Nuclear Geometry Research Articles

Motility and Segregation of Hsp104-Associated Protein Aggregates in Budding Yeast

During yeast cell division, aggregates of damaged proteins are segregated asymmetrically between the bud and the mother. It is thought that protein aggregates are cleared from the bud via actin cable-based retrograde transport toward the mother and that Bni1p formin regulates this transport. Here, we examined the dynamics of Hsp104-associated protein aggregates by video microscopy, particle tracking, and image correlation analysis. We show that protein aggregates undergo random walk without directional bias. Clearance of heat-induced aggregates from the bud does not depend on formin proteins but occurs mostly through dissolution via Hsp104p chaperon. Aggregates formed naturally in aged cells also exhibit random walk but do not dissolve during observation. Although our data do not disagree with a role for actin or cell polarity in aggregate segregation, modeling suggests that their asymmetric inheritance can be a predictable outcome of aggregates' slow diffusion and the geometry of yeast cells.

Analytical optimization of orbital exponents in Gaussian-type functions for molecular systems based on MCSCF and MP2 levels of fully variational molecular orbital method

We have analyzed the basis function series in molecular systems by optimization of orbital exponents in Gaussian-type functions (GTFs) including the electron correlation effects with multiconfiguration self-consistent field (MCSCF) and Moller–Plesset second-order perturbation (MP2) methods. First, we have derived and implemented the gradient formulas of MCSCF and MP2 energies with respect to GTF exponent, as well as GTF center and nuclear geometry, based on the fully variational molecular orbital (FVMO) method. Second, we have applied these electron-correlated FVMO methods to H2, LiH, and hydrocarbon (CH4, C2H6, C2H4, and C2H2) molecules. We have clearly demonstrated that the optimized exponent values with electron-correlated methods are different from those with simple Hartree–Fock method, since adequate basis functions for adequate virtual orbitals are indispensable to describe the accurate wave function and geometry for electron-correlated calculations.

Creating geometry and mesh models for nuclear reactor core geometries using a lattice hierarchy-based approach

Nuclear reactor cores are constructed as rectangular or hexagonal lattices of assemblies, where each assembly is itself a lattice of fuel, control, and instrumentation pins, surrounded by water or other material that moderates neutron energy and carries away fission heat. We describe a system for generating geometry and mesh for these systems. The method takes advantage of information about repeated structures in both assembly and core lattices to simplify the overall process. The system allows targeted user intervention midway through the process, enabling modification and manipulation of models for meshing or other purposes. Starting from text files describing assemblies and core, the tool can generate geometry and mesh for these models automatically as well. Simple and complex examples of tool operation are given, with the latter demonstrating generation of meshes with 12 million hexahedral elements in less than 30 minutes on a desktop workstation, using about 4 GB of memory. The tool is released as open source software as part of the MeshKit mesh generation library.

Quantum states for quantum processes: A toy model for ammonia inversion spectra

Chemical transformations are viewed here as quantum processes modulated by external fields, that is, as shifts in reactant to product amplitudes within a quantum state represented by a linear (coherent) superposition of electronuclear basis functions; their electronic quantum numbers identify the ``chemical species.'' This basis set can be mapped from attractors built from a unique electronic configurational space that is invariant with respect to the nuclear geometry. In turn, the quantum numbers that label these basis functions and the semiclassical potentials for the electronic attractors may be used to derive reaction coordinates to monitor progress as a function of the applied field. A generalization of Feynman's three-state model for the ammonia inversion process illustrates the scheme; to enforce symmetry for the entire inversion process model and ensure invariance with respect to nuclear configurations, the three attractors and their basis functions are computed with a grid of fixed floating Gaussian functions. The external-field modulation of the effective inversion barrier is discussed within this conceptual approach. This analysis brings the descriptions of chemical processes near modern technologies that employ molecules to encode information by means of confinement and external fields.

