Dynamics and intrinsic statistical fluctuations of a gene switch

We studied a simple gene regulatory network, the toggle switch. Specifically, we examined the means and statistical fluctuations in numbers of proteins. We found that when omega, the ratio of rates of protein-gene unbinding to protein degradation, was between similar to 10(-3) and similar to 10, the fluctuations were much larger than those we would have expected from Poisson statistics. In addition, we examined characteristic time values for system relaxation and found both that they increased with omega and that they have significant phase transition effects, with a secondary time scale appearing near the boundary between bistable and other phases. Last, we discuss the bistability of the toggle switch.

Context and conformation dictate function of a transcription antitermination switch

In bacteriophage, transcription elongation is regulated by the N protein, which binds a nascent mRNA hairpin ( termed boxB) and enables RNA polymerase to read through distal terminators. We have examined the structure, energetics and in vivo function of a number of N boxB complexes derived from in vitro protein selection. Trp18 fully stacks on the RNA loop in the wild-type structure, and can become partially or completely unstacked when the sequence context is changed three or four residues away, resulting in a recognition interface in which the best binding residues depend on the sequence context. Notably, in vivo antitermination activity correlates with the presence of a stacked aromatic residue at position 18, but not with N boxB binding affinity. Our work demonstrates that RNA polymerase responds to subtle conformational changes in cis-acting regulatory complexes and that approximation of components is not sufficient to generate a fully functional transcription switch.

Electromechanical Model of RF MEMS Switches

With the recent rapid growth of Radio Frequency Micro-Electro-Mechanical Systems (RF MEMS) switches, there has developed an emergent requirement for more accurate theoretical models to predict their electromechanical behaviors. Many parameters exist in the analysis of the behavior of the switch, and it is inconvenient for further study. In this paper, an improved model is introduced, considering simultaneously axial stress, residual stress, and fringing-field effect of the fixed-fixed bridge structure. To avoid any unnecessary repetitive model tests and numerical simulation for RF MEMS switches, some dimensionless numbers are derived by making governing equation dimensionless. The electromechanical behavior of the fixed-fixed bridge structure of RF MEMS switches is totally determined by these dimensionless numbers.

Stiction and Anti-Stiction in Mems and Nems

Stiction in microelectromechanical systems (MEMS) has been a major failure mode ever since the advent of surface micromachining in the 80s of the last century due to large surface-area-to-volume ratio. Even now when solutions to this problem are emerging, such as self-assembled monolayer (SAM) and other measures, stiction remains one of the most catastrophic failure modes in MEMS. A review is presented in this paper on stiction and anti-stiction in MEMS and nanoelectromechanical systems (NEMS). First, some new experimental observations of stiction in radio frequency (RF) MEMS switch and micromachined accelerometers are presented. Second, some criteria for stiction of microstructures in MEMS and NEMS due to surface forces (such as capillary, electrostatic, van der Waals, Casimir forces, etc.) are reviewed. The influence of surface roughness and environmental conditions (relative humidity and temperature) on stiction are also discussed. As hydrophobic films, the self-assembled monolayers (SAMs) turn out able to prevent release-related stiction effectively. The anti-stiction of SAMs in MEMS is reviewed in the last part.

Energy Principle And Nonlinear Electric-Mechanical Behavior Of Ferroelectric Ceramics

Many experimental observations have shown that a single domain in a ferroelectric material switches by progressive movement of domain walls, driven by a combination of electric field and stress. The mechanism of the domain switch involves the following steps: initially, the domain has a uniform spontaneous polarization; new domains with the reverse polarization direction nucleate, mainly at the surface, and grow though the crystal thickness; the new domain expands sideways as a new domain continues to form; finally, the domain switch coalesces to complete the polarization reversal. According to this mechanism, the volume fraction of the domain switching is introduced in the constitutive law of the ferroelectric material and used to study the nonlinear constitutive behavior of a ferroelectric body in this paper. The principle of stationary total potential energy is put forward in which the basic unknown quantities are the displacement u(i), electric displacement D-i and volume fraction rho(I) of the domain switching for the variant I. The mechanical field equation and a new domain switching criterion are obtained from the principle of stationary total potential energy. The domain switching criterion proposed in this paper is an expansion and development of the energy criterion established by Hwang et al. [ 1]. Based on the domain switching criterion, a set of linear algebraic equations for determining the volume fraction rho(I) of domain switching is obtained, in which the coefficients of the linear algebraic equations only contain the unknown strain and electric fields. If the volume fraction rho(I) of domain switching for each domain is prescribed, the unknown displacement and electric potential can be obtained based on the conventional finite element procedure. It is assumed that a domain switches if the reduction in potential energy exceeds a critical energy barrier. According to the experimental results, the energy barrier will strengthen when the volume fraction of the domain switching increases. The external mechanical and electric loads are increased step by step. The volume fraction rho(I) of domain switching for each element obtained from the last loading step is used as input to the constitutive equations. Then the strain and electric fields are calculated based on the conventional finite element procedure. The finite element analysis is carried out on the specimens subjected to uniaxial coupling stress and electric field. Numerical results and available experimental data are compared and discussed. The present theoretic prediction agrees reasonably with the experimental results.

