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At least 433 records · Page 24Linked to original sources
PubMed1987

Presaccadic spike potential: a computer model based upon motor unit recruitment patterns in the extraocular muscles.

Details are presented of a computer model of the presaccadic 'spike' potential based upon the discharge properties of motor units in the extraocular muscles. The model provides support for the hypothesis that the spike potential represents the summated electrical activity from the near-synchronous recruitment of motor units in the extraocular muscles by the presaccadic burst of motoneurone activity.

Action Potentials↗
PubMed2002

Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction.

Experimental observations suggest that electronic characteristics play a role in the rates of substrate oxidation for cytochrome P450 enzymes. For example, the tendency for oxidation of a certain functional group generally follows the relative stability of the radicals that are formed (e.g., N-dealkylation > O-dealkylation > 2 degrees carbon oxidation > 1 degree carbon oxidation). In addition, results show that useful correlations between the rates of product formation can be developed using electronic models. In this article, we attempt to determine whether a combined computational model for aromatic and aliphatic hydroxylation can be developed. Toward this goal, we used a combination of experimental data and semiempirical molecular orbital calculations to predicted activation energies for aromatic and aliphatic hydroxylation. The resulting model extends the predictive capacity of our previous aliphatic hydroxylation model to include the second most important group of oxidations, aromatic hydroxylation. The combined model can account for about 83% of the variance in the data for the 20 compounds in the training set and has an error of about 0.7 kcal/mol.

Computer Simulation↗
PubMed1979

The anterior cerebral artery. II. A computer model of its cortical branches estereotaxically obtained from anatomical specimens.

This article is a corrollary of a previously published anatomical study of the anterior cerebral artery. The authors propose a method to obtain a computer model of the anterior cerebral artery, based on a combined system of stereotaxic coordinates and a specially developed computer program. The graphic analysis, thus obtained, is projected on a model atlas brain and an ideal diagram of this anatomical structure is obtained. Forty anatomical specimens were used for this study.

Brain↗
PubMed1995

Computer modeling of the effects of chewing sugar-free and sucrose-containing gums on the pH changes in dental plaque associated with a cariogenic challenge at different intra-oral sites.

Variation in salivary access to different intra-oral sites is an important factor in the site-dependence of dental caries. This study explored, theoretically, how access is modified by chewing sugar-free and sugar-containing gums. A finite difference computer model, described elsewhere, was used. This allowed for diffusion and/or reaction of substrate, acid product, salivary buffers, and fixed-acid groups. Site-dependent saliva/plaque exchange was modeled in terms of a 100-microns-thick salivary film covering the plaque (a) flowing directly from the salivary ducts, (b) flowing from the intra-oral salivary pool, or (c) exchanging with the pool. Computed flow-velocities or rates of exchange were based on previous intra-oral measurements. The model was also tested against an in vitro study conducted by two of the authors. In addition, the three proposed models of saliva/plaque interaction were compared, and the effect of salivary film thickness investigate. Results suggested that: (1) although sugar-free gum chewed during a cariogenic challenge causes a rapid rise in plaque pH, sucrose-containing gums cause the pH, after a temporary rise resulting from increased salivary flow, to stay low for an extended period; (2) the computer model reproduced in vitro tests reasonably well; (3) although the three models of the plaque/saliva interaction start from different assumptions, two lead to closely related predictions; and (4) increasing the assumed salivary film thickness by a large amount (e.g., from 50 to 200 microns) caused no change in modeled Stephan curves, as long as these changes were accompanied by appropriate reductions in film velocity, in accord, theoretically, with the practical clearance data.

Acids↗
PubMedDate not supplied

Wave form decomposition of 'giant SEP' and its computer model for scalp topography.

By using the decomposition technique developed by ourselves to investigate the scalp topography of evoked potentials, a computer model for the scalp topography of giant SEPs was computed from 5 patients with progressive myoclonic epilepsy and was compared with those obtained from 6 normal subjects. Components of giant SEPs were similar to those of normal SEPs with respect to various parameters, although the former were much larger than the latter. An experimental enlargement of some of the early cortical components of the normal SEP model gave rise to a wave form closely resembling that of the giant SEP. These findings support our previous conclusion, derived from study of the scalp topography of the original SEP wave form, that the giant SEP results from a pathological enhancement of certain early cortical components of the normal SEP. The underlying neuronal hyperexcitability seems to involve more than one subunit of the sensorimotor cortex.

Adolescent↗
PubMed1983

A computer model analysis of the active-site coupling mechanism in the pyruvate dehydrogenase multienzyme complex of Escherichia coli.

A computer modeling system developed to analyze experimental data for inactivation of the Escherichia coli alpha-ketoglutarate dehydrogenase complex (KGDC) accompanying release of lipoyl moieties by lipoamidase and by trypsin [Hackert, M.L., Oliver, R.M. & Reed, L.J. (1983) Proc. Natl. Acad. Sci. USA 80, 2226-2230] was used to analyze analogous data for the E. coli pyruvate dehydrogenase complex (PDC). The model studies indicate that the activity of PDC, as found for KGDC, is influenced by redundancies and random processes, which we describe as a multiple random coupling mechanism. In both complexes more than one lipoyl moiety services each pyruvate dehydrogenase (EC 1.2.4.1) or alpha-ketoglutarate dehydrogenase (EC 1.2.4.2) (E1) subunit, and an extensive lipoyl-lipoyl interaction network for exchange of electrons and possibly acyl groups must also be present. The best fit between computed and experimental data for PDC was obtained with a model that has four lipoyl domains with four or, more probably, eight lipoyl moieties servicing each E1 subunit. The lipoyl-lipoyl interaction network for PDC has lipoyl domain interactions similar to those found for KGDC plus the additional possibility of interaction of a lipoyl moiety and its paired mate on each dihydrolipoamide acetyltransferase (EC 2.3.1.12) (E2) subunit. The two lipoyl moieties on an E2 subunit in PDC appear to be functionally indistinguishable, each servicing the acetyltransferase site of that E2 subunit and a dihydrolipoamide dehydrogenase (EC 1.6.4.3) (E3) subunit if the latter is bound to that particular E2 subunit. The observed difference between inactivation of PDC by lipoamidase and by trypsin appears to be due to dead-end competitive inhibition by lipoyl domains that have been modified by excision of lipoyl moieties by lipoamidase.

Amidohydrolases↗
PubMed2001

Computational modeling of ligament mechanics.

This article provides a critical review of past and current techniques for the computational modeling of ligaments and tendons. A brief overview of relevant concepts from the fields of continuum mechanics and finite element analysis is provided. The structure and function of ligaments and tendons are reviewed in detail, with emphasis on the relationship of microstructural tissue features to the continuum mechanical hehavior. Experimental techniques for the material characterization of biological soft tissues are discussed. Past and current efforts related to the constitutive modeling of ligaments and tendons are classified by the particular technique and dimensionality. Applications of one-dimensional and three-dimensional constitutive models in the representation of the mechanical behavior of joints are presented. Future research directions are identified.

Animals↗
PubMed1994

Spiral waves in a computer model of cardiac excitation.

Spiral excitation fronts have been demonstrated in association with reentry in a computer model of propagated excitation. Fronts were initiated by the reentrant circuits but the spiral configurations themselves occurred outside the circuits. Excitation initiated near the initial portion of reentrant circuits propagated greater distances during a particular time period than excitation initiated from later portions of the circuit. This resulted in spiral configuration of excitation fronts in which the front was located at increasing distance from the latest initiating event. Excitation fronts that did not themselves have spiral configurations in certain matrices were identifiable as parts of spiral configurations that occurred when the same reentrant events were present in other matrices. Spiral waves were initiated by either leading circle reentry associated with functional block to propagation or reentry associated with structural obstacles. They also occurred in the presence of initially uniform refractory periods and resulted in self-sustained reentrant excitation. This however, required particular conditions of excitation such that recovery times constituted a functional block permitting leading circle reentry.

Action Potentials↗
PubMed2006

Improved perfusion system for bipolar radiofrequency ablation of liver: preliminary findings from a computer modeling study.

Current systems for radiofrequency ablation of liver tumors are unable to consistently treat tumors larger than 3 cm in diameter with a single electrode in a single application. One of the strategies for enlarging coagulation zone dimensions is to infuse saline solutions into the tissue through the active electrodes. Nevertheless, the uncontrolled and undirected diffusion of boiling saline into the tissue has been associated with irregular coagulation zones and severe complications, mainly due to reflux of saline along the electrode path. In order to improve the perfusion bipolar ablation method, we hypothesized that the creation of small monopolar coagulation zones adjacent to the bipolar electrodes and previous to the saline infusion would create preferential paths for the saline to concentrate on the targeted coagulation zone. Firstly, we conducted ex vivo experiments in order to characterize the monopolar coagulation zones. We observed that they are practically impermeable to the infused saline. On the basis of this finding, we built theoretical models and conducted computer simulations to assess the feasibility of our hypothesis. Temperature distributions during bipolar ablations with and without previous monopolar coagulation zones were obtained. The results showed that in the case of monopolar coagulation zones the temperature of the tissue took longer to reach 100 degrees C. Since this temperature value is related to rise of impedance, and the time necessary for this process is directly related to the volume of the coagulation zone, our results suggest that monopolar sealing would allow larger coagulation zones to be created. Future experimental studies should confirm this benefit.

Animals↗
PubMed2005

A computer modelling study of the uptake, structure and distribution of carbonate defects in hydroxy-apatite.

Computer modelling techniques have been employed to qualitatively and quantitatively investigate the uptake and distribution of carbonate groups in the hydroxyapatite lattice. Two substitutional defects are considered: the type-A defect, where the carbonate group is located in the hydroxy channel, and the type-B defect, where the carbonate group is located at the position of a phosphate group. A combined type A-B defect is also considered and different charge compensations have been taken into account. The lowest energy configuration of the A-type carbonate has the O-C-O axis aligned with the channel in the c-direction of the apatite lattice and the third oxygen atom lying in the a/b plane. The orientation of the carbonate of the B-type defect is strongly affected by the composition of the apatite material, varying from a position (almost) flat in the a/b plane to being orientated with its plane in the b/c plane. However, Ca-O interactions are always maximised and charge compensating ions are located near the carbonate ion. When we make a direct comparison of the energies per substitutional carbonate group, the results of the different defect simulations show that the type-A defect where two hydroxy groups are replaced by one carbonate group is energetically preferred (DeltaH = -404 kJ mol(-1)), followed by the combined A-B defect, where both a phosphate and a hydroxy group are replaced by two carbonate groups (DeltaH = -259 kJ mol(-1)). The type-B defect, where we have replaced a phosphate group by both a carbonate group and another hydroxy group in the same location is energetically neutral (DeltaH = -1 kJ mol(-1)), but when the replacement of the phosphate group by a carbonate is charge compensated by the substitution of a sodium or potassium ion for a calcium ion, the resulting type-B defect is energetically favourable (DeltaH(Na) = -71 kJ mol(-1),DeltaH(K) = -6 kJ mol(-1)) and its formation is also promoted by A-type defects present in the lattice. Our simulations suggest that it is energetically possible for all substitutions to occur, which are calculated as ion-exchange reactions from aqueous solution. Carbonate defects are widely found in biological hydroxy-apatite and our simulations, showing that incorporation of carbonate from solution into the hydroxyapatite lattice is thermodynamically feasible, hence agree with experiment.

Bone Substitutes↗
PubMed1991

Computer model of excitation and recovery in the anisotropic myocardium. II. Excitation in the simplified left ventricle.

A computer model of propagated excitation and recovery in anisotropic cardiac tissue was described in the first report of this series. The model consists of a large number of excitable elements whose subthreshold interactions are governed by the anisotropic bidomain theory but whose suprathreshold behavior (action potential) is largely preassigned. As described in the first report, the model's performance was tested in rectangular and cubic arrays of excitable elements. This second report deals with three-dimensional simulations in a simplified left ventricle with anisotropy; specifically, the activation process in the "normal" ventricle is described (exemplified by the activation sequences started from various endocardial, intramural, and epicardial sites). To further substantiate our model's validity, we compare simulated epicardial and body-surface potential distributions with experimental findings in isolated canine hearts and with clinical evidence provided by electrocardiographic body-surface mapping.

Action Potentials↗
PubMed2006

Efficient solvability of Hamiltonians and limits on the power of some quantum computational models.

One way to specify a model of quantum computing is to give a set of control Hamiltonians acting on a quantum state space whose initial state and final measurement are specified in terms of the Hamiltonians. We formalize such models and show that they can be simulated classically in a time polynomial in the dimension of the Lie algebra generated by the Hamiltonians and logarithmic in the dimension of the state space. This leads to a definition of Lie-algebraic "generalized mean-field Hamiltonians." We show that they are efficiently (exactly) solvable. Our results generalize the known weakness of fermionic linear optics computation and give conditions on control needed to exploit the full power of quantum computing.