The effect of light-induced conical intersections on the alignment of diatomic molecules

It has already been shown that dressing of diatomic molecules by standing or by running linearly polarized laser waves gives rise to conical intersections (CIs). Due to the presence of such light-induced CIs (LICI), the rovibronic molecular motions are strongly coupled. Here we investigate an impact of LICI on molecular alignment. We show that the degree of alignment of a diatomic molecule as a function of time as obtained from the rigid rotor calculations (where the LICI is ignored) is very different from the exact calculations (where the LICI is taken into consideration). This claim is valid under an assumption that the initially prepared wavepacket has a significant amplitude at the nuclear geometry where the LICI is located. Moreover, our results clearly show that the LICI increases the electronic excitation of the diatom. In particular for weak laser fields this effect is very significant. Our prediction of the LICI’s effect on the alignment of diatomic molecules can be confirmed by a two-laser experiment. Here, the first laser should have weak intensity and its duration should be sufficiently long as to align the molecules. The wavelength should be tuned in such a way as to ensure that the initial nuclear wavepacket has a significant amplitude at the internuclear distance corresponding to the LICI. The second laser pulse should be strong to produce measurable high-order harmonics. The high-order harmonic generation spectra should be measured as a function of the time delay between the two laser pulses, and are predicted to give an experimental evidence for the LICI effect on the alignment.

A simplified model for calculating R AA and R CP of cold nuclear matter effects

An incoherent binary nucleon-nucleon collision model of AA collisions is presented for simulating particle production in cold nuclear matter. With a simple phenomenological parameter, the mean nucleon energy loss fraction, this model yields pseudorapidity density distributions that are comparable to those of experiment, as well as those of HIJING. Particle production data for a given binary collision is extracted from the PYTHIA event generator. The nuclear geometry is described by the Glauber model. The preliminary RAA and RCP results are also presented and discussed, with a proposal that RAA be redefined.

On the determination of partial differential cross sections for photodetachment and photoionization processes producing polyatomic molecules with electronic states coupled by conical intersections

A formalism is derived for the computation of partial differential cross sections for electron photodetachment and photoionization processes that leave the residual or target molecule in electronic states that are strongly coupled by conical intersections. Because the electronic states of the target are nonadiabatically coupled, the standard adiabatic states approach of solving the electronic Schrödinger equation for the detached electron at fixed nuclear geometries and then vibrationally averaging must be fundamentally modified. We use a Lippmann-Schwinger equation based approach, which leads naturally to a partitioning of the transition amplitude into a Dyson orbital like part plus a scattering correction. The requisite Green's function is that developed in our previous paper for the direct determination of total integral cross sections. The method takes proper account of electron exchange, possible nonorthogonality of the orbital describing the detached electron, and nonadiabatic effects in the product molecule. The Green's function is constructed in an L(2) basis using complex scaling techniques. The accurate treatment of nonadiabatic effects in the residual molecule is accomplished using the multimode vibronic coupling model. For photodetachment, an approximate approach, which is less computationally demanding, is suggested.

Modified DGLAP evolution for fragmentation functions in nuclei and QGP

Within the framework of generalized factorization of higher-twist contributions, including modification to splitting functions of both quark and gluon, we get and numerically resolve the medium-modified DGLAP (mDGLAP) evolution equations. With Woods-Saxon nuclear geometry and Hirano 3D ideal hydrodynamic simulations of hot medium, we study the medium modified fragmentation functions (mFF) in DIS and Au+Au collisions in RHIC. Our calculations imply that the parton density in the hot medium produced in RHIC is about 30 times larger than in a cold nucleus.

Non-Condon Effects in the One- and Two-Photon Absorption Spectra of the Green Fluorescent Protein

We report calculations of one and two photon absorption (OPA and TPA, respectively) spectra of the green fluorescent protein (GFP) chromophore using the double-harmonic parallel-mode approximation and including explicit dependence of the electronic transition moments on nuclear geometry. The non-Condon effects are found to be more significant for TPA resulting in a different shape of the spectra and a blue shift of 500 cm−1 of the TPA peak absorption relative to OPA. The computed shift is in excellent agreement with the experimentally observed 700 cm−1.

