ترغب بنشر مسار تعليمي؟ اضغط هنا

Cross-diffusion induced patterns for a single-step enzymatic reaction

65   0   0.0 ( 0 )
 نشر من قبل Giovanni Giunta
 تاريخ النشر 2020
  مجال البحث فيزياء
والبحث باللغة English




اسأل ChatGPT حول البحث

Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for these transport dynamics. Here, we analyze whether the enzymatic reactions can generate a significant feedback from enzyme transport onto the substrate profile. We find that this feedback can generate spatial patterns in the enzyme distribution, with just a single-step catalytic reaction. However, patterns are formed only for a subclass of transport models. For such models, nonspecific repulsive interactions between the enzyme and the substrate cause the enzyme to accumulate in regions of low substrate concentration. Reactions then amplify local substrate fluctuations, causing enzymes to further accumulate where substrate is low. Experimental analysis of this pattern formation process could discriminate between different transport models.



قيم البحث

اقرأ أيضاً

Computing based on biochemical processes is a newest rapidly developing field of unconventional information and signal processing. In this paper we present results of our research in the field of biochemical computing and summarize the obtained numer ical and experimental data for implementations of the standard two-input OR and AND gates with double-sigmoid shape of the output signal. This form of response was obtained as a function of the two inputs in each of the realized biochemical systems. The enzymatic gate processes in the first system were activated with two chemical inputs and resulted in optically detected chromogen oxidation, which happens when either one or both of the inputs are present. In this case, the biochemical system is functioning as the OR gate. We demonstrate that the addition of a filtering biocatalytic process leads to a considerable reduction of the noise transmission factor and the resulting gate response has sigmoid shape in both inputs. The second system was developed for functioning as an AND gate, where the output signal was activated only by a simultaneous action of two enzymatic biomarkers. This response can be used as an indicator of liver damage, but only if both of these of the inputs are present at their elevated, pathophysiological values of concentrations. A kinetic numerical model was developed and used to estimate the range of parameters for which the experimentally realized logic gate is close to optimal. We also analyzed the system to evaluate its noise-handling properties.
We report the first systematic study of designed two-input biochemical systems as information processing gates with favorable noise-transmission properties accomplished by modifying the gates response from convex shape to sigmoid in both inputs. This is realized by an added chemical filter process which recycles some of the output back into one of the inputs. We study a system involving the biocatalytic function of the enzyme horseradish peroxidase, functioning as an AND gate. We consider modularity properties, such as the use of three different input chromogens that, when oxidized yield signal-detection outputs for various ranges of the primary input, hydrogen peroxide. We also examine possible uses of different filter-effect chemicals (reducing agents) to induce the sigmoid-response. A modeling approach is developed and applied to our data, allowing us to describe the enzymatic kinetics in the framework of a formulation suitable for evaluating the noise-handling properties of the studied systems as logic gates for information processing steps.
We study a minimal cognitive flocking model, which assumes that the moving entities navigate using exclusively the available instantaneous visual information. The model consists of active particles, with no memory, that interact by a short-ranged, po sition-based, attractive force that acts inside a vision cone (VC) and lack velocity-velocity alignment. We show that this active system can exhibit -- due to the VC that breaks Newtons third law -- various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or milling-like patterns, the formation of moving -- locally polar -- files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and non-linear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and non-living active systems.
137 - T. Zhao , J. D. Weeks 2004
We study current-induced step bunching and wandering instabilities with subsequent pattern formations on vicinal surfaces. A novel two-region diffusion model is developed, where we assume that there are different diffusion rates on terraces and in a small region around a step, generally arising from local differences in surface reconstruction. We determine the steady state solutions for a uniform train of straight steps, from which step bunching and in-phase wandering instabilities are deduced. The physically suggestive parameters of the two-region model are then mapped to the effective parameters in the usual sharp step models. Interestingly, a negative kinetic coefficient results when the diffusion in the step region is faster than on terraces. A consistent physical picture of current-induced instabilities on Si(111) is suggested based on the results of linear stability analysis. In this picture the step wandering instability is driven by step edge diffusion and is not of the Mullins-Sekerka type. Step bunching and wandering patterns at longer times are determined numerically by solving a set of coupled equations relating the velocity of a step to local properties of the step and its neighbors. We use a geometric representation of the step to derive a nonlinear evolution equation describing step wandering, which can explain experimental results where the peaks of the wandering steps align with the direction of the driving field.
152 - Chia-Lung Hsieh 2013
Supported lipid bilayers have been studied intensively over the past two decades. In this work, we study the diffusion of single gold nanoparticles (GNPs) with diameter of 20 nm attached to GM1 ganglioside or DOPE lipids at different concentrations i n supported DOPC bilayers. The indefinite photostability of GNPs combined with the high sensitivity of interferometric scattering microscopy (iSCAT) allows us to achieve 1.9 nm spatial precision at 1 ms temporal resolution, while maintaining long recording times. Our trajectories visualize strong transient confinements within domains as small as 20 nm, and the statistical analysis of the data reveals multiple mobilities and deviations from normal diffusion. We present a detailed analysis of our findings and provide interpretations regarding the effect of the supporting substrate and GM1 clustering. We also comment on the use of high-speed iSCAT for investigating diffusion of lipids, proteins or viruses in lipid membranes with unprecedented spatial and temporal resolution.
التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا