Normal vibrations of N,N-dimethylacetamide

Infrared and Raman spectra of N,N-dimethylacetamide (DMA) are recorded and the normal vibrational analysis of the DMA skeleton as well as the entire molecule carried out employing the Urey-Bradley and modified Urey-Bradley force fields. Vibrational frequencies are assigned on the basis of the normal coordinate calculations and are compared with those of related molecules. Infrared spectra of metal complexes are examined to substantiate the band assignments.

Infrared Spectra of Dimethylquinolines in the Gas Phase: Experiment and Theory

Infrared spectra of atmospherically important dimethylquinolines (DMQs), namely 2,4-DMQ, 2,6-DMQ, 2,7-DMQ, and 2,8-DMQ in the gas phase at 80 degrees C were recorded using a long variable path-length cell. DFT calculations were carried out to assign the bands in the experimentally observed spectra at the B3LYP/6-31G* level of theory. The spectral assignments particularly for the C-H stretching modes could not be made unambiguously using calculated anharmonic or scaled harmonic frequencies. To resolve this problem, a scaled force field method of assignment was used. Assignment of fundamental modes was confirmed by potential energy distributions (PEDs) of the normal modes derived by the scaled force fields using a modified version of the UMAT program in the QCPE package. We demonstrate that for large molecules such as the DMQs, the scaling of the force field is more effective in arriving at the correct assignment of the fundamentals for a quantitative vibrational analysis. An error analysis of the mean deviation of the calculated harmonic, anharmonic, and force field fitted frequencies from the observed frequency provides strong evidence for the correctness of the assignment.

Isomeric identification of methylated naphthalenes using gas phase infrared spectroscopy

We report gas phase mid-infrared spectra of 1- and 2- methyl naphthalenes at 0.2 cm(-1) resolution. Assignment of observed bands have been made using scaled quantum mechanical (SQM) calculations where the force fields rather the frequencies are scaled to find a close fit between observed and calculated bands. The structure of the molecules has been optimized using B3LYP level of theory in conjunction with standard 6-311G** basis set to obtain the harmonic frequencies. Using the force constants in Cartesian coordinates from the Gaussian output, scaled force field calculations are carried out using a modified version of the UMAT program in the QCPE package. Potential energy distributions of the normal modes obtained from such calculations helped us assign the observed bands and identify the unique features of the spectra of 1- and 2-MNs which are important for their isomeric identification.

Infrared Spectra of Dimethylphenanthrenes in the Gas phase

Infrared spectra of atmospherically and astronomically important dimethylphenanthrenes (DMPs), namely 1,9-DMP, 2,4-DMP, and 3,9-DMP, were recorded in the gas phase from 400 to 4000 cm(-1) with a resolution of 0.5 cm(-1) at 110 degrees C using a 7.2 m gas cell. DFT calculations at the B3LYP/6-311G** level were carried out to get the harmonic and anharmonic frequencies and their corresponding intensities for the assignment of the observed bands. However, spectral assignments could not be made unambiguously using anharmonic or selectively scaled harmonic frequencies. Therefore, the scaled quantum mechanical (SQM) force field analysis method was adopted to achieve more accurate assignments. In this method force fields instead of frequencies were scaled. The Cartesian force field matrix obtained from the Gaussian calculations was converted to a nonredundant local coordinate force field matrix and then the force fields were scaled to match experimental frequencies in a consistent manner using a modified version of the UMAT program of the QCPE package. Potential energy distributions (PEDs) of the normal modes in terms of nonredundant local coordinates obtained from these calculations helped us derive the nature of the vibration at each frequency. The intensity of observed bands in the experimental spectra was calculated using estimated vapor pressures of the DMPs. An error analysis of the mean deviation between experimental and calculated intensities reveal that the observed methyl C-H stretching intensity deviates more compared to the aromatic C-H and non C-H stretching bands.

Structure Prediction of G-Protein Coupled Receptors

G-protein coupled receptors (GPCRs) form a large family of proteins and are very important drug targets. They are membrane proteins, which makes computational prediction of their structure challenging. Homology modeling is further complicated by low sequence similarly of the GPCR superfamily.

In this dissertation, we analyze the conserved inter-helical contacts of recently solved crystal structures, and we develop a unified sequence-structural alignment of the GPCR superfamily. We use this method to align 817 human GPCRs, 399 of which are nonolfactory. This alignment can be used to generate high quality homology models for the 817 GPCRs.

To refine the provided GPCR homology models we developed the Trihelix sampling method. We use a multi-scale approach to simplify the problem by treating the transmembrane helices as rigid bodies. In contrast to Monte Carlo structure prediction methods, the Trihelix method does a complete local sampling using discretized coordinates for the transmembrane helices. We validate the method on existing structures and apply it to predict the structure of the lactate receptor, HCAR1. For this receptor, we also build extracellular loops by taking into account constraints from three disulfide bonds. Docking of lactate and 3,5-dihydroxybenzoic acid shows likely involvement of three Arg residues on different transmembrane helices in binding a single ligand molecule.

Protein structure prediction relies on accurate force fields. We next present an effort to improve the quality of charge assignment for large atomic models. In particular, we introduce the formalism of the polarizable charge equilibration scheme (PQEQ) and we describe its implementation in the molecular simulation package Lammps. PQEQ allows fast on the fly charge assignment even for reactive force fields.

Impedance control reduces instability that arises from motor noise.

There is ample evidence that humans are able to control the endpoint impedance of their arms in response to active destabilizing force fields. However, such fields are uncommon in daily life. Here, we examine whether the CNS selectively controls the endpoint impedance of the arm in the absence of active force fields but in the presence of instability arising from task geometry and signal-dependent noise (SDN) in the neuromuscular system. Subjects were required to generate forces, in two orthogonal directions, onto four differently curved rigid objects simulated by a robotic manipulandum. The endpoint stiffness of the limb was estimated for each object curvature. With increasing curvature, the endpoint stiffness increased mainly parallel to the object surface and to a lesser extent in the orthogonal direction. Therefore, the orientation of the stiffness ellipses did not orient to the direction of instability. Simulations showed that the observed stiffness geometries and their pattern of change with instability are the result of a tradeoff between maximizing the mechanical stability and minimizing the destabilizing effects of SDN. Therefore, it would have been suboptimal to align the stiffness ellipse in the direction of instability. The time course of the changes in stiffness geometry suggests that modulation takes place both within and across trials. Our results show that an increase in stiffness relative to the increase in noise can be sufficient to reduce kinematic variability, thereby allowing stiffness control to improve stability in natural tasks.

Separate representations of dynamics in rhythmic and discrete movements: evidence from motor learning.

Rhythmic and discrete arm movements occur ubiquitously in everyday life, and there is a debate as to whether these two classes of movements arise from the same or different underlying neural mechanisms. Here we examine interference in a motor-learning paradigm to test whether rhythmic and discrete movements employ at least partially separate neural representations. Subjects were required to make circular movements of their right hand while they were exposed to a velocity-dependent force field that perturbed the circularity of the movement path. The direction of the force-field perturbation reversed at the end of each block of 20 revolutions. When subjects made only rhythmic or only discrete circular movements, interference was observed when switching between the two opposing force fields. However, when subjects alternated between blocks of rhythmic and discrete movements, such that each was uniquely associated with one of the perturbation directions, interference was significantly reduced. Only in this case did subjects learn to corepresent the two opposing perturbations, suggesting that different neural resources were employed for the two movement types. Our results provide further evidence that rhythmic and discrete movements employ at least partially separate control mechanisms in the motor system.

Composition and decomposition in bimanual dynamic learning.

Our ability to skillfully manipulate an object often involves the motor system learning to compensate for the dynamics of the object. When the two arms learn to manipulate a single object they can act cooperatively, whereas when they manipulate separate objects they control each object independently. We examined how learning transfers between these two bimanual contexts by applying force fields to the arms. In a coupled context, a single dynamic is shared between the arms, and in an uncoupled context separate dynamics are experienced independently by each arm. In a composition experiment, we found that when subjects had learned uncoupled force fields they were able to transfer to a coupled field that was the sum of the two fields. However, the contribution of each arm repartitioned over time so that, when they returned to the uncoupled fields, the error initially increased but rapidly reverted to the previous level. In a decomposition experiment, after subjects learned a coupled field, their error increased when exposed to uncoupled fields that were orthogonal components of the coupled field. However, when the coupled field was reintroduced, subjects rapidly readapted. These results suggest that the representations of dynamics for uncoupled and coupled contexts are partially independent. We found additional support for this hypothesis by showing significant learning of opposing curl fields when the context, coupled versus uncoupled, was alternated with the curl field direction. These results suggest that the motor system is able to use partially separate representations for dynamics of the two arms acting on a single object and two arms acting on separate objects.

Functional significance of stiffness in adaptation of multijoint arm movements to stable and unstable dynamics.

This study compared the mechanisms of adaptation to stable and unstable dynamics from the perspective of changes in joint mechanics. Subjects were instructed to make point to point movements in force fields generated by a robotic manipulandum which interacted with the arm in either a stable or an unstable manner. After subjects adjusted to the initial disturbing effects of the force fields they were able to produce normal straight movements to the target. In the case of the stable interaction, subjects modified the joint torques in order to appropriately compensate for the force field. No change in joint torque or endpoint force was required or observed in the case of the unstable interaction. After adaptation, the endpoint stiffness of the arm was measured by applying displacements to the hand in eight different directions midway through the movements. This was compared to the stiffness measured similarly during movements in a null force field. After adaptation, the endpoint stiffness under both the stable and unstable dynamics was modified relative to the null field. Adaptation to unstable dynamics was achieved by selective modification of endpoint stiffness in the direction of the instability. To investigate whether the change in endpoint stiffness could be accounted for by change in joint torque or endpoint force, we estimated the change in stiffness on each trial based on the change in joint torque relative to the null field. For stable dynamics the change in endpoint stiffness was accurately predicted. However, for unstable dynamics the change in endpoint stiffness could not be reproduced. In fact, the predicted endpoint stiffness was similar to that in the null force field. Thus, the change in endpoint stiffness seen after adaptation to stable dynamics was directly related to changes in net joint torque necessary to compensate for the dynamics in contrast to adaptation to unstable dynamics, where a selective change in endpoint stiffness occurred without any modification of net joint torque.

Adaptation to stable and unstable dynamics achieved by combined impedance control and inverse dynamics model.

This study compared adaptation in novel force fields where trajectories were initially either stable or unstable to elucidate the processes of learning novel skills and adapting to new environments. Subjects learned to move in a null force field (NF), which was unexpectedly changed either to a velocity-dependent force field (VF), which resulted in perturbed but stable hand trajectories, or a position-dependent divergent force field (DF), which resulted in unstable trajectories. With practice, subjects learned to compensate for the perturbations produced by both force fields. Adaptation was characterized by an initial increase in the activation of all muscles followed by a gradual reduction. The time course of the increase in activation was correlated with a reduction in hand-path error for the DF but not for the VF. Adaptation to the VF could have been achieved solely by formation of an inverse dynamics model and adaptation to the DF solely by impedance control. However, indices of learning, such as hand-path error, joint torque, and electromyographic activation and deactivation suggest that the CNS combined these processes during adaptation to both force fields. Our results suggest that during the early phase of learning there is an increase in endpoint stiffness that serves to reduce hand-path error and provides additional stability, regardless of whether the dynamics are stable or unstable. We suggest that the motor control system utilizes an inverse dynamics model to learn the mean dynamics and an impedance controller to assist in the formation of the inverse dynamics model and to generate needed stability.

Impedance control balances stability with metabolically costly muscle activation.

Humans are able to stabilize their movements in environments with unstable dynamics by selectively modifying arm impedance independently of force and torque. We further investigated adaptation to unstable dynamics to determine whether the CNS maintains a constant overall level of stability as the instability of the environmental dynamics is varied. Subjects performed reaching movements in unstable force fields of varying strength, generated by a robotic manipulator. Although the force fields disrupted the initial movements, subjects were able to adapt to the novel dynamics and learned to produce straight trajectories. After adaptation, the endpoint stiffness of the arm was measured at the midpoint of the movement. The stiffness had been selectively modified in the direction of the instability. The stiffness in the stable direction was relatively unchanged from that measured during movements in a null force field prior to exposure to the unstable force field. This impedance modification was achieved without changes in force and torque. The overall stiffness of the arm and environment in the direction of instability was adapted to the force field strength such that it remained equivalent to that of the null force field. This suggests that the CNS attempts both to maintain a minimum level of stability and minimize energy expenditure.