The spin-free analogue of Mukherjee's state-specific multireference coupled cluster theory

In this paper, we develop a rigorously spin-adapted version of Mukherjee's state-specific multireference coupled cluster theory (SS-MRCC, also known as Mk-MRCC) [U. S. Mahapatra, B. Datta, and D. Mukherjee, J. Chem. Phys. 110, 6171 (1999)] for reference spaces comprising open-shell configurations. The principal features of our approach are as follows: (1) The wave operator Ω is written as Ω = ∑(μ)Ω(μ)|φ(μ)>c(μ), where {φ(μ)} is the set of configuration state functions spanning a complete active space. (2) In contrast to the Jeziorski-Monkhorst Ansatz in spin-orbital basis, we write Ω(μ) as a power series expansion of cluster operators R(μ) defined in terms of spin-free unitary generators. (3) The operators R(μ) are either closed-shell-like n hole-n particle excitations (denoted as T(μ)) or they involve valence (active) destruction operators (denoted as S(μ)); these latter type of operators can have active-active scatterings, which can also carry the same active orbital labels (such S(μ)'s are called to have spectator excitations). (4) To simulate multiple excitations involving powers of cluster operators, we allow the S(μ)'s carrying the same active orbital labels to contract among themselves. (5) We exclude S(μ)'s with direct spectator scatterings. (6) Most crucially, the factors associated with contracted composites are chosen as the inverse of the number of ways the S(μ)'s can be joined among one another leading to the same excitation. The factors introduced in (6) have been called the automorphic factors by us. One principal thrust of this paper is to show that the use of the automorphic factors imparts a remarkable simplicity to the final amplitude equations: the equations consist of terms that are at most quartic in cluster amplitudes, barring only a few. In close analogy to the Mk-MRCC theory, the inherent linear dependence of the cluster amplitudes leading to redundancy is resolved by invoking sufficiency conditions, which are exact spin-free analogues of the spin-orbital based Mk-MRCC theory. This leads to manifest size-extensivity and an intruder-free formulation. Our formalism provides a relaxed description of the nondynamical correlation in presence of dynamical correlation. Pilot numerical applications to doublet systems, e.g., potential energy surfaces for the first two excited (2)A' states of asymmetric H(2)S(+) ion and the ground (2)Σ(+)state of BeH radical are presented to assess the viability of our formalism over an wide range of nuclear geometries and the manifest avoidance of intruder state problem.

Attosecond pumping of nonstationary electronic states of LiH: Charge shake-up and electron density distortion

Electronic reorganization during and after excitation by an intense ultrashort pulse is computed for LiH in a many-electron multireference time-dependent approach at a fixed nuclear geometry. The electronic dipole moment is used to probe the temporal response of the charge density. Above a field-strength threshold, there is an extensive Stark shifting and Rabi broadening of levels with corresponding distortion of the charge distribution whose response at strong fields is neither adiabatic nor diabatic. A nonresonant IR pulse is more effective in inducing charge shake-up during the pulse.

Nuclear Geometry and Rapid Mitosis Ensure Asymmetric Episome Segregation in Yeast

Asymmetric cell division drives the generation of differentiated cells and maintenance of stem cells. In budding yeast, autonomously replicating sequence (ARS) plasmids lacking centromere elements are asymmetrically segregated into the mother cell, where they are thought to contribute to cellular senescence. This phenomenon has been proposed to result from the active retention of plasmids through an interaction with nuclear pores. To investigate the mother-daughter segregation bias of plasmids, we used live-cell imaging to follow the behavior of extrachromosomal DNA. We show that both an excised DNA ring and a centromere-deficient ARS plasmid move freely in the nucleoplasm yet show a strong segregation bias for the mother cell. Computational modeling shows that the geometrical shape of the dividing yeast nucleus and length of mitosis severely restrict the passive diffusion of episomes into daughter nuclei. Predictions based on simulated nuclear division were tested with mutants that extend the length of mitosis. Finally, explaining how various anchors can improve mitotic segregation, we show that plasmid partitioning is improved by tethering the plasmid to segregating structures, such as the nuclear envelope and telomeres. The morphology and brevity of mitotic division in budding yeast impose physical constraints on the diffusion of material into the daughter, obviating the need for a retention mechanism to generate rejuvenated offspring.

