Effects of environmental fluctuation on plankton allelopathy

 This paper studies a two-dimensional system that arises in plankton allelopathy involving discrete time delays and environmental fluctuations. The environmental parameters are assumed to be perturbed by white noise characterized by a Gaussian distribution with mean zero and unit spectral density. The dynamic behaviour of the stochastic system is studied and the fluctuations in population are measured both analytically and numerically by computer simulation. Received: 7 September 1998 / Revised version: 14 October 1998     

Integrated system for bioprocess monitoring and diagnosis using a local area network

Bioprocess monitoring and data analysis utilizing a local area network (LAN) is described in which an integrated computer environment provides for real-time monitoring from several remote personal computers with easy evaluation of the current process status and providing a common utilization of fermentation data. The computer network also enhances the decision-making process in the management of the production plant. Bioprocess control utilizing a LAN environment is expected to promote better utilization of fermentation data accumulated through repeated operations and to realize advanced control of fermentation processes. © Rapid Science Ltd. 1998     

Modeling the exponential growth of filamentous fungi during batch cultivation

In certain conditions, filamentous fungi are observed to grow exponentially during batch submerged growth. It is shown for three cases, with simple mechanistic models, that an exponential growth assumption is reasonable. The basis of these models is the identification of a growth unit, and a mechanism for its doubling with a constant generation time. The importance of the variation of morphological properties within populations is demonstrated by the comparison of computer simulations of simplified models using average values and either experimental data or computer simulations of detailed stochastic models. Copyright 1998 John Wiley & Sons, Inc.     

用计算机折叠蛋白质:我们走了多远?(英文)

蛋白质折叠是现代科学最具挑战性的难题之一。Anfinsen的先驱性工作已经过去数十年了,我们对蛋白质折叠的机理仍不甚了然。但值得庆幸的是,科学工作者们在解析几个模型蛋白质的折叠机理上已经取得了明显的进展。这篇综述将主要回顾在蛋白质折叠的计算研究方面的进展。受益于计算机技术的迅猛发展,在1998年首次实现了一个微秒的全原子水平的蛋白质折叠,从2000年开始,folding@home将全球分布式计算技术应用于蛋白质折叠。在经历了数十年艰苦的努力之后,天然蛋白质亚埃精度的折叠终于在2007年成功实现。近年来,一种全新的概念开始出现,人们越来越多地用网络来解释蛋白质折叠的机理。随着分子力场的不断完善,分子模拟将会在解析蛋白质折叠的机理上起到越来越重要的作用。     

A new model for how O6-methylguanine-DNA methyltransferase binds DNA

Human methyltransferase (hAT) catalyzes the transfer of an alkyl group from the 6-position of guanine to an active site Cys residue. The physiological role of hAT is the repair of alkylated guanine residues in DNA. However, the repair of methylated or chloroethylated guanine bases negates the effects of certain chemotherapeutic agents. A model of how hAT binds DNA might be useful in the design of compounds that could inactivate hAT. We have used computer modeling studies to generate such a model. The model utilizes a helix-loop-wing DNA binding motif found in Mu transposase. The model incorporates a flipped out guanine base in order to bring the methylated oxygen atom close to the active site Cys residue. The model is consistent with a variety of chemical and biochemical data. Proteins 32:3–6, 1998. © 1998 Wiley-Liss, Inc.     

Time-lapse infrared videography for animal behavior observations

Although videography has been used for many years to record episodes of animal behavior, the availability of increasingly complex equipment can make selection difficult. Most equipment developed for round-the-clock observations was designed for security surveillance, so informed purchasing, installation, and usage decisions need to be made to monitor animal behavior effectively. During 7 years of using video and infrared equipment for animal behavior research and monitoring in a zoo setting, we tested many models, evaluated options, and modified components. We now have well-integrated systems that are compatible with our video/computer review and analysis program. New equipment will continue to become available, but familiarity with basic features and applications can help to narrow the selection. Zoo Biol 17:535–543, 1998. © 1998 Wiley-Liss, Inc.     

