R-3 Repository :: Browsing by Author "Hutchinson, John S."

Browsing by Author "Hutchinson, John S."

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A flexible lattice model to study protein folding
(1996) Nunes, Nicole Lynne; Hutchinson, John S.
The biological activity of protein molecules is central to life. It has been known for decades that this biological activity is dependent on the protein molecule achieving a particular geometric conformation. Simple lattice models have been developed to investigate the protein folding pathway since all-atom molecular dynamics simulations on the time scale of folding are beyond the current capabilities of computers. We present a new Monte Carlo lattice model to study the folding of heteropolymer chains. Previous lattice model studies of two-dimensional chains have been performed on square grids using pre-defined "move sets" of allowed moves. The motion of the polymer chain in these models is thus highly constrained. In order to add greater flexibility, we use a triangular lattice and allow the chain to choose its own moves. Physically unrealistic moves are prevented by including kinetic energy effects in the Metropolis algorithm. By looking at the results, we are able to characterize all of the possible one and two particle moves in the two-dimensional model and sort them according to relative importance. This information will be used to guide simplified molecular dynamics studies. We also find that the initial phase of the folding process is a rapid collapse to a relatively compact state which is entropically driven. The model has been extended to three dimensions. The increased difficulty of working in three-dimensions as well as the preliminary results will be discussed.
A phase-based analysis of reaction dynamics
(1997) Wright, Karin Ringer; Hutchinson, John S.
The reaction dynamics of realistic molecular Hamiltonians including both mode coupling and anharmonicity may be profitably explored by classical trajectories. However even if such trajectories begin in phase the energy dependence of individual orbital periods of anharmonic oscillators quickly results in an incoherent ensemble, thereby obscuring organization present in the reaction dynamics of a given Hamiltonian. One solution to these difficulties is to compare trajectories in phase on a cycle by cycle basis (i.e. coherently). In this work a model independent means for phase based, or coherent, comparison was developed utilizing the Hilbert transform. Phase based analysis reveals that in particular unimolecular reactions correlated motion occurs when energy transfer between an orthogonal mode and the reaction coordinate forces synchronization in their motions, resulting in convergence of their phases. Thus a restricted and systematic set of states (i.e. points in phase space) precedes reaction, apparently contradicting the RRKM assumption that all states are equally likely to react. Detailed examination of the fundamental RRKM equation shows that this assumption differs from requiring that all states are equally likely to react per unit of time. States involved in correlated motion react sooner than others, but all states ultimately react, so their reaction probabilities are equal, therefore correlated motion can be consistent with RRKM kinetics. To explore the properties of different distributions of internal energy within a microcanonical ensemble a variant of phase space is proposed wherein every point is indexed by time remaining until reaction. (In the absence of trapping all unimolecular trajectories reside in the bound region of phase space for only a finite duration.) Under this variant points belonging to a particular allocation of internal energy are not scattered randomly across the lifetime distribution mapping (e.g. states in close time proximity to the transition state obviously all share the property of having sufficient energy in the reaction coordinate to clear the barrier). The microcanonical rate constant is an average of those for all component distributions of available internal energy, so the existence of rate constants with mode specificity can also be consistent with RRKM kinetics.
An efficient method for analyzing the optimal modes of vibration for polyatomic molecules
(1994) Aiani, Karen Ellen; Hutchinson, John S.
A quantitative analysis of the vibrational spectra of polyatomic molecules in the high energy regime requires a determination of the proper modes that optimally describe the vibrational motions of the nuclei at these energies. Observed vibrational spectra in small polyatomics indicate substantial regularity in the vibrational motion, implying that such a set of "optimal modes"should exist. Experiments have not provided a direct means of characterizing these modes. We present a computationally efficient theoretical method for performing an optimal modes analysis of multi-dimensional vibrational eigenstates. This algorithm consists of direct numerical integration of selected projection coefficients which reveals the extent of zeroth-order character of these eigenstates and is very accurate and significantly less time-intensive than previously employed methods of analysis. Demonstration of this method is presented for the analysis of selected high energy vibrations in hydrogen cyanide, monodeuterioacetylene, and propyne. The propyne analysis demonstrates the quantum mechanical intramolecular vibrational energy redistribution process in addition to the optimal mode analysis.
