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At least 127 records · Page 7Linked to original sources
PubMed2001

Incorporating dynamic collimator motion in Monte Carlo simulations: an application in modelling a dynamic wedge.

In radiation therapy, new treatment modalities employing dynamic collimation and intensity modulation increase the complexity of dose calculation because a new dimension, time, has to be incorporated into the traditional three-dimensional problem. In this work, we investigated two classes of sampling technique to incorporate dynamic collimator motion in Monte Carlo simulation. The methods were initially evaluated for modelling enhanced dynamic wedges (EDWs) from Varian accelerators (Varian Medical Systems, Palo Alto, USA). In the position-probability-sampling or PPS method, a cumulative probability distribution function (CPDF) was computed for the collimator position, which could then be sampled during simulations. In the static-component-simulation or SCS method, a dynamic field is approximated by multiple static fields in a step-shoot fashion. The weights of the particles or the number of particles simulated for each component field are computed from the probability distribution function (PDF) of the collimator position. The CPDF and PDF were computed from the segmented treatment tables (STTs) for the EDWs. An output correction factor had to be applied in this calculation to account for the backscattered radiation affecting monitor chamber readings. Comparison of the phase-space data from the PPS method (with the step-shoot motion) with those from the SCS method showed excellent agreement. The accuracy of the PPS method was further verified from the agreement between the measured and calculated dose distributions. Compared to the SCS method, the PPS method is more automated and efficient from an operational point of view. The principle of the PPS method can be extended to simulate other dynamic motions, and in particular, intensity-modulated beams using multileaf collimators.

Biophysical Phenomena↗
PubMed2005

Single-strand conformation polymorphism (SSCP) of oligodeoxyribonucleotides: an insight into solution structural dynamics of DNAs provided by gel electrophoresis and molecular dynamics simulations.

Studies on the solution structure dynamics of RNA/DNA are becoming crucially important. The phenomena of SSCP (single-strand conformation polymorphism), small RNA dynamics in a cell, and others can be related to the conformational changes of single-stranded (ss) RNAs/DNAs in solution. However, little is known about those dynamics. Only the intra-structural transition of ssDNAs in solution has been reported based on Watson-Crick (W-C) base-pairing. Here, we found a general feature of the SSCP phenomenon by studying the simpler molecules of ss-oligodeoxyribonucleotides. A single base substitution or a positional exchange of nucleotide in a highly homologous series of ss-dodecanucleotides led to a change in the mobility-in-gel. This was unexpected, since most of these nucleotides [such as d(A(11)G) or d(A(11)C)] have no possibility of forming W-C base-pairing. MD (molecular dynamics) experiments revealed differences in shape and size between the dynamic structures of these molecules which could affect their mobility-in-gel. In addition, a high correlation was observed between the electrophoretic mobility and the size-related parameters such as end-to-end distance obtained from MD simulations. Because the simulation was considerably shorter (nanosecond) than the experimental time-scale (second), the result must be considered conservatively; but it is nevertheless encouraging for utilizing MD simulation for structural analysis of oligonucleotides.

Base Sequence↗
PubMed1993

Hierarchical functional organization of formal biological systems: a dynamical approach. III. The concept of non-locality leads to a field theory describing the dynamics at each level of organization of the (D-FBS) sub-system.

