21-residue peptide's dynamics at and between elementary structural transitions

Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions.

Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Comparative numerical study of energy deposition in femtosecond laser microfabrication with fundamental and second harmonics of Yb-doped laser

We present the results of comparative numerical study of femtosecond laser inscription for fundamental and second harmonic of Yb-doped laser. We have found that second harmonic is more efficient in terms of amount of absorbed energy which leads to lower inscription threshold. Hence this regime is more attractive for applications in femtosecond laser microfabrication. We observed the different size of modified domain on initial pulse energy and different spectrum dynamics during the pulse propagation for fundamental and second harmonics.

Intra-cavity dynamics in high power mode-locked fiber lasers

A theoretical model allows for the characterization and optimization of the intra-cavity pulse evolutions in high-power fiber lasers. Multi-parameter analysis of laser performance can be made at a fraction of the computational cost. © 2010 Optical Society of America.

Enhanced renewable energy adoption for sustainable development in India:interpretive structural modeling approach

Poverty alleviation and social upliftment of rural India is closely linked with the availability and use of energy for development. At the same time, sustainable supply of clean and affordable renewable energy sources is required if development is to be sustainable, so that it does not cause any environmental problems. The purpose of this paper is to determine the key variables of renewable energy implementation for sustainable development, on which the top management should focus. In this paper, an interpretive structural modeling (ISM) - based approach has been employed to model the implementation variables of renewable energy for sustainable development. These variables have been categorized under ‘enablers’ that help to increase the implementation of renewable energy for sustainable development. A major finding of this research is that public awareness regarding renewable energy for sustainable development is a very significant enabler. In this paper, an interpretation of variables of renewable energy for sustainable development in terms of their driving and dependence powers has been examined. For better results, top management should focus on improving the high-driving power enablers such as leadership, strategic planning, public awareness, top management support, availability of finance, government support, and support from interest groups.

Molecular dynamics simulations:bring biomolecular structures alive on a computer

The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation.

Stress-induced platelet formation in silicon:a molecular dynamics study

The effect of stress on vacancy cluster configurations in silicon is examined using molecular dynamics. At zero pressure, the shape and stability of the vacancy clusters agrees with previous atomistic results. When stress is applied the orientation of small planar clusters changes to reduce the strain energy. The preferred orientation for the vacancy clusters under stress agrees with the experimentally observed orientations of hydrogen platelets in the high stress regions of hydrogen implanted silicon. These results suggest a theory for hydrogen platelet formation. © 2005 The American Physical Society.

Real and imaginary parts of the vibrational relaxation of acetonitrile in its electrolyte solutions:new results for the dynamics of solvent molecules

Isotropic scattering Raman spectra of liquid acetonitrile (AN) solutions of LiBF4 and NaI at various temperatures and concentrations have been investigated. For the first time imaginary as well as real parts of the solvent vibrational correlation functions have been extracted from the spectra. Such imaginary parts are currently an important component of modern theories of vibrational relaxation in liquids. This investigation thus provides the first experimental data on imaginary parts of a correlation function in AN solutions. Using the fitting algorithm we recently developed, statistically confident models for the Raman spectra were deduced. The parameters of the band shapes, with an additional correction, of the ν2 AN vibration (CN stretching), together with their confidence intervals are also reported for the first time. It is shown that three distinct species, with lifetimes greater than ∼10−13 s, of the AN molecules can be detected in solutions containing Li+ and Na+. These species are attributed to AN molecules directly solvating cations; the single oriented and polarised molecules interleaving the cation and anion of a Solvent Shared Ion Pair (SShIP); and molecules solvating anions. These last are considered to be equivalent to the next layer of solvent molecules, because the CN end of the molecule is distant from the anion and thus less affected by the ionic charge compared with the anion situation. Calculations showed that at the concentrations employed, 1 and 0.3 M, there were essentially no other solvent molecules remaining that could be considered as bulk solvent. Calculations also showed that the internuclear distance in these solutions supported the proposal that the ionic entity dominating in solution was the SShIP, and other evidence was adduced that confirmed the absence of Contact Ion Pairs at these concentrations. The parameters of the shape of the vibrational correlation functions of all three species are reported. The parameters of intramolecular anharmonic coupling between the potential surfaces in AN and the dynamics of the intermolecular environment fluctuations and intermolecular energy transfer are presented. These results will assist investigations made at higher and lower concentrations, when additional species and interactions with AN molecules will be present.