Application of quantum mechanical methods to chemical reactions
(1990) Jiang, Jun; Hutchinson, John S.
A variety of quantum mechanical methods have been developed and applied to the study of highly energized "pre-reactive" species involved in chemical reactions. We have examined the character of transition states for both unimolecular systems and bimolecular collisions. For unimolecular reactions, we have studied vibrational predissociation of hydrogen peroxide. The nodal lines of the predissociative resonance states are found to bend toward the dissociative side. This character should be largely responsible for the dissociation of the molecule. To compute the dissociation rates, we have combined the complex coordinate method and the Lanczos algorithm. The complex Lanczos recursion method is found to be insufficient to produce well converged resonance widths for this large system due to round-off errors. For bimolecular collisions, we have computed the absorption spectra of the transition states of the reaction K + NaCl + hv $\to$ KCl + Na$\sp{\*}$. The absorption probabilities show a strong dependence on laser frequency. This dependence is well explained by Franck-Condon calculations. By contrast, a linear curve crossing model is quantitatively incorrect. After carefully examining the excited wave packet dynamics and the time evolution of the transition probabilities, we believe the excitation process is not localized to the crossings of the field-dressed potential curves. We have also studied the effects of overall molecular rotation on the vibrational dynamics and unimolecular reaction rates. For a simple collinear triatomic model, the dissociation rates are uniformly increased as a function of angular momentum J, generally in a manner close to $J\sp2$. The reaction rates could be changed by a factor of three for some predissociative states, while remain almost unchanged for some other ones. The differences in the J-dependency correlate well with the existence of Fermi resonance conditions. The rotational effects are further investigated using a more realistic three dimensional model for HCN/HNC isomerization. We have developed a parameter dependent basis set for the study of this particular system. The importance of overall molecular rotation is confirmed in this study. However, the overall rotation is found to have non-uniform effects for different initial states.
Characterization of the dynamics of unimolecular reaction of hydrazoic acid and hydrogen peroxide
(1993) Julien, Veronique; Hutchinson, John S.
Studies of intramolecular dynamics during unimolecular reactions are important in characterizing the energy transfer into the reaction coordinate responsible for the reactive event. We investigated the dynamics and mode-mode energy transfer immediately prior to the dissociation of hydrazoic acid and hydrogen peroxide. Hydrazoic acid decomposes into NH and N$\sb2$ when energy is "deposited" in the N-H stretch of the ground electronic state molecule by a pump laser. A specific vibrational motion generates an impulsive energy transfer, which leads to a singlet-triplet transition and subsequent central N-N bond fragmentation. Hydrogen peroxide decomposes into two OH fragments following overtone excitation of an O-H stretch via a specific bending motion capable of producing an impulse of energy flow into the reaction coordinate at the time of the O-O bond dissociation. Modeling the dynamics of overtone-excited HN$\sb3$, and using an existing model for the dynamics of overtone-excited H$\sb2$O$\sb2$, respectively, we first characterize the specificity of the vibrational dynamics preceding the reaction, then establish that these dynamics are stable, that is non-chaotic, and unique in the reaction.
Concept Development Studies in Chemistry
(Rice University, 2013-10-07) Hutchinson, John S.
"Concept Development Studies in Chemistry" is an on-line textbook for an Introductory General Chemistry course. Each module develops a central concept in Chemistry from experimental observations and inductive reasoning. This approach complements an interactive or active learning teaching approach.
Concept Development Studies in Chemistry 2013
(Rice University, 2017-02-15) Hutchinson, John S.
General Chemistry I
(Rice University, 2008-06-20) Hutchinson, John S.
Concept Development Studies associated with the first semester of a two semester General Chemistry course at Rice University
General Chemistry II
(Rice University, 2010-03-29) Hutchinson, John S.
