Analytic expressions for correlations in coarse-grained simple fluids.

Coarse-graining of fluids is challenging because fluid particles are unbound and diffuse long distances in time. One approach creates coarse-grain variables that group all particles within a region centered on specific points in space and accounts for the movement of particles among such regions. In our previous work, we showed that in many cases, potential interactions for such a scheme adopted a generalized quadratic form, whose parameters depend on means, variances, and correlation coefficients among the coarse-grain variables.

Conservative Potentials for a Lattice-Mapped, Coarse-Grain Scheme with Fuzzy Switching Functions.

We extend our previous work (Luo, S.; Thachuk, M. , , 64866497) on determining conservative potentials for lattice-like, coarse-grain (CG) mapping schemes to the case where the boundaries between different spatial regions are not sharply defined but are fuzzy.

Conservative Potentials for a Lattice-Mapped Coarse-Grained Scheme.

The conservative potential, arising from a coarse-grain (CG) mapping scheme for nonbonded atomistic particles, is studied. This is a bottom-up approach from first-principles that maps atomistic particles to fluid element-like subcells whose centers lie on a regular, cubic lattice. Unlike standard CG mapping schemes, the current one uses dynamic labeling which on-the-fly changes the CG labels of the particles.

Bayesian optimization for inverse problems in time-dependent quantum dynamics.

We demonstrate an efficient algorithm for inverse problems in time-dependent quantum dynamics based on feedback loops between Hamiltonian parameters and the solutions of the Schrödinger equation. Our approach formulates the inverse problem as a target vector estimation problem and uses Bayesian surrogate models of the Schrödinger equation solutions to direct the optimization of feedback loops. For the surrogate models, we use Gaussian processes with vector outputs and composite kernels built by an iterative algorithm with the Bayesian information criterion (BIC) as a kernel selection metric.

Equations of motion for position-dependent coarse-grain mappings obtained with Mori-Zwanzig theory.

A position-dependent transformation is introduced for mapping a system of atomistic particles to a system of coarse-grained (CG) variables, which under some circumstances might be considered particles. This CG mapping allows atomistic particles to simultaneously contribute to more than a single CG particle and to change in time the CG particle they are associated with. That is, the CG mapping is dynamic.

A general, rotating, hard sphere model applied to the transport properties of a low density gas.

A general, spherical, rigid model is introduced for describing rotating and translating particles. The model contains a parameter, which we label γ, that smoothly interpolates between the smooth hard sphere (γ = 0) and rough hard sphere (γ = 1) limits. Analytic expressions for transport coefficients are determined for the general model in the low density limit and compared with those for the smooth and rough hard sphere cases.

Relaxation of hot and massive tracers using numerical solutions of the Boltzmann equation.

A numerical method using B-splines is used to solve the linear Boltzmann equation describing the energy relaxation of massive tracer particles moving through a dilute bath gas. The smooth and rough hard sphere and Maxwell molecule models are used with a variety of mass ratios and initial energies to test the capability of the numerical method. Massive tracers are initialized with energies typically found in energy loss experiments in mass spectrometry using biomolecules.

Controlling dissociation channels of gas-phase protein complexes using charge manipulation.

Coarse-grained simulations with charge hopping were performed for a positively charged tetrameric transthyretin (TTR) protein complex with a total charge of +20. Charges were allowed to move among basic amino acid sites as well as N-termini. Charge distributions and radii of gyration were calculated for complexes simulated at two temperatures, 300 and 600 K, under different scenarios.

Kernels of the linear Boltzmann equation for spherical particles and rough hard sphere particles.

Kernels for the collision integral of the linear Boltzmann equation are presented for several cases. First, a rigorous and complete derivation of the velocity kernel for spherical particles is given, along with reductions to the smooth, rigid sphere case. This combines and extends various derivations for this kernel which have appeared previously in the literature.

A Charge Moving Algorithm for Molecular Dynamics Simulations of Gas-Phase Proteins.