Molecular dynamics simulation of brittle fracture in silicon

The fracture process involves converting potential energy from a strained body into surface energy, thermal energy, and the energy needed to create lattice defects. In dynamic fracture, energy is also initially converted into kinetic energy. This paper uses molecular dynamics (MD) to simulate brittle frcture in silicon and determine how energy is converted from potential energy (strain energy) into other forms.

Thermalized polarization dynamics of a discrete optical-waveguide system with four-wave mixing

Statistical mechanics of two coupled vector fields is studied in the tight-binding model that describes propagation of polarized light in discrete waveguides in the presence of the four-wave mixing. The energy and power conservation laws enable the formulation of the equilibrium properties of the polarization state in terms of the Gibbs measure with positive temperature. The transition line T=∞ is established beyond which the discrete vector solitons are created. Also in the limit of the large nonlinearity an analytical expression for the distribution of Stokes parameters is obtained, which is found to be dependent only on the statistical properties of the initial polarization state and not on the strength of nonlinearity. The evolution of the system to the final equilibrium state is shown to pass through the intermediate stage when the energy exchange between the waveguides is still negligible. The distribution of the Stokes parameters in this regime has a complex multimodal structure strongly dependent on the nonlinear coupling coefficients and the initial conditions.

Comprehensive secondary pyrolysis in fluidized-bed fast pyrolysis of biomass, a fluid dynamics based modelling effort

Homogenous secondary pyrolysis is category of reactions following the primary pyrolysis and presumed important for fast pyrolysis. For the comprehensive chemistry and fluid dynamics, a probability density functional (PDF) approach is used; with a kinetic scheme comprising 134 species and 4169 reactions being implemented. With aid of acceleration techniques, most importantly Dimension Reduction, Chemistry Agglomeration and In-situ Tabulation (ISAT), a solution within reasonable time was obtained. More work is required; however, a solution for levoglucosan (C6H10O5) being fed through the inlet with fluidizing gas at 500 °C, has been obtained. 88.6% of the levoglucosan remained non-decomposed, and 19 different decomposition product species were found above 0.01% by weight. A homogenous secondary pyrolysis scheme proposed can thus be implemented in a CFD environment and acceleration techniques can speed-up the calculation for application in engineering settings.

Control of the in-cavity dynamics in mode-locked fibre lasers

At the level of fundamental research, fibre lasers provide convenient and reproducible experimental settings for the study of a variety of nonlinear dynamical processes, while at the applied research level, pulses with different and optimised features – e.g., in terms of pulse duration, temporal and/or spectral intensity profile, energy, repetition rate and emission bandwidth – are sought with the general constraint of developing efficient cavity architectures. In this talk, we review our recent progress on the realisation of different regimes of pulse generation in passively mode-locked fibre lasers through control of the in-cavity propagation dynamics. We report on the possibility to achieve both parabolic self-similar and triangular pulse shaping in a mode-locked fibre laser via adjustment of the net normal dispersion and integrated gain of the cavity [1]. We also show that careful control of the gain/loss parameters of a net-normal dispersion laser cavity provides the means of achieving switching among Gaussian pulse, dissipative soliton and similariton pulse solutions in the cavity [2,3]. Furthermore, we report on our recent theoretical and experimental studies of pulse shaping by inclusion of an amplitude and phase spectral filter into the cavity of a laser. We numerically demonstrate that a mode-locked fibre laser can operate in dif- ferent pulse-generation regimes, including parabolic, flattop and triangular waveform generations, depending on the amplitude profile of the in-cavity spectral filter [4]. An application of technique using a flat-top spectral filter is demonstrated to achieve the direct generation of sinc-shaped optical Nyquist pulses of high quality and of a widely tuneable bandwidth from the laser [5]. We also report on a recently-developed versa- tile erbium-doped fibre laser, in which conventional soliton, dispersion-managed soli- ton (stretched-pulse) and dissipative soliton mode-locking regimes can be selectively and reliably targeted by programming different group-velocity dispersion profiles and bandwidths on an in-cavity programmable filter [6]. References: 1. S. Boscolo and S. K. Turitsyn, Phys. Rev. A 85, 043811 (2012). 2. J. Peng et al., Phys. Rev. A 86, 033808 (2012). 3. J. Peng, Opt. Express 24, 3046-3054 (2016). 4. S. Boscolo, C. Finot, H. Karakuzu, and P. Petropoulos, Opt. Lett. 39, 438-441 (2014). 5. S. Boscolo, C. Finot, and S. K. Turitsyn, IEEE Photon. J. 7, 7802008 (2015). 6. J. Peng and S. Boscolo, Sci. Rep. 6, 25995 (2016).