Long-range automaton models of earthquakes: Power-law accelerations, correlation evolution, and mode-switching

We introduce a conceptual model for the in-plane physics of an earthquake fault. The model employs cellular automaton techniques to simulate tectonic loading, earthquake rupture, and strain redistribution. The impact of a hypothetical crustal elastodynamic Green's function is approximated by a long-range strain redistribution law with a r(-p) dependance. We investigate the influence of the effective elastodynamic interaction range upon the dynamical behaviour of the model by conducting experiments with different values of the exponent (p). The results indicate that this model has two distinct, stable modes of behaviour. The first mode produces a characteristic earthquake distribution with moderate to large events preceeded by an interval of time in which the rate of energy release accelerates. A correlation function analysis reveals that accelerating sequences are associated with a systematic, global evolution of strain energy correlations within the system. The second stable mode produces Gutenberg-Richter statistics, with near-linear energy release and no significant global correlation evolution. A model with effectively short-range interactions preferentially displays Gutenberg-Richter behaviour. However, models with long-range interactions appear to switch between the characteristic and GR modes. As the range of elastodynamic interactions is increased, characteristic behaviour begins to dominate GR behaviour. These models demonstrate that evolution of strain energy correlations may occur within systems with a fixed elastodynamic interaction range. Supposing that similar mode-switching dynamical behaviour occurs within earthquake faults then intermediate-term forecasting of large earthquakes may be feasible for some earthquakes but not for others, in alignment with certain empirical seismological observations. Further numerical investigation of dynamical models of this type may lead to advances in earthquake forecasting research and theoretical seismology.

Numerical exploration of new features on three-dimensional transition of a cylinder wake

The three-dimensional transition of the wake flow behind a circular cylinder is studied in detail by direct numerical simulations using 3D incompressible N-S equations for Reynolds number ranging from 200 to 300. New features and vortex dynamics of the 3D transition of the wake are found and investigated. At Re = 200, the flow pattern is characterized by mode A instability. However, the spanwise characteristic length of the cylinder determines the transition features. Particularly for the specific spanwise characteristic length linear stable mode may dominate the wake in place of mode A and determine the spanwise phase difference of the primary vortices shedding. At Re = 250 and 300 it is found that the streamwise vortices evolve into a new type of mode - "dual vortex pair mode" downstream. The streamwise vortex structures switch among mode A, mode B and dual vortex pair mode from near wake to downstream wake. At Re = 250, an independent low frequency f(m) in addition to the vortex shedding frequency f(s) is identified. Frequency coupling between f(m) and f(s) occurs. These result in the irregularity of the temporal signals and become a key feature in the transition of the wake. Based on the formation analysis of the streamwise vorticity in the vicinity of cylinder, it is suggested that mode A is caused by the emergence of the spanwise velocity due to three dimensionality of the incoming flow past the cylinder. Energy distribution on various wave numbers and the frequency variation in the wake are also described.

Electric characteristics of pseudo-spark during breakdown phase

An analysis of the time-dependent resistive voltage and power deposition during the breakdown phase of pseudo-spark is presented. The voltage and current were measured by specially designed low-inductance capacitive voltage divider and current measuring resistor. The measured waveforms of voltage and current are digitized and processed by a computer program to remove the inductive component, so as to obtain resistive voltage and power deposition. The influence of pressure, cathode geometry and charging voltage of storage capacitors on the electrical properties in the breakdown phase are investigated. The results suggest that the breakdown phase of pseudo-spark consists of three stages. The first stage is mainly hollow cathode discharge. In the second stage, field-enhanced thermionic emission takes place, resulting in a fast voltage drop and sharp rise of discharge current. The third stage of discharge depends simply on the parameters of the discharge circuit.

The permanence of density waves of galaxy and the numerical investigation of waser mechanism

This paper deals with in detail the permanence of the spiral structure of galaxies andthe characters of waser mechanism. A simplified model of galaxy is adopted. Variousdynamical characters of density waves are studied using numerical calculation method. Theresults verify very well the switch character f waser and the tunnel effect of density wavesat the potential barrier of corotation circle as is shown in a previous work of the author.

