Thermodynamics of nano-spheres encapsulated in virus capsids

We investigate the thermodynamics of complexation of functionalized charged nano-spheres with viral proteins. The physics of this problem is governed by electrostatic interaction between the proteins and the nano-sphere cores (screened by salt ions), but also by configurational degrees of freedom of the charged protein N-tails. We approach the problem by constructing an appropriate complexation free energy functional. On the basis of both numerical and analytical studies of this functional we construct the phase diagram for the assembly which contains the information on the assembled structures that appear in the thermodynamical equilibrium, depending on the size and surface charge density of the nano-sphere cores. We show that both the nano-sphere core charge as well as its radius determine the size of the capsid that forms around the core.Comment: Submitte

What drives the translocation of stiff chains?

We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the length of the chain inside, for different concentrations of binding particles. As a consequence of the interactions with these particles, the chain experiences a net force along its length whose calculated value from the simulations accounts for the velocity at which it enters the cell. This force can in turn be obtained from the solution of a generalized diffusion equation incorporating an effective Langmuir adsorption free energy for the chain plus binding particles. These results suggest a role of binding particles in the translocation process which is in general quite different from that of a Brownian ratchet. Furthermore, non-equilibrium effects contribute significantly to the dynamics, \emph{e.g.}, the chain often enters the cell faster than particle binding can be saturated, resulting in a force several times smaller than the equilibrium value.Comment: 7 pages, 4 figure

Implementation and modeling of a femtosecond laser-activated streak camera

8 June 2017) A laser-activated streak camera was built to measure the duration of femtosecond electron pulses. The streak velocity of the device is 1.89 mrad/ps, which corresponds to a sensitivity of 34.9 fs/pixels. The streak camera also measures changes in the relative time of arrival between the laser and electron pulses with a resolution of 70 fs RMS. A full circuit analysis of the structure is presented to describe the streaking field and the general behavior of the device. We have developed a general mathematical model to analyze the streaked images. The model provides an accurate method to extract the pulse duration based on the changes of the electron beam profile when the streaking field is applied

Elastic Lattice Polymers

We study a model of "elastic" lattice polymer in which a fixed number of monomers $m$ is hosted by a self-avoiding walk with fluctuating length $l$. We show that the stored length density $\rho_m = 1 - /m$ scales asymptotically for large $m$ as $\rho_m=\rho_\infty(1-\theta/m + ...)$, where $\theta$ is the polymer entropic exponent, so that $\theta$ can be determined from the analysis of $\rho_m$. We perform simulations for elastic lattice polymer loops with various sizes and knots, in which we measure $\rho_m$. The resulting estimates support the hypothesis that the exponent $\theta$ is determined only by the number of prime knots and not by their type. However, if knots are present, we observe strong corrections to scaling, which help to understand how an entropic competition between knots is affected by the finite length of the chain.Comment: 10 page

Implementation and modeling of a femtosecond laser-activated streak camera

8 June 2017) A laser-activated streak camera was built to measure the duration of femtosecond electron pulses. The streak velocity of the device is 1.89 mrad/ps, which corresponds to a sensitivity of 34.9 fs/pixels. The streak camera also measures changes in the relative time of arrival between the laser and electron pulses with a resolution of 70 fs RMS. A full circuit analysis of the structure is presented to describe the streaking field and the general behavior of the device. We have developed a general mathematical model to analyze the streaked images. The model provides an accurate method to extract the pulse duration based on the changes of the electron beam profile when the streaking field is applied

