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Biological and Chemical Physics Commons™
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- Ab initio calculations (8)
- Chemical reactions (4)
- Dimers (4)
- Electron transfer (4)
- Electronic structure (4)
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- Ground states (4)
- Alkali halides (3)
- Charge exchange (3)
- Excited states (3)
- Perturbation theory (3)
- Quantum chemistry (3)
- Wave functions (3)
- Binding energy (2)
- Bond angle (2)
- Butadiene (2)
- Ethylene (2)
- Geometry (2)
- Ionization potential (2)
- Lithium (2)
- Matrix elements (2)
- Molecular configurations (2)
- Molecular electronic states (2)
- Morphogenesis (2)
- Orientation (2)
- Positive ions (2)
- Triplet state (2)
- Variational methods (2)
- Vibrational states (2)
- Zinc (2)
- Ab initio calculation (1)
Articles 1 - 21 of 21
Full-Text Articles in Biological and Chemical Physics
3d Imaging And Mechanical Modeling Of Helical Buckling In Medicago Truncatula Plant Roots, Jesse L. Silverberg, Roslyn D. Noar, Michael S. Packer, Maria J. Harrison, Christopher L. Henley, Itai Cohen, Sharon J. Gerbode
3d Imaging And Mechanical Modeling Of Helical Buckling In Medicago Truncatula Plant Roots, Jesse L. Silverberg, Roslyn D. Noar, Michael S. Packer, Maria J. Harrison, Christopher L. Henley, Itai Cohen, Sharon J. Gerbode
All HMC Faculty Publications and Research
We study the primary root growth of wild-type Medicago truncatula plants in heterogeneous environments using 3D time-lapse imaging. The growth medium is a transparent hydrogel consisting of a stiff lower layer and a compliant upper layer. We find that the roots deform into a helical shape just above the gel layer interface before penetrating into the lower layer. This geometry is interpreted as a combination of growth-induced mechanical buckling modulated by the growth medium and a simultaneous twisting near the root tip. We study the helical morphology as the modulus of the upper gel layer is varied and demonstrate that …
How The Cucumber Tendril Coils And Overwinds, Sharon J. Gerbode, Joshua R. Puzey, Andrew G. Mccormick, L. Mahadevan
How The Cucumber Tendril Coils And Overwinds, Sharon J. Gerbode, Joshua R. Puzey, Andrew G. Mccormick, L. Mahadevan
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The helical coiling of plant tendrils has fascinated scientists for centuries, yet the underlying mechanism remains elusive. Moreover, despite Darwin’s widely accepted interpretation of coiled tendrils as soft springs, their mechanical behavior remains unknown. Our experiments on cucumber tendrils demonstrate that tendril coiling occurs via asymmetric contraction of an internal fiber ribbon of specialized cells. Under tension, both extracted fiber ribbons and old tendrils exhibit twistless overwinding rather than unwinding, with an initially soft response followed by strong strain-stiffening at large extensions. We explain this behavior using physical models of prestrained rubber strips, geometric arguments, and mathematical models of elastic …
Evolution Of Spur-Length Diversity In Aquilegia Petals Is Achieved Solely Through Cell-Shape Anisotropy, Joshua R. Puzey, Sharon J. Gerbode, Scott A. Hodges, Elena M. Kramer, L. Mahadevan
Evolution Of Spur-Length Diversity In Aquilegia Petals Is Achieved Solely Through Cell-Shape Anisotropy, Joshua R. Puzey, Sharon J. Gerbode, Scott A. Hodges, Elena M. Kramer, L. Mahadevan
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The role of petal spurs and specialized pollinator interactions has been studied since Darwin. Aquilegia petal spurs exhibit striking size and shape diversity, correlated with specialized pollinators ranging from bees to hawkmoths in a textbook example of adaptive radiation. Despite the evolutionary significance of spur length, remarkably little is known about Aquilegia spur morphogenesis and its evolution. Using experimental measurements, both at tissue and cellular levels, combined with numerical modelling, we have investigated the relative roles of cell divisions and cell shape in determining the morphology of the Aquilegia petal spur. Contrary to decades-old hypotheses implicating a discrete meristematic zone …
Kinematic Evidence For Superfast Locomotory Muscle In Two Species Of Teneriffiid Mites, Grace C. Wu, Jonathan C. Wright, Dwight L. Whitaker, Anna N. Ahn
Kinematic Evidence For Superfast Locomotory Muscle In Two Species Of Teneriffiid Mites, Grace C. Wu, Jonathan C. Wright, Dwight L. Whitaker, Anna N. Ahn
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Locomotory muscles typically operate over a narrow range of contraction frequencies, characterized by the predominant fiber types and functional roles. The highest documented frequencies in the synchronous sound-producing muscles of insects (550 Hz) and toadfish (200 Hz) far exceed the contraction frequencies observed in weight-bearing locomotory muscles, which have maximum documented frequencies below 15-30 Hz. Laws of scaling, however, predict that smaller arthropods may employ stride frequencies exceeding this range. In this study we measured running speed and stride frequency in two undescribed species of teneriffiid mites from the coastal sage scrub of southern California. Relative speeds of both species …
Constructing Diabatic States From Adiabatic States: Extending Generalized Mulliken–Hush To Multiple Charge Centers With Boys Localization, Joseph E. Subotnik, Robert J. Cave, Sina Yeganeh, Mark A. Ratner
Constructing Diabatic States From Adiabatic States: Extending Generalized Mulliken–Hush To Multiple Charge Centers With Boys Localization, Joseph E. Subotnik, Robert J. Cave, Sina Yeganeh, Mark A. Ratner
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This article shows that, although Boys localization is usually applied to single-electron orbitals, the Boys method itself can be applied to many electron molecular states. For the two-state charge-transfer problem, we show analytically that Boys localization yields the same charge-localized diabatic states as those found by generalized Mulliken–Hush theory. We suggest that for future work in electron transfer, where systems have more than two charge centers, one may benefit by using a variant of Boys localization to construct diabatic potential energy surfaces and extract electronic coupling matrix elements. We discuss two chemical examples of Boys localization and propose a generalization …
Erratum: The Structure Of Alkali Halide Dimers: A Critical Test Of Ionic Models And New Ab Initio Results, T. Törring, S. Biermann, J. Hoeft, Richard J. Mawhorter, Robert J. Cave, C. Szemenyei
Erratum: The Structure Of Alkali Halide Dimers: A Critical Test Of Ionic Models And New Ab Initio Results, T. Törring, S. Biermann, J. Hoeft, Richard J. Mawhorter, Robert J. Cave, C. Szemenyei
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It has come to our attention that some of the ab initio results presented are incorrect due to errors in the Cs and C1 basis sets, and a small error in the binding energy of Rb2F2. The corrected results are presented below for the species that were affected, modifying the results in Table III of the original paper. Only those values which are different from the results of the original Table III are included. Note that some of these results are used for comparison with the ionic models in later tables. In addition, some HF data quoted in Tables V …
Double Excitations Within Time-Dependent Density Functional Theory Linear Response, Neepa T. Maitra, Fan Zhang, Robert J. Cave, Kieron Burke
Double Excitations Within Time-Dependent Density Functional Theory Linear Response, Neepa T. Maitra, Fan Zhang, Robert J. Cave, Kieron Burke
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Within the adiabatic approximation, time-dependent density functional theory yields only single excitations. Near states of double excitation character, the exact exchange–correlation kernel has a strong dependence on frequency. We derive the exact frequency-dependent kernel when a double excitation mixes with a single excitation, well separated from the other excitations, in the limit that the electron–electron interaction is weak. Building on this, we construct a nonempirical approximation for the general case, and illustrate our results on a simple model.