A Proteomic Study on Cell Cycle Progression of Endothelium Exposed to Tumor Conditioned Medium and the Possible Role of Cyclin D-1/E

This study was designed to comprehensively analyze the differential expression of proteins from human umbilical vein endothelial cells (HUVECs) exposed to tumor conditioned medium (TCM) and to identify the key regulator in the cell cycle progression. The HUVECs were exposed to TCM from breast carcinoma cell line MDA-MB-231, then their cell cycle distribution was measured by flow cytometer (FCM). The role of protein in cell cycle progression was detected via two-dimensional polyacrylamide gel electrophoresis (2-DE) and western blotting. Following the stimulation of TCM, HUVECs showed a more cells in the S phase than did the negative control group (ECGF-free medium with 20% FBS), but the HUVECs' level was similar to the positive control group (medium with 25 mug/ml ECGF and 20% FBS). Increased expression of cyclin D-1/E and some changes in other related proteins occurred after incubation with TCM. From our results, we can conclude that breast carcinoma cell line MDA-MB-231 may secrete soluble pro-angiogenic factors that induce the HUVEC angiogenic switch, during which the expression of cell cycle regulator cyclin D-1/E increases and related proteins play an important role in this process.

Research on Q-Switched Nd : YAG laser engraving

IN this paper, the engraving process with Q-Switched Nd:YAG laser is investigated. High power density is the pre- requisition to vapor materials, and high repetition rate makes the engraving process highly efficient. An acousto- optic Q-Switch is applied in the cavity of CW 200 W Nd:YAG laser to achieve the high peak power density and the high pulse repetition rate. Different shape craters are formed in a patterned structure on the material surface when the laser beam irradiates on it by controlling power density, pulse repetition rate, pulse quantity and pulse interval. In addition, assisting oxygen gas is used for not only improving combustion to deepen the craters but also removing the plasma that generated on the top of craters. Off-focus length classified as negative and positive has a substantial effect on crater diameters. According to the message of rotating angle positions from material to be engraved and the information of graph pixels from computer, a special graph is imparted to the material by integrating the Q- Switched Nd:YAG laser with the computer graph manipulation and the numerically controlled worktable. The crater diameter depends on laser beam divergence and laser focal length. The crater diameter changes from 50 micrometers to 300 micrometers , and the maximum of crater depth reaches one millimeter.

Energy Functions And Basic Equations For Ferroelectrics

Energy functions (or characteristic functions) and basic equations for ferroelectrics in use today are given by those for ordinary dielectrics in the physical and mechanical communications. Based on these basic equations and energy functions, the finite element computation of the nonlinear behavior of the ferroelectrics has been carried out by several research groups. However, it is difficult to process the finite element computation further after domain switching, and the computation results are remarkably deviating from the experimental results. For the crack problem, the iterative solution of the finite element calculation could not converge and the solutions for fields near the crack tip oscillate. In order to finish the calculation smoothly, the finite element formulation should be modified to neglect the equivalent nodal load produced by spontaneous polarization gradient. Meanwhile, certain energy functions for ferroelectrics in use today are not compatible with the constitutive equations of ferroelectrics and need to be modified. This paper proposes a set of new formulae of the energy functions for ferroelectrics. With regard to the new formulae of the energy functions, the new basic equations for ferroelectrics are derived and can reasonably explain the question in the current finite element analysis for ferroelectrics.

Donut-Shaped Fingerprint In Homologous Polypeptide Relationships-A Topological Feature Related To Pathogenic Structural Changes In Conformational Disease

Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.

A delay model for noise-induced bi-directional switching

Many biological systems can switch between two distinct states. Once switched, the system remains stable for a period of time and may switch back to its original state. A gene network with bistability is usually required for the switching and stochastic effect in the gene expression may induce such switching. A typical bistable system allows one-directional switching, in which the switch from the low state to the high state or from the high state to the low state occurs under different conditions. It is usually difficult to enable bi-directional switching such that the two switches can occur under the same condition. Here, we present a model consisting of standard positive feedback loops and an extra negative feedback loop with a time delay to study its capability to produce bi-directional switching induced by noise. We find that the time delay in the negative feedback is critical for robust bi-directional switching and the length of delay affects its switching frequency.

Ultrafast control of multiple filamentation by ultrafast laser pulses

Control of multiple filamentation by laser-induced microlens effect due to a nonlinear interaction of two overlapping laser beams inside a glass plate was demonstrated. Individual or multiple spots on the white light pattern which is a product of multiple filamentation through a mesh can be switched on and off with a very high contrast ratio on a femtosecond time scale. This phenomenon can find applications such as ultrafast optical switch and high-speed sampling. (C) 2005 American Institute of Physics.