Hydrotalcite intercalated siRNA:computational characterization of the interlayer environment

Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a Mg:Al 2:1 Layered Double Hydroxide (LDH) nanoparticle. An ab initio force field (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies: COMPASS) is used for the MD simulations of the hybrid organic-inorganic systems. The structure, arrangement, mobility, close contacts and hydrogen bonds associated with the intercalated RNA are examined and contrasted with those of the isolated RNA. Computed powder X-ray diffraction patterns are also compared with related LDH-DNA experiments. As a method of probing whether the intercalated environment approximates the crystalline or rather the aqueous state, we explore the stability of the principle parameters (e.g., the major groove width) that differentiate both A- and A'- crystalline forms of siRNA and contrast this with recent findings for the same siRNA simulated in water. We find the crystalline forms remain structurally distinct when intercalated, whereas this is not the case in water. Implications for the stability of hybrid LDH-RNA systems are discussed.

Resonant gradient force on atom interacting with laser field

The gradient force, as a function of position and velocity, is derived for a two-level atom interacting with a standing-wave laser field. Basing on optical Bloch equations, the numerical solutions for the gradient force f_(|_;n) (n = 0, 1, 2, 3, 4, ...) pointing in the direction of the transverse of the laser beam are given. It is shown the higher order gradient force plays important role at strong intensity (G = 64), the contribution of them can not be neglected.

Signal processing for molecular and cellular biological physics:an emerging field

Recent advances in our ability to watch the molecular and cellular processes of life in action-such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer-raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.

Using overlay test to evaluate fracture properties of field-aged asphalt concrete

Field material testing provides firsthand information on pavement conditions which are most helpful in evaluating performance and identifying preventive maintenance or overlay strategies. High variability of field asphalt concrete due to construction raises the demand for accuracy of the test. Accordingly, the objective of this study is to propose a reliable and repeatable methodology to evaluate the fracture properties of field-aged asphalt concrete using the overlay test (OT). The OT is selected because of its efficiency and feasibility for asphalt field cores with diverse dimensions. The fracture properties refer to the Paris’ law parameters based on the pseudo J-integral (A and n) because of the sound physical significance of the pseudo J-integral with respect to characterizing the cracking process. In order to determine A and n, a two-step OT protocol is designed to characterize the undamaged and damaged behaviors of asphalt field cores. To ensure the accuracy of determined undamaged and fracture properties, a new analysis method is then developed for data processing, which combines the finite element simulations and mechanical analysis of viscoelastic force equilibrium and evolution of pseudo displacement work in the OT specimen. Finally, theoretical equations are derived to calculate A and n directly from the OT test data. The accuracy of the determined fracture properties is verified. The proposed methodology is applied to a total of 27 asphalt field cores obtained from a field project in Texas, including the control Hot Mix Asphalt (HMA) and two types of warm mix asphalt (WMA). The results demonstrate a high linear correlation between n and −log A for all the tested field cores. Investigations of the effect of field aging on the fracture properties confirm that n is a good indicator to quantify the cracking resistance of asphalt concrete. It is also indicated that summer climatic condition clearly accelerates the rate of aging. The impact of the WMA technologies on fracture properties of asphalt concrete is visualized by comparing the n-values. It shows that the Evotherm WMA technology slightly improves the cracking resistance, while the foaming WMA technology provides the comparable fracture properties with the HMA. After 15 months aging in the field, the cracking resistance does not exhibit significant difference between HMA and WMAs, which is confirmed by the observations of field distresses.