Note: A pure-sampling quantum Monte Carlo algorithm with independent Metropolis.

Recently, Ospadov and Rothstein published a pure-sampling quantum Monte Carlo algorithm (PSQMC) that features an auxiliary Path Z that connects the midpoints of the current and proposed Paths X and Y, respectively. When sufficiently long, Path Z provides statistical independence of Paths X and Y. Under those conditions, the Metropolis decision used in PSQMC is done without any approximation, i.

A pure-sampling quantum Monte Carlo algorithm.

The objective of pure-sampling quantum Monte Carlo is to calculate physical properties that are independent of the importance sampling function being employed in the calculation, save for the mismatch of its nodal hypersurface with that of the exact wave function. To achieve this objective, we report a pure-sampling algorithm that combines features of forward walking methods of pure-sampling and reptation quantum Monte Carlo (RQMC). The new algorithm accurately samples properties from the mixed and pure distributions simultaneously in runs performed at a single set of time-steps, over which extrapolation to zero time-step is performed.

Ground-state properties of LiH by reptation quantum Monte Carlo methods.

We apply reptation quantum Monte Carlo to calculate one- and two-electron properties for ground-state LiH, including all tensor components for static polarizabilities and hyperpolarizabilities to fourth-order in the field. The importance sampling is performed with a large (QZ4P) STO basis set single determinant, directly obtained from commercial software, without incurring the overhead of optimizing many-parameter Jastrow-type functions of the inter-electronic and internuclear distances. We present formulas for the electrical response properties free from the finite-field approximation, which can be problematic for the purposes of stochastic estimation.

Structure propensities in mutated polyglutamine peptides.

Polyglutamine is a naturally occurring peptide found within several proteins in neuronal cells of the brain, and its aggregation has been implicated in several neurodegenerative diseases, including Huntington's disease. The resulting aggregates have been demonstrated to possess β-sheet structure, and experimental evidence has demonstrated that aggregation begins with a nucleus composed of a single peptide. In this paper, we computationally examined the structural tendencies of mutant polyglutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies.

Comparative characterization of short monomeric polyglutamine peptides by replica exchange molecular dynamics simulation.

Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume beta-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q(15)), we performed replica exchange molecular dynamics (REMD) simulations.

Procrustean rotation in concert with principal component analysis of molecular dynamics trajectories: Quantifying global and local differences between conformational samples.

Given the principal component analysis (PCA) of a molecular dynamics (MD) conformational trajectory for a model protein, we perform orthogonal Procrustean rotation to "best fit" the PCA squared-loading matrix to that of a target matrix computed for a related but different molecular system. The sum of squared deviations of the elements of the rotated matrix from those of the target, known as the error of fit (EOF), provides a quantitative measure of the dissimilarity between the two conformational samples. To estimate precision of the EOF, we perform bootstrap resampling of the molecular conformations within the trajectories, generating a distribution of EOF values for the system and target.

Mutation effects on structural stability of polyglutamine peptides by molecular dynamics simulation.

Huntington's disease patients commonly have glutamine (Q) repeats longer than 37 residues in the Huntingtin protein. This unusual protein will misfold and aggregate to form insoluble amyloid-like fibrils. Although the determination of polyQ structure is very important for elucidation of the aggregation mechanism, this has not yet been accomplished due to the experimental difficulties.

Water-mediated interactions in the CRP-cAMP-DNA complex: does water mediate sequence-specific binding at the DNA primary-kink site?

The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated.

Gamma distribution model to provide a direct assessment of the overall quality of quantum Monte Carlo-generated electron distributions.

Our objective is to assess the accuracy of simulated quantum Monte Carlo electron distributions of atoms and molecules. Our approach is first to model the exact electron distribution by a linear combination of gamma distribution functions, with parameters chosen to exactly reproduce highly accurate literature values for a number of selected moments for the system of interest. In application to the ground-state electron distributions of helium and dihydrogen, a high level of accuracy of the model was confirmed upon comparing its predicted moments, not used in the model's parametrization, to those calculated from high-level theory.

Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides.

It is known that Huntington's disease patients commonly have glutamine (Q) repeat sequences longer than a critical length in the coding area of Huntingtin protein in their genes. As the polyglutamine (polyQ) region becomes longer than the critical length, the disease occurs and Huntingtin protein aggregates, both in vitro and in vivo, as suggested by experimental and clinical data. The determination of polyglutamine structure is thus very important for elucidation of the aggregation and disease mechanisms.

Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method.

A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFIEs are usually analyzed in a matrix form called an IFIE matrix.

Local-structural diversity and protein folding: application to all-beta off-lattice protein models.

Global measures of structural diversity within a distribution of biopolymers, such as the radius of gyration and percent native contacts, have proven useful in the analysis of simulation data for protein folding. In this paper we describe a statistical-based methodology to quantify the local structural variability of a distribution of biopolymers, applied to 46- and 69-"residue" off-lattice, three-color model proteins. Each folds into beta-barrel structures.

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories.

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation.

Unbiased expectation values from diffusion quantum Monte Carlo simulations with a fixed number of walkers.

We append forward walking to a diffusion Monte Carlo algorithm which maintains a fixed number of walkers. This removes the importance sampling bias of expectation values of operators which do not commute with the Hamiltonian. We demonstrate the effectiveness of this approach by employing three importance sampling functions for the hydrogen atom ground state, two very crude.