1,356 papers in this slice of arXiv.
Andrej Vilfan, Thomas Duke
Motivated by the operation of myogenic (self-oscillatory) insect flight muscle, we study a model consisting of a large number of identical oscillatory contractile elements joined in a chain, whose end is attached to a damped mass-spring oscillator. When the inertial load is small, the serial coupling favors an antisynchronous state in which the extension of one oscillator is compensated by the contraction of another, in order to preserve the total length. However, a sufficiently massive load can sychronize the oscillators and can even induce oscillation in situations where isolated elements would be stable. The system has a complex phase diagram displaying quiescent, synchronous and antisynchrononous phases, as well as an unsual asynchronous phase in which the total length of the chain oscillates at a different frequency from the individual active elements.
P. Ao, L. Yin
We discuss two aspects, the in vivo and in vitro difference and the modeling of noise, of integrative modeling of network dynamics in biology, using phage lambda as an example. We believe those two aspects have not been seriously considered, and the including of them may be enough to solve the outstanding stability and robustness puzzle of in gene regulatory network dynamics.
Pier Paolo Delsanto, Caterina Guiot, Piero Giorgio Degiorgis +3
Most organisms grow according to simple laws, which in principle can be derived from energy conservation and scaling arguments, critically dependent on the relation between the metabolic rate B of energy flow and the organism mass m. Although this relation is generally recognized to be of the form B(m) = mp, the specific value of the exponent p is the object of an ongoing debate, with many mechanisms being postulated to support different predictions. We propose that multicellular tumor spheroids provide an ideal experimental model system for testing these allometric growth theories, especially under controlled conditions of malnourishment and applied mechanical stress.
Frank Emmert-Streib
We demonstrate that our recently introduced stochastic Hebb-like learning rule is capable of learning the problem of timing in general network topologies generated by an algorithm of Watts and Strogatz. We compare our results with a learning rule proposed by Bak and Chialvo and obtain not only a significantly better convergence behavior but also a dependence of the presentation order of the patterns to be learned by introduction of an additional degree of freedom which allows the neural network to select the next pattern itself whereas the learning rule of Bak and Chialvo stays uneffected. This dependence offers a bidirectional communication between a neuronal and a behavioural level and hence completes the action-perception-cycle which is a characteristics of any living being with a brain.
Frank Emmert-Streib
We present a novel stochastic Hebb-like learning rule for neural networks. This learning rule is stochastic with respect to the selection of the time points when a synaptic modification is induced by pre- and postsynaptic activation. Moreover, the learning rule does not only affect the synapse between pre- and postsynaptic neuron which is called homosynaptic plasticity but also on further remote synapses of the pre- and postsynaptic neuron. This form of plasticity has recently come into the light of interest of experimental investigations and is called heterosynaptic plasticity. Our learning rule gives a qualitative explanation of this kind of synaptic modification.
Josh E. Baker
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions, challenging the classic view (in Brownian motor models) that work can only be performed within biochemical states. An alternative class of models (chemical motor models) has emerged in which motors perform work with biochemical transitions, but many of these models lack a solid physicochemical foundation. In this paper, I develop a self consistent framework for chemical motor models. This novel framework accommodates multiple pathways for free energy transfer, predicts rich behaviors from the simplest multi motor systems, and provides important new insights into muscle and motor function.
G. J. Ackland
We investigate whether the equilibrium time averaged state of a self-organising system with many internal degrees of freedom, 2D- daisyworld, can be described by optimising a single quantity. Unlike physical systems where a principle of maximum energy production has been observed, Daisyworld follows evolutionary dynamics rather than Hamiltonian dynamics. We find that this is sufficient to invalidate the MEP principle, finding instead a different principle, that the system self-organises to a state which maximises the amount of life.