Bone health in patients with multiple sclerosis relapses

OBJECTIVES: To evaluate the bone health and vitamin D levels of a cohort of patients with relapses of multiple sclerosis (MS) and to propose an algorithm for the management of bone health in this patient group. METHODS: We prospectively studied 56 consecutive patients from our acute relapse clinic. 3 patients were excluded from analysis as they were not deemed to have experienced an acute MS relapse. Bone health was assessed with vitamin D levels and Dual Energy X-ray Absorptiometry (DEXA) scanning (10 patients failed to attend for DEXA). Statistical analyses were used to compare groups and identify predictive variables. A review of the literature led to a proposed management protocol. RESULTS: Pre-relapse the baseline EDSS was ≤6.5 in all subjects, and <4.0 in the majority (66%). Most received corticosteroids. 51% had low bone mineral density (BMD) as defined by a T-score less than −1.0 on DEXA scanning. Three were osteoporotic (T-score less than −2.5). Thirty one of fifty (62%) subjects were Vitamin D deficient (25(OH)D less than 50 nmol/L). A range of variables, including previous corticosteroid usage, were not significantly predictive of reduced BMD. CONCLUSIONS: There was a high frequency of both low BMD and Vitamin D deficiency in this cohort of relatively young and largely ambulatory patients experiencing MS relapses. Current tools, such as the WHO FRAX algorithm, are inadequate in assessing bone status and fracture risk in this patient group, predominantly as they are focused on older age groups. We propose a simple clinical management algorithm

Experimental and theoretical investigation of angular dependence of the Casimir force between sinusoidally corrugated surfaces

In the current work we present the complete results for the measurement of normal Casimir force between shallow and smooth sinusoidally corrugated gold coated sphere and a plate at various angles between the corrugations using an atomic force microscope. All measured data were compared with the theoretical approach using the proximity force approximation and theory based on derivative expansion. In both cases real material properties of the surfaces and non-zero temperature were taken into account. Special attention is paid to the description of electrostatic interactions between corrugated surfaces at different angels between corrugations and samples reparation and characterization. The measured forces are found to be in good agreement with the theory including correlation effects of geometry and material properties and deviate significantly from the predictions of the proximity force approximation approach. This provides the quantitative confirmation for the observation of diffraction-type effects that are disregarded within the PFA approach. The obtained results open new opportunities for control of the Casimir effect in micromechanical systems

Completeness and properness of refinement operators in inductive logic programming

AbstractWithin Inductive Logic Programming, refinement operators compute a set of specializations or generalizations of a clause. They are applied in model inference algorithms to search in a quasi-ordered set for clauses of a logical theory that consistently describes an unknown concept. Ideally, a refinement operator is locally finite, complete, and proper. In this article we show that if an element in a quasi-ordered set 〈S, ≥〉 has an infinite or incomplete cover set, then an ideal refinement operator for 〈S, ≥〉 does not exist. We translate the nonexistence conditions to a specific kind of infinite ascending and descending chains and show that these chains exist in unrestricted sets of clauses that are ordered by θ-subsumption. Next we discuss how the restriction to a finite ordered subset can enable the construction of ideal refinement operators. Finally, we define an ideal refinement operator for restricted θ-subsumption ordered sets of clauses

Modeling and computational homogenization of chloride diffusion in three-phase meso-scale concrete

A computational homogenization technique for modeling diffusion in concrete is introduced with emphasis on the influence of the aggregate content and variability. The highly heterogeneous material is investigated on different scales by combining Variationally Consistent Homogenization on numerical microstructures with analytical techniques accounting for lower, unresolved, length scales. The concrete structure consists of the cement paste, the embedded aggregates, and the Interfacial Transition Zone (ITZ) in between the two. Diffusion takes place in the cement phase, as well as in the ITZ. Since the thickness of the ITZ is, typically, much smaller than the diameter of the aggregates, the effect of the ITZ can be modelled as a surface transport around the aggregates. The occurrence of different aggregate sizes is described via the Particle Size Distribution for given sieve curves, as described in design codes. The Particle Size Distribution curve is split into two parts. The effect of smaller aggregates is homogenized analytically using a mixture rule. This results in an effective matrix material consisting of cement paste and the smaller aggregates. Synthetic structures are then generated numerically to account for the larger aggregates. At first, a dense sphere packing is created based on the Particle Size Distribution. This information is used to generate a weighted Voronoi diagram, which is modified by a shrinking process. This procedure allows us to create periodic Representative Volume Elements for numerical investigations. The overall diffusivity of the concrete mixture is evaluated upon using Variationally Consistent Homogenization, in the context of Finite Element analysis, for the generated RVEs and compared with analytical homogenization results and experimental data. It is found that, depending on the Particle Size Distribution, the ITZ has a large effect on the effective properties