Concept Development Studies used for the second semester of first year general chemistry at Rice University.
Incorporation of Conceptual Understanding of Chemistry in Assessments, Undergraduate General Chemistry Classrooms and Laboratories, and High School Classrooms
(2012-11-02) Cloonan, Carrie; Hutchinson, John S.; Matsuda, Seiichi P. T.; Lopez Turley, Ruth N.
The novel assessment models and studies developed in this work provided new insight on effective teaching practices in chemistry classrooms and laboratories through the framework of constructivism. Each project aimed to promote greater levels of understanding and inspire interest in chemistry, both of which are great challenges within the U.S. educational system. Assessment drives learning, so appropriate tests are essential to good courses. However, large classes often make written exams impractical. A multiple-choice test of conceptual knowledge in general chemistry was created and validated to provide the chemical education community with a reliable and functional tool that correlates with open-ended General Chemistry exams. Large classes make active-learning implementation challenging, as not all students can participate. Students in a large General Chemistry course taught via active-learning were studied through surveys and interviews. The data revealed that “silent” students are engaged in the active-learning experience, yet “vocal” students outperform silent students on measures of conceptual understanding in chemistry. The motivation behind being vocal suggested students participate in order to improve their grade, and while doing so, also see the benefit to their learning. Another mixed-methods study focused on the traditionally formatted General Chemistry Laboratories. Initial data on student expectations lead to the creation of a pilot lab section and ultimately a new format of the labs with the inclusion of a discussion session. The changes resulted in the students being better prepared, focusing on the content rather than the process of the labs, and reporting better understanding of chemistry due to labs. Two novel laboratory experiences were also developed to promote conceptual understanding, and their creation and use are outlined. The impact of a professional development program on high school chemistry courses was analyzed via interviews, teacher observations and a case study. The professional development exposed teachers to novel chemistry teaching practices of inquiry-based concept development and active-learning methods. The case study showed implementation of the instructional strategies to be successful within an existing exemplary chemistry classroom. Each of these projects advanced best practices in teaching chemistry by expanding the current understanding of teaching concepts and analyzing applications of research-based pedagogies.
Nanotechnology: Content and Context
(Rice University, 2009-06-02) Kelty, Christopher; Hutchinson, John S.
This is an NSF-funded (Grant No. EEC-0407237) Rice University course called "Nanotechnology: Context and Content." The goal is to teach students some basic nanoscience/nanotechnology by putting it in a social and cultural context. Students are expected to learn both some basic science and technology and at the same time, some techniques for understanding the social and cultural significance, role, and possible effects of this emerging science. Students from from all majors are encouraged to take this class. In addition, students are expected to assist each other in learning and discussing the content and the context, and to maintain respect for both the scientific and the social and cultural approaches. Many modules in this course are the result of students work in previous iterations of the class.
Quantum-mechanical correspondences of regularity and mode-mode specific impulsive energy transfer in the classical dynamics of unimolecular reactions
(1995) Yahara, Hiroki; Hutchinson, John S.
First, the parameter-dependent zeroth-order basis (PDZOB) method was employed in the study of the quantum mechanical dynamics of a HCN/HNC isomerization model reaction for a few hundred femtoseconds before the time of the unimolecular reaction. From this study, it was learned that the dominant mode-mode specific energy flow incorporated with large and sudden energy transfer is responsible for the isomerization. The classical dynamics study of the same isomerization also reveals the mode-mode specific impulsive energy transfer. Second, the HEG-Wigner distribution (HEGWD) method was applied to study phase space in the quantum dynamics of a two-mode hindered rotor isomerization. We discovered that regularity in the phase space lasts for about 200 fs after the initiation of this reaction. Strong correspondence between the semi-classical result with $\hbar$ = 0.5 and that in the classical result has been observed; however, there was no clear correspondence between the full-quantum result with $\hbar$ = 1.0 and the classical result.
The dynamics of a model chain by constrained molecular dynamics
(1996) Chen, Kaiqi; Hutchinson, John S.
