publications
2022
- PRAAdaptive variational preparation of the Fermi-Hubbard eigenstatesGaurav Gyawali, and Michael J. LawlerPhys. Rev. A Jan 2022
2021
- IOPscienceGlass phenomenology in the hard matrix modelJunkai Dong, Veit Elser, Gaurav Gyawali, and 5 more authorsSep 2021
We introduce a new toy model for the study of glasses: the hardmatrix model (HMM). This may be viewed as a single particle moving on SO(N), where there is a potential proportional to the 1-norm of the matrix. The ground states of the model are “crystals” where all matrix elements have the same magnitude. These are the Hadamard matrices when N is divisible by four. Just as finding the latter has challenged mathematicians, our model fails to find them upon cooling and instead shows all the behaviors that characterize physical glasses. With simulations we have located the first-order crystallization temperature, the Kauzmann temperature where the glass would have the same entropy as the crystal, as well as the standard, measurement-time dependent glass transition temperature. Our model also brings to light a new kind of elementary excitation special to the glass phase: the rubicon. In our model these are associated with the finite density of matrix elements near zero, the maximum in their contribution to the energy. Rubicons enable the system to cross between basins without thermal activation, a possibility not much discussed in the standard landscape picture. We use these modes to explain the slow dynamics in our model and speculate about their role in its quantum extension in the context of manybody localization.
2019
- JCTCCoarse-Grained Models for Constant pH Simulations of Carboxylic AcidsNaeyma N. Islam, Arjun Sharma, Gaurav Gyawali, and 2 more authorsJournal of Chemical Theory and Computation Aug 2019
A model for carboxylic acids, in both the protonated and deprotonated states, is developed in which hydrogen interaction sites are not used and all interactions are short-ranged. A method for constant pH simulations, which exploits these features of the model, is developed. The constant pH method samples protonation states by making discrete Monte Carlo steps and is able to efficiently move between states in two steps. The method is applied to the polymer poly(methacrylic acid), a pH-responsive polymer that undergoes structural changes as a function of pH. The model is able to reproduce the structural changes induced by pH.
2018
- MDPICoarse-Grained Simulations of Aqueous Thermoresponsive PolyethersBryan Raubenolt, Gaurav Gyawali, Wenwen Tang, and 2 more authorsPolymers Aug 2018
Thermoresponsive polymers can change structure or solubility as a function of temperature. Block co-polymers of polyethers have a response that depends on polymer molecular weight and co-polymer composition. A coarse-grained model for aqueous polyethers is developed and applied to polyethylene oxide and polyethylene oxide-polypropylene oxide-polyethylene oxide triblock co-polymers. In this model, no interaction sites on hydrogen atoms are included, no Coulombic interactions are present, and all interactions are short-ranged, treated with a combination of two- and three-body terms. Our simulations find that The triblock co-polymers tend to associate at temperatures above 350 K. The aggregation is stabilized by contact between The hydrophobic methyl groups on The propylene oxide monomers and involves a large, favorable change in entropy.
2017
- JCTCCoarse-Grained Models of Aqueous and Pure Liquid AlkanesGaurav Gyawali, Samuel Sternfield, Revati Kumar, and 1 more authorJournal of Chemical Theory and Computation Aug 2017
A model for linear alkanes is presented in which interaction sites are only on the carbon atoms, and the range of the potential is reduced using the Stillinger–Weber potential. The model is optimized for aqueous and liquid alkane properties and can match thermodynamic and structural properties, including solvation free energies, liquid densities, and liquid/vapor and liquid/water surface tensions for alkanes over a range of lengths. The results for long alkanes indicate that such models can be useful as accurate, yet efficient, coarse-grained potentials for macromolecules in water and other environments.
- ELSEVIERAtomistic Study of Intramolecular Interactions in the Closed-State Channelrhodopsin Chimera, C1C2Monika R. VanGordon, Gaurav Gyawali, Steven W. Rick, and 1 more authorBiophysical Journal Aug 2017
Channelrhodopsins (ChR1 and ChR2) are light-activated ion channels that enable photomobility of microalgae from the genus Chlamydomonas. Despite common use of ChR2 in optogenetics for selective control and monitoring of individual neurons in living tissue, the protein structures remain unresolved. Instead, a crystal structure of the ChR chimera (C1C2), an engineered combination of helices I–V from ChR1, without its C-terminus, and helices VI–VII from ChR2, is used as a template for ChR2 structure prediction. Surprisingly few studies have focused in detail on the chimera. Here, we present atomistic molecular dynamics studies of the closed-state, non-conducting C1C2 structure and protonation states. A new and comprehensive characterization of interactions in the vicinity of the gating region of the pore, namely between residues E90, E123, D253, N258, and the protonated Schiff base (SBH), as well as nearby residues K93, T127, and C128, indicates that the equilibrated C1C2 structure with both E123 and D253 deprotonated closely resembles the available crystal structure. In agreement with experimental studies on C1C2, no direct or water-mediated hydrogen bonding between an aspartate and a cysteine (D156-O…S-C128) that would define a direct-current gate in C1C2 was observed in our simulations. Finally, we show that a single hydrogen bond between a glutamic acid (E90) and an asparagine (N258) residue suffices to keep the gate of C1C2 closed and to disable free water and ion passage through the putative pore, in contrast to the double bond proposed earlier for ChR2. We anticipate that this work will provide context for studies of both the gating process and water and ion transport in C1C2, and will spark interest in further experimental studies on the chimera.