Difference between revisions of "Publications"

We studied the influence of dispersion energy corrections on the free energy of formation for sodium-water clusters computed with DFT and wound up discovering that dispersion and split-range exchange functionals can somewhat counter-balance each other. The charged sodium ion pulls on the water's electrons, clearly showing which density functionals over-polarize compared to CCSD. Split-range exchange can reduce this over-polarization, but results in reduced electrostatic interaction. Dispersion can lower the binding energy again to counter-balance. So, functionals fit to experimental formation energies need both effects to avoid lowering energies by over-polarizing.

I introduce sets of point charges that are able to simultaneously reproduce all multipole (spherical harmonic) expansions up to arbitrary order. The number of points is space-optimal. Translations are described from the usual harmonics and from Cartesian moments (dipole, quadrupole, etc.) on supersymmetric tensors to directional moments using the point weight distribution. Many applications are possible, including trivial implementation of multipoles in molecular mechanics and representing probability distributions over rotation space.

A fully atomistic potential of mean force for association of the viral envelope protein from Dengue virus was compared to a Poisson-Boltzmann electrostatic plus dispersion model. The results are consistent, showing hope for this type of combined scale simulation.

This paper with our experimental collaborators carried out blocked peptide synthesis by vapor-depositing Boc-L-alanine to create a uniform thin film of polypeptides grown on a silica substrate activated by aminopropyltrimethoxysilane.

We show how the interpretation of thermodynamic states as representing system information leads naturally to thermodynamic cycles and the first and second laws of thermodynamics as well as similar formulations for nontrivial nonequilibrium problems. The logical development of the theory also leads naturally to correct indistinguishability factors in the partition function.

We review the development of models for understanding the physical basis of selectivity for K+ ions over Na+, its sibling only one row behind, in membrane channels and transporters. Although the problem is subtle because of the morass of competing effects, we emphasize work analyzing the systematic influence of the environment on tipping local binding site structure toward selective configurations.

We presented an extension of the Quasi-Chemical theory for quantifying the impact of local structure on ion complexation thermodynamics. The theory can be simply represented using a set of thermodynamic cycles involving binding site structural and compositional states as reaction intermediates.

We summarize work on designing polymer coatings for salt exclusion in water transporting nanopores. In this work, I collected available molecular dynamics results for these systems and performed a novel energy efficiency analysis able to relate atomistic and experimental scales as well as identify important design goals and chemical principles for material performance.

We investigated the central quantity of free energies in a Bayesian context and provide estimators for solvation free energies as well as optimal potential of mean force approximations to model polymer coarse-grained dynamics from atomistic simulations.

Dr. Zhao's ab-initio analysis of the charge distribution in water-ion clusters highlighted the importance of many-body water-water interactions and charge transfer effects in determining cluster structural and energetic properties. These are still challenging to represent in modern polarizable forcefields and have implications for anion properties at interfaces.

The role of polarizability in forcefield-based models of ions and water was examined. Utilizing some of our recent developments on quasi-chemical theory, we have been able to quantify the tightened, asymmetric nature of the ion's local solvation waters induced by increased polarizability as well as the exact effects of polarization on the solvation free energy. The results suggest some potential problems and diagnostics for such models.

This force matching software implements and tests coarse-graining for general molecular systems in a mere 4000 lines of code. It is able to parametrize coarse Hamiltonians from atomic trajectory data given arbitrary definitions of coarse united-atom type models as well as carry out short Langevin Dynamics simulations on the coarse scale. The program's main drawbacks are its slow speed and high memory usage due to its simplistic design, attributable to the interpreted nature of python.

Fresh insight is provided into long-standing mathematical issues surrounding computational modeling of continuous functions from a few sampled data points. The present research lays the groundwork for predicting the behavior of complicated many-body systems using advanced regression techniques.