Dynamics of Structural Elements of GB1 β-Hairpin Revealed by Tryptophan-Cysteine Contact Formation Experiments

Quenching of the triplet state of tryptophan by close contact with cysteine provides a tool for measuring the rate of intramolecular contact formation, one of the most elementary events in the folding process, in peptides and proteins using only natural probes. Here we present a study performed on a stabilized mutant of the second \u3b2-hairpin of the GB1 domain, where we combine steady-state fluorescence, laser-induced temperature-jump, and contact formation measurements to unveil the role of elementary structural components on hairpin dynamics and overall stability. In particular, our methodology provides access to the conformational dynamics of both the folded and unfolded state of the hairpin under native conditions, revealing the presence of extremely slow dynamics on the microsecond time scale in the unfolded state and coexistence of structures with partial pairing of the tails in the folded state. Comparing model peptides that mimic the turn sequence, we found that both ion pairing and hydrogen bonding due to the threonine side chain contribute to the propensity of turn formation but not to the much slower dynamics of the hydrophobic core formation. Interestingly, the dynamics of the turn region in isolation are significantly faster than the dynamics measured for the unfolded state of the complete hairpin, suggesting that non-native hydrophobic contacts slow down the reconfiguration dynamics of the unfolded state. Overall, the information extracted from these experiments provides kinetic limits on interconversions among conformational populations, hence enabling a simplified multistate free-energy landscape for the GB1 hairpin to be drawn

Plasduino: an inexpensive, general purpose data acquisition framework for educational experiments

Based on the Arduino development platform, Plasduino is an open-source data acquisition framework specifically designed for educational physics experiments. The source code, schematics and documentation are in the public domain under a GPL license and the system, streamlined for low cost and ease of use, can be replicated on the scale of a typical didactic lab with minimal effort. We describe the basic architecture of the system and illustrate its potential with some real-life examples.Comment: 11 pages, 10 figures, presented at the XCIX conference of the Societ\`a Italiana di Fisic

Space/Time Noncommutativity in String Theories without Background Electric Field

The appearance of space/time non-commutativity in theories of open strings with a constant non-diagonal background metric is considered. We show that, even if the space-time coordinates commute, when there is a metric with a time-space component, no electric field and the boundary condition along the spatial direction is Dirichlet, a Moyal phase still arises in products of vertex operators. The theory is in fact dual to the non-commutatitive open string (NCOS) theory. The correct definition of the vertex operators for this theory is provided. We study the system also in the presence of a $B$ field. We consider the case in which the Dirichlet spatial direction is compactified and analyze the effect of these background on the closed string spectrum. We then heat up the system. We find that the Hagedorn temperature depends in a non-extensive way on the parameters of the background and it is the same for the closed and the open string sectors.Comment: 18 pages, JHEP styl

Thermodynamics of the hot BIon

We investigate the thermodynamics of the recently obtained finite temperature BIon solution of arXiv:1012.1494, focusing on two aspects. The first concerns comparison of the free energy of the three available phases for the finite temperature brane-antibrane wormhole configuration. Based on this we propose a heuristic picture for the dynamics of the phases that involves a critical temperature below which a stable phase exists. This stable phase is the finite temperature analogue of the thin throat branch of the extremal brane anti-brane wormhole configuration. The second aspect that we consider is the possibility of constructing a finite temperature generalization of the infinite spike configuration of the extremal BIon. To this end we identify a correspondence point at the end of the throat where the thermodynamics of the D3-F1 blackfold configuration can be matched to that of k non-extremal black fundamental strings.Comment: 19 pages, 7 figure

Thermal Giant Gravitons

We study the giant graviton solution as the AdS_5 X S^5 background is heated up to finite temperature. The analysis employs the thermal brane probe technique based on the blackfold approach. We focus mainly on the thermal giant graviton corresponding to a thermal D3-brane probe wrapped on an S^3 moving on the S^5 of the background at finite temperature. We find several interesting new effects, including that the thermal giant graviton has a minimal possible value for the angular momentum and correspondingly also a minimal possible radius of the S^3. We compute the free energy of the thermal giant graviton in the low temperature regime, which potentially could be compared to that of a thermal state on the gauge theory side. Moreover, we analyze the space of solutions and stability of the thermal giant graviton and find that, in parallel with the extremal case, there are two available solutions for a given temperature and angular momentum, one stable and one unstable. In order to write down the equations of motion, action and conserved charges for the thermal giant graviton we present a slight generalization of the blackfold formalism for charged black branes. Finally, we also briefly consider the thermal giant graviton moving in the AdS_5 part.Comment: v1: 32 pages + 11 pages appendices, 13 figures, v2: typos fixed in Sec.2 and other misprints, references adde