In paper I, the construction of the graph of interactions, called (O-FBS), was deduced from the 'self-association hypothesis'. In paper II, a criterion of evolution during development for the (O-FBS), which represents the topology of the biological system, was deduced from an optimum principle leading to specific dynamics. Experimental verification of the proposed extremum hypothesis is possible because precise knowledge of the dynamics is not necessary; only knowledge of the monotonic variation of the number of sinks is required for given initial conditions. Essentially, the properties of the (O-FBS) are based on the concept of non-symmetry of functional interactions, as shown by the 'orgatropy' function (paper II). In this paper, a field theory is proposed to describe the (D-FBS), i.e. the physiological processes expressed by functional interactions: (i) physiological processes are conceived as the transport of a field variable submitted to the action of a field operator; (ii) because of hierarchy, this field theory is based on the concept of non-locality, and includes a non-local and non-symmetric interaction operator; (iii) the geometry of the structure contributes to the dynamics via the densities of structural units; and (iv) because a physiological process evolves on a particular timescale, it is possible to classify the levels of organization according to distinct timescales, and, therefore, to obtain a 'decoupling' of dynamics at each level. Thus, a property of structurality for a biological system is proposed, which is based on the finiteness of the velocity of the interaction, thus, with distinct values of timescales for the construction of the hierarchy of the system. Three axioms are introduced to define the fields associated with the topology of the system: (i) the existence of the fields; (ii) the decoupling of the dynamics; and (iii) the ability of activation-inhibition. This formulation leads to a self-coherent definition of auto-organization: an FBS is self-organized if it goes from one stable state for the (D-FBS) to another under the influence of certain modifications of its topology, i.e. a modification of the (O-FBS). It is shown that properties deduced with this formalism give the relationship between topology and geometry in an FBS, and particularly, the geometrical re-distribution of units.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2002

Dynamic critical behavior of an extended reptation dynamics for self-avoiding walks.

We consider lattice self-avoiding walks and discuss the dynamic critical behavior of two dynamics that use local and bilocal moves and generalize the usual reptation dynamics. We determine the integrated and exponential autocorrelation times for several observables, perform a dynamic finite-size scaling study of the autocorrelation functions, and compute the associated dynamic critical exponents z. For the variables that describe the size of the walks, in the absence of interactions we find z approximately 2.2 in two dimensions and z approximately 2.1 in three dimensions. At the theta point in two dimensions we have z approximately 2.3.

Journal Article↗
PubMed2005

Geometry of dynamically available empty space is the key to near-arrest dynamics.

We study several examples of kinetically constrained lattice models using dynamically accessible volume as an order parameter. Thereby we identify two distinct regimes exhibiting dynamical slowing, with a sharp threshold between them. These regimes are identified both by a new response function in dynamically available volume, as well as directly in the dynamics. Results for the self-diffusion constant in terms of the connected hole density are presented, and some evidence is given for scaling in the limit of dynamical arrest.

Journal Article↗
PubMed2003

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.

Adaptation, Physiological↗
PubMed2003

Demand dynamic bio-girdling in heart failure: improved efficacy of dynamic cardiomyoplasty by LD contraction during aortic out-flow.

PURPOSE: The value of dynamic cardiomyoplasty has been brought into question by the disappointing results produced by slow contraction-relaxation cycle and possibly degeneration of the latissimus dorsi muscle (LD) secondary to temporary tenotomy and chronic daily electrical stimulation. Objective of our study is to determine whether daily periods of rest introduced by demand stimulation in the continuous contraction protocol produce systolic assistance and improve clinical results. METHODS: Twelve dynamic cardiomyoplasty patients (mean age 58.2 +/- 5.8 years, M/F=11/1, sinus rhythm/atrial fibrillation=11/1) with dilated myocardiopathy were enrolled in an unrandomized trial of Demand Dynamic Heart Bio-Girdling in a public regional teaching hospital. Periods of LD inactivity, each lasting several hours, were introduced daily on a heart rate-based demand regime. To avoid full transformation of LD, fewer impulses per day were delivered, daily providing the LD with long periods of rest (Demand light stimulation). The contractile properties were measured by transcutaneous non-invasive LD tensiomyogram interrogation (LD tensiomyogram). Bio-Girdle activation was synchronized to heart beat by combining tensiomyogram and echocardiography. Clinical, echocardiographic and hemodynamic records, as well as aortic flow measurements by Doppler aortic flow wire were taken during the follow-up. MAIN FINDINGS: Mean duration of the demand stimulation follow-up was 40.2+13.8 months. At five years, "Demand stimulation" shows: 1) no operative death; 2) 83% actuarial survival; 3) highly significant 47.4% decrease of the NYHA class (from 3.17 +/- 0.38 to 1.67 +/- 0.77, p=0.0001); 4) 41.6% improvement of LVEF (from 22.6 +/- 4.38 to 32.0 +/- 7.0, p=0.001); 5) 7.5 +/- 3.0% increase in aortic flow velocity peak in assisted vs. unassisted beats, and 6) preservation of LD from slowness (TFF value 33 +/- 7.86 at follow-up versus 15.8 +/- 11.1 Hz just before switching from continuous to demand stimulation, p=0.0001) and muscle degenerative atrophy. CONCLUSIONS: In dynamic cardiomyoplasty the demand light stimulation maintains LD contraction properties over time, produces effective systolic assistance, and improves clinical results. Demand dynamic bio-girdling is a safe and effective treatment for end-stage heart failure in selected patients.