Scroll Waves In The Presence Of Slowly Varying Anisotropy With Application To The Heart, S. Setayeshgar, Andrew J. Bernoff
Scroll Waves In The Presence Of Slowly Varying Anisotropy With Application To The Heart, S. Setayeshgar, Andrew J. Bernoff
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We consider the dynamics of scroll waves in the presence of rotating anisotropy, a model of the left ventricle of the heart in which the orientation of fibers in successive layers of tissue rotates. By choosing a coordinate system aligned with the fiber rotation and studying the phase dynamics of a straight but twisted scroll wave, we derive a Burgers’ equation with forcing associated with the fiber rotation rate. We present asymptotic solutions for scroll twist, verified by numerics, using a realistic fiber distribution profile. We make connection with earlier numerical and analytical work on scroll dynamics.
An Ab Initio Study Of The Mono- And Difluorides Of Krypton, Gerald J. Hoffman, Laura A. Swafford '97, Robert J. Cave
An Ab Initio Study Of The Mono- And Difluorides Of Krypton, Gerald J. Hoffman, Laura A. Swafford '97, Robert J. Cave
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Results from ab initio calculations at the CCSD(T) level of theory are presented for krypton monofluoride (KrF), krypton monofluoride cation (KrF+), linear, ground-state krypton difluoride (KrF2), the triplet state of krypton difluoride, and the krypton–fluorine van der Waals complex (Kr–F2). These are the first calculations demonstrating that KrF is a bound molecule, in agreement with experimental observation. When corrected for basis-set superposition error, the calculated potential displays quantitative agreement with the attractive wall of the experimentally measured potential curve. Results are also presented for KrF+ and linear KrF2 which yield accurate values for their dissociation energies. The triplet state of …
An Ab Initio Study Of Specific Solvent Effects On The Electronic Coupling Element In Electron Transfer Reactions, Thomas M. Henderson '98, Robert J. Cave
An Ab Initio Study Of Specific Solvent Effects On The Electronic Coupling Element In Electron Transfer Reactions, Thomas M. Henderson '98, Robert J. Cave
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Specific solvent effects on the electronic coupling element for electron transfer are examined using two model donor–acceptor systems (Zn2+ and Li2+) and several model “solvent” species (He, Ne, H2O, and NH3). The effects are evaluated relative to the given donor–acceptor pair without solvent present. The electronic coupling element (Hab) is found to depend strongly on the identity of the intervening solvent, with He atoms decreasing Hab, whereas H2O and NH3 significantly increase Hab. The distance dependence (essentially exponential decay) is weakly affected by a single intervening solvent atom–molecule. However, when the donor–acceptor distance increases in concert with addition of successively …
Calculation Of Electronic Coupling Matrix Elements For Ground And Excited State Electron Transfer Reactions: Comparison Of The Generalized Mulliken–Hush And Block Diagonalization Methods, Robert J. Cave, Marshall D. Newton
Calculation Of Electronic Coupling Matrix Elements For Ground And Excited State Electron Transfer Reactions: Comparison Of The Generalized Mulliken–Hush And Block Diagonalization Methods, Robert J. Cave, Marshall D. Newton
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Two independent methods are presented for the nonperturbative calculation of the electronic coupling matrix element (Hab) for electron transfer reactions using ab initio electronic structure theory. The first is based on the generalized Mulliken–Hush (GMH) model, a multistate generalization of the Mulliken Hush formalism for the electronic coupling. The second is based on the block diagonalization (BD) approach of Cederbaum, Domcke, and co-workers. Detailed quantitative comparisons of the two methods are carried out based on results for (a) several states of the system Zn2OH2+ and (b) the low-lying states of the benzene–Cl atom complex and its contact ion pair. Generally …
The Structure Of Alkali Halide Dimers: A Critical Test Of Ionic Models And New Ab Initio Results, T. Törring, S. Biermann, J. Hoeft, Richard J. Mawhorter, Robert J. Cave, C. Szemenyei
The Structure Of Alkali Halide Dimers: A Critical Test Of Ionic Models And New Ab Initio Results, T. Törring, S. Biermann, J. Hoeft, Richard J. Mawhorter, Robert J. Cave, C. Szemenyei