Divergence Cancellation and Loop Corrections in String Field Theory on a Plane Wave Background

We investigate the one-loop energy shift E to certain two-impurity string states in light-cone string field theory on a plane wave background. We find that there exist logarithmic divergences in the sums over intermediate mode numbers which cancel between the cubic Hamiltonian and quartic ``contact term''. Analyzing the impurity non-conserving channel we find that the non-perturbative, order g_2^2 sqrt(lambda') contribution to E/mu predicted in hep-th/0211220 is in fact an artifact of these logarithmic divergences and vanishes with them, leaving an order g_2^2 lambda' contribution. Exploiting the supersymmetry algebra, we present a form for the energy shift which appears to be manifestly convergent and free of non-perturbative terms. We use this form to argue that E/mu receives order g_2^2 lambda' contributions at every order in intermediate state impurities.Comment: 27 pages; added references, acknowledgments, missing normalization in equations 2.3 - 2.8, also cleaned up notation, and added a few footnote

DLCQ String Spectrum from N=2{\cal N}=2 SYM Theory

We study non planar corrections to the spectrum of operators in the ${\mathcal N}=2$ supersymmetric Yang Mills theory which are dual to string states in the maximally supersymmetric pp-wave background with a {\em compact} light-cone direction. The existence of a positive definite discrete light-cone momentum greatly simplifies the operator mixing problem. We give some examples where the contribution of all orders in non-planar diagrams can be found analytically. On the string theory side this corresponds to finding the spectrum of a string state to all orders in string loop corrections.Comment: 35 pages, no figure

Holographic 3-point function at one loop

We explore the recent weak/strong coupling match of three-point functions in the AdS/CFT correspondence for two semi-classical operators and one light chiral primary operator found by Escobedo et al. This match is between the tree-level three-point function with the two semi-classical operators described by coherent states while on the string side the three-point function is found in the Frolov-Tseytlin limit. We compute the one-loop correction to the three-point function on the gauge theory side and compare this to the corresponding correction on the string theory side. We find that the corrections do not match. Finally, we discuss the possibility of further contributions on the gauge theory side that can alter our results.Comment: 24 pages, 2 figures. v2: Typos fixed, Ref. added, figure improved. v3: Several typos and misprints fixed, Ref. updated, figures improved, new section 2.3 added on correction from spin-flipped coherent state, computations on string theory side improve

Non-planar ABJM Theory and Integrability

Using an effective vertex method we explicitly derive the two-loop dilatation generator of ABJM theory in its SU(2)xSU(2) sector, including all non-planar corrections. Subsequently, we apply this generator to a series of finite length operators as well as to two different types of BMN operators. As in N=4 SYM, at the planar level the finite length operators are found to exhibit a degeneracy between certain pairs of operators with opposite parity - a degeneracy which can be attributed to the existence of an extra conserved charge and thus to the integrability of the planar theory. When non-planar corrections are taken into account the degeneracies between parity pairs disappear hinting the absence of higher conserved charges. The analysis of the BMN operators resembles that of N=4 SYM. Additional non-planar terms appear for BMN operators of finite length but once the strict BMN limit is taken these terms disappear.Comment: 1+26 pages, uses axodraw.sty. v2: typos fixed, references added. v3: more typos fixed, minor correction

Measurement of the atmospheric muon depth intensity relation with the NEMO Phase-2 tower

The results of the analysis of the data collected with the NEMO Phase-2 tower, deployed at 3500 m depth about 80 km off-shore Capo Passero (Italy), are presented. Cherenkov photons detected with the photomultipliers tubes were used to reconstruct the tracks of atmospheric muons. Their zenith-angle distribution was measured and the results compared with Monte Carlo simulations. An evaluation of the systematic effects due to uncertainties on environmental and detector parameters is also included. The associated depth intensity relation was evaluated and compared with previous measurements and theoretical predictions. With the present analysis, the muon depth intensity relation has been measured up to 13 km of water equivalent.Comment: submitted to Astroparticle Physic