Simulation of electronic structure Hamiltonians using quantum computers

Over the last century, a large number of physical and mathematical developments paired with rapidly advancing technology have allowed the field of quantum chemistry to advance dramatically. However, the lack of computationally efficient methods for the exact simulation of quantum systems on classical computers presents a limitation of current computational approaches. We report, in detail, how a set of pre-computed molecular integrals can be used to explicitly create a quantum circuit, i.e. a sequence of elementary quantum operations, that, when run on a quantum computer, obtains the energy of a molecular system with fixed nuclear geometry using the quantum phase estimation algorithm. We extend several known results related to this idea and discuss the adiabatic state preparation procedure for preparing the input states used in the algorithm. With current and near future quantum devices in mind, we provide a complete example using the hydrogen molecule of how a chemical Hamiltonian can be simulated using a quantum computer.

Triplet Excited State Distortions in a Pyrazolate Bridged Platinum Dimer Measured by X-ray Transient Absorption Spectroscopy

The excited-state structure of a dinuclear platinum(II) complex with tert-butyl substituted pyrazolate bridging units, [Pt(ppy)(μ-(t)Bu(2)pz)](2) (ppy = 2-phenylpyridine; (t)Bu(2)pz = 3,5-di-tert-butylpyrazolate) is studied by X-ray transient absorption (XTA) spectroscopy to reveal the transient electronic and nuclear geometry. DFT calculations predict that the lowest energy triplet excited state, assigned to a metal-metal-to-ligand charge transfer (MMLCT) transition, has a contraction in the Pt-Pt distance. The Pt-Pt bond length and other structural parameters extracted from fitting the experimental XTA difference spectra from full multiple scattering (FMS) and multidimensional interpolation calculations indicates a metal-metal distance decrease by approximately 0.2 Å in the triplet excited state. The advantages and challenges of this approach in resolving dynamic transient structures of nonbonding or weak-bonding dinuclear metal complexes in solution are discussed.

Erratum: Collision-geometry fluctuations and triangular flow in heavy-ion collisions [Phys. Rev. C81, 054905 (2010)

We introduce the concepts of participant triangularity and triangular flow in heavy-ion collisions, analogous to the definitions of participant eccentricity and elliptic flow. The participant triangularity characterizes the triangular anisotropy of the initial nuclear overlap geometry and arises from event-by-event fluctuations in the participant-nucleon collision points. In studies using a multi-phase transport model (AMPT), a triangular flow signal is observed that is proportional to the participant triangularity and corresponds to a large third Fourier coefficient in two-particle azimuthal correlation functions. Using two-particle azimuthal correlations at large pseudorapidity separations measured by the PHOBOS and STAR experiments, we show that this Fourier component is also present in data. Ratios of the second and third Fourier coefficients in data exhibit similar trends as a function of centrality and transverse momentum as in AMPT calculations. These findings suggest a significant contribution of triangular flow to the ridge and broad away-side features observed in data. Triangular flow provides a new handle on the initial collision geometry and collective expansion dynamics in heavy-ion collisions.

Improved Design of Orbital Domains within the Cluster-in-Molecule Local Correlation Framework: Single-Environment Cluster-in-Molecule Ansatz and Its Application to Local Coupled-Cluster Approach with Singles and Doubles†

The improved variant of the local correlation coupled-cluster (CC) framework termed "cluster-in-molecule" (CIM), defining the single-environment (SE) CIM-CC approach, is presented and tested at the CC singles and doubles (CCSD) level. In the proposed SECIM-CC method, the previous design of the CIM orbital subsystems [Li, W.; Gour, J. R.; Piecuch, P.; Li, S. J. Chem. Phys. 2009, 131, 114109], referred to as the dual-environment (DE) CIM-CC approach, which is based on the ideas of central orbitals and the associated primary and secondary environments, is replaced by the simplified design in which the central localized molecular orbitals (LMOs) and the corresponding environment LMOs are first assigned to each nonhydrogen atom and the hydrogen atoms that are bound to it. The SECIM-CC approach offers improvements in the DECIM-CC results, particularly for weakly bound molecular clusters using diffuse basis functions. Through the use of a single parameter to define the environment LMOs and through the assignment of subsystem LMOs to atoms, the SECIM-CC calculations are easy to control and the CIM subsystems do not unnecessarily vary with the nuclear geometry, creating smoother potential energy surfaces. The performance of SECIM-CCSD is illustrated by the calculations for normal alkanes and water clusters described by the 6-31G(d), 6-31++G(d,p), and 6-311++G(d,p) basis sets.