Aorta↗
PubMed1999

E-MAP-115 (ensconsin) associates dynamically with microtubules in vivo and is not a physiological modulator of microtubule dynamics.

Microtubule-associated proteins (MAPs) have been hypothesized to regulate microtubule dynamics and/or functions. To test hypotheses concerning E-MAP-115 (ensconsin) function, we prepared stable cell lines expressing conjugates in which the full-length MAP (Ensc) or its microtubule-binding domain (EMTB) was conjugated to one or more green fluorescent protein (GFP) molecules. Because both distribution and microtubule-binding properties of GFP-Ensc, GFP-EMTB, and 2x, 3x, or 4xGFP-EMTB chimeras all appeared to be identical to those of endogenous E-MAP-115 (ensconsin), we used the 2xGFP-EMTB molecule as a reporter for the behavior and microtubule-binding function of endogenous MAP. Dual wavelength time-lapse fluorescence imaging of 2xGFP-EMTB in cells microinjected with labeled tubulin revealed that this GFP-MAP chimera associated with the lattice of all microtubules immediately upon polymerization and dissociated concomitant with depolymerization, suggesting that dynamics of MAP:microtubule interactions were at least as rapid as tubulin:microtubule dynamics in the polymerization reaction. Presence of both GFP-EMTB chimeras and endogenous E-MAP-115 (ensconsin) along apparently all cellular microtubules at all cell cycle stages suggested that the MAP might function in modulating stability or dynamics of microtubules, a capability shown previously in transiently transfected cells. Although cells with extremely high expression levels of GFP-EMTB chimera exhibited stabilized microtubules, cells expressing four to ten times the physiological level of endogenous MAP exhibited microtubule dynamics indistinguishable from those of untransfected cells. This result shows that E-MAP-115 (ensconsin) is unlikely to function as a microtubule stabilizer in vivo. Instead, this MAP most likely serves to modulate microtubule functions or interactions with other cytoskeletal elements.

Female↗
PubMed2005

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.

Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide basepair steps are reported. The objective is to obtain the calculated dynamical structure for at least two copies of each case, use the results to examine issues with regard to convergence and dynamical stability of MD on DNA, and determine the significance of sequence context effects on all unique dinucleotide steps. This information is essential to understand sequence effects on DNA structure and has implications on diverse problems in the structural biology of DNA. Calculations were carried out on the 136 cases embedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All simulations were carried out using a well-defined state-of-the-art MD protocol, the AMBER suite of programs, and the parm94 force field. In a previous article (Beveridge et al. 2004. Biophysical Journal. 87:3799-3813), the research design, details of the simulation protocol, and informatics issues were described. Preliminary results from 15 ns MD trajectories were presented for the d(CpG) step in all 10 unique sequence contexts. The results indicated the sequence context effects to be small for this step, but revealed that MD on DNA at this length of trajectory is subject to surprisingly persistent cooperative transitions of the sugar-phosphate backbone torsion angles alpha and gamma. In this article, we report detailed analysis of the entire trajectory database and occurrence of various conformational substates and its impact on studies of context effects. The analysis reveals a possible direct correspondence between the sequence-dependent dynamical tendencies of DNA structure and the tendency to undergo transitions that "trap" them in nonstandard conformational substates. The difference in mean of the observed basepair step helicoidal parameter distribution with different flanking sequence sometimes differs by as much as one standard deviation, indicating that the extent of sequence effects could be significant. The observations reveal that the impact of a flexible dinucleotide such as CpG could extend beyond the immediate basepair neighbors. The results in general provide new insight into MD on DNA and the sequence-dependent dynamical structural characteristics of DNA.