A note on the propagation of quantized vortex rings through a quantum turbulence tangle:energy transport or energy dissipation?

We investigate quantum vortex ring dynamics at scales smaller than the inter-vortex spacing in quantum turbulence. Through geometrical arguments and high-resolution numerical simulations, we examine the validity of simple estimates for the mean free path and the structure of vortex rings post-reconnection. We find that a large proportion of vortex rings remain coherent objects where approximately 75% of their energy is preserved. This leads us to consider the effectiveness of energy transport in turbulent tangles. Moreover, we show that in low density tangles, appropriate for the ultra-quantum regime, ring emission cannot be ruled out as an important mechanism for energy dissipation. However at higher vortex line densities, typically associated with the quasi-classical regime, loop emission is expected to make a negligible contribution to energy dissipation, even allowing for the fact that our work shows rings can survive multiple reconnection events. Hence the Kelvin wave cascade seems the most plausible mechanism leading to energy dissipation

Exact solution for the energy spectrum of Kelvin-wave turbulence in superfluids

We study the statistical and dynamical behavior of turbulent Kelvin waves propagating on quantized vortices in superfluids and address the controversy concerning the energy spectrum that is associated with these excitations. Finding the correct energy spectrum is important because Kelvin waves play a major role in the dissipation of energy in superfluid turbulence at near-zero temperatures. In this paper, we show analytically that the solution proposed by [L’vov and Nazarenko, JETP Lett. 91, 428 (2010)] enjoys existence, uniqueness, and regularity of the prefactor. Furthermore, we present numerical results of the dynamical equation that describes to leading order the nonlocal regime of the Kelvin-wave dynamics. We compare our findings with the analytical results from the proposed local and nonlocal theories for Kelvin-wave dynamics and show an agreement with the nonlocal predictions. Accordingly, the spectrum proposed by L’vov and Nazarenko should be used in future theories of quantum turbulence. Finally, for weaker wave forcing we observe an intermittent behavior of the wave spectrum with a fluctuating dissipative scale, which we interpreted as a finite-size effect characteristic of mesoscopic wave turbulence.

Interaction of Kelvin waves and nonlocality of energy transfer in superfluids

We argue that the physics of interacting Kelvin Waves (KWs) is highly nontrivial and cannot be understood on the basis of pure dimensional reasoning. A consistent theory of KW turbulence in superfluids should be based upon explicit knowledge of their interactions. To achieve this, we present a detailed calculation and comprehensive analysis of the interaction coefficients for KW turbuelence, thereby, resolving previous mistakes stemming from unaccounted contributions. As a first application of this analysis, we derive a local nonlinear (partial differential) equation. This equation is much simpler for analysis and numerical simulations of KWs than the Biot-Savart equation, and in contrast to the completely integrable local induction approximation (in which the energy exchange between KWs is absent), describes the nonlinear dynamics of KWs. Second, we show that the previously suggested Kozik-Svistunov energy spectrum for KWs, which has often been used in the analysis of experimental and numerical data in superfluid turbulence, is irrelevant, because it is based upon an erroneous assumption of the locality of the energy transfer through scales. Moreover, we demonstrate the weak nonlocality of the inverse cascade spectrum with a constant particle-number flux and find resulting logarithmic corrections to this spectrum.