A Finite-Size Scaling Study of a Model of Globular Proteins

Grand canonical Monte Carlo simulations are used to explore the metastable fluid-fluid coexistence curve of the modified Lennard-Jones model of globular proteins of ten Wolde and Frenkel (Science, v277, 1975 (1997)). Using both mixed-field finite-size scaling and histogram reweighting methods, the joint distribution of density and energy fluctuations is analyzed at coexistence to accurately determine the critical-point parameters. The subcritical coexistence region is explored using the recently developed hyper-parallel tempering Monte Carlo simulation method along with histogram reweighting to obtain the density distributions. The phase diagram for the metastable fluid-fluid coexistence curve is calculated in close proximity to the critical point, a region previously unattained by simulation.Comment: 17 pages, 10 figures, 2 Table

Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more than the third order coupling terms since we take a normal mode picture as a zeroth order approximation. When we invoke the Markov approximation, our theory reduces to the Maradudin-Fein formula which is used to describe VER properties of glass and proteins. When the system anharmonicity and the renormalization effect due to the environment vanishes, our formulas reduce to those derived by Mikami and Okazaki invoking the path-integral influence functional method [J. Chem. Phys. 121 (2004) 10052]. We apply our formulas to VER of the amide I mode of a small amino-acide like molecule, N-methylacetamide, in heavy water.Comment: 16 pages, 5 figures, 5 tables, submitted to J. Chem. Phy

Stability of critical bubble in stretched fluid of square-gradient density-functional model with triple-parabolic free energy

The square-gradient density-functional model with triple-parabolic free energy, that was used previously to study the homogeneous bubble nucleation [J. Chem. Phys. 129, 104508 (2008)], is used to study the stability of the critical bubble nucleated within the bulk under-saturated stretched fluid. The stability of the bubble is studied by solving the Schr\"odinger equation for the fluctuation. The negative eigenvalue corresponds to the unstable growing mode of the fluctuation. Our results show that there is only one negative eigenvalue whose eigenfunction represents the fluctuation that corresponds to the isotropically growing or shrinking nucleus. In particular, this negative eigenvalue survives up to the spinodal point. Therefore the critical bubble is not fractal or ramified near the spinodal.Comment: 9 pages, 8 figures, Journal of Chemical Physics accepted for publicatio

Instantaneous Pair Theory for High-Frequency Vibrational Energy Relaxation in Fluids

Notwithstanding the long and distinguished history of studies of vibrational energy relaxation, exactly how it is that high frequency vibrations manage to relax in a liquid remains somewhat of a mystery. Both experimental and theoretical approaches seem to say that there is a natural frequency range associated with intermolecular motions in liquids, typically spanning no more than a few hundred cm^{-1}. Landau-Teller-like theories explain how a solvent can absorb any vibrational energy within this "band", but how is it that molecules can rid themselves of superfluous vibrational energies significantly in excess of these values? We develop a theory for such processes based on the idea that the crucial liquid motions are those that most rapidly modulate the force on the vibrating coordinate -- and that by far the most important of these motions are those involving what we have called the mutual nearest neighbors of the vibrating solute. Specifically, we suggest that whenever there is a single solvent molecule sufficiently close to the solute that the solvent and solute are each other's nearest neighbors, then the instantaneous scattering dynamics of the solute-solvent pair alone suffices to explain the high frequency relaxation. The many-body features of the liquid only appear in the guise of a purely equilibrium problem, that of finding the likelihood of particularly effective solvent arrangements around the solute. These results are tested numerically on model diatomic solutes dissolved in atomic fluids (including the experimentally and theoretically interesting case of I_2 in Xe). The instantaneous pair theory leads to results in quantitative agreement with those obtained from far more laborious exact molecular dynamics simulations.Comment: 55 pages, 6 figures Scheduled to appear in J. Chem. Phys., Jan, 199

Noise in detection of qubit states using a quantum point contact

We present a model for detection of the states of a coupled quantum dots (qubit) by a quantum point contact. Most proposals for measurements of states of quantum systems are idealized. However in a real laboratory the measurements cannot be perfect due to practical devices and circuits. The models using ideal devices are not sufficient for describing the detection information of the states of the quantum systems. Our model therefore includes the extension to a non-ideal measurement device case using an equivalent circuit. We derive a quantum trajectory that describes the stochastic evolution of the state of the system of the qubit and the measuring device. We calculate the noise power spectrum of tunnelling events in an ideal and a non-ideal quantum point contact measurement respectively. We found that, for the strong coupling case it is difficult to obtain information of the quantum processes in the qubit by measurements using a non-ideal quantum point contact. The noise spectra can also be used to estimate the limits of applicability of the ideal model

Beyond Crossing Fibers: Tractography Exploiting Sub-voxel Fibre Dispersion and Neighbourhood Structure