Base Pairing↗
PubMed2002

Dynamic MR cholangiography after fatty meal loading: cystic contractility and dynamic evaluation of biliary stasis.

PURPOSE: Dynamic MR cholangiography was conducted on patients with cholelithiasis or choledocholithiasis who had consumed a fatty test meal (Molyork) and the cystic contractility and dynamics of biliary stasis was evaluated. SUBJECTS AND METHOD: The subjects were 25 with intracystic cholelithiasis, 10 with choledocholithiasis and 10 normal controls. For an imaging sequence, the rapid acquisition with relaxation enhancement (RARE) method was employed and imaging was conducted for 40 min (every 30 s following Molyork administration) without breath-holding. The gallbladder contraction ratio was computed and the contractile ratio for the common bile duct was calculated. To determine the bile flow to the duodenum, the high-intensity signal, indicating the flow from the lower common bile duct, and perfusion of the duodenum were observed in dynamic mode on the monitor with the naked eye and interpreted as positive bile flow. The frequency of this flow was visually monitored. RESULTS: The gallbladder contractile ratio was significantly reduced in patients with cholelithiasis or choledocholithiasis compared with the controls. In a comparison with the normal controls, no sequential changes were noted in the mean contractile ratio of the common bile duct of the patients with cholelithiasis or choledocholithiasis. The mean frequency of bile flow observed for each 40 min period was 13+/-2.4, 6+/-2.2, and 4+/-1.3 times for the controls, those with intracystic cholelithiasis, and those with choledocholithiasis, respectively. Compared with the controls, the latter two patient groups showed evident reductions in the frequency of bile flow to the duodenum (p<0.001). CONCLUSION: Dynamic MRC combined with Molyork loading makes it possible to compute cystic contractile ratios and perform a dynamic examination of bile flow under non-invasive, near-physiological conditions.

Adult↗
PubMed2006

Limits of dynamic object perception in pigeons: dynamic stimulus presentation does not enhance perception and discrimination of complex shape.

A go/no-go procedure was used to train pigeons to discriminate pictures of human faces differing only in shape, with either static images or movies of human faces dynamically rotating in depth. On the basis of experimental findings in humans and some earlier studies on three-dimensional object perception in pigeons, we expected dynamic stimulus presentation to support the pigeon's perception of the complex morphology of a human face. However, the performance of the subjects presented with movies was either worse than (AVI format movies) or did not differ from (uncompressed dynamic presentation) that of the subjects trained with a single or with multiple static images of the faces. Furthermore, generalization tests to other presentation conditions and to novel static views revealed no promoting effect of dynamic training. Except for the subjects trained on multiple static views, performance dropped to chance level with views outside the training range. These results are in contrast to some prior reports from the literature, since they suggest that pigeons, unlike humans, have difficulty using the additional structural information provided by the dynamic presentation and integrating the multiple views into a three-dimensional object.

Animals↗
PubMed2001

[Comparison of enhancement patterns of multi-phase scan of dynamic MRI and dynamic CT in small hepatocellular carcinoma].

OBJECTIVE: To study prospectively the enhancement features of multi-phase scan of dynamic MRI and spiral CT in the diagnosis of small hepatocellular carcinoma (SHCC) and to discuss the cause of dynamic MRI being superior to spiral CT. METHODS: Multi-phase contrast scanning of dynamic MR and spiral CT were done in 53 SHCC patients. The lesions were proved by surgery and pathology. The arterial-phase, portal venous-phase and delayed phase scan of spiral CT were carried out after the pre-contrast scanning of the entire liver. MRI was performed with SE sequence and FMPSPGR sequence dynamic multi-phase contrast scans. RESULTS: Seventy-six lesions were found in 53 patients. Sixty-nine lesions and 54 lesions were enhanced obviously in MR and spiral CT arterial-phase scans. The typical enhancement patterns of SHCC in the arterial-phase, portal venous-phase and delayed phase scan of MRI and spiral CT were hyper-hypo-hypointense (dense) and hyperintense (hyperdense), -isointense (isodense) and -hypointense (hypodense). Atypical enhancement patterns were hyperintense (hyperdense), -hyperintense (hyperdense), -hyperintense (hyperdense), -hyperintense (hyperdense), -isointense (isodense), -isointense (isodense) and -hypointense- (hypodense), -hypointense (hypodense) and -hypointense (hypodense). CONCLUSION: Both dynamic MRI and spiral CT multi-phase contrast scanning are able to demonstrate the enhancement features of SHCC, with arterial-phase scan of MRI being superior to spiral CT in reflecting the hypervascular characterization of SHCC. Combined with SE sequence in characterizing the SHCC, MRI is better than spiral CT.