Influence of Nuclear Geometry on the Formation of Genetic Rearrangements in Human Cells

Interphase chromosomes are divided into discrete domains, with limited overlapping and movement. We explored the role of nuclear topology in the formation of chromosome aberrations by irradiating normal human fibroblasts with high-energy heavy ions from different directions. Cells with elliptical nuclei were grown in an aligned manner onto micrometer grooved culturing substrates to have a predetermined orientation with respect to the accelerated iron ions. Particles were directed either perpendicular to the cell layer or along the major or minor axis of the nucleus. Analysis of chromosome aberrations by mFISH showed that, at the same radiation dose, the yield of chromosomal damage and its complexity are largely modified by the irradiation geometry. The results demonstrate that the architecture of the cell nucleus determines the formation of chromosomal rearrangements.

Accurate and computationally efficient third-nearest-neighbor tight-binding model for large graphene fragments

Owing to the large sizes involved, most calculations of the electronic properties of graphene and its fragments involve empirical tight-binding models restricted to nearest-neighbor interactions only. Such approaches fail to predict key electronic and magnetic properties, however, and rely on assumed geometries. While alternative approaches based on density-functional theory are much more successful in predicting properties, they are often computationally prohibitive to apply. We introduce a simple third-nearest-neighbor $\ensuremath{\pi}$-only tight-binding approach that maintains the computational efficiency of the empirical method while achieving the accuracy of the density-functional methods to which it is parametrized. It yields both nuclear geometries and electronic structures of graphene fragments, providing an efficient and accurate replacement for traditional tight-binding models of graphene.

Collision-geometry fluctuations and triangular flow in heavy-ion collisions

We introduce the concepts of participant triangularity and triangular flow in heavy-ion collisions, analogous to the definitions of participant eccentricity and elliptic flow. The participant triangularity characterizes the triangular anisotropy of the initial nuclear overlap geometry and arises from event-by-event fluctuations in the participant-nucleon collision points. In studies using a multiphase transport model (AMPT), a triangular flow signal is observed that is proportional to the participant triangularity and corresponds to a large third Fourier coefficient in two-particle azimuthal correlation functions. Using two-particle azimuthal correlations at large pseudorapidity separations measured by the PHOBOS and STAR experiments, we show that this Fourier component is also present in data. Ratios of the second and third Fourier coefficients in data exhibit similar trends as a function of centrality and transverse momentum as in AMPT calculations. These findings suggest a significant contribution of triangular flow to the ridge and broad away-side features observed in data. Triangular flow provides a new handle on the initial collision geometry and collective expansion dynamics in heavy-ion collisions.

The anomalous effect of surface diffusion on the nuclear magnetic resonance signal inrestricted geometry

Anisotropy of diffusion properties in a specimen plays a key role in numerousapplications of nuclear magnetic resonance (NMR) imaging, like non-invasivetracking of fibers in the central nervous system. We suggest that contrastingfiber structures with certain diameters could be improved if second-order effectsare taken into account. We introduce a procedure consisting of two standarddiffusion NMR experiments differing in their gradient pulse characteristics. Thesetwo echo signals will be called the background and principal signals. We showthat the difference obtained by subtracting one echo signal from the other haseither typical or anomalous properties. In the typical case, as the duration of thegradient pulse in the second experiment is set to smaller and smaller values, thedifference from the background echo signal tends toward its maximum. In contrast, inthe anomalous case the difference between the background and the principalsignals has a maximum at a certain nonzero duration of the pulse in the secondexperiment. This critical duration is determined by different characteristics, includingthe diameters of fibers. For this anomalous effect to take place the fast surfacediffusion channel coupled to the surrounding media is required. The diffusionof magnetic molecules along the surface of restricted media and the couplingof the surface and the bulk translational motions can strongly modify the echoattenuation NMR signal. The origin of this strong anomalous effect is the change of thesymmetry of the lowest diffusion eigenmode of the system. We illustrate the effect ofsurface diffusion for a cylindrically symmetric system and describe the experimentalconditions under which the anomalous behavior of the echo signals can be observed.