J. -Y. Chen, W. Cox, E. Tehan +3
A number of researchers are attempting to develop a biosensor based on terahertz sensing. Key to the realization of any biosensor system is the access of the target molecules to the sensor. In the case of using terahertz spectroscopy, there are limitations due to high attenuation by water and sensitivity levels. In order to have a significant response at THz frequencies generally requires a minimum pathlength of 100 microns. Solid thin films of this thickness will have limited interaction with target molecules. We propose to use xerogels as biomolecular probe substrates. We have characterized the THz transmission of xerogel substrates as a function of hydration and protein content. These measurements demonstrate that xerogels are excellent candidates for biomolecular probe substrates to realize THz biosensors.
J. -Y. Chen, J. Cerne, A. G. Markelz
We propose a biosensor based on the change of terahertz (THz) dielectric response when a biotarget binds to a probe. The feasibility of this biosensor is examined by studying the change of THz transmission for thin films of heme proteins myoglobin (Mb) and cytochrome C (CytC) as a function oxygen binding. We measure a strong increase in both the index and absorbance with oxygen binding for both Mb and CytC. The measured changes occur for both dried and samples hydrated at 80% r.h. suggesting that using terahertz time domain spectroscopy (TTDS) to monitor the transmitted terahertz pulse through a biomolecular probe thin film in ambient environmental conditions could be used to determine the presence of a biomolecular target.
Alexei A. Koulakov, Dmitry N. Tsigankov
We present a theoretical model for retinocollicular map development, which can account for intriguing behaviors observed in gain-of-function experiments in knock-in mice by Brown et al., including bifurcation in heterozygous Isl2/EphA3 knock-ins. The model is based on known chemical labels, axonal repulsion/competition, stochasticity and uses Markov chain description. Our model suggests that the map in heterozygotes is single-valued in the temporal region of retina due to reduced gradient of ephrin in the corresponding region of SC. The remaining map is double-valued since the gradient of ephrin is high there. We predict therefore that if gradient of ephrin is reduced by a genetic manipulation, the single-valued region of the map should occupy a larger portion of temporal retina, i.e. the point of transition between single- and doulble-valued maps should move to a more nasal position in Isl2-EphA3 heterozygotes. We also discuss the importance of inhomogeneous EphA gradient and mapping in Isl2/EphB knock-ins.
Somendra M. Bhattacharjee
We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.
Og DeSouza, Octavio Miramontes
Survival in groups of termites is known to be socially facilitated since individual longevity is increased together with the size of the group. Here we report on experimental evidence that survival as a function of group size in Cornitermes cumulans (Kollar) does not increase asysmptotically but it peaks in a group size range at which individual longevity is maximal. Strinkly, this same effect in other social insects was noted more than fifty years ago, but it was regarded as ``aberrant'' since it has been generally assumed that individual survival should increase with the size of the group. We also provide evidence that individual activity --measured as mobility-- is maximal at approximately the same group-size range as the observed survival
Yukio Hayashi
We investigate mechanisms of the typically observed recoverable prevalence in epidemic spreading. Assuming the time-independent connectivity correlations, we analyze the dynamics of spreading on linearly growing scale-free (SF) networks, and derive the extinction condition related to the rates of network growth, infection, and immunization of viruses. The behavior is consistent with the previous results for SF networks by a mean-field approximation without connectivity correlations. In particular, it is suggested that the growing must be stopped to prevent the spreading of infection. This insight helps to understand the spreading phenomena on communication or social networks.
Manoranjan P. Singh
We study the synchronous dynamics of the Hopfield model when a random antisymmetric part is added to the otherwise symmetric synaptic matrix. We use a generating functional technique to derive analytical expressions for the order parameters at the first time step (t=1) and the second time step (t=2). We find that the overlap between the target pattern and the state of the network at t=1 is independent of the symmetry of the additional random part of the synaptic interaction matrix. The result may have bearing on the theories which use the results at t=1 to estimate quantities relevant to the retrieval performance of the network. The symmetry of the synaptic interaction matrix becomes effective from the second time step, explicitly through a correlation function involving spin configurations at different times. This suggests that the prediction of the long time behavior of the network from the first few time steps may not be always correct. This was confirmed by the numerical simulation which shows that the difference in the long time and the short time behavior of the network becomes pronounced in presence of asymmetry in the synaptic interaction matrix. It is also found in simulations that the size of the basins of attraction of the stored patterns decreases with an increase in the asymmetry. Moreover, the convergence time for the retrieval increases. These results are contrary to the expectations from the earlier studies based on the counting of fixed points. However, the convergence time for the spurious fixed points increases faster than that for the retrieval fixed points in the presence of asymmetry in the synapses. This is a positive feature of the asymmetry so far as the retrieval performance of the network is concerned.