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In semiempirical ionic models a number of adjustable parameters have to be fitted to experimental data of either monomer molecules or crystals. This leads to strong correlations between these constants and prevents a unique test and a clear physical interpretation of the fit parameters. Moreover, it is not clear whether these constants remain unchanged when the model is applied to dimers or larger clusters. It is shown that these correlations can be substantially reduced when reliable information about dimers is available from experiments or ab initio calculations. Starting with Dunham coefficients of the monomer potential determined from microwave measurements, we …
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Mixed Alkali Halide Dimers, Robert J. Cave, Ian Ono '94
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Mixed Alkali Halide Dimers, Robert J. Cave, Ian Ono '94
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Results are presented from ab initio calculations on several mixed alkali halide dimers made up of Li, Na, F, and Cl. All of the dimers are investigated at the restricted Hartree–Fock level to provide ab initio estimates of geometries, vibrational frequencies, and binding energies. The dimer LiNaF2 is then treated using a variety of basis sets at the Hartree–Fock level, as well as at correlated levels (second‐order Møller–Plesset and coupled‐cluster singles and doubles) to examine the sensitivity of the calculations to use of higher levels of theory. The results are then compared to the experimental data available for the LiNaF2 …
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Alkali Halide Dimers, Robert P. Dickey '93, David Maurice '91, Robert J. Cave, Richard J. Mawhorter
A Theoretical Investigation Of The Geometries, Vibrational Frequencies, And Binding Energies Of Several Alkali Halide Dimers, Robert P. Dickey '93, David Maurice '91, Robert J. Cave, Richard J. Mawhorter
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Results are presented from ab initio calculations on the symmetrical alkali halide dimers made up of Li, Na, K, F, and Cl. We examine the sensitivity of representative monomer and dimer geometries to the variation of the basis set with and without polarization and diffuse functions. The geometries are then compared with available experimental results. We have also calculated vibrational frequencies at the restricted Hartree–Fock level and examined the changes in geometry brought about by correlation using second‐order Møller–Plesset perturbation theory. It is found that Hartree–Fock theory in a modest basis set with diffuse and polarization functions yields results comparable …
A Theoretical Investigation Of The Ground And Low‐Lying Excited States Of Butadiene Radical Cation, Robert J. Cave, Michael G. Perrott '90
A Theoretical Investigation Of The Ground And Low‐Lying Excited States Of Butadiene Radical Cation, Robert J. Cave, Michael G. Perrott '90
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Results are presented from ab initio calculations on the ground and several low‐lying excited states of the butadiene radical cation. In particular, we have calculated geometries for the ground and several excited states at the multiconfiguration self‐consistent field level and characterized the planar stationary points. The vertical ionization potentials from the neutral molecule ground state and vertical excitation energies at the computed equilibrium geometry of the cation were also examined. A variety of methods were tested for the calculation of ionization potentials and excitation energies, including multiconfiguration self‐consistent field, multireference singles and doubles configuration interaction (with and without size‐consistency correction), …
Size‐Inconsistency Effects In Molecular Properties For States With Valence‐Rydberg Mixing: The Low‐Lying Π→Π∗ States Of Ethylene And Butadiene, Robert J. Cave
Size‐Inconsistency Effects In Molecular Properties For States With Valence‐Rydberg Mixing: The Low‐Lying Π→Π∗ States Of Ethylene And Butadiene, Robert J. Cave
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Ab initio results for the low‐lying 1B1u states of ethylene are used to discuss size‐inconsistency effects on calculated molecular properties for states where valence‐Rydberg mixing is important. Results for the expectation value of x2, x being the coordinate perpendicular to the plane of the molecule, are presented from quasidegenerate variational perturbation theory and multireference configuration‐interaction calculations. These results are compared with values from previous studies. It is argued that size inconsistency in configuration‐interaction studies can have a significant effect on estimated molecular properties. Calculations on several low‐lying states of butadiene are also reported where similar size‐inconsistency effects are found.
Quasidegenerate Variational Perturbation Theory And The Calculation Of First‐Order Properties From Variational Perturbation Theory Wave Functions, Robert J. Cave, Ernest R. Davidson
Quasidegenerate Variational Perturbation Theory And The Calculation Of First‐Order Properties From Variational Perturbation Theory Wave Functions, Robert J. Cave, Ernest R. Davidson
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In previous work on the treatment of correlation in molecular systems we have applied a multireference version of second‐order Hylleraas variational perturbation theory. The choice made for the partitioning of H treated the interactions between the correlating functions to infinite order and gave the corrections to the wave function to first order. The method was shown to be accurate in many cases, but became less so when near degeneracies occurred between the reference energy and other eigenvalues of H0. In this article we introduce an effective Hamiltonian method that is analogous to variational perturbation theory, but which is significantly more …
Hylleraas Variational Perturbation Theory: Application To Correlation Problems In Molecular Systems, Robert J. Cave, Ernest R. Davidson
Hylleraas Variational Perturbation Theory: Application To Correlation Problems In Molecular Systems, Robert J. Cave, Ernest R. Davidson
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Hylleraas variational perturbation theory is applied through second order in energy to estimate the correlation energy in several molecular systems. The specific choices for H0 and V which are made lead to equations nearly identical to the multireference linearized coupled‐cluster method of Laidig and Bartlett. The results obtained are in virtually exact agreement where comparisons have been made. Results from test calculations are presented for BeH2, CH2, and C2H4. In addition, the utility of perturbation theory for selecting correlating configurations is examined. This procedure is found to be quite accurate while …
Theoretical Studies Of Electron Transfer In Metal Dimers: Xy+→X+Y, Where X, Y=Be, Mg, Ca, Zn, Cd, Robert J. Cave, David V. Baxter, William A. Goddard Iii, John D. Baldeschwieler
Theoretical Studies Of Electron Transfer In Metal Dimers: Xy+→X+Y, Where X, Y=Be, Mg, Ca, Zn, Cd, Robert J. Cave, David V. Baxter, William A. Goddard Iii, John D. Baldeschwieler
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The electronic matrix element responsible for electron exchange in a series of metal dimers was calculated using ab initio wave functions. The distance dependence is approximately exponential for a large range of internuclear separations. A localized description, where the two nonorthogonal structures characterizing the electron localized at the left and right sites are each obtained self‐consistently, is found to provide the best description of the electron exchange process. We find that Gaussian basis sets are capable of predicting the expected exponential decay of the electronic interactions even at quite large internuclear distances.
A Semiclassical Model For Orientation Effects In Electron Transfer Reactions, Robert J. Cave, Stephen J. Klippenstein, R.A. Marcus
A Semiclassical Model For Orientation Effects In Electron Transfer Reactions, Robert J. Cave, Stephen J. Klippenstein, R.A. Marcus
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An approximate solution to the single‐particle Schrödinger equation with an oblate spheroidal potential well of finite depth is presented. The electronic matrix element HBA for thermal electron transfer is calculated using these wave functions, and is compared with values of HBA obtained using the exact solution of the same Schrödinger equation. The present method yields accurate results for HBA, within the oblate spheroidal potential well model, and is useful for examining the orientational effects of the two centers on the rate of electron transfer.
A Model For Orientation Effects In Electron‐Transfer Reactions, Paul Siders, Robert J. Cave, R.A. Marcus
A Model For Orientation Effects In Electron‐Transfer Reactions, Paul Siders, Robert J. Cave, R.A. Marcus
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A method for solving the single‐particle Schrödinger equation with an oblate spheroidal potential of finite depth is presented. The wave functions are then used to calculate the matrix element TBA which appears in theories of nonadiabatic electron transfer. The results illustrate the effects of mutual orientation and separation of the two centers on TBA. Trends in these results are discussed in terms of geometrical and nodal structure effects. Analytical expressions related to TBA for states of spherical wells are presented and used to analyze the nodal structure effects for TBA for the spheroidal wells.