A comparison of shoot-forming and non-shoot-forming somatic embryos of sweet potato [Ipomoea batatas (L.) Lam.] using computer vision and histological analyses

Diagnostic structural features for competence to form shoots were tested among sweet potato embryos by combining morphological image capture (using a computer vision system) with anatomical analyses (using light microscopy). Five major morphological variants (`perfect', `near perfect', `limited/no meristematic activity', `disrupted internal anatomy', and `proliferating') were identified among torpedo- and cotyledonary-stage embryos. Among these, only the first two were found to be competent for conversion into plantlets. Lack of organized shoot development in somatic embryos of sweet potato was associated with the following abnormalities: lack of an organized apical meristem, sparcity of dividing cells in the apical region, flattened apical meristem, and multiple meristemoids and/or diffuse meristematic activity throughout the embryo. Diagnostic separation of most shoot-forming and non-shoot-forming torpedo and cotyledonary embryo variants was achieved. Received: 27 January 1997 / Revision received: 28 January 1998 / Accepted: 12 February 1998     

Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program

The hydrodynamic properties of macromolecules and bioparticles, represented by bead models, can be calculated using methods implemented in the computer routine HYDRO. Recently, a new computer routine, SOLPRO, has been presented for the calculation of various SOLution PROperties. These include (1) time-dependent electro-optic and spectroscopic properties related to rotational diffusion, (2) non-dynamic properties like scattering curves, and (3) dimensionless quantities that combine two or more solution properties in a form which depends on the shape of the macromolecule but not on its size. In the present work we describe the inclusion of more of those types of properties in a new version of SOLPRO. Particularly, we describe the calculation of relaxation rates in nuclear magnetic resonance (NMR). For dipolar coupling, given the direction of the dipole the program calculates values of the spectral density, from which the NMR relaxation times can be obtained. We also consider scattering-related properties, namely the distribution of distances for the bead model, which is directly related to the angular dependence of scattered intensity, and the particle's longest distance. We have devised and programmed a procedure to calculate the covolume of the bead model, related to the second virial coefficient and, in general, to the concentration dependence of solution properties. Various shape-dependent dimensionless quantities involving the covolume are calculated. In this paper we also discuss some aspects, namely bead overlapping and hydration, that are not explicitely included in SOLPRO, but should be considered by the user. Received: 25 May 1998 / Revised version: 30 July 1998 / Accepted: 30 July 1998     

Quantifying livestock responses for heat stress management: a review

 Hot weather challenges livestock production but technology exists to offset the challenge if producers have made appropriate strategic decisions. Key issues include understanding the hazards of heat stress, being prepared to offer relief from the heat, recognizing when an animal is in danger, and taking appropriate action. This paper describes our efforts to develop biological response functions; assesses climatic probabilities and performs associated risk analyses; provides inputs for computer models used to make environmental management decisions; and evaluates threshold temperatures as estimates of critical temperature limits for swine, cattle and sheep. Received: 3 September 1998/Accepted: 5 October 1998     

Influence of protein structure databases on the predictive power of statistical pair potentials

A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139–149, 1998. © 1998 Wiley-Liss, Inc.     

Computer-assisted paleoanthropology

Paleoanthropologists are confronted by a steadily growing number of fossil specimens exhibiting diversity in both apparent morphology and state of preservation. Studying this material to answer phylogenetic and functional questions requires extensive qualitative assessment accompanied by quantitative evaluation of large volumes of data. Over the past decade, major new developments in both respects have been made possible through the advent of medical imaging technologies, most notably computer tomography (CT), and through concomitant progress in computer graphics technology. In paleoanthropology, these techniques offer noninvasive tools for visualization of inaccessible regions of the skeleton, computer-assisted reconstruction of fragmentary fossil specimens, and morphometric or biomechanical analysis of data derived from CT images. A series of CT based studies has already yielded new insights into character differences between fossil hominid species. © 1998 Wiley-Liss, Inc.     

Coefficient of variation of interspike intervals greater than 0.5. How and when?