A method for moving charges in a coarse-grained simulation of gas-phase proteins is presented which uses a Monte Carlo approach to move charges between charge sites. The method is used to study the role of charge movement in the dissociation mechanism of protein complexes in order to better understand experimentally observed mass spectra from CID studies. The charge hopping process is analyzed using energy distributions and a pair correlation plot.

Suitability of the MARTINI Force Field for Use with Gas-Phase Protein Complexes.

The MARTINI coarse-grained force field [Monticelli, L. et al. J.

A numerical solution of the linear Boltzmann equation using cubic B-splines.

A numerical method using cubic B-splines is presented for solving the linear Boltzmann equation. The collision kernel for the system is chosen as the Wigner-Wilkins kernel. A total of three different representations for the distribution function are presented.

Transport properties of the rough hard sphere fluid.

Results are presented of a systematic study of the transport properties of the rough hard sphere fluid. The rough hard sphere fluid is a simple model consisting of spherical particles that exchange linear and angular momenta, and energy upon collision. This allows a study of the sole effect of particle rotation upon fluid properties.

The effect of rotational and translational energy exchange on tracer diffusion in rough hard sphere fluids.

A study is presented of tracer diffusion in a rough hard sphere fluid. Unlike smooth hard spheres, collisions between rough hard spheres can exchange rotational and translational energy and momentum. It is expected that as tracer particles become larger, their diffusion constants will tend toward the Stokes-Einstein hydrodynamic result.

Toward an improved understanding of the dissociation mechanism of gas phase protein complexes.

Understanding the dissociation mechanism of multimeric protein complex ions is important for deciphering gas phase dissociation experiments. The dissociation of cytochrome c' dimer ions in the gas phase was investigated in the present study by constrained molecular dynamics simulations. The center of mass (COM) distance between two monomers was selected as the constrained coordinate.

Free energy barrier estimation for the dissociation of charged protein complexes in the gas phase.

Free energies are calculated for the protonated cytochrome c' dimer ion in the gas phase as a function of the center of mass distance between the monomers. A number of different charge partitionings are examined as well as the behavior of the neutral complex. It is found that monomer unfolding competes with complex dissociation and that the relative importance of these two factors depends upon the charge partitioning in the complex.

Gas-phase proton-transfer pathways in protonated histidylglycine.

Pathways for proton transfer in the histidylglycine cation are examined in the gas-phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero-point energy are included, it is found that all the lowest energy barriers for proton transfer between the N-terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring.

Theoretical investigations of the dissociation of charged protein complexes in the gas phase.

A series of calculations, varying from simple electrostatic to more detailed semi-empirical based molecular dynamics ones, were carried out on charged gas phase ions of the cytochrome c(') dimer. The energetics of differing charge states, charge partitionings, and charge configurations were examined in both the low and high charge regimes. As well, preliminary free energy calculations of dissociation barriers are presented.

Tracer diffusion in hard sphere fluids from molecular to hydrodynamic regimes.

Molecular dynamics is employed to investigate tracer diffusion in hard sphere fluids. Reduced densities (rho*=rhosigma(3), sigma is the diameter of bath fluid particles) ranging from 0.02 to 0.

Collision-induced alignment of H2O+ drifting in helium.

The collision-induced alignment of H(2)O(+) drifting in helium is studied with a molecular dynamics method that has been extended to treat nonlinear rigid ions. Rotational distribution functions and averaged quantities are presented in terms of the rho formalism [M. Thachuk, Phys.

Affinity capillary electrophoresis using a low-concentration additive with the consideration of relative mobilities.

Most affinity studies in capillary electrophoresis assume that the analyte concentration is much smaller than the additive concentration so that the migration of the analyte has no effect on the concentration of the additive in the capillary. However, in most medium- to high-affinity interactions, the additive concentration has to be kept rather low to observe the changes in analyte mobility before saturation is reached. In this paper, a mathematical model is developed to describe the migration behavior of the analyte in a system where the complex formed becomes concentrated to levels much greater than the original concentration of the additive due to the differences in the mobilities of the analyte, additive, and complex.