A new method for the treatment of holonomic constraints in molecular dynamics simulation has been developed. In this method, constraint forces are solved explicitly. The method explores the special mathematical property (sparse and symmetric positive definite) of an matrix inherent to the molecule under study. The method is especially useful when some bond angles are constrained. A lattice model for proteins is proposed. The connection between implicit-solvent model and explicit-solvent model has been established. The structural features of globular proteins are studied by the model. It is found that the proteins are driven to compact conformations by strong water-water interactions. The constrained molecular dynamics simulations are applied to a short chain in solvent to infer the possible move set for Monte Carlo simulations. It is found that the end monomers should be more mobile than the inner ones and that one and two-monomer moves are the integral part of the set of basic moves. The moves involving four or more monomers can be modeled as the result of several basic moves.
Theoretical investigations of the vibrational behavior of large molecular systems
(1989) Marshall, Kenneth Todd; Hutchinson, John S.
While the dynamics of model systems has been widely studied, the sizes of the systems has been limited. We present the dynamics for two large systems: a 9 degrees of freedom molecule and a 10000 state tier model. Classical non-linear resonance analysis and its quantum analog have been instrumental in providing insight into the pathways and rates of IVR processes in the overtone excitation of small molecules such as benzene and cyanoacetylene. It has been observed that the fourth overtone OH excitation of propargyl alcohol (PPA) is anomalously broad in comparison to the corresponding band of other small alcohols, possibly the result of rapid IVR out of the excited mode. An accurate model displayed no classical relaxation, but the quantum dynamics indicated an approximate degeneracy between the excited OH stretch and a combination band that can explain the observed broadening. To better understand the tier-to-tier relaxation process, an abstract model consisting of ten tiers of states was developed with the final tier representing the vibrational bath-states via a 50 state/cm$\sp{-1}$ state density. The survival dynamics showed irreversible relaxation out of the initial tier without the usual Poincare recursions. Interestingly, a calculation of the time-dependent spectrum showed the presence of only a few large features up to 720 fs which could not be attributed in a simple fashion to the dynamics of sub-models consisting the first n tiers. The early appearance and long persistence of a few broad bands implied the presence of "IVR resonances". In an attempt to elucidate these resonances, a imaginary damping function or optical potential was added to the model. An eigenvalue calculation on the resulting Hamiltonian did yield several long-lived resonances, and in fact, a spectrum calculated using only the first five resonances qualitatively reproduced the short pulse-length spectrum calculated from the original model. The "discovery" of these resonances is a step towards understanding and interpreting future pulselength dependent spectra in terms of the underlying tier structure of the systems studied.
Vibrational coordinate transformation and optimization
(1989) Fleming, Patrick R.; Hutchinson, John S.
The nature of molecular vibrational coordinates is elucidated through the use of canonical coordinate transformations of the Hamiltonian. The importance of studying molecular vibrations with quantum mechanical calculational techniques is discussed and the methods for doing these calculations in rectilinear rotations of the bond coordinates are presented. Chief among these methods are prediagonalization and the transformation method, also known as the discrete variable representation. The results of coordinate rotation calculations on a three-coordinate stretching-only model of acetylene are presented and discussed. The results of calculations on two two-coordinate subsystems of acetylene are also presented. In all of these cases prediagonalization and rotated coordinates result in a substantial improvement in the quality of the zero order basis as measured by the projection of the eigenstate of interest onto the product function basis state with the same quantum numbers. Optimized coordinate rotation calculations for a two-coordinate stretching-only model of hydrogen cyanide are presented. The results are similar to those of the acetylene calculations. The physical interpretation of the hydrogen cyanide calculations is easier because contour plots of the entire system are possible. An unexpected and previously unexplained intensity pattern in the hydrogen cyanide vibrational overtone spectrum is analyzed and clarified. Finally, drawbacks to these calculational techniques are discussed and possible improvements and future uses are suggested.

Browsing by Author "Hutchinson, John S."

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