Role of higher order interactions on spiral waves in excitable media.

When nodes in excitable system are stimulated, the system tends to form traveling waves or self-organized spiral waves, such as electrical signals in the heart and the spread of epidemics. Networks composed of these nodes can be influenced by higher-order interactions. We utilized the FitzHugh-Nagumo (FHN) model for nodes to construct a three-layer lattice network, incorporating higher-order interactions applicable to neuronal models.

Theoretical description of logical stochastic resonance and its enhancement: Fast Fourier transform filtering method.

Over the past decade, dynamic schemes have been proposed for the use of bistable systems in the design of logic devices. A bistable system in a noisy background can operate as a reliable logic gate in a moderate noise level, which is called a logical stochastic resonance (LSR). In this paper, we theoretically explore the emergence of LSR in general bistable systems and identify the dynamical mechanisms of LSR.

Effects of noise and time delay on E2F's expression level in a bistable Rb-E2F gene's regulatory network.

The bistable Rb-E2F gene regulatory network plays a central role in regulating cellular proliferation-quiescence transition. Based on Gillespie's chemical Langevin method, the stochastic bistable Rb-E2F gene's regulatory network with time delays is proposed. It is found that under the moderate intensity of internal noise, delay in the Cyclin E synthesis rate can greatly increase the average concentration value of E2F.

Termite's Twisted Mandible Presents Fast, Powerful, and Precise Strikes.

The asymmetric mandibles of termites are hypothetically more efficient, rapid, and powerful than the symmetric mandibles of snap-jaw ants or termites. We investigated the velocity, force, precision, and defensive performance of the asymmetric mandibular snaps of a termite species, Pericapritermes nitobei. Ultrahigh-speed recordings of termites revealed a new record in biological movement, with a peak linear velocity of 89.

Modeling of mesenchymal hybrid epithelial state and phenotypic transitions in EMT and MET processes of cancer cells.

Based on the transcriptional regulatory mechanisms between microRNA-200 and transcription factor ZEB in an individual cancer cell, a minimal dynamic model is proposed to study the epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) processes of cancer cells. It is shown that each cancer cell can exit in any of three phenotypic states: the epithelial (E) state, the mesenchymal (M) state, and the epithelial/mesenchymal (E/M) hybrid state, and the state of cancer cell can interconvert between different states. The phase diagram shows that there are monostable, bistable, and tristable phenotypic states regions in a parameters plane.

Effect of external periodic signals and electromagnetic radiation on autaptic regulation of neuronal firing.

An improved Hindmarsh-Rose (HR) neuron model, where the memristor is a bridge between membrane potential and magnetic flux, can be used to investigate the effect of periodic signals on autaptic regulation of neurons under electromagnetic radiation. Based on the improved HR model driven by periodic high-low-frequency current and electromagnetic radiation, the responses of electrical autaptic regulation with diverse high-low-frequency signals are investigated using bifurcation analysis. It is found that the electrical modes of neurons are determined by the selecting parameters of both periodic high and low-frequency current and electromagnetic radiation, and the Hamiltonian energy depends on the neuronal firing modes.

Noise Decomposition Principle in a Coherent Feed-Forward Transcriptional Regulatory Loop.

Coherent feed-forward loops exist extensively in realistic biological regulatory systems, and are common signaling motifs. Here, we study the characteristics and the propagation mechanism of the output noise in a coherent feed-forward transcriptional regulatory loop that can be divided into a main road and branch. Using the linear noise approximation, we derive analytical formulae for the total noise of the full loop, the noise of the branch, and the noise of the main road, which are verified by the Gillespie algorithm.

3DRobot: automated generation of diverse and well-packed protein structure decoys.

Motivation: Computationally generated non-native protein structure conformations (or decoys) are often used for designing protein folding simulation methods and force fields. However, almost all the decoy sets currently used in literature suffer from uneven root mean square deviation (RMSD) distribution with bias to non-protein like hydrogen-bonding and compactness patterns. Meanwhile, most protein decoy sets are pre-calculated and there is a lack of methods for automated generation of high-quality decoys for any target proteins.

Underwater attachment using hairs: the functioning of spatula and sucker setae from male diving beetles.

Males of Dytiscinae beetles use specialized adhesive setae to adhere to female elytra during underwater courtship. This coevolution of male setae and female elytra has attracted much attention since Darwin. However, there has been little examination of their biomechanical functioning despite increasing knowledge on biofibrillar adhesion.

Fluctuations of cell population in a colonic crypt.

The number of stem cells in a colonic crypt is often very small, which leads to large intrinsic fluctuations in the cell population. Based on the model of cell population dynamics with linear feedback in a colonic crypt, we present a stochastic dynamics of the cell population [including stem cells (SCs), transit amplifying cells (TACs), and fully differentiated cells (FDCs)]. The Fano factor, covariance, and susceptibility formulas of the cell population around the steady state are derived by using the Langevin theory.

Enhancement of tunability of MAPK cascade due to coexistence of processive and distributive phosphorylation mechanisms.

The processive phosphorylation mechanism becomes important when there is macromolecular crowding in the cytoplasm. Integrating the processive phosphorylation mechanism with the traditional distributive one, we propose a mixed dual-site phosphorylation (MDP) mechanism in a single-layer phosphorylation cycle. Further, we build a degree model by applying the MDP mechanism to a three-layer mitogen-activated protein kinase (MAPK) cascade.