D. Bolle
Recent results are reviewed on both the time evolution and retrieval properties of multi-state neural networks that are based upon spin-glass models. In particular, the properties of models with neuron states having Q-Ising symmetry are discussed for various architectures. The main common features and differences are highlighted.
Tsunehiro Kobayashi
A mechanism of memories, especially biological memories, is studied in terms of quantum fluids. Two-dimensional flows in central potentials Va(ρ)=−a2gaρ2(a−1) (a=0 and ρ=x2+y2) have zero-energy eigenstates that degenerate infinitely for all a. It is shown that stable standing waves constructed from the zero-energy flows are confined in various types of polygons which can be the minimum units of memory systems. Vortex patterns awoken in the units by stimuli correspond to the memories of the stimuli. This memory system is not a system for preserving memories as usual but that for awaking memories. The system has interesting properties; (i) the absolute economy as for the energy consumption, (ii) the infinite variety for a huge number of memories, (iii) the perfect recovery of the system from any disturbances by stimuli, and (iv) the large flexibility in the construction of the system. A process for thinking is also proposed in terms of this memory system.
E. Allahyarov, H. Löwen, G. Gompper
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.
Joerg Uhde, Manfred Keller, Erich Sackmann +2
We present a study on filamentous actin solutions containing heavy meromyosin subfragments of myosin II motor molecules. We focus on the viscoelastic phase behavior and internal dynamics of such networks during ATP depletion. Upon simultaneously using micro-rheology and fluorescence microscopy as complementary experimental tools, we find a sol-gel transition accompanied by a sudden onset of directed filament motion. We interpret the sol-gel transition in terms of myosin II enzymology, and suggest a "zipping" mechanism to explain the filament motion in the vicinity of the sol-gel transition.
Bao-Quan Ai, Xian-Ju Wang, Guo-Tao Liu +3
The SIRM (Stochastic Inclined Rods Model) proposed by H. Matsuura and M. Nakano can explain the muscle's motion perfectly, but the intermolecular potential between myosin head and G-actin is too simple and only repulsive potential is considered. In this paper we study the SIRM with different complex potential and discuss the effect of the spring on the system. The calculation results show that the spring, the effective radius of the G-actin and the intermolecular potential play key roles in the motion. The sliding speed is about 4.7×10−6m/s calculated from the model which well agrees with the experimental data.
Michael Knott, Huseyin Kaya, Hue Sun Chan
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric Gō-like models with a coarse-grained Cα chain representation. We study a series of models in which the (local) bond- and torsion-angle terms have different strengths relative to the (nonlocal) pairwise contact energy terms. Conformational distributions in these models are sampled by Langevin dynamics. Thermodynamic cooperativity is characterized by the experimental criteria requiring the van't Hoff to calorimetric enthalpy ratio ΔHvH/ΔHcal≈1 (the calorimetric criterion), as well as a two-state-like variation of the average radius of gyration upon denaturation. We find that both local and nonlocal interactions are critical for thermodynamic cooperativity. Chain models with either much weakened local conformational propensities or much weakened favorable nonlocal interactions are significantly less cooperative than chain models with both strong local propensities and strong favorable nonlocal interactions. These findings are compared with results from a recently proposed lattice model with a local-nonlocal coupling mechanism; their relationship with experimental measurements of protein cooperativity and chain compactness is discussed.