Reflex contributions to the directional tuning of arm stiffness

It has been shown that during arm movement, humans selectively change the endpoint stiffness of their arm to compensate for the instability in an unstable environment. When the direction of the instability is rotated with respect to the direction of movement, it was found that humans modify the antisymmetric component of their endpoint stiffness. The antisymmetric component of stiffness arises due to reflex responses suggesting that the subjects may have tuned their reflex responses as part of the feedforward adaptive control. The goal of this study was to examine whether the CNS modulates the gain of the reflex response for selective tuning of endpoint impedance. Subjects performed reaching movements in three unstable force fields produced by a robotic manipulandum, each field differing only in the rotational component. After subjects had learned to compensate for the field, allowing them to make unperturbed movements to the target, the endpoint stiffness of the arm was estimated in the middle of the movements. At the same time electromyographic activity (EMG) of six arm muscles was recorded. Analysis of the EMG revealed differences across force fields in the reflex gain of these muscles consistent with stiffness changes. This study suggests that the CNS modulates the reflex gain as part of the adaptive feedforward command in which the endpoint impedance is selectively tuned to overcome environmental instability. © 2008 Springer-Verlag Berlin Heidelberg.

Generalization in Adaptation to Stable and Unstable Dynamics

Humans skillfully manipulate objects and tools despite the inherent instability. In order to succeed at these tasks, the sensorimotor control system must build an internal representation of both the force and mechanical impedance. As it is not practical to either learn or store motor commands for every possible future action, the sensorimotor control system generalizes a control strategy for a range of movements based on learning performed over a set of movements. Here, we introduce a computational model for this learning and generalization, which specifies how to learn feedforward muscle activity in a function of the state space. Specifically, by incorporating co-activation as a function of error into the feedback command, we are able to derive an algorithm from a gradient descent minimization of motion error and effort, subject to maintaining a stability margin. This algorithm can be used to learn to coordinate any of a variety of motor primitives such as force fields, muscle synergies, physical models or artificial neural networks. This model for human learning and generalization is able to adapt to both stable and unstable dynamics, and provides a controller for generating efficient adaptive motor behavior in robots. Simulation results exhibit predictions consistent with all experiments on learning of novel dynamics requiring adaptation of force and impedance, and enable us to re-examine some of the previous interpretations of experiments on generalization. © 2012 Kadiallah et al.

The effect of contextual cues on the encoding of motor memories.

Several studies have shown that sensory contextual cues can reduce the interference observed during learning of opposing force fields. However, because each study examined a small set of cues, often in a unique paradigm, the relative efficacy of different sensory contextual cues is unclear. In the present study we quantify how seven contextual cues, some investigated previously and some novel, affect the formation and recall of motor memories. Subjects made movements in a velocity-dependent curl field, with direction varying randomly from trial to trial but always associated with a unique contextual cue. Linking field direction to the cursor or background color, or to peripheral visual motion cues, did not reduce interference. In contrast, the orientation of a visual object attached to the hand cursor significantly reduced interference, albeit by a small amount. When the fields were associated with movement in different locations in the workspace, a substantial reduction in interference was observed. We tested whether this reduction in interference was due to the different locations of the visual feedback (targets and cursor) or the movements (proprioceptive). When the fields were associated only with changes in visual display location (movements always made centrally) or only with changes in the movement location (visual feedback always displayed centrally), a substantial reduction in interference was observed. These results show that although some visual cues can lead to the formation and recall of distinct representations in motor memory, changes in spatial visual and proprioceptive states of the movement are far more effective than changes in simple visual contextual cues.

Motor learning of novel dynamics is not represented in a single global coordinate system: evaluation of mixed coordinate representations and local learning.

Successful motor performance requires the ability to adapt motor commands to task dynamics. A central question in movement neuroscience is how these dynamics are represented. Although it is widely assumed that dynamics (e.g., force fields) are represented in intrinsic, joint-based coordinates (Shadmehr R, Mussa-Ivaldi FA. J Neurosci 14: 3208-3224, 1994), recent evidence has questioned this proposal. Here we reexamine the representation of dynamics in two experiments. By testing generalization following changes in shoulder, elbow, or wrist configurations, the first experiment tested for extrinsic, intrinsic, or object-centered representations. No single coordinate frame accounted for the pattern of generalization. Rather, generalization patterns were better accounted for by a mixture of representations or by models that assumed local learning and graded, decaying generalization. A second experiment, in which we replicated the design of an influential study that had suggested encoding in intrinsic coordinates (Shadmehr and Mussa-Ivaldi 1994), yielded similar results. That is, we could not find evidence that dynamics are represented in a single coordinate system. Taken together, our experiments suggest that internal models do not employ a single coordinate system when generalizing and may well be represented as a mixture of coordinate systems, as a single system with local learning, or both.