Using Stein's model with and without reversal potentials, we investigated the mechanism of production of spike trains with a CV (ISI) (standard deviation/mean interspike interval) greater than 0.5, as observed in the visual cortex. When the attractor of the deterministic part of the dynamics is below the firing threshold, spike generation results primarily from random fluctuations. Using computer simulation for a range of membrane decay times and with other model parameters set to values appropriate for the visual cortex, we demonstrate that CV (ISI) is then usually greater than 0.5; if the attractor is above the threshold, spike generation is mainly due to deterministic forces, and CV (ISI) is then usually lower than 0.5. The critical value of the inhibitory postsynaptic potential (IPSP) rate at which CV (ISI) becomes greater than 0.5 is determined, resulting in specifications of how neurones might adjust their synaptic inputs to elicit irregular spike trains. Received: 25 June 1998/Accepted in revised form: 16 December 1998     

Design,construction, crystallization,and preliminary X-ray studies of a fine-tuning mutant (F133V) of module-substituted chimera hemoglobin

A chimera βα-subunit of human hemoglobin was crystallized into a carbonmonoxy form. The protein was assembled by substituting the structural portion of a β-subunit of hemoglobin (M4 module of the subunit) for its counterpart in the α-subunit. In order to overcome the inherent instability in the crystallization of the chimera subunit, a site-directed mutagenesis (F133V) technique was employed based on a computer model. The crystal was used for an X-ray diffraction study yielding a data set with a resolution of 2.5 Å. The crystal belongs to the monoclinic space group P2₁, with cell dimensions of a = 62.9, b = 81.3, c = 55.1 Å, and β = 91.0°. These dimensions are similar to the crystallographic parameters of the native β-subunit tetramers in three different ligand states, one of which is a cyanide form that was also crystallized in this study. Proteins 32:263–267, 1998. © 1998 Wiley-Liss, Inc.     

The cellular environment in computer simulations of radiation-induced damage to DNA

Radiation-induced DNA single- and double-strand breaks were modeled for 660 keV photon radiation and scavenger capacity mimicking the cellular environment. Atomistic representation of DNA in B form with a first hydration shell was utilized to model direct and indirect damage. Monte Carlo generated electron tracks were used to model energy deposition in matter and to derive initial spatial distributions of species which appear in the medium following radiolysis. Diffusion of species was followed with time, and their reactions with DNA and each other were modeled in an encounter-controlled manner. Three methods to account for hydroxyl radical diffusion in a cellular environment were tested: assumed exponential survival, time-limited modeling and modeling of reactions between hydroxyl radicals and scavengers in an encounter-controlled manner. Although the method based on modeling scavenging in an encounter-controlled manner is more precise, it requires substantially more computer resources than either the exponential or time-limiting method. Scavenger concentrations of 0.5 and 0.15 M were considered using exponential and encounter-controlled methods with reaction rate set at 3×10⁹ dm³ mol^–1 s^–1. Diffusion length and strand break yields, predicted by these two methods for the same scavenger molarity, were different by 20%–30%. The method based on limiting time of chemistry follow-up to 10^–9 s leads to DNA damage and radical diffusion estimates similar to 0.5 M scavenger concentration in the other two methods. The difference observed in predictions made by the methods considered could be tolerated in computer simulations of DNA damage. Received: 3 June 1998 / Accepted in revised form: 16 July 1998     

Interaction of ON and OFF pathways for visual contrast measurement

We propose a novel model of visual contrast measurement based on segregated On and Off pathways. Two driving forces have shaped our investigation: (1) establishing a mechanism selective for sharp local transitions in the luminance distribution; (2) generating a robust scheme of oriented contrast detection. Our starting point was the architecture of early stages in the mammalian visual system. We show that the circuit behaves as a soft AND-gate and analyze the scale-space selectivity properties of the model in detail. The theoretical analysis is supplemented by computer simulations in which we selectively investigate key functionalities of the proposed contrast detection scheme. We demonstrate that the model is capable of successfully processing synthetic as well as natural images, thus illustrating the potential of the method for computer vision applications. Received: 5 June 1998 / Accepted in revised form: 12 May 1999     

