Magnetic friction due to vortex fluctuation

We use Monte Carlo and molecular dynamics simulation to study a magnetic tip-sample interaction. Our interest is to understand the mechanism of heat dissipation when the forces involved in the system are magnetic in essence. We consider a magnetic crystalline substrate composed of several layers interacting magnetically with a tip. The set is put thermally in equilibrium at temperature T by using a numerical Monte Carlo technique. By using that configuration we study its dynamical evolution by integrating numerically the equations of motion. Our results suggests that the heat dissipation in this system is closed related to the appearing of vortices in the sample.Comment: 6 pages, 41 figure

Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc

Glucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5’ diphospho N-acetyl-D-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target for antifungal, antibacterial and antidiabetic therapy. The crystal structure of the isomerase domain of GlcN-6-P synthase from human pathogenic fungus Candida albicans, in complex with UDP-GlcNAc has been solved recently but it has not revealed the molecular mechanism of inhibition taking place under UDP-GlcNAc influence, the unique feature of the eukaryotic enzyme. UDP-GlcNAc is a physiological inhibitor of GlcN-6-P synthase, binding about 1 nm away from the active site of the enzyme. In the present work, comparative molecular dynamics simulations of the free and UDP-GlcNAc-bounded structures of GlcN-6-P synthase have been performed. The aim was to complete static X-ray structural data and detect possible changes in the dynamics of the two structures. Results of the simulation studies demonstrated higher mobility of the free structure when compared to the liganded one. Several amino acid residues were identified, flexibility of which is strongly affected upon UDP-GlcNAc binding. Importantly, the most fixed residues are those related to the inhibitor binding process and to the catalytic reaction. The obtained results constitute an important step toward understanding of mechanism of GlcN-6-P synthase inhibition by UDP-GlcNAc molecule

High frequency longitudinal and transverse dynamics in water

High-resolution, inelastic x-ray scattering measurements of the dynamic structure factor S(Q,\omega) of liquid water have been performed for wave vectors Q between 4 and 30 nm^-1 in distinctly different thermodynamic conditions (T= 263 - 420 K ; at, or close to, ambient pressure and at P = 2 kbar). In agreement with previous inelastic x-ray and neutron studies, the presence of two inelastic contributions (one dispersing with Q and the other almost non-dispersive) is confirmed. The study of their temperature- and Q-dependence provides strong support for a dynamics of liquid water controlled by the structural relaxation process. A viscoelastic analysis of the Q-dispersing mode, associated with the longitudinal dynamics, reveals that the sound velocity undergoes the complete transition from the adiabatic sound velocity (c_0) (viscous limit) to the infinite frequency sound velocity (c_\infinity) (elastic limit). On decreasing Q, as the transition regime is approached from the elastic side, we observe a decrease of the intensity of the second, weakly dispersing feature, which completely disappears when the viscous regime is reached. These findings unambiguously identify the second excitation to be a signature of the transverse dynamics with a longitudinal symmetry component, which becomes visible in the S(Q,\omega) as soon as the purely viscous regime is left.Comment: 28 pages, 12 figure

Amorphous carbon nanoparticles: a versatile label for rapid diagnostic (immuno)assays

Carbon nanoparticles (CNPs) labeled with reporter molecules can serve as signaling labels in rapid diagnostic assays as an alternative to gold, colored latex, silica, quantum dots, or up-converting phosphor nanoparticles. Detailed here is the preparation of biomolecule-labeled CNPs and examples of their use as a versatile label. CNPs can be loaded with a range of biomolecules, such as DNA, antibodies, and proteins (e.g., neutravidin or a fusion protein of neutravidin with an enzyme), and the resulting conjugates can be used to detect analytes of high or low molecular mass

Supercooled confined water and the Mode Coupling crossover temperature

We present a Molecular Dynamics study of the single particle dynamics of supercooled water confined in a silica pore. Two dynamical regimes are found: close to the hydrophilic substrate molecules are below the Mode Coupling crossover temperature, $T_C$, already at ambient temperature. The water closer to the center of the pore (free water) approaches upon supercooling $T_C$ as predicted by Mode Coupling Theories. For free water the crossover temperature and crossover exponent $\gamma$ are extracted from power-law fits to both the diffusion coefficient and the relaxation time of the late $\alpha$ region.Comment: To be published, Phys. Rev. Lett., 4 pages, 3 figures, revTeX, minor changes in the figures, references added, changes in the tex

Molecular dynamics simulation of polymer helix formation using rigid-link methods

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under gradual cooling are followed until each reaches a state from which no further change is possible. The interactions are chosen so that the true ground state is a helix, and a high proportion of simulation runs succeed in reaching this state; the fraction that manage to form defect-free helices is a function of both chain length and cooling rate. In order to demonstrate behavior analogous to the formation of protein tertiary structure, additional attractive interactions are introduced into the model, leading to the appearance of aligned, antiparallel helix pairs. The simulations employ a computational approach that deals directly with the internal coordinates in a recursive manner; this representation is able to maintain constant bond lengths and angles without the necessity of treating them as an algebraic constraint problem supplementary to the equations of motion.Comment: 15 pages, 14 figure

Diagnostic accuracy of follow-up tests for detecting colorectal cancer recurrences in primary care:A systematic review and meta-analysis

Introduction Traditionally, follow-up of colorectal cancer (CRC) is performed in secondary care. In new models of care, the screening part care could be replaced to primary care. We aimed to synthesise evidence on the diagnostic accuracy of commonly used screeners in CRC follow-up applicable in primary care: carcinoembryonic antigen (CEA), ultrasound and physical examination. Methods Medline, EMBASE, Cochrane Trial Register and Web of Science databases were systematically searched. Studies were included if they provided sufficient data for a 2 × 2 contingency tables. QUADAS-2 was used to assess methodological quality. We performed bivariate random effects meta-analysis, generated a hypothetical cohort, and reported sensitivity and specificity. Results We included 12 studies (n = 3223, median recurrence rate 19.6%). Pooled estimates showed a sensitivity for CEA (≤ 5 μg/l) of 59% [47%–70%] and a specificity of 89% [80%–95%]. Only few studies reported sensitivities and specificities for ultrasound (36–70% and 97–100%, respectively) and clinical examination (23% and 27%, respectively). Conclusion In practice, GPs could perform CEA screening. Radiological examination in a hospital setting should remain part of the surveillance strategy. Personalised algorithms accounting for recurrence risk and changes of CEA-values over time might add to the diagnostic value of CEA in primary care

Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding