K. E. Schmidt

Femtosecond x-ray protein nanocrystallography

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

Correlated Monte Carlo wave functions for the atoms He through Ne

We apply the variational Monte Carlo method to the atoms He through Ne. Our trial wave function is of the form introduced by Boys and Handy. We use the Monte Carlo method to calculate the first and second derivatives of an unreweighted variance and apply Newton’s method to minimize this variance. We motivate the form of the correlation function using the local current conservation arguments of Feynman and Cohen. Using a self‐consistent field wave function multiplied by a Boys and Handy correlation function, we recover a large fraction of the correlation energy of these atoms. We give the value of all variational parameters necessary to reproduce our wave functions. The method can be extended easily to other atoms and to molecules.

Implementing the fast multipole method in three dimensions

The Rokhlin-Greengard fast multipole algorithm for evaluating Coulomb and multipole potentials has been implemented and analyzed in three dimensions. The implementation is presented for bounded charged systems and systems with periodic boundary conditions. The results include timings and error characterizations.

Time-resolved protein nanocrystallography using an X-ray free-electron laser

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

A new look at correlation energy in atomic and molecular systems. II. The application of the Green’s function Monte Carlo method to LiH

The potential energy surface of the LiH molecule is calculated using the Green’s function Monte Carlo method. The calculated correlation energy is 0.078±0.001 hartree and the binding energy is 2.56 eV. These results are within 6% and 2% of the experimental values, respectively. The Green’s function Monte Carlo method is discussed in some detail with particular emphasis on problems of chemical interest.

A path integral ground state method

Ground state expectation values are obtained by using a path integral ground state Monte Carlo method. The method allows calculations of ground state expectation values without the extrapolations often used with Green’s function and diffusion Monte Carlo methods. We compare our results with those of Green’s function Monte Carlo by calculating some ground state properties of the van der Waals complex He2Cl2 as well as the infinite systems liquid and solid 4He. Advantages and disadvantages of the present method with respect to previous ones are discussed.

Quantum Monte Carlo methods for nuclear physics

Quantum Monte Carlo methods have proved very valuable to study the structure and reactions of light nuclei and nucleonic matter starting from realistic nuclear interactions and currents. These ab-initio calculations reproduce many low-lying states, moments and transitions in light nuclei, and simultaneously predict many properties of light nuclei and neutron matter over a rather wide range of energy and momenta. We review the nuclear interactions and currents, and describe the continuum Quantum Monte Carlo methods used in nuclear physics. These methods are similar to those used in condensed matter and electronic structure but naturally include spin-isospin, tensor, spin-orbit, and three-body interactions. We present a variety of results including the low-lying spectra of light nuclei, nuclear form factors, and transition matrix elements. We also describe low-energy scattering techniques, studies of the electroweak response of nuclei relevant in electron and neutrino scattering, and the properties of dense nucleonic matter as found in neutron stars. A coherent picture of nuclear structure and dynamics emerges based upon rather simple but realistic interactions and currents.

Conformational Analysis of Flexible Molecules: Location of the Global Minimum Energy Conformation by the Simulated Annealing Method

Abstract A new computational method for the location of the lowest energy conformation of flexible molecules is reported. The technique, called simulated annealing, is discussed and several applications are described.

Green’s function Monte Carlo for few fermion problems

The Green’s function Monte Carlo method used for obtaining exact solutions to the Schrodinger equation of boson systems is generalized to treat systems of several fermions. We show that when it is possible to select eigenfunctions of the Hamiltonian based on physical symmetries, the GFMC method can be used to yield the lowest energy state of that symmetry. In particular, the lowest totally antisymmetric eigenfunction, the fermion ground state, can be obtained. Calculations on several two‐ and three‐body model problems show the method to be computationally feasible for few‐body systems.

Equilibrium structures and approximate HF vibrational red shifts for ArnHF (n=1-14) van der Waals clusters

This paper presents a theoretical study of the size evolution of equilibrium structures and approximate HF vibrational red shifts for ArnHF van der Waals clusters, with n=1–14. Pairwise additive ArnHF intermolecular potential energy surfaces were constructed from spectroscopically accurate Ar–Ar and anisotropic Ar–HF potentials. The latter depend on vibrational excitation of the HF monomer. The global and energetically close‐lying local minima of ArnHF, n=1–14, for HF v=0 and v=1, were determined using simulated annealing followed by a direct minimization scheme. For ArnHF clusters with n≤8, the lowest‐energy structure always has HF bound to the surface of the Arn subunit. In contrast, for n≥9, the global minimum of ArnHF corresponds to HF inside a cage. Ar12HF has the minimum‐energy configuration of an HF‐centered icosahedron, which appears to be unusually stable. Size dependence of the HF vibrational red shift in ArnHF (n=1–14) clusters was investigated by means of a simple approximation, where the red ...