Adult↗
PubMed1992

["Dynamic" MR imaging of the cervical cord in patients with cervical spondylosis and ossification of the posterior longitudinal ligament--significance of dynamic cord compression].

This investigation was designed to assess the influence of dynamic cord compression on severity and course of myelopathy. Sixty-seven patients studied comprised 54 cases of cervical spondylosis and 13 cases of ossification of the posterior longitudinal ligament. These patients underwent "dynamic" MR imaging of the cervical spine. MR images in the sagittal view were obtained in three different neck positions: flexion, neutral, and extension. MR imaging was performed with a 0.15 T resistive unit. For technical reasons, the body coil was used. The pulse sequence was 500/30 (Tr msec/echo time msec) for T1 images. The spinal cord compression was accelerated in 32 cases when extended, in 2 cases when flexed, and in 4 cases when both extended and flexed. In 21 cases, we compared myelograms with MR images in a same neck position. Findings of myelograms well corresponded with those of MR images on 83 percent of intervertebral levels. The patients with dynamic cord compression were proved to have severer long tract signs, and their disability was regressive or progressive case by case for an average of 21-month follow-up. The "dynamic" MR imaging can provide dynamic nature of spinal cord compression, and prognostic clues.

Cervical Vertebrae↗
PubMed1996

[Approximation to the dynamics of meningococcal meningitis through dynamic systems and time series].

Meningococcal meningitis is subjected to epidemiological surveillance due to its severity and the occasional presentation of epidemic outbreaks. This work analyses previous disease models, generate new ones and analyses monthly cases using ARIMA time series models. The results show that disease dynamics for closed populations is epidemic and the epidemic size is related to the proportion of carriers and the transmissiveness of the agent. In open populations, disease dynamics depends on the admission rate of susceptible and the relative admission of infected individuals. Our model considers a logistic populational growth and carrier admission proportional to populational size, generating an endemic dynamics. Considering a non-instantaneous system response, a greater realism is obtained establishing that the endemic situation may present a dynamics highly sensitive to initial conditions, depending on the transmissiveness and proportion of susceptible individuals in the population. Time series model showed an adequate predictive capacity in terms no longer than 10 months. The lack of long term predictability was attributed to local changes in the proportion of carriers or on transmissiveness that lead to chaotic dynamics over a seasonal pattern. Predictions for 1995 and 1996 were obtained.

Humans↗
PubMed1998

The dynamics of drug action on the within-host population growth of infectious agents: melding pharmacokinetics with pathogen population dynamics.

The use of simple mathematical models to study the kinetics of drug action and decay within vertebrate hosts has a long history with a major objective being to derive drug dosage regimens that optimize efficacy and minimize toxicity to the patient. Mathematical models of the relationship between dosage, route of delivery, drug concentration in defined sites and effect on a particular pathogen are widely used in the pharmacological literature. A more recent literature is that concerned with the population dynamics of pathogen replication within the host subjected to pressures exerted by the human immune system. In this paper we develop a theoretical framework to meld both approaches with the aim of identifying threshold criteria that dictate the optimum pattern of drug administration for pathogen clearance from the host. In particular we show how the percentage reduction in microparasite abundance is related to the pharmacokinetic parameter, AUC, recording the area under the drug concentration-time curve within the treated patient, in terms of the parameters that define the population dynamics of the pathogen and the properties of the drug. Two particular pathogens are examined to illustrate the principles underpinning the dynamics of the pharmacokinetic-population dynamic models, namely HIV and Plasmodium falciparum. Criteria for pathogen persistence or elimination are derived for these specific models based on the definition of a basic reproductive number, R0, which measures the average number of secondary infected target cells in a host generated by a single infected cell (CD4 lymphocyte for HIV, and erythrocyte for P. falciparum) within a population of susceptible cells. For the pathogen to invade the host and persist over time, R0</=1. Under chemotherapeutic regimens, expressions for R0 are derived allowing estimates to be made of the ideal treatment regime required to eliminate the pathogen, both for HIV and P. falciparum malaria.