Direct sum matrix game with prisoner's dilemma and snowdrift game.

A direct sum form is proposed for constructing a composite game from two 2 x 2 games, prisoner's dilemma and snowdrift game. This kind of direct sum form game is called a multiple roles game. The replicator dynamics of the multiple roles game with will-mixed populations is explored.

Vibrational resonance induced by transition of phase-locking modes in excitable systems.

We study the occurrence of vibrational resonance as well as the underlying mechanism in excitable systems. The single vibration resonance and vibration bi-resonance are observed when tuning the amplitude and frequency of high-frequency force simultaneously. Furthermore, by virtue of the phase diagram of low-frequency-signal-free FitzHugh-Nagumo model, it is found that each maxima of response measure is located exactly at the transition boundary of phase patterns.

What is the best reference state for designing statistical atomic potentials in protein structure prediction?

Many statistical potentials were developed in last two decades for protein folding and protein structure recognition. The major difference of these potentials is on the selection of reference states to offset sampling bias. However, since these potentials used different databases and parameter cutoffs, it is difficult to judge what the best reference states are by examining the original programs.

Studies on electrostatic interactions of colloidal particles in two dimensions: a modeling approach.

We study the effective electrostatic interactions between a pair of charged colloidal particles without salt ions while the system is confined in two dimensions. In particular, we use a simplified model to elucidate the effects of rotational fluctuations in counterion distribution. The results exhibit effective colloidal attractions under appropriate conditions.

Dynamics of biomembranes with active multiple-state inclusions.

Nonequilibrium dynamics of biomembranes with active multiple-state inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with adenosine triphosphate (ATP) ligands. As protein conformations cyclically change, this induces hydrodynamical flows and also directly affects the local curvature of a membrane.

Adhesion-induced lateral phase separation of multicomponent membranes: the effect of repellers and confinement.

We present a theoretical study of adhesion-induced lateral phase separation for a membrane with short stickers, long stickers, and repellers confined between two hard walls. The effects of confinement and repellers on lateral phase separation are investigated. We find that the critical potential depth of the stickers for lateral phase separation increases as the distance between the hard walls decreases.

Intrinsic noise in post-transcriptional gene regulation by small non-coding RNA.

Small non-coding RNA (sRNA) plays very important role in the post transcriptional regulation in various organisms. In complex regulatory networks, highly significant relative fluctuations in RNAs copy numbers can not be neglected due to very small copy number of individual RNA molecules. Here we consider two simple regulation schemes, where one is single target gene regulated by a sRNA and the other is two target mRNAs (mRNA(R) and mRNA(T)) regulated by one sRNA.

Multiplicative-noise-induced coherence resonance via two different mechanisms in bistable neural models.

The bistable FitzHugh-Nagumo (FHN) neural model driven by two multiplicative noises and one additive noise is investigated. Two different potential mechanisms for enhancing coherence of bistable FHN model are presented, that is, the first multiplicative noise changes the system from the bistable to the oscillatory regime, and the second multiplicative noise can enhance the symmetry of two stable states of the system. The two mechanisms are analytically or numerically explained.

Critical condition for the occurrence of a noise-reduction effect.

Based on a copy number control model of bacterial plasmid, the internal noise near a given steady state is investigated by using the linear noise approximation. All the parameters are restricted to a certain region so that the time spent near the steady state is long enough and the absorbing state can be neglected. For the noise in the plasmid molecules, a transition occurs with increasing the noise in the signal molecules under certain conditions.

RyR channels and glucose-regulated pancreatic beta-cells.

Ryanodine receptor channel model is introduced to a dynamical model of pancreatic beta-cells to discuss the effects of RyR channels and glucose concentration on membrane potential. The results show Ca2+ concentration changes responding to enhance of glucose concentration is more quickly than that of activating RyR channels, and both methods can induce bursting action potential and increase free cytosolic Ca2+ concentration. An interesting finding is that moderate stimulation to RyR channels will result in a kind of "complex bursting", which is more effective in enhancing average Ca2+ concentration and insulin section.

Protein folding in confined and crowded environments.

Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10k(B)T but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate.

Mean-field coupling of calcium oscillations in a multicellular system of rat hepatocytes.

In a multicellular system of rat hepatocytes and even in an intact liver, cytoplasmic calcium oscillations are synchronized and highly coordinated. In this paper, the mean-field coupling term has been introduced to describe the coupling flux, which is more efficient than gap junctional coupling terms. An optimal coupling strength and an optimal stimulation level for the synchronization of the coupled system have been observed in this paper.

Enhancement of internal-noise coherence resonance by modulation of external noise in a circadian oscillator.

A circadian oscillator driven by external noise and internal noise has been studied by use of the chemical Langevin equation method. When the system is near a Hopf bifurcation and driven by internal noise only, it is found that the coherence resonance phenomenon can be induced by the internal noise. When the system is simultaneously driven by internal and external noise, it is found that external-noise coherence resonance can be suppressed by internal noise, while internal-noise coherence resonance can be enhanced by modulation of the external noise intensity in a certain range of noise intensity.