Journal Article↗
PubMed2005

Computer modeling and analysis of heterogeneous structures of microporous carbonaceous materials.

The aim of this work was to study the problems connected with computer modeling and analysis of heterogeneous structures of microporous carbonaceous materials. The research was focused on the numerical properties of original mathematical models for heterogeneous multilayer adsorption on microporous carbonaceous materials presented in our earlier papers and their applicability to examination of real microporous materials. These models are aimed at drawing information on pore structure and capacity on the basis of adsorption isotherms of small molecule adsorbates. They easily fit typical adsorption data in wide relative pressure ranges. In the theory presented, adsorption of small nearly spherical molecules in irregular pores of molecular size has been considered and side adsorbate-adsorbate interactions are neglected. The molecules mentioned are located in pores by forming aggregates, the size of which is limited by the geometry of the pores. The set of adsorbate molecules, which were adsorbed mainly due to adhesive interactions with the adsorbent matter, is treated as the first layer adsorption. Joining further molecules is viewed as the second, third,... layer adsorption. The main idea of the approach to modeling microporous structure presented, consists of introducing of realistic relationships between geometrical properties of pores and adsorption energy. Special attention was focused on the analysis of the influence of the number of model parameters on identification reliability and evaluation errors of porous structure parameters. This paper gives more information on properties of the identification technique presented in our earlier papers. The five-parameter and six-parameter identification reliability is analyzed in more detail, for different values of the system parameters. In this context, the efficiency of simultaneous examination of two isotherms is also studied.

Adsorption↗
PubMed1992

A computer model to predict the effects of level of nutrition on composition of empty body gain in beef cattle: I. Theory and development.

A computer model was developed to simulate differences in the composition of empty body gain of beef cattle resulting from differences in postweaning level of nutrition that are not associated with empty BW. Differences in rate of empty body gain of cattle of similar genotype reflect differences in the level of nutrition; hence, empty body gain was used to represent level of nutrition. The model was based on four assumptions: 1) as animals mature, the proportion of fat is greater in gain than in body weight, 2) effects on body composition caused by plane of nutrition that are not associated with empty BW are predictable from rate of empty BW gain, 3) effects resulting from changes in nutrition are not exerted immediately nor are they permanent, and 4) cattle approach an empty body composition equilibrium when empty body gain is zero. Six parameters were used to characterize mature fat-free matter, rate of change to body composition equilibrium, minimum and maximum fractional growth rate relative to fractional growth rate for empty BW, time lag of response to change in nutrition, and influence of stage of maturity and nutrition on rate of change for fat-free matter. Two parameters were specific for genotype and gender. Using results from the model, we were able to explain conflicting results obtained from compensatory gain experiments.

Adipose Tissue↗
PubMed1993

A novel computer modeling approach to the structures of small bioactive peptides: the structure of gonadotropin releasing hormone.

A novel computer modeling approach suitable for the structure analysis of small bioactive peptides has been developed. This approach involves identification of conformational patterns in protein structure data bank based on the sequence homology with the bioactive peptide. The models built on the basis of this homology and having common conformational patterns are analyzed under the structural constraints derived from the activity data of various synthetic analogs of the peptide. Application of this procedure to the gonadotropin-releasing hormone (GnRH) resulted in a library of possible structures for GnRH, 9 among which shared a common beta-turn. Further analysis of the structures containing the beta-turn motif, in the context of the structure-activity data, led to a model for the active conformation of GnRH. The topology of the putative receptor binding site of the hormone is defined by a contiguous surface formed through an appropriate juxtaposition of the N-terminal pGlu1, the guanidyl group of Arg8, aromatic side chain of Trp3, and the Gly10-NH2 at the C-terminal end.

Amino Acid Sequence↗
PubMed2007

Computer modelling of the sinoatrial node.

Over the past decades patch-clamp experiments have provided us with detailed information on the different types of ion channels that are present in the cardiac cell membrane. Sophisticated cardiac cell models based on these data can help us understand how the different types of ion channels act together to produce the cardiac action potential. In the field of biological pacemaker engineering, such models provide important instruments for the assessment of the functional implications of changes in density of specific ion channels aimed at producing stable pacemaker activity. In this review, an overview is given of the progress made in cardiac cell modelling, with particular emphasis on the development of sinoatrial (SA) nodal cell models. Also, attention is given to the increasing number of publicly available tools for non-experts in computer modelling to run cardiac cell models.

Action Potentials↗