Animals↗
PubMed2004

Dynamical resetting of the human brain at epileptic seizures: application of nonlinear dynamics and global optimization techniques.

Epileptic seizures occur intermittently as a result of complex dynamical interactions among many regions of the brain. By applying signal processing techniques from the theory of nonlinear dynamics and global optimization to the analysis of long-term (3.6 to 12 days) continuous multichannel electroencephalographic recordings from four epileptic patients, we present evidence that epileptic seizures appear to serve as dynamical resetting mechanisms of the brain, that is the dynamically entrained brain areas before seizures disentrain faster and more frequently (p < 0.05) at epileptic seizures than any other periods. We expect these results to shed light into the mechanisms of epileptogenesis, seizure intervention and control, as well as into investigations of intermittent spatiotemporal state transitions in other complex biological and physical systems.

Adaptation, Physiological↗
PubMed2005

Slow dynamics and anomalous nonlinear fast dynamics in diverse solids.

Results are reported of the first systematic study of anomalous nonlinear fast dynamics and slow dynamics in a number of solids. Observations are presented from seven diverse materials showing that anomalous nonlinear fast dynamics (ANFD) and slow dynamics (SD) occur together, significantly expanding the nonlinear mesoscopic elasticity class. The materials include samples of gray iron, alumina ceramic, quartzite, cracked Pyrex, marble, sintered metal, and perovskite ceramic. In addition, it is shown that materials which exhibit ANFD have very similar ratios of amplitude-dependent internal-friction to the resonance-frequency shift with strain amplitude. The ratios range between 0.28 and 0.63, except for cracked Pyrex glass, which exhibits a ratio of 1.1, and the ratio appears to be a material characteristic. The ratio of internal friction to resonance frequency shift as a function of time during SD is time independent, ranging from 0.23 to 0.43 for the materials studied.

Elasticity↗
PubMed2002

Effect of molecular confinement on internal enzyme dynamics: frequency domain fluorometry and molecular dynamics simulation studies.

The tryptophanyl emission decay of the mesophilic beta-galactosidase from Aspergillus oryzae free in buffer and entrapped in agarose gel is investigated as a function of temperature and compared to that of the hyperthermophilic enzyme from Sulfolobus solfataricus. Both enzymes are tetrameric proteins with a large number of tryptophanyl residues, so the fluorescence emission can provide information on the conformational dynamics of the overall protein structure rather than that of the local environment. The tryptophanyl emission decays are best fitted by bimodal Lorentzian distributions. The long-lived component is ascribed to close, deeply buried tryptophanyl residues with reduced mobility; the short-lived one arises from tryptophanyl residues located in more flexible external regions of each subunit, some of which are involved in forming the catalytic site. The center of both lifetime distribution components at each temperature increases when going from the free in solution mesophilic enzyme to the gel-entrapped and hyperthermophilic enzyme, thus indicating that confinement of the mesophilic enzyme in the agarose gel limits the freedom of the polypeptide chain. A more complex dependence is observed for the distribution widths. Computer modeling techniques are used to recognize that the catalytic sites are similar for the mesophilic and hyperthermophilic beta-galactosidases. The effect due to gel entrapment is considered in dynamic simulations by imposing harmonic restraints to solvent-exposed atoms of the protein with the exclusion of those around the active site. The temperature dependence of the tryptophanyl fluorescence emission decay and the dynamic simulation confirm that more rigid structures, as in the case of the immobilized and/or hyperthermophilic enzyme, require higher temperatures to achieve the requisite conformational dynamics for an effective catalytic action and strongly suggest a link between conformational rigidity and enhanced thermal stability.

Aspergillus oryzae↗