In this paper we propose a novel algorithm which leverages models of white matter fibre dispersion to improve tractography. Tractography methods exploit directional information from diffusion weighted magnetic resonance (DW-MR) imaging to infer connectivity between different brain regions. Most tractography methods use a single direction (e.g. the principal eigenvector of the diffusion tensor) or a small set of discrete directions (e.g. from the peaks of an orientation distribution function) to guide streamline propagation. This strategy ignores the effects of within-bundle orientation dispersion, which arises from fanning or bending at the sub-voxel scale, and can lead to missing connections. Various recent DW-MR imaging techniques estimate the fibre dispersion in each bundle directly and model it as a continuous distribution. Here we introduce an algorithm to exploit this information to improve tractography. The algorithm further uses a particle filter to probe local neighbourhood structure during streamline propagation. Using information gathered from neighbourhood structure enables the algorithm to resolve ambiguities between converging and diverging fanning structures, which cannot be distinguished from isolated orientation distribution functions. We demonstrate the advantages of the new approach in synthetic experiments and in vivo data. Synthetic experiments demonstrate the effectiveness of the particle filter in gathering and exploiting neighbourhood information in recovering various canonical fibre configurations and experiments with in vivo brain data demonstrate the advantages of utilising dispersion in tractography, providing benefits in practical situations. © 2013 Springer-Verlag

Model for monitoring of a charge qubit using a radio-frequency quantum point contact including experimental imperfections

The extension of quantum trajectory theory to incorporate realistic imperfections in the measurement of solid-state qubits is important for quantum computation, particularly for the purposes of state preparation and error-correction as well as for readout of computations. Previously this has been achieved for low-frequency (dc) weak measurements. In this paper we extend realistic quantum trajectory theory to include radio frequency (rf) weak measurements where a low-transparency quantum point contact (QPC), coupled to a charge qubit, is used to damp a classical oscillator circuit. The resulting realistic quantum trajectory equation must be solved numerically. We present an analytical result for the limit of large dissipation within the oscillator (relative to the QPC), where the oscillator slaves to the qubit. The rf+dc mode of operation is considered. Here the QPC is biased (dc) as well as subjected to a small-amplitude sinusoidal carrier signal (rf). The rf+dc QPC is shown to be a low-efficiency charge-qubit detector, that may nevertheless be higher than the dc-QPC (which is subject to 1/f noise).Comment: 12 pages, 2 colour figures. v3 is published version (minor changes since v2

Phase separation in solutions with specific and nonspecific interactions.

Protein solutions, which tend to be thermodynamically stable under physiological conditions, can demix into protein-enriched and protein-depleted phases when stressed. Using a lattice-gas model of proteins with both isotropic and specific, directional interactions, we calculate the critical conditions for phase separation for model proteins with up to four patches via Monte Carlo simulations and statistical associating fluid theory. Given a fixed specific interaction strength, the critical value of the isotropic energy, which accounts for dispersion forces and nonspecific interactions, measures the stability of the solution with respect to nonspecific interactions. Phase separation is suppressed by the formation of protein complexes, which effectively passivate the strongly associating sites on the monomers. Nevertheless, we find that protein models with three or more patches can form extended aggregates that phase separate despite the assembly of passivated complexes, even in the absence of nonspecific interactions. We present a unified view of the critical behavior of model fluids with anisotropic interactions, and we discuss the implications of these results for the thermodynamic stability of protein solutions.Protein solutions, which tend to be thermodynamically stable under physiological conditions, can demix into protein-enriched and protein-depleted phases when stressed. Using a lattice-gas model of proteins with both isotropic and specific, directional interactions, we calculate the critical conditions for phase separation for model proteins with up to four patches via Monte Carlo simulations and statistical associating fluid theory. Given a fixed specific interaction strength, the critical value of the isotropic energy, which accounts for dispersion forces and nonspecific interactions, measures the stability of the solution with respect to nonspecific interactions. Phase separation is suppressed by the formation of protein complexes, which effectively passivate the strongly associating sites on the monomers. Nevertheless, we find that protein models with three or more patches can form extended aggregates that phase separate despite the assembly of passivated complexes, even in the absence of nonspecific interactions. We present a unified view of the critical behavior of model fluids with anisotropic interactions, and we discuss the implications of these results for the thermodynamic stability of protein solutions.This is the final published version, which can also be found on the publisher's website at: http://scitation.aip.org/content/aip/journal/jcp/140/20/10.1063/1.4878836 © 2014 AIP Publishing LL

Freezing of He-4 and its liquid-solid interface from Density Functional Theory

We show that, at high densities, fully variational solutions of solid-like type can be obtained from a density functional formalism originally designed for liquid 4He. Motivated by this finding, we propose an extension of the method that accurately describes the solid phase and the freezing transition of liquid 4He at zero temperature. The density profile of the interface between liquid and the (0001) surface of the 4He crystal is also investigated, and its surface energy evaluated. The interfacial tension is found to be in semiquantitative agreement with experiments and with other microscopic calculations. This opens the possibility to use unbiased DF methods to study highly non-homogeneous systems, like 4He interacting with strongly attractive impurities/substrates, or the nucleation of the solid phase in the metastable liquid.Comment: 5 pages, 4 figures, submitted to Phys. Rev.

A diffusion-induced transition in the phase separation of binary fluid mixtures subjected to a temperature ramp

Demixing of binary fluids subjected to slow temperature ramps shows repeated waves of nucleation which arise as a consequence of the competition between generation of supersaturation by the temperature ramp and relaxation of supersaturation by diffusive transport and flow. Here, we use an advection-reaction-diffusion model to study the oscillations in the weak- and strong-diffusion regime. There is a sharp transition between the two regimes, which can only be understood based on the probability distribution function of the composition rather than in terms of the average composition. We argue that this transition might be responsible for some yet unclear features of experiments, like the appearance of secondary oscillations and bimodal droplet size distributions.Comment: 6 pages, 3 color figure