon Migration in Mb
Haydar Taylan Turan, Eric Boittier, Markus Meuwly
The transport of ligands, such as NO or O, through internal cavities is essential for the function of globular proteins, including hemoglobin, myoglobin (Mb), neuroglobin, trun…
Neural Network Potentials for Chemistry: Concepts, Applications and Prospects
Silvan Käser, Luis Itza Vazquez-Salazar, Markus Meuwly +1
Artificial Neural Networks (ANN) are already heavily involved in methods and applications for frequent tasks in the field of computational chemistry such as representation of poten…
Combining Machine Learning and Spectroscopy to Model Reactive Atom + Diatom Collisions
Juan Carlos San Vicente Veliz, Julian Arnold, Raymond J. Bemish +1
The prediction of product translational, vibrational, and rotational energy distributions for arbitrary initial conditions for reactive atom+diatom collisions is of considerable pr…
Transfer learning for affordable and high quality tunneling splittings from instanton calculations
Silvan Käser, Jeremy O. Richardson, Markus Meuwly
The combination of transfer learning (TL) a low level potential energy surface (PES) to a higher level of electronic structure theory together with ring-polymer instanton (RPI) the…
Uncertainty quantification for predictions of atomistic neural networks
Luis Itza Vazquez-Salazar, Eric D. Boittier, M. Meuwly
The value of uncertainty quantification on predictions for trained neural networks (NNs) on quantum chemical reference data is quantitatively explored. For this, the architecture o…
Structure, Organization and Heterogeneity of Water-Containing Deep Eutectic Solvents
Kai Töpfer, Andrea Pasti, Anuradha Das +6
The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SC…
Molecular Dynamics with Conformationally Dependent, Distributed Charges
Eric D. Boittier, Mike Devereux, Markus Meuwly
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polariz…
Quantum and Quasi-classical Dynamics of the C(P) + O() CO()+ O(D) Reaction on Its Electronic Ground State
Sugata Goswami, Juan Carlos San Vicente Veliz, Meenu Upadhyay +2
The dynamics of the C(P) + O() CO()+ O(D) reaction on its electronic ground state is investigated by using time-dependent wa…
Hydration Dynamics and IR Spectroscopy of 4-Fluorophenol
Seyedeh Maryam Salehi, Silvan Käser, Kai Töpfer +5
Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infr…
Computational Vibrational Spectroscopy
Markus Meuwly
Vibrational spectroscopy is a powerful technique to characterize the near-equilibrium dynamics of molecules in the gas- and the condensed-phase. This contribution summarizes effort…
Quantitative Molecular Simulations
K. Töpfer, M. Upadhyay, M. Meuwly
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realist…
Photodissociation dynamics of N
Sarbani Patra, Juan Carlos San Vicente Veliz, Debasish Koner +2
The photodissociation dynamics of N excited from its ground to the first excited singlet and triplet states is investigated. Three dimensional potential en…
Atomistic Simulations for Reactions and Spectroscopy in the Era of Machine Learning -- Quo Vadis?
M. Meuwly
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with…