Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. (49/235)

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.  (+info)

Performance analysis of a dual-buffer architecture for digital flow cytometry. (50/235)

BACKGROUND: Most current commercial flow cytometers employ analog circuitry to provide feature values describing the pulse waveforms produced from suspended cells and particles. This restricts the type of features that can be extracted (typically pulse height, width, and integral) and consequently places a limit on classification performance. In previous work, we described a first-generation digital data acquisition and processing system that was used to demonstrate the classification advantages provided by the extraction of additional waveform features. An improved version of the system is discussed in this paper, focusing on dual-buffering to ensure increased pulse capture. A mathematical model of the system is also presented for performance analysis. METHODS: The second-generation system incorporates fast digitization of analog pulse waveforms, instantaneous pulse detection hardware, and a novel dual-buffering scheme. A mathematical model of the system was developed to theoretically compute the capture-rate performance. RESULTS: The capture rate of the system was theoretically analyzed and empirically measured. Under typical conditions, a capture rate of 8,000 pulses/s was experimentally achieved. CONCLUSIONS: Based on these results, the dual-buffer architecture shows great potential for use in flow cytometry.  (+info)

Transition from stochastic to deterministic behavior in calcium oscillations. (51/235)

Simulation and modeling is becoming more and more important when studying complex biochemical systems. Most often, ordinary differential equations are employed for this purpose. However, these are only applicable when the numbers of participating molecules in the biochemical systems are large enough to be treated as concentrations. For smaller systems, stochastic simulations on discrete particle basis are more accurate. Unfortunately, there are no general rules for determining which method should be employed for exactly which problem to get the most realistic result. Therefore, we study the transition from stochastic to deterministic behavior in a widely studied system, namely the signal transduction via calcium, especially calcium oscillations. We observe that the transition occurs within a range of particle numbers, which roughly corresponds to the number of receptors and channels in the cell, and depends heavily on the attractive properties of the phase space of the respective systems dynamics. We conclude that the attractive properties of a system, expressed, e.g., by the divergence of the system, are a good measure for determining which simulation algorithm is appropriate in terms of speed and realism.  (+info)

Internal models in sensorimotor integration: perspectives from adaptive control theory. (52/235)

Internal models and adaptive controls are empirical and mathematical paradigms that have evolved separately to describe learning control processes in brain systems and engineering systems, respectively. This paper presents a comprehensive appraisal of the correlation between these paradigms with a view to forging a unified theoretical framework that may benefit both disciplines. It is suggested that the classic equilibrium-point theory of impedance control of arm movement is analogous to continuous gain-scheduling or high-gain adaptive control within or across movement trials, respectively, and that the recently proposed inverse internal model is akin to adaptive sliding control originally for robotic manipulator applications. Modular internal models' architecture for multiple motor tasks is a form of multi-model adaptive control. Stochastic methods, such as generalized predictive control, reinforcement learning, Bayesian learning and Hebbian feedback covariance learning, are reviewed and their possible relevance to motor control is discussed. Possible applicability of a Luenberger observer and an extended Kalman filter to state estimation problems-such as sensorimotor prediction or the resolution of vestibular sensory ambiguity-is also discussed. The important role played by vestibular system identification in postural control suggests an indirect adaptive control scheme whereby system states or parameters are explicitly estimated prior to the implementation of control. This interdisciplinary framework should facilitate the experimental elucidation of the mechanisms of internal models in sensorimotor systems and the reverse engineering of such neural mechanisms into novel brain-inspired adaptive control paradigms in future.  (+info)

Dynamic properties of network motifs contribute to biological network organization. (53/235)

Biological networks, such as those describing gene regulation, signal transduction, and neural synapses, are representations of large-scale dynamic systems. Discovery of organizing principles of biological networks can be enhanced by embracing the notion that there is a deep interplay between network structure and system dynamics. Recently, many structural characteristics of these non-random networks have been identified, but dynamical implications of the features have not been explored comprehensively. We demonstrate by exhaustive computational analysis that a dynamical property--stability or robustness to small perturbations--is highly correlated with the relative abundance of small subnetworks (network motifs) in several previously determined biological networks. We propose that robust dynamical stability is an influential property that can determine the non-random structure of biological networks.  (+info)

A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. (54/235)

Signal transduction pathways control cellular responses to stimuli, but it is unclear how molecular information is processed as a network. We constructed a systems model of 7980 intracellular signaling events that directly links measurements to 1440 response outputs associated with apoptosis. The model accurately predicted multiple time-dependent apoptotic responses induced by a combination of the death-inducing cytokine tumor necrosis factor with the prosurvival factors epidermal growth factor and insulin. By capturing the role of unsuspected autocrine circuits activated by transforming growth factor-alpha and interleukin-1alpha, the model revealed new molecular mechanisms connecting signaling to apoptosis. The model derived two groupings of intracellular signals that constitute fundamental dimensions (molecular "basis axes") within the apoptotic signaling network. Projection along these axes captures the entire measured apoptotic network, suggesting that cell survival is determined by signaling through this canonical basis set.  (+info)

Unique contribution of family functioning in caregivers of patients with mild to moderate dementia. (55/235)

The relationship between family functioning and dementia caregiving is complex. The present study examined the interrelationships between family functioning, caregiver burden, and patient characteristics. Participants were 72 live-in, family caregivers of patients with mild (n = 47) or moderate dementia (n = 25). Caregivers completed measures of burden, family functioning, depression, and anxiety. Ratings of patients' memory/behavior problems and patients' activities of daily living were also collected. Results indicated that higher levels of caregiver burden were significantly associated with increased caregiver depression and anxiety, greater frequency of memory and behavior problems in the dementia patient, worse activities of daily living, and poorer family functioning. Even after controlling for caregiver depression, caregiver anxiety, and frequency of memory/behavior problems in dementia patients, poorer family functioning continued to be associated with higher levels of caregiver burden. Caregivers with high levels of burden reported greater family dysfunction in communication and roles, regardless of their relationship to the patient (i.e., spouse or child). These findings suggest that including a family systems component in caregiver interventions may be beneficial in reducing burden in these very distressed individuals.  (+info)

The EUHPID Health Development Model for the classification of public health indicators. (56/235)

The European Community Health Promotion Indicator Development Model has been developed as the basis for establishing a European set of indicators for monitoring health promotion interventions. This paper offers the model more generally as a common frame of reference for broader public health practice and indicator development. The model builds around the physical, mental and social health of individuals and shows how health develops by interaction between individual and environmental health determinants. It demonstrates that health development can be analysed from a salutogenic and a pathogenic perspective and explains how the differing starting points of different intervention approaches such as health promotion and health care are related to these two perspectives. Finally, a classification system for pathogenic and salutogenic public health outcome indicators is derived from the model and has been applied to the current core list of the European Community Health Indicator system. The model and its application highlight the need for systematic salutogenic indicator development in the field of public health and for strengthening the health promotion perspective in the future.  (+info)