A passive dynamic walking robot that has a deterministic nonlinear gait

There is a growing body of evidence that the step-to-step variations present in human walking are related to the biomechanics of the locomotive system. However, we still have limited understanding of what biomechanical variables influence the observed nonlinear gait variations. It is necessary to develop reliable models that closely resemble the nonlinear gait dynamics in order to advance our knowledge in this scientific field. Previously, Goswami et al. [1998. A study of the passive gait of a compass-like biped robot: symmetry and chaos. International Journal of Robotic Research 17(12)] and Garcia et al. [1998. The simplest walking model: stability, complexity, and scaling. Journal of Biomechanical Engineering 120(2), 281-288] have demonstrated that passive dynamic walking computer models can exhibit a cascade of bifurcations in their gait pattern that lead to a deterministic nonlinear gait pattern. These computer models suggest that the intrinsic mechanical dynamics may be at least partially responsible for the deterministic nonlinear gait pattern; however, this has not been shown for a physical walking robot. Here we use the largest Laypunov exponent and a surrogation analysis method to confirm and extend Garcia et al.'s and Goswami et al.'s original results to a physical passive dynamic walking robot. Experimental outcomes from our walking robot further support the notion that the deterministic nonlinear step-to-step variations present in gait may be partly governed by the intrinsic mechanical dynamics of the locomotive system. Furthermore the nonlinear analysis techniques used in this investigation offer novel methods for quantifying the nature of the step-to-step variations found in human and robotic gait.     

Bifurcations in the decremental propagation of a spike train in the Hodgkin-Huxley model of low excitability

Response of a nerve fiber of low excitability to periodic stimulus pulses is studied with computer simulation of the Hodgkin-Huxley model. The excitability of the Hodgkin-Huxley model is reduced by decreasing the equilibrium potential for the sodium ion and by increasing the temperature, so that the decremental propagation of spikes occurs in the refractory period. It is shown that, as the period of stimulus pulses is decreased, the propagation length of the spikes is continuously changed, and period-doubling bifurcations occur. The response of a nerve fiber of low excitability is then qualitatively different from that of a normal fiber. Received: 6 December 1996 / Accepted in revised form: 12 June 1998     

Models for the length distributions of actin filaments: II. Polymerization and fragmentation by gelsolin acting together

In a previous paper, we studied elementary models for polymerization, depolymerization, and fragmentation of actin filaments (Edelstein-Keshet and Ermentrout, 1998, Bull. Math. Biol. 60, 449–475). When these processes act together, more complicated dynamics occur. We concentrate on a particular case study, using the actin-fragmenting protein gelsolin. A set of biological parameter values (drawn from the experimental literature) is used in computer simulations of the kinetics of gelsolin-mediated actin filament fragmentation.     

Hysteresis Dynamics,Bursting Oscillations and Evolution to Chaotic Regimes

This article describes new aspects of hysteresis dynamics which have been uncovered through computer experiments. There are several motivations to be interested in fast-slow dynamics. For instance, many physiological or biological systems display different time scales. The bursting oscillations which can be observed in neurons, beta-cells of the pancreas and population dynamics are essentially studied via bifurcation theory and analysis of fast-slow systems (Keener and Sneyd, 1998; Rinzel, 1987). Hysteresis is a possible mechanism to generate bursting oscillations. A first part of this article presents the computer techniques (the dotted-phase portrait, the bifurcation of the fast dynamics and the wave form) we have used to represent several patterns specific to hysteresis dynamics. This framework yields a natural generalization to the notion of bursting oscillations where, for instance, the active phase is chaotic and alternates with a quiescent phase. In a second part of the article, we emphasize the evolution to chaos which is often associated with bursting oscillations on the specific example of the Hindmarsh-Rose system. This evolution to chaos has already been studied with classical tools of dynamical systems but we give here numerical evidence on hysteresis dynamics and on some aspects of the wave form. The analytical proofs will be given elsewhere.